US20070136839A1 - Promoter, promoter control elements, and combinations, and uses thereof - Google Patents

Promoter, promoter control elements, and combinations, and uses thereof Download PDF

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US20070136839A1
US20070136839A1 US11/598,118 US59811806A US2007136839A1 US 20070136839 A1 US20070136839 A1 US 20070136839A1 US 59811806 A US59811806 A US 59811806A US 2007136839 A1 US2007136839 A1 US 2007136839A1
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Prior art keywords
promoter
transcription
plant
nucleic acid
sequence
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Zhihong Cook
Yiwen Fang
Ken Feldmann
Edward Kiegle
Shing Kwok
Yu-Ping Lu
Leonard Medrano
Roger Pennell
Richard Schneeberger
Chuan-Yin Wu
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Ceres Inc
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Ceres Inc
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Priority claimed from US10/950,321 external-priority patent/US7173121B2/en
Application filed by Ceres Inc filed Critical Ceres Inc
Priority to US11/598,118 priority Critical patent/US20070136839A1/en
Publication of US20070136839A1 publication Critical patent/US20070136839A1/en
Priority to US12/504,863 priority patent/US8278434B2/en
Priority to US13/664,313 priority patent/US20130117881A1/en
Priority to US15/967,437 priority patent/US10851383B2/en
Priority to US16/938,557 priority patent/US11634723B2/en
Priority to US16/938,550 priority patent/US11739340B2/en
Abandoned legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8216—Methods for controlling, regulating or enhancing expression of transgenes in plant cells
    • C12N15/8222—Developmentally regulated expression systems, tissue, organ specific, temporal or spatial regulation

Definitions

  • the present invention relates to promoters and promoter control elements that are useful for modulating transcription of a desired polynucleotide.
  • Such promoters and promoter control elements can be included in polynucleotide constructs, expression cassettes, vectors, or inserted into the chromosome or as an exogenous element, to modulate in vivo and in vitro transcription of a polynucleotide.
  • Host cells, including plant cells, and organisms, such as regenerated plants therefrom, with desired traits or characteristics using polynucleotides comprising the promoters and promoter control elements of the present invention are also a part of the invention.
  • This invention relates to the field of biotechnology and, in particular, to specific promoter sequences and promoter control element sequences which are useful for the transcription of polynucleotides in a host cell or transformed host organism.
  • One of the primary goals of biotechnology is to obtain organisms, such as plants, mammals, yeast, and prokaryotes having particular desired characteristics or traits. Examples of these characteristic or traits abound and may include, for example, in plants, virus resistance, insect resistance, herbicide resistance, enhanced stability or additional nutritional value.
  • Recent advances in genetic engineering have enabled researchers in the field to incorporate polynucleotide sequences into host cells to obtain the desired qualities in the organism of choice.
  • This technology permits one or more polynucleotides from a source different than the organism of choice to be transcribed by the organism of choice. If desired, the transcription and/or translation of these new polynucleotides can be modulated in the organism to exhibit a desired characteristic or trait. Alternatively, new patterns of transcription and/or translation of polynucleotides endogenous to the organism can be produced. Both approaches can be used at the same time.
  • the present invention is directed to isolated polynucleotide sequences that comprise promoters and promoter control elements from plants, especially Arabidopsis thaliana, Glycine max, Oryza sativa , and Zea mays , and other promoters and promoter control elements functional in plants.
  • promoter sequences comprise, for example,
  • promoter control element sequences comprise, for example,
  • Promoter or promoter control element sequences of the present invention are capable of modulating preferential transcription.
  • the present promoter control elements are capable of serving as or fulfilling the function, for example, as a core promoter, a TATA box, a polymerase binding site, an initiator site, a transcription binding site, an enhancer, an inverted repeat, a locus control region, or a scaffold/matrix attachment region.
  • the first promoter control element is a promoter control element sequence as discussed above, and the second promoter control element is heterologous to the first control element. Moreover, the first and second control elements are operably linked.
  • Such promoters may modulate transcript levels preferentially in a tissue or under particular conditions.
  • the present isolated polynucleotide comprises a promoter or a promoter control element as described above, wherein the promoter or promoter control element is operably linked to a polynucleotide to be transcribed.
  • the promoter and promoter control elements of the instant invention are operably linked to a heterologous polynucleotide that is a regulatory sequence.
  • Host cells include, for instance, bacterial, yeast, insect, mammalian, and plant.
  • the host cell can comprise a promoter or promoter control element exogenous to the genome. Such a promoter can modulate transcription in cis- and in trans-.
  • the present host cell is a plant cell capable of regenerating into a plant.
  • This method comprises providing a polynucleotide or vector according to the present invention as described above, and contacting the sample of the polynucleotide or vector with conditions that permit transcription.
  • the polynucleotide or vector preferentially modulates
  • Table 1 consists of the Expression Reports for each promoter of the invention providing the nucleotide sequence for each promoter and details for expression driven by each of the nucleic acid promoter sequences as observed in transgenic plants.
  • the results are presented as summaries of the spatial expression, which provides information as to gross and/or specific expression in various plant organs and tissues.
  • the observed expression pattern is also presented, which gives details of expression during different generations or different developmental stages within a generation. Additional information is provided regarding the associated gene, the GenBank reference, the source organism of the promoter, and the vector and marker genes used for the construct. The following symbols are used consistently throughout the Table:
  • Each row of the table begins with heading of the data to be found in the section.
  • the following provides a description of the data to be found in each section: Heading in Table 1 Description
  • Promoter Identifies the particular promoter by its construct ID. Modulates the gene: This row states the name of the gene modulated by the promoter
  • GenBank description of the gene This field gives the Locus Number of the gene as well as the accession number.
  • the predicted promoter sequence Identifies the nucleic acid promoter sequence in question.
  • the experimental promoter sequence Identifies the nucleic acid sequence in planta driving expression of the reporter gene.
  • the promoter was cloned in the vector: Identifies the vector used into which a promoter was cloned. When cloned into the vector the promoter was Identifies the type of marker linked to the promoter. operably linked to a marker, which was the type: The marker is used to determine patterns of gene expression in plant tissue.
  • Promoter-marker vector was tested in: Identifies the organism in which the promoter- marker vector was tested.
  • Generation screened T1 Mature T2 Identifies the plant generation(s) used in the Seedling T2 Mature T3 Seedling screening process. T1 plants are those plants subjected to the transformation event while the T2 generation plants are from the seeds collected from the T1 plants and T3 plants are from the seeds of T2 plants.
  • the spatial expression of the promoter-marker Identifies the specific parts of the plant where vector was found observed in and would be useful in various levels of GFP expression are observed. expression in any or all of the following: Expression levels are noted as either low (L), medium (M), or high (H). Observed expression pattern of the promoter-marker Identifies a general explanation of where GFP vector was in: expression in different generations of plants was T1 mature: observed. T2 seedling: The promoter can be of use in the following trait Identifies which traits and subtraits the promoter and sub-trait areas: (search for the trait and sub-trait cDNA can modulate table) The promoter has utility in: Identifies a specific function or functions that can be modulated using the promoter cDNA.
  • Bidirectionality is determined by the number of Bidirectionality: base pairs between the promoter and the start codon Exons: of a neighboring gene.
  • a promoter is considered Repeats: bidirectional if it is closer than 200 bp to a start codon of a gene 5′ or 3′ to the promoter.
  • “Exons” (or any coding sequence) identifies if the promoter has overlapped with either the modulating gene's or other neighboring gene's coding sequence.
  • a “fail” for exons means that this overlap has occurred.
  • Reppeats identifies the presence of normally occurring sequence repeats that randomly exist throughout the genome.
  • a “pass” for repeats indicates a lack of repeats in the promoter.
  • An overlap in an exon with the endogenous coding Identifies the specific nucleotides overlapping the sequence to the promoter occurs at base pairs: UTR region or exon of a neighboring gene.
  • the orientation relative to the promoter is designated with a 5′ or 3′.
  • the Ceres cDNA ID of the endogenous coding Identifies the number associated with the Ceres sequence to the promoter: cDNA that corresponds to the endogenous cDNA sequence of the promoter.
  • cDNA nucleotide sequence The nucleic acid sequence of the Ceres cDNA matching the endogenous cDNA region of the promoter.
  • Coding sequence A translated protein sequence of the gene modulated by a protein encoded by a cDNA Microarray Data shows that the coding sequence Microarray data is identified along with the was expressed in the following experiments, which corresponding experiments along with the shows that the promoter would useful to modulate corresponding gene expression. Gene expression is expression in situations similar to the following: identified by a “+” or a “ ⁇ ” in the “SIGN(LOG_RATIO)” column. A “+” notation indicates the cDNA is upregulated while a “ ⁇ ” indicates that the cDNA is downregulated. The “SHORT_NAME” field describes the experimental conditions.
  • the parameters for the microarray experiments Parameters for microarray experiments include age, listed above by EXPT_REP_ID and Short_Name organism, specific tissues, age, treatments and other are as follow below: distinguishing characteristics or features. Table 2
  • Table 1 provides the results of differential expression experiments indicating if the expression levels were increased (“+”) or decreased (“ ⁇ ”). Such increase or decrease expression levels indicates the utility of the corresponding promoter.
  • Table 2 correlates the various differential expression experiments with the utility for the promoter that would be understood from an increased or decreased expression.
  • Table 2 includes three columns, the first column (“EXPT_REP_ID”) lists the microarray experiments by their experimental prep ID number and correspond to the same number listings in Table 1 in the “Microarray data” section.
  • the second column lists the Short_Name of the experiment that corresponds to the EXPT_REP_ID.
  • FIG. 1 A first figure.
  • FIG. 1 is a schematic representation of the vector pNewBin4-HAP1-GFP.
  • the definitions of the abbreviations used in the vector map are as follows:
  • Chimeric is used to describe polynucleotides or genes, as defined supra, or constructs wherein at least two of the elements of the polynucleotide or gene or construct, such as the promoter and the polynucleotide to be transcribed and/or other regulatory sequences and/or filler sequences and/or complements thereof, are heterologous to each other.
  • Constitutive Promoter Promoters referred to herein as “constitutive promoters” actively promote transcription under most, but not necessarily all, environmental conditions and states of development or cell differentiation.
  • constitutive promoters include the cauliflower mosaic virus (CaMV) 35S transcript initiation region and the 1′ or 2′ promoter derived from T-DNA of Agrobacterium tumefaciens , and other transcription initiation regions from various plant genes, such as the maize ubiquitin-1 promoter, known to those of skill.
  • Core Promoter This is the minimal stretch of contiguous DNA sequence that is sufficient to direct accurate initiation of transcription by the RNA polymerase II machinery (for review see: Struhl, 1987 , Cell 49: 295-297; Smale, 1994, In Transcription: Mechanisms and Regulation (eds R. C. Conaway and J. W. Conaway), pp 63-81/Raven Press, Ltd., New York; Smale, 1997 , Biochim. Biophys. Acta 1351: 73-88; Smale et al., 1998 , Cold Spring Harb. Symp. Quant. Biol. 58: 21-31; Smale, 2001 , Genes & Dev. 15: 2503-2508; Weis and Reinberg, 1992 , FASEB J.
  • Domains are fingerprints or signatures that can be used to characterize protein families and/or parts of proteins. Such fingerprints or signatures can comprise conserved (1) primary sequence, (2) secondary structure, and/or (3) three-dimensional conformation. A similar analysis can be applied to polynucleotides. Generally, each domain has been associated with either a conserved primary sequence or a sequence motif. Generally these conserved primary sequence motifs have been correlated with specific in vitro and/or in vivo activities. A domain can be any length, including the entirety of the polynucleotide to be transcribed. Examples of domains include, without limitation, AP2, helicase, homeobox, zinc finger, etc.
  • Endogenous refers to any polynucleotide, polypeptide or protein sequence which is a natural part of a cell or organisms regenerated from said cell.
  • endogenous coding region or “endogenous cDNA” refers to the coding region that is naturally operably linked to the promoter.
  • Enhancer/Suppressor An “enhancer” is a DNA regulatory element that can increase the steady state level of a transcript, usually by increasing the rate of transcription initiation. Enhancers usually exert their effect regardless of the distance, upstream or downstream location, or orientation of the enhancer relative to the start site of transcription.
  • a “suppressor” is a corresponding DNA regulatory element that decreases the steady state level of a transcript, again usually by affecting the rate of transcription initiation.
  • the essential activity of enhancer and suppressor elements is to bind a protein factor(s). Such binding can be assayed, for example, by methods described below. The binding is typically in a manner that influences the steady state level of a transcript in a cell or in an in vitro transcription extract.
  • Exogenous is any polynucleotide, polypeptide or protein sequence, whether chimeric or not, that is introduced into the genome of a host cell or organism regenerated from said host cell by any means other than by a sexual cross. Examples of means by which this can be accomplished are described below, and include Agrobacterium -mediated transformation (of dicots—e.g. Salomon et al. EMBO J. 3:141 (1984); Herrera-Estrella et al. EMBO J. 2:987 (1983); of monocots, representative papers are those by Escudero et al., Plant J.
  • Agrobacterium -mediated transformation of dicots—e.g. Salomon et al. EMBO J. 3:141 (1984); Herrera-Estrella et al. EMBO J. 2:987 (1983); of monocots, representative papers are those by Escudero et al., Plant J.
  • exogenous nucleic acid is referred to here as a T 0 for the primary transgenic plant and T 1 for the first generation.
  • exogenous as used herein is also intended to encompass inserting a naturally found element into a non-naturally found location.
  • Gene encompasses all regulatory and coding sequence contiguously associated with a single hereditary unit with a genetic function.
  • Genes can include non-coding sequences that modulate the genetic function that include, but are not limited to, those that specify polyadenylation, transcriptional regulation, DNA conformation, chromatin conformation, extent and position of base methylation and binding sites of proteins that control all of these.
  • Genes encoding proteins are comprised of “exons” (coding sequences), which may be interrupted by “introns” (non-coding sequences). In some instances complexes of a plurality of protein or nucleic acids or other molecules, or of any two of the above, may be required for a gene's function.
  • a gene's genetic function may require only RNA expression or protein production, or may only require binding of proteins and/or nucleic acids without associated expression.
  • genes adjacent to one another may share sequence in such a way that one gene will overlap the other.
  • a gene can be found within the genome of an organism, in an artificial chromosome, in a plasmid, in any other sort of vector, or as a separate isolated entity.
  • Heterologous sequences are those that are not operatively linked or are not contiguous to each other in nature.
  • a promoter from corn is considered heterologous to an Arabidopsis coding region sequence.
  • a promoter from a gene encoding a growth factor from corn is considered heterologous to a sequence encoding the corn receptor for the growth factor.
  • Regulatory element sequences such as UTRs or 3′ end termination sequences that do not originate in nature from the same gene as the coding sequence originates from, are considered heterologous to said coding sequence.
  • Elements operatively linked in nature and contiguous to each other are not heterologous to each other.
  • a “homologous” gene or polynucleotide or polypeptide refers to a gene or polynucleotide or polypeptide that shares sequence similarity with the gene or polynucleotide or polypeptide of interest. This similarity may be in only a fragment of the sequence and often represents a functional domain such as, examples including without limitation a DNA binding domain or a domain with tyrosine kinase activity. The functional activities of homologous polynucleotide are not necessarily the same.
  • an “inducible promoter” in the context of the current invention refers to a promoter, the activity of which is influenced by certain conditions, such as light, temperature, chemical concentration, protein concentration, conditions in an organism, cell, or organelle, etc.
  • a typical example of an inducible promoter, which can be utilized with the polynucleotides of the present invention, is PARSK1, the promoter from an Arabidopsis gene encoding a serine-threonine kinase enzyme, and which promoter is induced by dehydration, abscissic acid and sodium chloride (Wang and Goodman, Plant J. 8:37 (1995)).
  • Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions, elevated temperature, the presence or absence of a nutrient or other chemical compound or the presence of light.
  • Modulate Transcription Level describes the biological activity of a promoter sequence or promoter control element. Such modulation includes, without limitation, includes up- and down-regulation of initiation of transcription, rate of transcription, and/or transcription levels.
  • Mutant refers to a heritable change in nucleotide sequence at a specific location. Mutant genes of the current invention may or may not have an associated identifiable phenotype.
  • Operable Linkage is a linkage in which a promoter sequence or promoter control element is connected to a polynucleotide sequence (or sequences) in such a way as to place transcription of the polynucleotide sequence under the influence or control of the promoter or promoter control element.
  • Two DNA sequences are said to be operably linked if induction of promoter function results in the transcription of mRNA encoding the polynucleotide and if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter sequence to direct the expression of the protein, antisense RNA or ribozyme, or (3) interfere with the ability of the DNA template to be transcribed.
  • a promoter sequence would be operably linked to a polynucleotide sequence if the promoter was capable of effecting transcription of that polynucleotide sequence.
  • Optional Promoter Fragments are used to refer to any sub-sequence of the promoter that is not required for driving transcription of an operationally linked coding region. These fragments comprise the 5′ UTR and any exon(s) of the endogenous coding region. The optional promoter fragments may also comprise any exon(s) and the 3′ or 5′ UTR of the gene residing upstream of the promoter (that is, 5′ to the promoter). Optional promoter fragments also include any intervening sequences that are introns or sequence that occurs between exons or an exon and the UTR.
  • Orthologous is a term used herein to describe a relationship between two or more polynucleotides or proteins. Two polynucleotides or proteins are “orthologous” to one another if they serve a similar function in different organisms. In general, orthologous polynucleotides or proteins will have similar catalytic functions (when they encode enzymes) or will serve similar structural functions (when they encode proteins or RNA that form part of the ultrastructure of a cell).
  • Percentage of sequence identity is determined by comparing two optimally aligned sequences over a comparison window, where the fragment of the polynucleotide or amino acid sequence in the comparison window may comprise additions or deletions (e.g., gaps or overhangs) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity.
  • Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Add. APL. Math. 2:482 (1981), by the homology alignment algorithm of Needleman and Wunsch J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson and Lipman Proc. Natl. Acad. Sci. (USA) 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, PASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection. Given that two sequences have been identified for comparison, GAP and BESTFIT are preferably employed to determine their optimal alignment. Typically, the default values of 5.00 for gap weight and 0.30 for gap weight length are used.
  • Plant Promoter is a promoter capable of initiating transcription in plant cells and can modulate transcription of a polynucleotide. Such promoters need not be of plant origin.
  • promoters derived from plant viruses such as the CaMV35S promoter or from Agrobacterium tumefaciens such as the T-DNA promoters, can be plant promoters.
  • a typical example of a plant promoter of plant origin is the maize ubiquitin-1 (ubi-1) promoter known to those of skill.
  • Plant Tissue includes differentiated and undifferentiated tissues or plants, including but not limited to roots, stems, shoots, cotyledons, epicotyl, hypocotyl, leaves, pollen, seeds, tumor tissue and various forms of cells in culture such as single cells, protoplast, embryos, and callus tissue.
  • the plant tissue may be in plants or in organ, tissue or cell culture.
  • Preferential Transcription is defined as transcription that occurs in a particular pattern of cell types or developmental times or in response to specific stimuli or combination thereof.
  • Non-limitive examples of preferential transcription include: high transcript levels of a desired sequence in root tissues; detectable transcript levels of a desired sequence in certain cell types during embryogenesis; and low transcript levels of a desired sequence under drought conditions. Such preferential transcription can be determined by measuring initiation, rate, and/or levels of transcription.
  • promoter is a DNA sequence that directs the transcription of a polynucleotide. Typically a promoter is located in the 5′ region of a polynucleotide to be transcribed, proximal to the transcriptional start site of such polynucleotide.
  • promoters are defined as the region upstream of the first exon; more typically, as a region upstream of the first of multiple transcription start sites; more typically, as the region downstream of the preceding gene and upstream of the first of multiple transcription start sites; more typically, the region downstream of the polyA signal and upstream of the first of multiple transcription start sites; even more typically, about 3,000 nucleotides upstream of the ATG of the first exon; even more typically, 2,000 nucleotides upstream of the first of multiple transcription start sites.
  • the promoters of the invention comprise at least a core promoter as defined above. Frequently promoters are capable of directing transcription of genes located on each of the complementary DNA strands that are 3′ to the promoter.
  • promoters exhibit bidirectionality and can direct transcription of a downstream gene when present in either orientation (i.e. 5′ to 3′ or 3′ to 5′ relative to the coding region of the gene).
  • the promoter may also include at least one control element such as an upstream element.
  • control elements include UARs and optionally, other DNA sequences that affect transcription of a polynucleotide such as a synthetic upstream element.
  • Promoter control element describes elements that influence the activity of the promoter.
  • Promoter control elements include transcriptional regulatory sequence determinants such as, but not limited to, enhancers, scaffold/matrix attachment regions, TATA boxes, transcription start locus control regions, UARs, URRs, other transcription factor binding sites and inverted repeats.
  • Public sequence refers to any sequence that has been deposited in a publicly accessible database prior to the filing date of the present application. This term encompasses both amino acid and nucleotide sequences. Such sequences are publicly accessible, for example, on the BLAST databases on the NCBI FTP web site (accessible at ncbi.nlm.nih.gov/ftp). The database at the NCBI FTP site utilizes “gi” numbers assigned by NCBI as a unique identifier for each sequence in the databases, thereby providing a non-redundant database for sequence from various databases, including GenBank, EMBL, DBBJ, (DNA Database of Japan) and PDB (Brookhaven Protein Data Bank).
  • regulatory sequence refers to any nucleotide sequence that influences transcription or translation initiation and rate, or stability and/or mobility of a transcript or polypeptide product. Regulatory sequences include, but are not limited to, promoters, promoter control elements, protein binding sequences, 5′ and 3′ UTRs, transcriptional start sites, termination sequences, polyadenylation sequences, introns, certain sequences within amino acid coding sequences such as secretory signals, protease cleavage sites, etc.
  • Related sequences refer to either a polypeptide or a nucleotide sequence that exhibits some degree of sequence similarity with a reference sequence.
  • specific promoters refers to a subset of promoters that have a high preference for modulating transcript levels in a specific tissue or organ or cell and/or at a specific time during development of an organism.
  • high preference is meant at least 3-fold, preferably 5-fold, more preferably at least 10-fold still more preferably at least 20-fold, 50-fold or 100-fold increase in transcript levels under the specific condition over the transcription under any other reference condition considered.
  • Typical examples of temporal and/or tissue or organ specific promoters of plant origin that can be used with the polynucleotides of the present invention, are: PTA29, a promoter which is capable of driving gene transcription specifically in tapetum and only during anther development (Koltonow et al., Plant Cell 2:1201 (1990); RCc2 and RCc3, promoters that direct root-specific gene transcription in rice (Xu et al., Plant Mol. Biol. 27:237 (1995); TobRB27, a root-specific promoter from tobacco (Yamamoto et al., Plant Cell 3:371 (1991)).
  • tissue-specific promoters under developmental control include promoters that initiate transcription only in certain tissues or organs, such as root, ovule, fruit, seeds, or flowers.
  • Other specific promoters include those from genes encoding seed storage proteins or the lipid body membrane protein, oleosin. A few root-specific promoters are noted above. See also “Preferential transcription”.
  • Stringency is a function of probe length, probe composition (G+C content), and salt concentration, organic solvent concentration, and temperature of hybridization or wash conditions. Stringency is typically compared by the parameter T m , which is the temperature at which 50% of the complementary molecules in the hybridization are hybridized, in terms of a temperature differential from T m . High stringency conditions are those providing a condition of T m ⁇ 5° C. to T m ⁇ 10° C. Medium or moderate stringency conditions are those providing T m ⁇ 20° C. to T m ⁇ 29° C. Low stringency conditions are those providing a condition of T m ⁇ 40° C. to T m ⁇ 48° C.
  • T m 81.5 ⁇ 16.6(log 10 [Na + ])+0.41(% G+C ) ⁇ (600 /N ) (1) where N is the length of the probe.
  • N is the length of the probe.
  • This equation works well for probes 14 to 70 nucleotides in length that are identical to the target sequence.
  • the equation below for T m of DNA-DNA hybrids is useful for probes in the range of 50 to greater than 500 nucleotides, and for conditions that include an organic solvent (formamide).
  • T m 81.5+16.6log ⁇ [Na + ]/(1+0.7[Na + ]) ⁇ +0.41(% G+C ) ⁇ 500 /L 0.63(% formamide) (2) where L is the length of the probe in the hybrid.
  • the T m of equation (2) is affected by the nature of the hybrid; for DNA-RNA hybrids T m is 10-15° C. higher than calculated, for RNA-RNA hybrids T m is 20-25° C. higher. Because the T m decreases about 1° C. for each 1% decrease in homology when a long probe is used (Bonner et al., J. Mol. Biol. 81:123 (1973)), stringency conditions can be adjusted to favor detection of identical genes or related family members.
  • Equation (2) is derived assuming equilibrium and therefore, hybridizations according to the present invention are most preferably performed under conditions of probe excess and for sufficient time to achieve equilibrium.
  • the time required to reach equilibrium can be shortened by inclusion of a hybridization accelerator such as dextran sulfate or another high volume polymer in the hybridization buffer.
  • Stringency can be controlled during the hybridization reaction or after hybridization has occurred by altering the salt and temperature conditions of the wash solutions used.
  • the formulas shown above are equally valid when used to compute the stringency of a wash solution.
  • Preferred wash solution stringencies lie within the ranges stated above; high stringency is 5-8° C. below T m , medium or moderate stringency is 26-29° C. below T m and low stringency is 45-48° C. below T m .
  • a composition containing A is “substantially free of” B when at least 85% by weight of the total A+B in the composition is A.
  • A comprises at least about 90% by weight of the total of A+B in the composition, more preferably at least about 95% or even 99% by weight.
  • a plant gene can be substantially free of other plant genes.
  • Other examples include, but are not limited to, ligands substantially free of receptors (and vice versa), a growth factor substantially free of other growth factors and a transcription binding factor substantially free of nucleic acids.
  • TATA to start shall mean the distance, in number of nucleotides, between the primary TATA motif and the start of transcription.
  • Transgenic plant is a plant having one or more plant cells that contain at least one exogenous polynucleotide introduced by recombinant nucleic acid methods.
  • Translational start site In the context of the present invention, a “translational start site” is usually an ATG or AUG in a transcript, often the first ATG or AUG. A single protein encoding transcript, however, may have multiple translational start sites.
  • Transcription start site is used in the current invention to describe the point at which transcription is initiated. This point is typically located about 25 nucleotides downstream from a TFIID binding site, such as a TATA box. Transcription can initiate at one or more sites within the gene, and a single polynucleotide to be transcribed may have multiple transcriptional start sites, some of which may be specific for transcription in a particular cell-type or tissue or organ. “+1” is stated relative to the transcription start site and indicates the first nucleotide in a transcript.
  • Upstream Activating Region An “Upstream Activating Region” or “UAR” is a position or orientation dependent nucleic acid element that primarily directs tissue, organ, cell type, or environmental regulation of transcript level, usually by affecting the rate of transcription initiation.
  • Corresponding DNA elements that have a transcription inhibitory effect are called herein “Upstream Repressor Regions” or “URR”s.
  • the essential activity of these elements is to bind a protein factor. Such binding can be assayed by methods described below. The binding is typically in a manner that influences the steady state level of a transcript in a cell or in vitro transcription extract.
  • UTR Untranslated region
  • a “UTR” is any contiguous series of nucleotide bases that is transcribed, but is not translated.
  • a 5′ UTR lies between the start site of the transcript and the translation initiation codon and includes the +1 nucleotide.
  • a 3′ UTR lies between the translation termination codon and the end of the transcript.
  • UTRs can have particular functions such as increasing mRNA message stability or translation attenuation. Examples of 3′ UTRs include, but are not limited to polyadenylation signals and transcription termination sequences.
  • variants are used herein to denote a polypeptide or protein or polynucleotide molecule that differs from others of its kind in some way.
  • polypeptide and protein variants can consist of changes in amino acid sequence and/or charge and/or post-translational modifications (such as glycosylation, etc).
  • polynucleotide variants can consist of changes that add or delete a specific UTR or exon sequence. It will be understood that there may be sequence variations within sequence or fragments used or disclosed in this application. Preferably, variants will be such that the sequences have at least 80%, preferably at least 90%, 95, 97, 98, or 99% sequence identity.
  • Variants preferably measure the primary biological function of the native polypeptide or protein or polynucleotide.
  • the polynucleotides of the invention comprise promoters and promoter control elements that are capable of modulating transcription.
  • promoters and promoter control elements can be used in combination with native or heterologous promoter fragments, control elements or other regulatory sequences to modulate transcription and/or translation.
  • promoters and control elements of the invention can be used to modulate transcription of a desired polynucleotide, which includes without limitation:
  • the promoters and promoter control elements of the instant invention are useful to produce preferential transcription which results in a desired pattern of transcript levels in a particular cells, tissues, or organs, or under particular conditions.
  • the promoters and promoter control elements of the present invention are presented in Table 1 in the section entitled “The predicted promoter” sequence and were identified from Arabidopsis thaliana or Oryza sativa . Additional promoter sequences encompassed by the invention can be identified as described below.
  • PCR polymerase chain reaction
  • Polynucleotide libraries comprising genomic sequences can be constructed according to Sambrook et al., Molecular Cloning: A Laboratory Manual, 2 nd Ed. (1989) Cold Spring Harbor Press, Cold Spring Harbor, N.Y.), for example.
  • tail-PCR for example, Liu et al., Plant J 8(3): 457-463 (September, 1995); Liu et al., Genomics 25: 674-681 (1995); Liu et al., Nucl. Acids Res. 21(14): 3333-3334 (1993); and Zoe et al., BioTechniques 27(2): 240-248 (1999); for RACE, see, for example, PCR Protocols: A Guide to Methods and Applications , (1990) Academic Press, Inc.
  • promoters and promoter control elements described in Table 1 in the section entitled “The predicted promoter” sequence can be chemically synthesized according to techniques in common use. See, for example, Beaucage et al., Tet. Lett . (1981) 22: 1859 and U.S. Pat. No. 4,668,777.
  • Such chemical oligonucleotide synthesis can be carried out using commercially available devices, such as, Biosearch 4600 or 8600 DNA synthesizer, by Applied Biosystems, a division of Perkin-Elmer Corp., Foster City, Calif., USA; and Expedite by Perceptive Biosystems, Framingham, Mass., USA.
  • Synthetic RNA including natural and/or analog building blocks, can be synthesized on the Biosearch 8600 machines, see above.
  • Oligonucleotides can be synthesized and then ligated together to construct the desired polynucleotide.
  • the reduced promoters can be isolated from the promoters of the invention by deleting at least one 5′ UTR, exon or 3′ UTR sequence present in the promoter sequence that is associated with a gene or coding region located 5′ to the promoter sequence or in the promoter's endogenous coding region.
  • the “core” promoter sequences can be generated by deleting all 5′ UTRs, exons and 3′ UTRs present in the promoter sequence and the associated intervening sequences that are related to the gene or coding region 5′ to the promoter region and the promoter's endogenous coding region.
  • promoter and promoter control elements that are related to those described in Table 1 in the section entitled “The predicted promoter sequence”. Such related sequence can be isolated utilizing
  • Relatives can include both naturally occurring promoters and non-natural promoter sequences.
  • Non-natural related promoters include nucleotide substitutions, insertions or deletions of naturally-occurring promoter sequences that do not substantially affect transcription modulation activity.
  • the binding of relevant DNA binding proteins can still occur with the non-natural promoter sequences and promoter control elements of the present invention.
  • promoter sequences and promoter control elements exist as functionally important regions, such as protein binding sites, and spacer regions. These spacer regions are apparently required for proper positioning of the protein binding sites. Thus, nucleotide substitutions, insertions and deletions can be tolerated in these spacer regions to a certain degree without loss of function.
  • the effects of substitutions, insertions and deletions to the promoter sequences or promoter control elements may be to increase or decrease the binding of relevant DNA binding proteins to modulate transcript levels of a polynucleotide to be transcribed. Effects may include tissue-specific or condition-specific modulation of transcript levels of the polypeptide to be transcribed.
  • Polynucleotides representing changes to the nucleotide sequence of the DNA-protein contact region by insertion of additional nucleotides, changes to identity of relevant nucleotides, including use of chemically-modified bases, or deletion of one or more nucleotides are considered encompassed by the present invention.
  • promoters exhibiting nucleotide sequence identity to those described in Table 1 in the section entitled “The predicted promoter sequence”.
  • such related promoters exhibit at least 80% sequence identity, preferably at least 85%, more preferably at least 90%, and most preferably at least 95%, even more preferably, at least 96%, 97%, 98% or 99% sequence identity compared to those shown in Table 1 in the section entitled “The predicted promoter” sequence.
  • sequence identity can be calculated by the algorithms and computers programs described above.
  • sequence identity is exhibited in an alignment region that is at least 75% of the length of a sequence shown in Table 1 in the section entitled “The predicted promoter” sequence or corresponding full-length sequence; more usually at least 80%; more usually, at least 85%, more usually at least 90%, and most usually at least 95%, even more usually, at least 96%, 97%, 98% or 99% of the length of a sequence shown in Table 1 in the section entitled “The predicted promoter sequence”.
  • the percentage of the alignment length is calculated by counting the number of residues of the sequence in region of strongest alignment, e.g., a continuous region of the sequence that contains the greatest number of residues that are identical to the residues between two sequences that are being aligned. The number of residues in the region of strongest alignment is divided by the total residue length of a sequence in Table 1 in the section entitled “The predicted promoter sequence”.
  • These related promoters may exhibit similar preferential transcription as those promoters described in Table 1 in the section entitled “The predicted promoter sequence”.
  • Naturally occurring promoters that exhibit nucleotide sequence identity to those shown in Table 1 in the section entitled “The predicted promoter sequence” can be isolated using the techniques as described above. More specifically, such related promoters can be identified by varying stringencies, as defined above, in typical hybridization procedures such as Southern blots or probing of polynucleotide libraries, for example.
  • Non-natural promoter variants of those shown in Table 1 can be constructed using cloning methods that incorporate the desired nucleotide variation. See, for example, Ho, S. N., et al. Gene 77:51-59 1989, describing a procedure site directed mutagenesis using PCR.
  • the present invention includes non-natural promoters that exhibit the above-sequence identity to those in Table 1.
  • the promoters and promoter control elements of the present invention may also be synthesized with 5′ or 3′ extensions, to facilitate additional manipulation, for instance.
  • the present invention also includes reduced promoter sequences. These sequences have at least one of the optional promoter fragments deleted.
  • Core promoter sequences are another embodiment of the present invention.
  • the core promoter sequences have all of the optional promoter fragments deleted.
  • Polynucleotides of the invention were tested for activity by cloning the sequence into an appropriate vector, transforming plants with the construct and assaying for marker gene expression.
  • Recombinant DNA constructs were prepared which comprise the polynucleotide sequences of the invention inserted into a vector suitable for transformation of plant cells.
  • the construct can be made using standard recombinant DNA techniques (Sambrook et al. 1989) and can be introduced to the species of interest by Agrobacterium -mediated transformation or by other means of transformation as referenced below.
  • the vector backbone can be any of those typical in the art such as plasmids, viruses, artificial chromosomes, BACs, YACs and PACs and vectors of the sort described by
  • the construct comprises a vector containing a sequence of the present invention operationally linked to any marker gene.
  • the polynucleotide was identified as a promoter by the expression of the marker gene.
  • GFP Green Fluorescent Protein
  • the vector may also comprise a marker gene that confers a selectable phenotype on plant cells.
  • the marker may encode biocide resistance, particularly antibiotic resistance, such as resistance to kanamycin, G418, bleomycin, hygromycin, or herbicide resistance, such as resistance to chlorosulfuron or phosphinotricin.
  • Vectors can also include origins of replication, scaffold attachment regions (SARs), markers, homologous sequences, introns, etc.
  • the promoter control elements of the present invention include those that comprise a sequence shown in Table 1 in the section entitled “The predicted promoter sequence” and fragments thereof.
  • the size of the fragments of the row titled “The predicted promoter sequence” can range from 5 bases to 10 kilobases (kb).
  • the fragment size is no smaller than 8 bases; more typically, no smaller than 12; more typically, no smaller than 15 bases; more typically, no smaller than 20 bases; more typically, no smaller than 25 bases; even more typically, no more than 30, 35, 40 or 50 bases.
  • the fragment size in no larger than 5 kb bases; more usually, no larger than 2 kb; more usually, no larger than 1 kb; more usually, no larger than 800 bases; more usually, no larger than 500 bases; even more usually, no more than 250, 200, 150 or 100 bases.
  • promoter control elements exhibiting nucleotide sequence identity to those described in Table 1 in the section entitled “The predicted promoter sequence” of fragments thereof.
  • such related promoters exhibit at least 80% sequence identity, preferably at least 85%, more preferably at least 90%, and most preferably at least 95%, even more preferably, at least 96%, 97%, 98% or 99% sequence identity compared to those shown in Table 1 in the section entitled “The predicted promoter sequence”.
  • sequence identity can be calculated by the algorithms and computers programs described above.
  • RNA polymerase II promoters A common configuration of the promoter control elements in RNA polymerase II promoters is shown below:
  • Promoters are generally modular in nature. Promoters can consist of a basal promoter which functions as a site for assembly of a transcription complex comprising an RNA polymerase, for example RNA polymerase II.
  • a typical transcription complex will include additional factors such as TF II B, TF II D, and TF II E. Of these, TF II D appears to be the only one to bind DNA directly.
  • the promoter might also contain one or more promoter control elements such as the elements discussed above. These additional control elements may function as binding sites for additional transcription factors that have the function of modulating the level of transcription with respect to tissue specificity and of transcriptional responses to particular environmental or nutritional factors, and the like.
  • promoter control element is a polynucleotide sequence representing a binding site for proteins.
  • protein binding sites constitute regions of 5 to 60, preferably 10 to 30, more preferably 10 to 20 nucleotides. Within such binding sites, there are typically 2 to 6 nucleotides which specifically contact amino acids of the nucleic acid binding protein.
  • the protein binding sites are usually separated from each other by 10 to several hundred nucleotides, typically by 15 to 150 nucleotides, often by 20 to 50 nucleotides.
  • protein binding sites in promoter control elements often display dyad symmetry in their sequence. Such elements can bind several different proteins, and/or a plurality of sites can bind the same protein. Both types of elements may be combined in a region of 50 to 1,000 base pairs.
  • Binding sites for any specific factor have been known to occur almost anywhere in a promoter.
  • functional AP-1 binding sites can be located far upstream, as in the rat bone sialoprotein gene, where an AP-1 site located about 900 nucleotides upstream of the transcription start site suppresses expression.
  • an AP-1 site located close to the transcription start site plays an important role in the expression of Moloney murine leukemia virus. Sap et al., Nature, 340, 242-244, (1989).
  • Promoter control elements from the promoters of the instant invention can be identified utilizing bioinformatic or computer driven techniques.
  • One method uses a computer program AlignACE to identify regulatory motifs in genes that exhibit common preferential transcription across a number of time points.
  • the program identifies common sequence motifs in such genes. See, Roth et al., Nature Biotechnol. 16: 949-945 (1998); Tavazoie et al., Nat Genet 1999 July; 22(3):281-5;
  • Genomatix also makes available a GEMS Launcher program and other programs to identify promoter control elements and configuration of such elements. Genomatix is located in Kunststoff, Germany.
  • Protein binding sites of promoters can be identified as reported in “Computer-assisted prediction, classification, and delimination of protein binding sites in nucleic acids”, Frech, et al., Nucleic Acids Research, Vol. 21, No. 7, 1655-1664, 1993.
  • Promoter control elements also can be identified with in-vitro assays, such as transcription detection methods; and with in-vivo assays, such as enhancer trapping protocols.
  • in-vitro assays include detection of binding of protein factors that bind promoter control elements. Fragments of the instant promoters can be used to identify the location of promoter control elements. Another option for obtaining a promoter control element with desired properties is to modify known promoter sequences. This is based on the fact that the function of a promoter is dependent on the interplay of regulatory proteins that bind to specific, discrete nucleotide sequences in the promoter, termed motifs. Such interplay subsequently affects the general transcription machinery and regulates transcription efficiency. These proteins are positive regulators or negative regulators (repressors), and one protein can have a dual role depending on the context (Johnson, P. F. and McKnight, S. L. Annu. Rev. Biochem. 58:799-839 (1989)).
  • in-vitro assay utilizes a known DNA binding factor to isolate DNA fragments that bind. If a fragment or promoter variant does not bind, then a promoter control element has been removed or disrupted.
  • a promoter control element For specific assays, see, for instance, B. Luo et al., J. Mol. Biol. 266:470 (1997), S. Chusacultanachai et al., J. Biol. Chem. 274:23591 (1999), D. Fabbro et al., Biochem. Biophys. Res. Comm. 213:781 (1995)).
  • a fragment of DNA suspected of conferring a particular pattern of specificity can be examined for activity in binding transcription factors involved in that specificity by methods such as DNA footprinting (e.g. D. J. Cousins et al., Immunology 99:101 (2000); V. Kolla et al., Biochem. Biophys. Res. Comm. 266:5 (1999)) or “mobility-shift” assays (E. D. Fabiani et al., J. Biochem. 347:147 (2000); N. Sugiura et al., J. Biochem 347:155 (2000)) or fluorescence polarization (e.g. Royer et al., U.S. Pat. No. 5,445,935). Both mobility shift and DNA footprinting assays can also be used to identify portions of large DNA fragments that are bound by proteins in unpurified transcription extracts prepared from tissues or organs of interest.
  • DNA footprinting e.g. D. J. Cousins et al., Immun
  • Cell-free transcription extracts can be prepared and used to directly assay in a reconstitutable system (Narayan et al., Biochemistry 39:818 (2000)).
  • Promoter control elements can be identified with reporter genes in in-vivo assays with the use of fragments of the instant promoters or variants of the instant promoter polynucleotides.
  • various fragments can be inserted into a vector, comprising a basal or “core” promoter, for example, operably linked to a reporter sequence, which, when transcribed, can produce a detectable label.
  • reporter genes include those encoding luciferase, green fluorescent protein, GUS, neo, cat and bar.
  • reporter sequence can be detected utilizing AFLP and microarray techniques.
  • probe vectors In promoter probe vector systems, genomic DNA fragments are inserted upstream of the coding sequence of a reporter gene that is expressed only when the cloned fragment contains DNA having transcription modulation activity (Neve, R. L. et al., Nature 277:324-325 (1979)). Control elements are disrupted when fragments or variants lacking any transcription modulation activity. Probe vectors have been designed for assaying transcription modulation in E. coli (An, G. et al., J. Bact. 140:400-407 (1979)) and other bacterial hosts (Band, L. et al., Gene 26:313-315 (1983); Achen, M. G., Gene 45:45-49 (1986)), yeast (Goodey, A. R. et al., Mol. Gen. Genet. 204:505-511 (1986)) and mammalian cells (Pater, M. M. et al., J. Mol. App. Gen. 2:363-371 (1984
  • a different design of a promoter/control element trap includes packaging into retroviruses for more efficient delivery into cells.
  • retroviral enhancer trap was described by von Melchner et al. (Genes Dev. 1992; U.S. Pat. No. 5,364,783).
  • the basic design of this vector includes a reporter protein coding sequence engineered into the U3 portion of the 3′ LTR. No splice acceptor consensus sequences are included, limiting its utility to work as an enhancer trap only.
  • a different approach to a gene trap using retroviral vectors was pursued by Friedrich and Soriano (Genes Dev. 1991), who engineered a lacZ-neo fusion protein linked to a splicing acceptor. LacZ-neo fusion protein expression from trapped loci allows not only for drug selection, but also for visualization of ⁇ -galatactosidase expression using the chromogenic substrate, X-gal.
  • Non-natural control elements can be constructed by inserting, deleting or substituting nucleotides into the promoter control elements described above. Such control elements are capable of transcription modulation that can be determined using any of the assays described above.
  • the promoter polynucleotides and promoter control elements of the present invention can be combined with each other to produce the desired preferential transcription.
  • the polynucleotides of the invention can be combined with other known sequences to obtain other useful promoters to modulate, for example, tissue transcription specific or transcription specific to certain conditions.
  • Such preferential transcription can be determined using the techniques or assays described above.
  • promoter control elements within a promoter can affect the ability of the promoter to modulate transcription.
  • the order and spacing of control elements is a factor when constructing promoters.
  • Promoters can contain any number of control elements.
  • a promoter can contain multiple transcription binding sites or other control elements.
  • One element may confer tissue or organ specificity; another element may limit transcription to specific time periods, etc.
  • promoters will contain at least a basal or core promoter as described above. Any additional element can be included as desired.
  • a fragment comprising a basal or “core” promoter can be fused with another fragment with any number of additional control elements.
  • control elements or the configuration or control elements can be determined or optimized to permit the desired protein-polynucleotide or polynucleotide interactions to occur.
  • the binding sites are spaced to allow each factor to bind without steric hinderance.
  • the spacing between two such hybridizing control elements can be as small as a profile of a protein bound to a control element.
  • two protein binding sites can be adjacent to each other when the proteins bind at different times during the transcription process.
  • control elements when two control elements hybridize the spacing between such elements will be sufficient to allow the promoter polynucleotide to hairpin or loop to permit the two elements to bind.
  • the spacing between two such hybridizing control elements can be as small as a t-RNA loop, to as large as 10 kb.
  • the spacing is no smaller than 5 bases; more typically, no smaller than 8;
  • the fragment size in no larger than 5 kb bases; more usually, no larger than 2 kb; more usually, no larger than 1 kb; more usually, no larger than 800 bases; more usually, no larger than 500 bases; even more usually, no more than 250, 200, 150 or 100 bases.
  • Such spacing between promoter control elements can be determined using the techniques and assays described above.
  • promoters that are induced under stress conditions and can be combined with those of the present invention: ldh1 (oxygen stress; tomato; see Germain and Ricard. 1997. Plant Mol Biol 35:949-54), GPx and CAT (oxygen stress; mouse; see Franco et al. 1999. Free Radic Biol Med 27:1122-32), ci7 (cold stress; potato; see Kirch et al. 1997. Plant Mol. Biol. 33:897-909), Bz2 (heavy metals; maize; see Marrs and Walbot. 1997. Plant Physiol 113:93-102), HSP32 (hyperthermia; rat; see Raju and Maines. 1994. Biochim Biophys Acta 1217:273-80); MAPKAPK-2 (heat shock; Drosophila ; see Larochelle and Suter. 1995. Gene 163:209-14).
  • promoters are induced by the presence or absence of light can be used in combination with those of the present invention: Topoisomerase II (pea; see Reddy et al. 1999. Plant Mol Biol 41:125-37), chalcone synthase (soybean; see Wingender et al. 1989. Mol Gen Genet 218:315-22) mdm2 gene (human tumor; see Saucedo et al. 1998. Cell Growth Differ 9:119-30), Clock and BMAL1 (rat; see Namihira et al. 1999. Neurosci Lett 271:1-4, PHYA (Arabidopsis; see Canton and Quail 1999.
  • the promoters and control elements of the following genes can be used in combination with the present invention to confer tissue specificity: MipB (iceplant; Yamada et al. 1995. Plant Cell 7:1129-42) and SUCS (root nodules; broadbean; Kuster et al. 1993. Mol Plant Microbe Interact 6:507-14) for roots, OsSUTI (rice; Hirose et al. 1997. Plant Cell Physiol 38:1389-96) for leaves, Msg (soybean; Stomvik et al. 1999. Plant Mol Biol 41:217-31) for siliques, cell (Arabidopsis; Shani et al. 1997. Plant Mol Biol 34(6):837-42) and ACT11 (Arabidopsis; Huang et al. 1997. Plant Mol Biol 33:125-39) for inflorescence.
  • MipB iceplant; Yamada et al. 1995. Plant Cell 7:1129-42
  • SUCS root no
  • Still other promoters are affected by hormones or participate in specific physiological processes, which can be used in combination with those of present invention.
  • Some examples are the ACC synthase gene that is induced differently by ethylene and brassinosteroids (mung bean; Yi et al. 1999. Plant Mol Biol 41:443-54), the TAPG1 gene that is active during abscission (tomato; Kalaitzis et al. 1995. Plant Mol Biol 28:647-56), and the 1-aminocyclopropane-1-carboxylate synthase gene (carnation; Jones et al. 19951 Plant Mol Biol 28:505-12) and the CP-2/cathepsin L gene (rat; Kim and Wright. 1997. Biol Reprod 57:1467-77), both active during senescence.
  • Vectors are a useful component of the present invention.
  • the present promoters and/or promoter control elements may be delivered to a system such as a cell by way of a vector.
  • delivery may range from simply introducing the promoter or promoter control element by itself randomly into a cell to integration of a cloning vector containing the present promoter or promoter control element.
  • a vector need not be limited to a DNA molecule such as a plasmid, cosmid or bacterial phage that has the capability of replicating autonomously in a host cell. All other manner of delivery of the promoters and promoter control elements of the invention are envisioned.
  • the various T-DNA vector types are a preferred vector for use with the present invention. Many useful vectors are commercially available.
  • Marker sequences typically include genes that provide antibiotic resistance, such as tetracycline resistance, hygromycin resistance or ampicillin resistance, or provide herbicide resistance.
  • Specific selectable marker genes may be used to confer resistance to herbicides such as glyphosate, glufosinate or broxynil (Comai et al., Nature 317: 741-744 (1985); Gordon-Kamm et al., Plant Cell 2: 603-618 (1990); and Stalker et al., Science 242: 419-423 (1988)).
  • Other marker genes exist which provide hormone responsiveness.
  • the promoter or promoter control element of the present invention may be operably linked to a polynucleotide to be transcribed. In this manner, the promoter or promoter control element may modify transcription by modulate transcript levels of that polynucleotide when inserted into a genome.
  • the promoter or promoter control element need not be linked, operably or otherwise, to a polynucleotide to be transcribed.
  • the promoter or promoter control element may be inserted alone into the genome in front of a polynucleotide already present in the genome. In this manner, the promoter or promoter control element may modulate the transcription of a polynucleotide that was already present in the genome.
  • This polynucleotide may be native to the genome or inserted at an earlier time.
  • the promoter or promoter control element may be inserted into a genome alone to modulate transcription. See, for example. Vaucheret, H et al. (1998) Plant J 16: 651-659. Rather, the promoter or promoter control element may be simply inserted into a genome or maintained extrachromosomally as a way to divert transcription resources of the system to itself. This approach may be used to downregulate the transcript levels of a group of polynucleotide(s).
  • polynucleotide to be transcribed is not limited.
  • the polynucleotide may include sequences that will have activity as RNA as well as sequences that result in a polypeptide product. These sequences may include, but are not limited to antisense sequences, ribozyme sequences, spliceosomes, amino acid coding sequences, and fragments thereof.
  • Specific coding sequences may include, but are not limited to endogenous proteins or fragments thereof, or heterologous proteins including marker genes or fragments thereof.
  • Promoters and control elements of the present invention are useful for modulating metabolic or catabolic processes. Such processes include, but are not limited to, secondary product metabolism, amino acid synthesis, seed protein storage, oil development, pest defense and nitrogen usage.
  • expression constructs can be used to inhibit expression of these
  • regulatory elements As explained above, several types of regulatory elements exist concerning transcription regulation. Each of these regulatory elements may be combined with the present vector if desired.
  • the vector of the present invention may contain additional components.
  • an origin of replication allows for replication of the vector in a host cell.
  • homologous sequences flanking a specific sequence allows for specific recombination of the specific sequence at a desired location in the target genome.
  • T-DNA sequences also allow for insertion of a specific sequence randomly into a target genome.
  • the vector may also be provided with a plurality of restriction sites for insertion of a polynucleotide to be transcribed as well as the promoter and/or promoter control elements of the present invention.
  • the vector may additionally contain selectable marker genes.
  • the vector may also contain a transcriptional and translational initiation region, and a transcriptional and translational termination region functional in the host cell.
  • the termination region may be native with the transcriptional initiation region, may be native with the polynucleotide to be transcribed, or may be derived from another source. Convenient termination regions are available from the Ti-plasmid of A. tumefaciens , such as the octopine synthase and nopaline synthase termination regions.
  • the polynucleotide to be transcribed may be optimized for increased expression in a certain host cell.
  • the polynucleotide can be synthesized using preferred codons for improved transcription and translation. See U.S. Pat. Nos. 5,380,831, 5,436, 391; see also and Murray et al., (1989) Nucleic Acids Res. 17:477-498.
  • Additional sequence modifications include elimination of sequences encoding spurious polyadenylation signals, exon intron splice site signals, transposon-like repeats, and other such sequences well characterized as deleterious to expression.
  • the G-C content of the polynucleotide may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell.
  • the polynucleotide sequence may be modified to avoid hairpin secondary mRNA structures.
  • GUS expression vectors and reporter genes can be found in Gruber, et al., “Vectors for Plant Transformation, in Methods in Plant Molecular Biology & Biotechnology” in Glich et al., (Eds. pp. 89-119, CRC Press, 1993). Moreover GUS expression vectors and GUS gene cassettes are available from Clonetech Laboratories, Inc., Palo Alto, Calif. while luciferase expression vectors and luciferase gene cassettes are available from Promega Corp. (Madison, Wis.). GFP vectors are available from Aurora Biosciences.
  • the polynucleotides according to the present invention can be inserted into a host cell.
  • a host cell includes but is not limited to a plant, mammalian, insect, yeast, and prokaryotic cell, preferably a plant cell.
  • the method of insertion into the host cell genome is chosen based on convenience.
  • the insertion into the host cell genome may either be accomplished by vectors that integrate into the host cell genome or by vectors which exist independent of the host cell genome.
  • polynucleotides of the present invention can exist autonomously or independent of the host cell genome.
  • Vectors of these types are known in the art and include, for example, certain type of non-integrating viral vectors, autonomously replicating plasmids, artificial chromosomes, and the like.
  • transient expression of a polynucleotide may be desired.
  • the promoter sequences, promoter control elements or vectors of the present invention may be transformed into host cells. These transformations may be into protoplasts or intact tissues or isolated cells. Preferably expression vectors are introduced into intact tissue.
  • General methods of culturing plant tissues are provided for example by Maki et al. “Procedures for Introducing Foreign DNA into Plants” in Methods in Plant Molecular Biology & Biotechnology, Glich et al. (Eds. pp. 67-88 CRC Press, 1993); and by Phillips et al. “Cell-Tissue Culture and In-Vitro Manipulation” in Corn & Corn Improvement, 3rd Edition 10Sprague et al. (Eds. pp. 345-387) American Society of Agronomy Inc. et al. 1988.
  • Methods of introducing polynucleotides into plant tissue include the direct infection or co-cultivation of plant cell with Agrobacterium tumefaciens , Horsch et al., Science, 227:1229 (1985). Descriptions of Agrobacterium vector systems and methods for Agrobacterium -mediated gene transfer provided by Gruber et al. supra.
  • polynucleotides are introduced into plant cells or other plant tissues using a direct gene transfer method such as microprojectile-mediated delivery, DNA injection, electroporation and the like. More preferably polynucleotides are introduced into plant tissues using the microprojectile media delivery with the biolistic device. See, for example, Tomes et al., “Direct DNA transfer into intact plant cells via microprojectile bombardment” In: Gamborg and Phillips (Eds.) Plant Cell, Tissue and Organ Culture: Fundamental Methods, Springer Verlag, Berlin (1995).
  • expression constructs can be used for gene expression in callus culture for the purpose of expressing marker genes encoding peptides or polypeptides that allow identification of transformed plants.
  • a promoter that is operatively linked to a polynucleotide to be transcribed is transformed into plant cells and the transformed tissue is then placed-on callus-inducing media. If the transformation is conducted with leaf discs, for example, callus will initiate along the cut edges. Once callus growth has initiated, callus cells can be transferred to callus shoot-inducing or callus root-inducing media. Gene expression will occur in the callus cells developing on the appropriate media: callus root-inducing promoters will be activated on callus root-inducing media, etc.
  • peptides or polypeptides useful as transformation markers include, but are not limited to barstar, glyphosate, chloramphenicol acetyltransferase (CAT), kanamycin, spectinomycin, streptomycin or other antibiotic resistance enzymes, green fluorescent protein (GFP), and ⁇ -glucuronidase (GUS), etc.
  • CAT chloramphenicol acetyltransferase
  • GFP green fluorescent protein
  • GUS ⁇ -glucuronidase
  • Some of the exemplary promoters of the row titled “The predicted promoter sequence” will also be capable of sustaining expression in some tissues or organs after the initiation or completion of regeneration. Examples of these tissues or organs are somatic embryos, cotyledon, hypocotyl, epicotyl, leaf, stems, roots, flowers and seed.
  • Integration into the host cell genome also can be accomplished by methods known in the art, for example, by the homologous sequences or T-DNA discussed above or using the cre-lox system (A. C. Vergunst et al., Plant Mol. Biol. 38:393 (1998)).
  • the promoters of the present invention can be used to further understand developmental mechanisms. For example, promoters that are specifically induced during callus formation, somatic embryo formation, shoot formation or root formation can be used to explore the effects of overexpression, repression or ectopic expression of target genes, or for isolation of trans-acting factors.
  • the vectors of the invention can be used not only for expression of coding regions but may also be used in exon-trap cloning, or promoter trap procedures to detect differential gene expression in various tissues, K. Lindsey et al., 1993 “Tagging Genomic Sequences That Direct Transgene Expression by Activation of a Promoter Trap in Plants”, Transgenic Research 2:3347. D. Auch & Reth, et al., “Exon Trap Cloning: Using PCR to Rapidly Detect and Clone Exons from Genomic DNA Fragments”, Nucleic Acids Research, Vol. 18, No. 22, p. 674.
  • Entrapment vectors first described for use in bacteria (Casadaban and Cohen, 1979, Proc. Nat. Aca. Sci. U.S.A., 76: 4530; Casadaban et al., 1980, J. Bacteriol., 143: 971) permit selection of insertional events that lie within coding sequences. Entrapment vectors can be introduced into pluripotent ES cells in culture and then passed into the germline via chimeras (Gossler et al., 1989, Science, 244: 463; Skarnes, 1990, Biotechnology, 8: 827).
  • Promoter or gene trap vectors often contain a reporter gene, e.g., lacZ, lacking its own promoter and/or splice acceptor sequence upstream. That is, promoter gene traps contain a reporter gene with a splice site but no promoter. If the vector lands in a gene and is spliced into the gene product, then the reporter gene is expressed.
  • a reporter gene e.g., lacZ
  • IVET innate promoter traps
  • various bacterial genome fragments are placed in front of a necessary metabolic gene coupled to a reporter gene.
  • the DNA constructs are inserted into a bacterial strain otherwise lacking the metabolic gene, and the resulting bacteria are used to infect the host organism. Only bacteria expressing the metabolic gene survive in the host organism; consequently, inactive constructs can be eliminated by harvesting only bacteria that survive for some minimum period in the host.
  • constitutively active constructs can be eliminated by screening only bacteria that do not express the reporter gene under laboratory conditions.
  • the bacteria selected by such a method contain constructs that are selectively induced only during infection of the host.
  • the IVET approach can be modified for use in plants to identify genes induced in either the bacteria or the plant cells upon pathogen infection or root colonization.
  • For information on IVET see the articles by Mahan et al. in Science 259:686-688 (1993), Mahan et al. in PNAS USA 92:669-673 (1995), Heithoff et al. in PNAS USA 94:934-939 (1997), and Wang et al. in PNAS USA. 93:10434 (1996).
  • promoters and control elements providing constitutive transcription is desired for modulation of transcription in most cells of an organism under most environmental conditions.
  • constitutive transcription is useful for modulating genes involved in defense, pest resistance, herbicide resistance, etc.
  • Constitutive up-regulation and transcription down-regulation is useful for these applications.
  • genes, transcripts, and/or polypeptides that increase defense, pest and herbicide resistance may require constitutive up-regulation of transcription.
  • constitutive transcriptional down-regulation may be desired to inhibit those genes, transcripts, and/or polypeptides that lower defense, pest and herbicide resistance.
  • promoter or control elements that provide constitutive transcription produce transcription levels that are statistically similar in many tissues and environmental conditions observed.
  • P-value is the probability that the difference of transcript levels is not statistically significant. The higher the P-value, the more likely the difference of transcript levels is not significant.
  • One formula used to calculate P-value is as follows: ⁇ (x) dx, integrated from a to ⁇ ,
  • the P-value from the formula ranges from 1.0 to 0.0.
  • each P-value of the transcript levels observed in a majority of cells, tissues, or organs under various environmental conditions produced by the promoter or control element is greater than 10 ⁇ 8 ; more usually, greater than 10 ⁇ 7 ; even more usually, greater than 10 ⁇ 6 ; even more usually, greater than 10 ⁇ 5 or 10 ⁇ 4 .
  • promoter and control elements For up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Promoters and control elements providing modulation of transcription under oxidative, drought, oxygen, wound, and methyl jasmonate stress are particularly useful for producing host cells or organisms that are more resistant to biotic and abiotic stresses.
  • modulation of genes, transcripts, and/or polypeptides in response to oxidative stress can protect cells against damage caused by oxidative agents, such as hydrogen peroxide and other free radicals.
  • the promoters and control elements of the present invention can modulate stresses similar to those described in, for example, stress conditions are VuPLD1 (drought stress; Cowpea; see Pham-Thi et al. 1999. Plant molecular Biology. 1257-65), pyruvate decarboxylase (oxygen stress; rice; see Rivosal et al. 1997. Plant Physiol. 114(3): 1021-29), chromoplast specific carotenoid gene (oxidative stress; capsicum ; see Bouvier et al. 1998. Journal of Biological Chemistry 273: 30651-59).
  • Promoters and control elements providing preferential transcription during wounding or induced by methyl jasmonate can produce a defense response in host cells or organisms.
  • preferential modulation of genes, transcripts, and/or polypeptides under such conditions is useful to induce a defense response to mechanical wounding, pest or pathogen attack or treatment with certain chemicals.
  • Promoters and control elements of the present invention also can trigger a response similar to those described for cf9 (viral pathogen; tomato; see O'Donnell et al. 1998.
  • the Plant journal: for cell and molecular biology 14(1): 137-42 hepatocyte growth factor activator inhibitor type 1 (HAI-1), which enhances tissue regeneration (tissue injury; human; Koono et al. 1999. Journal of Histochemistry and Cytochemistry 47: 673-82), copper amine oxidase (CuAO), induced during ontogenesis and wound healing (wounding; chick-pea; Rea et al. 1998.
  • HAI-1 hepatocyte growth factor activator inhibitor type 1
  • CuAO copper amine oxidase
  • Up-regulation and transcription down-regulation are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase oxidative, flood, or drought tolerance may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to inhibit those genes, transcripts, and/or polypeptides that lower such tolerance.
  • promoter or control elements which provide preferential transcription in wounding or under methyl jasmonate induction, produce transcript levels that are statistically significant as compared to cell types, organs or tissues under other conditions.
  • promoter and control elements For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Promoters and control elements providing preferential transcription when induced by light exposure can be utilized to modulate growth, metabolism, and development; to increase drought tolerance; and decrease damage from light stress for host cells or organisms.
  • modulation of genes, transcripts, and/or polypeptides in response to light is useful
  • Up-regulation and transcription down-regulation are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase drought or light tolerance may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to inhibit those genes, transcripts, and/or polypeptides that lower such tolerance.
  • promoter or control elements which provide preferential transcription in cells, tissues or organs exposed to light, produce transcript levels that are statistically significant as compared to cells, tissues, or organs under decreased light exposure (intensity or length of time).
  • promoter and control elements For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Promoters and control elements providing preferential transcription when induced by dark or decreased light intensity or decreased light exposure time can be utilized to time growth, metabolism, and development, to modulate photosynthesis capabilities for host cells or organisms.
  • modulation of genes, transcripts, and/or polypeptides in response to dark is useful, for example,
  • Up-regulation and transcription down-regulation is useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase growth and development may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to inhibit those genes, transcripts, and/or polypeptides that modulate photosynthesis capabilities.
  • promoter or control elements which provide preferential transcription under exposure to dark or decrease light intensity or decrease exposure time, produce transcript levels that are statistically significant.
  • promoter and control elements For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Promoters and control elements providing preferential transcription in a leaf can modulate growth, metabolism, and development or modulate energy and nutrient utilization in host cells or organisms.
  • preferential modulation of genes, transcripts, and/or polypeptide in a leaf is useful, for example,
  • genes, transcripts, and/or polypeptides that increase growth may require up-regulation of transcription.
  • transcriptional down-regulation may be desired to inhibit energy usage in a leaf to be directed to the fruit instead, for instance.
  • promoter or control elements which provide preferential transcription in the cells, tissues, or organs of a leaf, produce transcript levels that are statistically significant as compared to other cells, organs or tissues.
  • promoter and control elements For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Promoters and control elements providing preferential transcription in a root can modulate growth, metabolism, development, nutrient uptake, nitrogen fixation, or modulate energy and nutrient utilization in host cells or organisms.
  • preferential modulation of genes, transcripts, and/or in a leaf is useful
  • genes, transcripts, and/or polypeptides that increase growth may require up-regulation of transcription.
  • transcriptional down-regulation may be desired to inhibit nutrient usage in a root to be directed to the leaf instead, for instance.
  • promoter or control elements which provide preferential transcription in cells, tissues, or organs of a root, produce transcript levels that are statistically significant as compared to other cells, organs or tissues.
  • promoter and control elements For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Promoters and control elements providing preferential transcription in a stem or shoot can modulate growth, metabolism, and development or modulate energy and nutrient utilization in host cells or organisms.
  • preferential modulation of genes, transcripts, and/or polypeptide in a stem or shoot is useful, for example,
  • genes, transcripts, and/or polypeptides that increase growth may require up-regulation of transcription.
  • transcriptional down-regulation may be desired to inhibit energy usage in a stem/shoot to be directed to the fruit instead, for instance.
  • promoter or control elements which provide preferential transcription in the cells, tissues, or organs of a stem or shoot, produce transcript levels that are statistically significant as compared to other cells, organs or tissues.
  • promoter and control elements For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Promoters and control elements providing preferential transcription in a silique or fruit can time growth, development, or maturity; or modulate fertility; or modulate energy and nutrient utilization in host cells or organisms.
  • preferential modulation of genes, transcripts, and/or polypeptides in a fruit is useful
  • genes, transcripts, and/or polypeptides that increase growth may require up-regulation of transcription.
  • transcriptional down-regulation may be desired to inhibit late fruit maturity, for instance.
  • promoter or control elements which provide preferential transcription in the cells, tissues, or organs of siliques or fruits, produce transcript levels that are statistically significant as compared to other cells, organs or tissues.
  • promoter and control elements For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Promoters and control elements providing preferential transcription in a callus can be useful to modulating transcription in dedifferentiated host cells.
  • preferential modulation of genes, transcripts, in callus is useful to modulate transcription of a marker gene, which can facilitate selection of cells that are transformed with exogenous polynucleotides.
  • genes, transcripts, and/or polypeptides that increase marker gene detectability may require up-regulation of transcription.
  • transcriptional down-regulation may be desired to increase the ability of the calluses to later differentiate, for instance.
  • promoter or control elements which provide preferential transcription in callus, produce transcript levels that are statistically significant as compared to other cell types, tissues, or organs. Calculation of P-value from the different observed transcript levels is one means of determining whether a promoter or control element is providing such preferential transcription.
  • each P-value of the transcript levels observed in callus as compared to, at least one other cell type, tissue or organ is less than 10 ⁇ 4 ; more usually, less than 10 ⁇ 5 ; even more usually, less than 10 ⁇ 6 ; even more usually, less than 10 ⁇ 7 or 10 ⁇ 8 .
  • promoter and control elements For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Promoters and control elements providing preferential transcription in flowers can modulate pigmentation; or modulate fertility in host cells or organisms.
  • preferential modulation of genes, transcripts, and/or polypeptides in a flower is useful,
  • genes, transcripts, and/or polypeptides that increase pigmentation, for example, may require up-regulation of transcription.
  • transcriptional down-regulation may be desired to inhibit fertility, for instance.
  • promoter or control elements which provide preferential transcription in flowers, produce transcript levels that are statistically significant as compared to other cells, organs or tissues.
  • promoter and control elements For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Promoters and control elements providing preferential transcription in a immature bud or inflorescence can time growth, development, or maturity; or modulate fertility or viability in host cells or organisms.
  • preferential modulation of genes, transcripts, and/or polypeptide in a fruit is useful,
  • genes, transcripts, and/or polypeptides that increase growth may require up-regulation of transcription.
  • transcriptional down-regulation may be desired to decrease endosperm size, for instance.
  • promoter or control elements which provide preferential transcription in immature buds and inflorescences, produce transcript levels that are statistically significant as compared to other cell types, organs or tissues.
  • promoter and control elements For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Promoters and control elements providing preferential transcription during senescence can be used to modulate cell degeneration, nutrient mobilization, and scavenging of free radicals in host cells or organisms.
  • Other types of responses that can be modulated include, for example, senescence associated genes (SAG) that encode enzymes thought to be involved in cell degeneration and nutrient mobilization (Arabidopsis; see Hensel et al. 1993. Plant Cell 5: 553-64), and the CP-2/cathepsin L gene (rat; Kim and Wright. 1997. Biol Reprod 57: 1467-77), both induced during senescence.
  • SAG senescence associated genes
  • CP-2/cathepsin L gene rat; Kim and Wright. 1997. Biol Reprod 57: 1467-77
  • preferential modulation of genes, transcripts, and/or polypeptides during senescencing is useful to modulate fruit ripening.
  • genes, transcripts, and/or polypeptides that increase scavenging of free radicals may require up-regulation of transcription.
  • transcriptional down-regulation may be desired to inhibit cell degeneration, for instance.
  • promoter or control elements which provide preferential transcription in cells, tissues, or organs during senescence, produce transcript levels that are statistically significant as compared to other conditions.
  • promoter and control elements For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Promoters and control elements providing preferential transcription in a germinating seed can time growth, development, or maturity; or modulate viability in host cells or organisms.
  • preferential modulation of genes, transcripts, and/or polypeptide in a germinating seed is useful,
  • genes, transcripts, and/or polypeptides that increase growth may require up-regulation of transcription.
  • transcriptional down-regulation may be desired to decrease endosperm size, for instance.
  • promoter or control elements which provide preferential transcription in a germinating seed, produce transcript levels that are statistically significant as compared to other cell types, organs or tissues.
  • promoter and control elements For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • a major way that a cell controls its response to internal or external stimuli is by regulating the rate of transcription of specific genes.
  • the differentiation of cells during organogenensis into forms characteristic of the organ is associated with the selective activation and repression of large numbers of genes.
  • specific organs, tissues and cells are functionally distinct due to the different populations of mRNAs and protein products they possess.
  • Internal signals program the selective activation and repression programs.
  • internally synthesized hormones produce such signals. The level of hormone can be raised by increasing the level of transcription of genes encoding proteins concerned with hormone synthesis.
  • mRNA levels can be measured and used as an indicator for the extent of transcription of the gene.
  • Cells can be exposed to a stimulus, and mRNA can be isolated and assayed at different time points after stimulation. The mRNA from the stimulated cells can be compared to control cells that were not stimulated. The mRNA levels that are higher in the stimulated cell versus the control indicate a stimulus-specific response of the cell. The same is true of mRNA levels that are lower in stimulated cells versus the control condition.
  • Applicants have utilized microarray techniques to measure the levels of mRNAs in cells from plants transformed with a construct containing the promoter or control elements of the present invention together with their endogenous cDNA sequences.
  • transformants with the constructs were grown to an appropriate stage, and tissue samples were prepared for the microarray differential expression analysis. In this manner it is possible to determine the differential expression for the cDNAs under the control of the endogenous promoter under various conditions.
  • Tissue samples for each of the expression analysis experiments were prepared as follows:
  • Seeds of Arabidopsis thaliana were sterilized in full strength bleach for less than 5 min., washed more than 3 times in sterile distilled deionized water and plated on MS agar plates. The plates were placed at 4° C. for 3 nights and then placed vertically into a growth chamber having 16 hr light/8 hr dark cycles, 23° C., 70% relative humidity and ⁇ 11,000 LUX. After 2 weeks, the roots were cut from the agar, flash frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Arabidopsis thaliana (Ws) seed was vernalized at 4° C. for 3 days before sowing in Metro-mix soil type 350. Flats were placed in a growth chamber having 16 hr light/8 hr dark, 80% relative humidity, 23° C. and 13,000 LUX for germination and growth. After 3 weeks, rosette leaves, stems, and siliques were harvested, flash frozen in liquid nitrogen and stored at ⁇ 80° C. until use. After 4 weeks, siliques ( ⁇ 5 mm, 5-10 mm and >10 mm) were harvested, flash frozen in liquid nitrogen and stored at ⁇ 80° C. until use. 5 week old whole plants (used as controls) were harvested, flash frozen in liquid nitrogen and kept at ⁇ 80° C. until RNA was isolated.
  • Arabidopsis thaliana seeds (ecotype Ws) were sterilized in bleach and rinsed with sterile water. The seeds were placed in 100 mm petri plates containing soaked autoclaved filter paper. Plates were foil-wrapped and left at 4° C. for 3 nights to vernalize. After cold treatment, the foil was removed and plates were placed into a growth chamber having 16 hr light/8 hr dark cycles, 23° C., 70% relative humidity and ⁇ 11,000 lux. Seeds were collected 1 d, 2 d, 3 d and 4 d later, flash frozen in liquid nitrogen and stored at ⁇ 80° C. until RNA was isolated.
  • Seeds of Arabidopsis thaliana were sown in trays and left at 4° C. for 4 days to vernalize. They were then transferred to a growth chamber having grown 16 hr light/8 hr dark, 13,000 LUX, 70% humidity, and 20° C. and watered twice a week with 1 L of 1 ⁇ Hoagland's solution. Approximately 1,000 14 day old plants were spayed with 200-250 mls of 100 ⁇ M ABA in a 0.02% solution of the detergent Silwet L-77. Whole seedlings, including roots, were harvested within a 15 to 20 minute time period at 1 hr and 6 hr after treatment, flash-frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 100 ⁇ M ABA for treatment. Control plants were treated with water. After 6 hr and 24 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • tissue was prepared from two different mutants; (1) a dwf4-1 knock out mutant and (2) a mutant overexpressing the dwf4-1 gene.
  • Seeds of wild-type Arabidopsis thaliana (ecotype Wassilewskija) and of the dwf4-1 knock out and overexpressor mutants were sown in trays and left at 4° C. for 4 days to vernalize. They were then transferred to a growth chamber having 16 hr light/8 hr dark, 11,000 LUX, 70% humidity and 22° C. temperature. Tissue from shoot parts (unopened floral primordia and shoot apical meristems) was flash-frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in I-liter beakers with 0.1 ⁇ M epi-brassinolide for treatment. Control plants were treated with distilled deionized water. After 24 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • Wild type Arabidopsis thaliana seeds (ecotpye Ws) were surface sterilized with 30% Clorox, 0.1% Triton X-100 for 5 minutes. Seeds were then rinsed with 4-5 exchanges of sterile double distilled deionized water. Seeds were vernalized at 4° C. for 2-4 days in darkness. After cold treatment, seeds were plated on modified 1 ⁇ MS media (without NH 4 NO 3 or KNO 3 ), 0.5% sucrose, 0.5 g/L MES pH5.7, 1% phytagar and supplemented with KNO 3 to a final concentration of 60 mM (high nitrate modified 1 ⁇ MS media). Plates were then grown for 7 days in a Percival growth chamber at 22° C. with 16 hr. light/8 hr dark.
  • Germinated seedlings were then transferred to a sterile flask containing 50 mL of high nitrate modified 1 ⁇ MS liquid media. Seedlings were grown with mild shaking for 3 additional days at 22° C. in 16 hr. light/8 hr dark (in a Percival growth chamber) on the high nitrate modified 1 ⁇ MS liquid media.
  • seedlings were transferred either to a new sterile flask containing 50 mL of high nitrate modified 1 ⁇ MS liquid media or to low nitrate modified 1 ⁇ MS liquid media (containing 20 ⁇ M KNO 3 ). Seedlings were grown in these media conditions with mild shaking at 22° C. in 16 hr light/8 hr dark for the appropriate time points and whole seedlings harvested for total RNA isolation via the Trizol method (LifeTech.). The time points used for the microarray experiments were 10 min. and 1 hour time points for both the high and low nitrate modified 1 ⁇ MS media.
  • seeds that were surface sterilized in 30% bleach containing 0.1% Triton X-100 and further rinsed in sterile water were planted on MS agar, (0.5% sucrose) plates containing 50 mM KNO 3 (potassium nitrate).
  • the seedlings were grown under constant light (3500 LUX) at 22° C. After 12 days, seedlings were transferred to MS agar plates containing either 1 mM KNO 3 or 50 mM KNO 3 . Seedlings transferred to agar plates containing 50 mM KNO 3 were treated as controls in the experiment. Seedlings transferred to plates with 1 mM KNO 3 were rinsed thoroughly with sterile MS solution containing 1 mM KNO 3 . There were ten plates per transfer. Root tissue was collected and frozen in 15 mL Falcon tubes at various time points which included 1 hour, 2 hours, 3 hours, 4 hours, 6 hours, 9 hours, 12 hours, 16 hours, and 24 hours.
  • Corn root tissues isolated at the 4 hr and 16 hr time points were used for the microarray experiments. Both the high and low nitrate modified 1 ⁇ MS media were used.
  • Arabidopsis thaliana ecotype Ws seeds were sown on flats containing 4 L of a 1:2 mixture of Grace Zonolite vermiculite and soil. Flats were watered with 3 L of water and vernalized at 4° C. for five days. Flats were placed in a Conviron growth chamber having 16 hr light/8 hr dark at 20° C., 80% humidity and 17,450 LUX. Flats were watered with approximately 1.5 L of water every four days. Mature, bolting plants (24 days after germination) were bottom treated with 2 L of either a control (100 mM mannitol pH 5.5) or an experimental (50 mM ammonium nitrate, pH 5.5) solution. Roots, leaves and siliques were harvested separately 30, 120 and 240 minutes after treatment, flash frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Hybrid maize seed (Pioneer hybrid 35A19) were aerated overnight in deionized water. Thirty seeds were plated in each flat, which contained 4 liters of Grace zonolite vermiculite. Two liters of water were bottom fed and flats were kept in a Conviron growth chamber with 16 hr light/8 hr dark at 20° C. and 80% humidity. Flats were watered with 1 L of tap water every three days. Five day old seedlings were treated as described above with 2 L of either a control (100 mM mannitol pH 6.5) solution or 1 L of an experimental (50 mM ammonium nitrate, pH 6.8) solution. Fifteen shoots per time point per treatment were harvested 10, 90 and 180 minutes after treatment, flash frozen in liquid nitrogen and stored at ⁇ 80° C.
  • seeds of Arabidopsis thaliana were left at 4° C. for 3 days to vernalize. They were then sown on vermiculite in a growth chamber having 16 hours light/8 hours dark, 12,000-14,000 LUX, 70% humidity, and 20° C. They were bottom-watered with tap water, twice weekly. Twenty-four days old plants were sprayed with either water (control) or 0.6% ammonium nitrate at 4 ⁇ L/cm 2 of tray surface. Total shoots and some primary roots were cleaned of vermiculite, flash-frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Seeds of Arabidopsis thaliana were sown in trays and left at 4° C. for 4 days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr. dark, 13,000 LUX, 70% humidity, 20° C. temperature and watered twice a week with 1 L of a 1 ⁇ Hoagland's solution.
  • Approximately 1,000 14 day old plants were spayed with 200-250 mls of 0.001% methyl jasmonate in a 0.02% solution of the detergent Silwet L-77.
  • whole seedlings, including roots were harvested within a 15 to 20 minute time period, flash-frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 0.001% methyl jasmonate for treatment. Control plants were treated with water. After 24 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • Seeds of Arabidopsis thaliana were sown in trays and left at 4° C. for 4 days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr. dark, 13,000 LUX, 70% humidity, 20° C. temperature and watered twice a week with 1 L of a 1 ⁇ Hoagland's solution.
  • Approximately 1,000 14 day old plants were spayed with 200-250 mls of 5 mM salicylic acid (solubilized in 70% ethanol) in a 0.02% solution of the detergent Silwet L-77.
  • whole seedlings, including roots were harvested within a 15 to 20 minute time period flash-frozen in liquid nitrogen and stored at ⁇ 80° C.
  • seeds of wild-type Arabidopsis thaliana (ecotype Columbia) and mutant CS3726 were sown in soil type 200 mixed with osmocote fertilizer and Marathon insecticide and left at 4° C. for 3 days to vernalize. Flats were incubated at room temperature with continuous light. Sixteen days post germination plants were sprayed with 2 mM SA, 0.02% SilwettL-77 or control solution (0.02% SilwettL-77. Aerial parts or flowers were harvested 1 hr, 4 hr, 6 hr, 24 hr and 3 weeks post-treatment flash frozen and stored at ⁇ 80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 2 mM SA for treatment. Control plants were treated with water. After 12 hr and 24 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • Seeds of Arabidopsis thaliana were sown in pots and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 150,000-160,000 LUX, 20° C. and 70% humidity. After 14 days, aerial tissues were cut and left to dry on 3 MM Whatman paper in a Petri-plate for 1 hour and 6 hours. Aerial tissues exposed for 1 hour and 6 hours to 3 MM Whatman paper wetted with 1 ⁇ Hoagland's solution served as controls. Tissues were harvested, flash-frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Arabidopsis thaliana (Ws) seed was vernalized at 4° C. for 3 days before sowing in Metromix soil type 350. Flats were placed in a growth chamber with 23° C., 16 hr light/8 hr. dark, 80% relative humidity, ⁇ 13,000 LUX for germination and growth. Plants were watered with 1-1.5 L of water every four days. Watering was stopped 16 days after germination for the treated samples, but continued for the control samples. Rosette leaves and stems, flowers and siliques were harvested 2 d, 3 d, 4 d, 5 d, 6 d and 7 d after watering was stopped. Tissue was flash frozen in liquid nitrogen and kept at ⁇ 80° C. until RNA was isolated. Flowers and siliques were also harvested on day 8 from plants that had undergone a 7 d drought treatment followed by 1 day of watering. Control plants (whole plants) were harvested after 5 weeks, flash frozen in liquid nitrogen and stored as above.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in empty 1-liter beakers at room temperature for treatment. Control plants were placed in water. After 1 hr, 6 hr, 12 hr and 24 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • Seeds of Arabidopsis thaliana were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C., and 70% humidity. After 14 days, the aerial tissues were cut and placed on 3 MM Whatman paper in a petri-plate wetted with 20% PEG (polyethylene glycol-M r 8,000) in 1 ⁇ Hoagland's solution. Aerial tissues on 3 MM Whatman paper containing 1 ⁇ Hoagland's solution alone served as the control. Aerial tissues were harvested at 1 hour and 6 hours after treatment, flash-frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 10% PEG (polyethylene glycol-M r 8,000) for treatment. Control plants were treated with water. After 1 hr and 6 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 150 mM NaCl for treatment. Control plants were treated with water. After 1 hr, 6 hr, and 24 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • Seeds of Arabidopsis Thaliana were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber with 16 hr light/8 hr dark, 12,000-14,000 Lux, 70% humidity and 20° C., fourteen day old plants were transferred to a 42° C. growth chamber and aerial tissues were harvested 1 hr and 6 hr after transfer. Control plants were left at 20° C. and aerial tissues were harvested. Tissues were flash-frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers containing 42° C. water for treatment. Control plants were treated with water at 25° C. After 1 hr and 6 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • Seeds of Arabidopsis thaliana were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C. and 70% humidity. Fourteen day old plants were transferred to a 4° C. dark growth chamber and aerial tissues were harvested 1 hour and 6 hours later. Control plants were maintained at 20° C. and covered with foil to avoid exposure to light. Tissues were flash-frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers containing 4° C. water for treatment. Control plants were treated with water at 25° C. After 1 hr and 6 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • Seeds of Arabidopsis thaliana were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of Arabidopsis embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Green siliques 5-10 mm in length containing developing seeds 72-120 hours after fertilization (HAF)] were opened and the seeds removed. The remaining tissues (green pods minus seed) were harvested and flash frozen in liquid nitrogen.
  • HAF human embryonic stage
  • Seeds of Arabidopsis thaliana were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of Arabidopsis embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Green siliques>10 mm in length containing developing seeds up to 9 days after flowering (DAF)] were opened and the seeds removed and harvested and flash frozen in liquid nitrogen.
  • DAF flowering
  • Seeds of Arabidopsis thaliana were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of Arabidopsis embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Yellowing siliques>10 mm in length containing brown, dessicating seeds>11 days after flowering (DAF)] were opened and the seeds removed and harvested and flash frozen in liquid nitrogen.
  • DAF flowering
  • Seeds of Arabidopsis thaliana were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of Arabidopsis embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Green siliques>10 mm in length containing both green and brown seeds>9 days after flowering (DAF)] were opened and the seeds removed and harvested and flash frozen in liquid nitrogen.
  • DAF flowering
  • Mature dry seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown onto moistened filter paper and left at 4° C. for two to three days to vernalize. Imbibed seeds were then transferred to a growth chamber [16 hr light: 8 hr dark conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature], the emerging seedlings harvested after 48 hours and flash frozen in liquid nitrogen.
  • Seeds of Arabidopsis thaliana were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature and taken to maturity. Mature dry seeds are collected, dried for one week at 28° C., and vernalized for one week at 4° C. before used as a source of RNA.
  • Arabidopsis thaliana (Ws) seeds were sterilized for 5 min. with 30% bleach, 50 ⁇ l Triton in a total volume of 50 ml. Seeds were vernalized at 4° C. for 3 days before being plated onto GM agar plates at a density of about 144 seeds per plate. Plates were incubated in a Percival growth chamber having 16 hr light/8 hr dark, 80% relative humidity, 22° C. and 11,000 LUX for 14 days.
  • Seeds of Arabidopsis thaliana were placed on MS plates and vernalized at 4° C. for 3 days before being placed in a 25° C. growth chamber having 16 hr light/8 hr dark, 70% relative humidity and about 3 W/m 2 .
  • young seedlings were transferred to flasks containing B5 liquid medium, 1% sucrose and 0.05 mg/l indole-3-butyric acid. Flasks were incubated at room temperature with 100 rpm agitation. Media was replaced weekly. After three weeks, roots were harvested and incubated for 1 hr with 2% pectinase, 0.2% cellulase, pH 7 before straining through a #80 (Sigma) sieve.
  • the root body material remaining on the sieve (used as the control) was flash frozen and stored at ⁇ 80° C. until use.
  • the material that passed through the #80 sieve was strained through a #200 (Sigma) sieve and the material remaining on the sieve (root tips) was flash frozen and stored at ⁇ 80° C. until use. Approximately 10 mg of root tips were collected from one flask of root culture.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 8 days. Seedlings were carefully removed from the sand and the root tips ( ⁇ 2 mm long) were removed and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C. The tissues above the root tips ( ⁇ 1 cm long) were cut, treated as above and used as control tissue.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in covered flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX.
  • hr light 25° C.
  • hr dark 20° C.
  • 75% relative humidity 13,000-14,000 LUX.
  • One day after sowing whole seeds were flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • Two days after sowing, embryos and endosperm were isolated and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • aerial tissues, roots and endosperm were isolated and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • Seeds of Arabidopsis thaliana were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 70% humidity and 20° C. After 14 days, the leaves were wounded with forceps. Aerial tissues were harvested 1 hour and 6 hours after wounding. Aerial tissues from unwounded plants served as controls. Tissues were flash-frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were wounded (one leaf nicked by scissors) and placed in 1-liter beakers of water for treatment. Control plants were treated not wounded. After 1 hr and 6 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • Seeds of Arabidopsis thaliana were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C. and 70% humidity.
  • Fourteen day old plants were sprayed with 5 mM sodium nitroprusside in a 0.02% Silwett L-77 solution.
  • Control plants were sprayed with a 0.02% Silwett L-77 solution.
  • Aerial tissues were harvested 1 hour and 6 hours after spraying, flash-frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in I-liter beakers with 5 mM nitroprusside for treatment. Control plants were treated with water. After 1 hr, 6 hr and 12 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • Plants mutant at the rhl gene locus lack root hairs. This mutation is maintained as a heterozygote.
  • Seeds of Arabidopsis thaliana (Landsberg erecta) mutated at the rhl gene locus were sterilized using 30% bleach with 1 ul/ml 20% Triton-X 100 and then vernalized at 4° C. for 3 days before being plated onto GM agar plates. Plates were placed in growth chamber with 16 hr light/8 hr. dark, 23° C., 14,500-15,900 LUX, and 70% relative humidity for germination and growth.
  • seeds of Arabidopsis thaliana (Landsberg erecta), heterozygous for the rhl1 (root hairless) mutation, were surface-sterilized in 30% bleach containing 0.1% Triton X-100 and further rinsed in sterile water. They were then vernalized at 4° C. for 4 days before being plated onto MS agar plates. The plates were maintained in a growth chamber at 24° C. with 16 hr light/8 hr dark for germination and growth. After 10 days, seedling roots that expressed the phenotype (i.e. lacking root hairs) were cut below the hypocotyl junction, frozen in liquid nitrogen and stored at ⁇ 80° C. Those seedlings with the normal root phenotype (heterozygous or wt) were collected as described for the mutant and used as controls.
  • Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing in flats containing vermiculite soil. Flats were placed at 20° C. in a Conviron growth chamber having 16 hr light/8 hr dark. Whole plants (used as controls) received water. Other plants were treated with 100 mM NaCl. After 6 hr and 72 hr, aerial and root tissues were harvested and flash frozen in liquid nitrogen prior to storage at ⁇ 80° C.
  • Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing in flats containing vermiculite soil. Flats were watered placed at 20° C. in a Conviron growth chamber having 16 hr light/8 hr dark. Whole plants (used as the control) and petals from inflorescences 23-25 days after germination were harvested, flash frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing in flats containing vermiculite soil. Flats were watered and placed at 20° C. in a Conviron growth chamber having 16 hr light/8 hr dark. Whole plants (used as controls) and pollen from plants 38 dap was harvested, flash frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Interploidy crosses involving a 6 ⁇ parent are lethal.
  • Crosses involving a 4 ⁇ parent are complete and analyzed.
  • the imbalance in the maternal/paternal ratio produced from the cross can lead to big seeds.
  • Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing. Small siliques were harvested at 5 days after pollination, flash frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Alkaloid 35S over-expressing lines were used to monitor the expression levels of terpenoid/alkaloid biosynthetic and P450 genes to identify the transcriptional regulatory points I the biosynthesis pathway and the related P450 genes.
  • Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing in vermiculite soil (Zonolite) supplemented by Hoagland solution. Flats were placed in Conviron growth chambers under long day conditions (16 hr light, 23° C./8 hr dark, 20° C.) Basta spray and selection of the overexpressing lines was conducted about 2 weeks after germination. Approximately 2-3 weeks after bolting (approximately 5-6 weeks after germination), stem and siliques from the over-expressing lines and from wild-type plants were harvested, flash frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Demeter is a mutant of a methyl transferase gene and is similar to fie.
  • Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing.
  • Cauline leaves and closed flowers were isolated from 35S::DMT and dmt ⁇ / ⁇ plant lines, flash frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing on MS media (1%) sucrose on bactor-agar. Roots and shoots were separated 14 days after germination, flash frozen in liquid nitrogen and stored at ⁇ 80° C.
  • CS237 is an ethylene triple response mutant that is insensitive to ethylene and which has an etr1-1 phenotype.
  • Arabidopsis thaliana CS237 seeds were vernalized at 4° C. for 3 days before sowing.
  • Aerial tissue was collected from mutants and wild-type Columbia ecotype plants, flash frozen in liquid nitrogen and stored at ⁇ 80° C.
  • Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing. Leaves were harvested, homogenized and centrifuged to isolate the guard cell containing fraction. Homogenate from leaves served as the control. Samples were flash frozen in liquid nitrogen and stored at ⁇ 80° C. Identical experiments using leaf tissue from canola were performed.
  • 3642-1 is a T-DNA mutant that affects leaf development. This mutant segregates 3:1, wild-type:mutant. Arabidopsis thaliana 3642-1 mutant seeds were vernalized at 4° C. for 3 days before sowing in flats of MetroMix 200. Flats were placed in the greenhouse, watered and grown to the 8 leaf, pre-flower stage. Stems and rosette leaves were harvested from the mutants and the wild-type segregants, flash frozen and stored at ⁇ 80° C.
  • Carple factory is a double-stranded RNAse protein that is hypothesized to process small RNAs in Arabidopsis .
  • the protein is closely related to a Drosophila protein named DICER that functions in the RNA degradation steps of RNA interference.
  • Arabidopsis thaliana Caf mutant seeds were vernalized at 4° C. for 3 days before sowing in flats of MetroMix 200. Flats were placed in the greenhouse, watered and grown to the 8 leaf, pre-flower stage. Stems and rosette leaves were harvested from the mutants and the wild-type segregants, flash frozen and stored at ⁇ 80° C.
  • Microarray technology provides the ability to monitor mRNA transcript levels of thousands of genes in a single experiment. These experiments simultaneously hybridize two differentially labeled fluorescent cDNA pools to glass slides that have been previously spotted with cDNA clones of the same species. Each arrayed cDNA spot will have a corresponding ratio of fluorescence that represents the level of disparity between the respective mRNA species in the two sample pools. Thousands of polynucleotides can be spotted on one slide, and each experiment generates a global expression pattern.
  • the microarray consists of a chemically coated microscope slide, referred herein as a “chip” with numerous polynucleotide samples arrayed at a high density.
  • the poly-L-lysine coating allows for this spotting at high density by providing a hydrophobic surface, reducing the spreading of spots of DNA solution arrayed on the slides.
  • Glass microscope slides Gold Seal #3010 manufactured by Gold Seal Products, Portsmouth, N.H., USA
  • Polynucleotides were amplified from Arabidopsis cDNA clones using insert specific probes.
  • the resulting 100 uL PCR reactions were purified with Qiaquick 96 PCR purification columns (Qiagen, Valencia, Calif., USA) and eluted in 30 uL of 5 mM Tris. 8.5 uL of the elution were mixed with 1.5 uL of 20 ⁇ SSC to give a final spotting solution of DNA in 3 ⁇ SSC.
  • the concentrations of DNA generated from each clone varied between 10-100 ng/ul, but were usually about 50 ng/ul.
  • PCR products from cDNA clones were spotted onto the poly-L-Lysine coated glass slides using an arrangement of quill-tip pins (ChipMaker 3 spotting pins; Telechem, International, Inc., Sunnyvale, Calif., USA) and a robotic arrayer (PixSys 3500, Cartesian Technologies, Irvine, Calif., USA).
  • quill-tip pins ChipMaker 3 spotting pins; Telechem, International, Inc., Sunnyvale, Calif., USA
  • a robotic arrayer PanSys 3500, Cartesian Technologies, Irvine, Calif., USA.
  • Spot center-to-center spacing was from 180 um to 210 um depending on the array. Printing was conducted in a chamber with relative humidity set at 50%.
  • slides were processed through a series of steps—rehydration, UV cross-linking, blocking and denaturation—required prior to hybridization.
  • Slides were rehydrated by placing them over a beaker of warm water (DNA face down), for 2-3 sec, to distribute the DNA more evenly within the spots, and then snap dried on a hot plate (DNA side, face up).
  • the DNA was then cross-linked to the slides by UV irradiation (60-65 mJ; 2400 Stratalinker, Stratagene, La Jolla, Calif., USA).
  • 3 ⁇ 350-ml glass chambers (with metal tops) were set to one side, and a large round Pyrex dish with dH 2 O was placed ready in the microwave. At this time, 15 ml sodium borate was prepared in a 50 ml conical tube.
  • the slide rack was plunged rapidly and evenly in the solution. It was vigorously shaken up and down for a few seconds, making sure slides never left the solution.
  • the slide rack was gently plunge in the 95 C water (just stopped boiling) for 2 min. Then the slide rack was plunged 5 ⁇ in 95% ethanol. The slides and rack were centrifuged for 5 min. @ 500 rpm. The slides were loaded quickly and evenly onto the carriers to avoid streaking. The arrays were used immediately or store in slide box.
  • the Hybridization process began with the isolation of mRNA from the two tissues (see “Isolation of total RNA ” and “Isolation of mRNA ”, below) in question followed by their conversion to single stranded cDNA (see “Generation of probes for hybridization ”, below).
  • the cDNA from each tissue was independently labeled with a different fluorescent dye and then both samples were pooled together. This final differentially labeled cDNA pool was then placed on a processed microarray and allowed to hybridize (see “Hybridization and wash conditions”, below).
  • RNAse-free water was dissolved in either TE (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) or DEPC (diethylpyrocarbonate) treated deionized water (RNAse-free water). For subsequent isolation of mRNA using the Qiagen kit, the total RNA pellet was dissolved in RNAse-free water.
  • the pellet was resuspended in 400 ⁇ l OW2 buffer (10 mM Tris-Cl, pH 7.5, 150 mM NaCl, 1 mM EDTA) by vortexing, the resulting solution placed on a small spin column in a 1.5 ml RNase-free microcentrifuge tube and centrifuged for 1 min at 14,000-18,000 ⁇ g.
  • the spin column was transferred to a new 1.5 ml RNase-free microcentrifuge tube and washed with 400 ⁇ l of OW2 buffer.
  • the spin column was again transferred to a new RNase-free 1.5 ml microcentrifuge tube, 20-100 ⁇ l 70° C.
  • OEB buffer (5 mM Tris-Cl, pH 7.5) added and the resin resuspended in the resulting solution via pipeting.
  • the mRNA solution was collected after centrifuging for 1 min at 14,000-18,000 ⁇ g.
  • RNA was isolated using the Stratagene Poly(A) Quik mRNA Isolation Kit (Startagene, La Jolla, Calif.). Here, up to 0.5 mg of total RNA (maximum volume of 1 ml) was incubated at 65° C. for 5 minutes, snap cooled on ice and 0.1 ⁇ volumes of 10 ⁇ sample buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA (pH 8.0) 5 M NaCl) added. The RNA sample was applied to a prepared push column and passed through the column at a rate of ⁇ 1 drop every 2 sec. The solution collected was reapplied to the column and collected as above.
  • 10 ⁇ sample buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA (pH 8.0) 5 M NaCl
  • the elution buffer was passed through the column at a rate of 1 drop/sec.
  • the resulting mRNA solution was precipitated by adding 0.1 ⁇ volumes of 10 ⁇ sample buffer, 2,5 volumes of ice-cold 100% ethanol, incubating overnight at ⁇ 20° C. and centrifuging at 14,000-18,000 ⁇ g for 20-30 min at 4° C. The pellet was washed with 70% ethanol and air dried for 10 min. at room temperature before resuspension in RNase-free deionized water.
  • Plasmid DNA was isolated from the following yeast clones using Qiagen filtered maxiprep kits (Qiagen, Valencia, Calif.): YAL022c(Fun26), YAL031c(Fun21), YBR032w, YDL131w, YDL182w, YDL194w, YDL196w, YDR050c and YDR116c.
  • Plasmid DNA was linearized with either BsrBI (YAL022c(Fun26), YAL031c(Fun21), YDL131w, YDL182w, YDL194w, YDL196w, YDR050c) or AflIII (YBR032w, YDR116c) and isolated.
  • the solution was extracted with phenol/chloroform once before adding 0.1 volume 3M sodium acetate and 2.5 volumes of 100% ethanol.
  • the solution was centrifuged at 15,000 rpm, 4° C. for 20 minutes and the pellet resuspended in RNase-free deionized water.
  • the DNase I treatment was carried out at 37° C. for 30 minutes using 2 U of Ampli DNase I in the following reaction condition: 50 mM Tris-HCl (pH 7.5), 10 mM MgCl 2 .
  • the DNase I reaction was then stopped with the addition of NH 4 OAC and phenol:chloroform:isoamyl alcohol (25:24:1), and RNA isolated as described above.
  • Hybridization probes were generated from isolated mRNA using an AtlasTM Glass Fluorescent Labeling Kit (Clontech Laboratories, Inc., Palo Alto, Calif., USA). This entails a two step labeling procedure that first incorporates primary aliphatic amino groups during cDNA synthesis and then couples fluorescent dye to the cDNA by reaction with the amino functional groups.
  • oligo(dT) 18 primer d(TTTTTTTTTTTTTTTTTTV) was mixed with Poly A+ mRNA (1.5-2 ⁇ g mRNA isolated using the Qiagen Oligotex mRNA Spin-Column protocol or-the Stratagene Poly(A) Quik mRNA Isolation protocol (Stratagene, La Jolla, Calif., USA)) in a total volume of 25 ⁇ l.
  • the sample was incubated in a thermocycler at 70° C. for 5 min, cooled to 48° C.
  • 5 ⁇ cDNA Synthesis Buffer (kit supplied), 5 ⁇ l 10 ⁇ dNTP mix (dATP, dCTP, dGTP, dTTP and aminoallyl-dUTP; kit supplied), 7.5 ⁇ l deionized water and 2.5 ⁇ l MMLV Reverse Transcriptase (500 U) added.
  • the reaction was then incubated at 48° C. for 30 minutes, followed by 1 hr incubation at 42° C. At the end of the incubation the reaction was heated to 70° C. for 10 min, cooled to 37° C. and 0.5 ⁇ l (5 U) RNase H added, before incubating for 15 min at 37° C.
  • the solution was vortexed for 1 min after the addition of 0.5 ⁇ l 0.5 M EDTA and 5 ⁇ l of QuickClean Resin (kit supplied) then centrifuged at 14,000-18,000 ⁇ g for 1 min. After removing the supernatant to a 0.45 ⁇ m spin filter (kit supplied), the sample was again centrifuged at 14,000-18,000 ⁇ g for 1 min, and 5.5 ⁇ l 3 M sodium acetate and 137.5 ⁇ l of 100% ethanol added to the sample before incubating at ⁇ 20° C. for at least 1 hr. The sample was then centrifuged at 14,000-18,000 ⁇ g at 4° C.
  • the fluorescently labeled first strand cDNA was precipitated by adding 2 ⁇ l 3M sodium acetate and 50 ⁇ l 100% ethanol, incubated at ⁇ 20° C. for at least 2 hrs, centrifuged at 14,000-18,000 ⁇ g for 20 min, washed with 70% ethanol, air-dried for 10 min and dissolved in 100 ⁇ l of water.
  • 3-4 ⁇ g mRNA, 2.5 ( ⁇ 8.9 ng of in vitro translated mRNA) ⁇ l yeast control and 3 ⁇ g oligo dTV (TTTTTTTTTTTTTTTTTTTTTT(A/C/G) were mixed in a total volume of 24.7 ⁇ l.
  • the sample was incubated in a thermocycler at 70° C. for 10 min. before chilling on ice.
  • 8 ⁇ l of 5 ⁇ first strand buffer SuperScript II RNase H—Reverse Transcriptase kit from Invitrogen (Carlsbad, Calif. 92008); cat no. 18064022
  • aa-dUTP/dNTP mix 50 ⁇ ; 25 mM dATP, 25 mM dGTP, 25 mM dCTP, 15 mM dTTP, 10 mM aminoallyl-dUTP
  • 4 ⁇ l of 0.1 M DTT and 2.5 ⁇ l (500 units) of Superscript R.T.II enzyme (Stratagene) were added.
  • the sample was incubated at 42° C. for 2 hours before a mixture of 10° C. of 1 M NaOH and 10° C. of 0.5 M EDTA were added. After a 15 minute incubation at 65° C., 25 ⁇ l of 1 M Tris pH 7.4 was added.
  • the probe was purified using a Qiagen PCR cleanup kit (Qiagen, Valencia, Calif., USA), and eluted with 100 ul EB (kit provided). The sample was loaded on a Microcon YM-30 (Millipore, Bedford, Mass., USA) spin column and concentrated to 4-5 ul in volume. Probes for the maize microarrays were generated using the Fluorescent Linear Amplification Kit (cat. No. G2556A) from Agilent Technologies (Palo Alto, Calif.).
  • the probe was kept at 42 C. Prior to the hybridization, the probe was heated for 1 more min., added to the array, and then covered with a glass cover slip. Slides were placed in hybridization chambers (Telechem, Sunnyvale, Calif.) and incubated at 42° C. overnight.
  • Maize microarrays were hybridized according to the instructions included Fluorescent Linear Amplification Kit (cat. No. G2556A) from Agilent Technologies (Palo Alto, Calif.).
  • the chips were scanned using a ScanArray 3000 or 5000 (General Scanning, Watertown, Mass., USA). The chips were scanned at 543 and 633 nm, at 10 um resolution to measure the intensity of the two fluorescent dyes incorporated into the samples hybridized to the chips.
  • the images generated by scanning slides consisted of two 16-bit TIFF images representing the fluorescent emissions of the two samples at each arrayed spot. These images were then quantified and processed for expression analysis using the data extraction software ImageneTM (Biodiscovery, Los Angeles, Calif., USA). Imagene output was subsequently analyzed using the analysis program GenespringTM (Silicon Genetics, San Carlos, Calif., USA). In Genespring, the data was imported using median pixel intensity measurements derived from Imagene output. Background subtraction, ratio calculation and normalization were all conducted in Genespring. Normalization was achieved by breaking the data in to 32 groups, each of which represented one of the 32 pin printing regions on the microarray. Groups consist of 360 to 550 spots. Each group was independently normalized by setting the median of ratios to one and multiplying ratios by the appropriate factor.
  • sequences showing differential expression in a particular experiment (denoted by either a “+” or “ ⁇ ” in the column in Table 1 entitled “SIGNCLOG_RATIO”) thereby show utility for a function in a plant, and these functions/utilities are described in detail below, where the title of each section (i.e. a “utility section”) is correlated with the particular differential expression experiment in the section of Table 1 entitled “Microarray Experiment Parameters”.
  • Roots arise not only from harvested adventitious roots or tubers, but also from the ability of roots to funnel nutrients to support growth of all plants and increase their vegetative material, seeds, fruits, etc. Roots have four main functions. First, they anchor the plant in the soil. Second, they facilitate and regulate the molecular signals and molecular traffic between the plant, soil, and soil fauna. Third, the root provides a plant with nutrients gained from the soil or growth medium. Fourth, they condition local soil chemical and physical properties.
  • Root genes are active or potentially active to a greater extent in roots than in most other organs of the plant. These genes and gene products can regulate many plant traits from yield to stress tolerance. Root genes can be used to modulate root growth and development.
  • mRNA product in the root versus the aerial portion of the plant was measured. Specifically, mRNA was isolated from roots and root tips of Arabidopsis plants and compared to mRNA isolated from the aerial portion of the plants utilizing microarray procedures.
  • Root hairs are specialized outgrowths of single epidermal cells termed trichoblasts.
  • the trichoblasts are regularly arranged around the perimeter of the root.
  • trichoblasts tend to alternate with non-hair cells or atrichoblasts. This spatial patterning of the root epidermis is under genetic control, and a variety of mutants have been isolated in which this spacing is altered or in which root hairs are completely absent.
  • the root hair development genes of the instant invention are useful to modulate one or more processes of root hair structure and/or function including (1) development; (2) interaction with the soil and soil contents; (3) uptake and transport in the plant; and (4) interaction with microorganisms.
  • the surface cells of roots can develop into single epidermal cells termed trichoblasts or root hairs. Some of the root hairs will persist for the life of the plant; others will gradually die back; some may cease to function due to external influences. These genes and gene products can be used to modulate root hair density or root hair growth; including rate, timing, direction, and size, for example.
  • genes and gene products can also be used to modulate cell properties such as cell size, cell division, rate and direction and number, cell elongation, cell differentiation, lignified cell walls, epidermal cells (including trichoblasts) and root apical meristem cells (growth and initiation); and root hair architecture such as leaf cells under the trichome, cells forming the base of the trichome, trichome cells, and root hair responses.
  • cell properties such as cell size, cell division, rate and direction and number, cell elongation, cell differentiation, lignified cell walls, epidermal cells (including trichoblasts) and root apical meristem cells (growth and initiation); and root hair architecture such as leaf cells under the trichome, cells forming the base of the trichome, trichome cells, and root hair responses.
  • genes and gene products can be used to modulate one or more of the growth and development processes in response to internal plant programs or environmental stimuli in, for example, the seminal system, nodal system, hormone responses, Auxin, root cap abscission, root senescence, gravitropism, coordination of root growth and development with that of other organs (including leaves, flowers, seeds, fruits, and stems), and changes in soil environment (including water, minerals, Ph, and microfauna and flora).
  • Root hairs are sites of intense chemical and biological activity and as a result can strongly modify the soil they contact. Roots hairs can be coated with surfactants and mucilage to facilitate these activities. Specifically, roots hairs are responsible for nutrient uptake by mobilizing and assimilating water, reluctant ions, organic and inorganic compounds and chemicals. In addition, they attract and interact with beneficial microfauna and flora. Root hairs also help to mitigate the effects of toxic ions, pathogens and stress.
  • root hair genes and gene products can be used to modulate traits such as root hair surfactant and mucilage (including composition and secretion rate and time); nutrient uptake (including water, nitrate and other sources of nitrogen, phosphate, potassium, and micronutrients (e.g.
  • microbe and nematode associations such as bacteria including nitrogen-fixing bacteria, mycorrhizae, nodule-forming and other nematodes, and nitrogen fixation
  • oxygen transpiration ; detoxification effects of iron, aluminum, cadium, mercury, salt, and other soil constituents; pathogens (including chemical repellents) glucosinolates (GSLI), which release pathogen-controlling isothiocyanates; and changes in soil (such as Ph, mineral excess and depletion), and rhizosheath.
  • GSLI glucosinolates
  • root hair development genes and gene products can be used to modulate the vigor and yield of the overall plant as well as distinct cells, organs, or tissues of a plant.
  • the genes and gene products can modulate plant nutrition, growth rate (such as whole plant, including height, flowering time, etc., seedling, coleoptile elongation, young leaves, stems, flowers, seeds and fruit) and yield, including biomass (fresh and dry weight during any time in plant life, including maturation and senescence), number of flowers, number of seeds, seed yield, number, size, weight and harvest index (content and composition, e.g. amino acid, jasmonate, oil, protein and starch) and fruit yield (number, size, weight, harvest index, and post harvest quality).
  • growth rate such as whole plant, including height, flowering time, etc., seedling, coleoptile elongation, young leaves, stems, flowers, seeds and fruit
  • yield including biomass (fresh and dry weight during any time in plant life, including maturation and senescence), number of flowers, number of seeds, seed yield, number, size, weight and harvest index (content and composition, e.g. amino acid, jasmonate, oil, protein and starch)
  • Reproduction genes are defined as genes or components of genes capable of modulating any aspect of sexual reproduction from flowering time and inflorescence development to fertilization and finally seed and fruit development. These genes are of great economic interest as well as biological importance.
  • the fruit and vegetable industry grosses over $1 billion USD a year.
  • the flower formation is a precondition for the sexual propagation of plants and is therefore essential for the propagation of plants that cannot be propagated vegetatively as well as for the formation of seeds and fruits.
  • the point of time at which the merely vegetative growth of plants changes into flower formation is of vital importance for example in agriculture, horticulture and plant breeding.
  • the number of flowers is often of economic importance, for example in the case of various useful plants (tomato, cucumber, zucchini, cotton etc.) with which an increased number of flowers may lead to an increased yield, or in the case of growing ornamental plants and cut flowers.
  • Flowering plants exhibit one of two types of inflorescence architecture: indeterminate, in which the inflorescence grows indefinitely, or determinate, in which a terminal flower is produced.
  • Adult organs of flowering plants develop from groups of stem cells called meristems. The identity of a meristem is inferred from structures it produces: vegetative meristems give rise to roots and leaves, inflorescence meristems give rise to flower meristems, and flower meristems give rise to floral organs such as sepals and petals.
  • vegetative meristems give rise to roots and leaves
  • inflorescence meristems give rise to flower meristems
  • flower meristems give rise to floral organs such as sepals and petals.
  • floral organs such as sepals and petals.
  • meristems capable of generating new meristems of different identity, but their own identity can change during development.
  • a vegetative shoot meristem can be transformed into an inflorescence meristem upon floral induction, and in some species, the inflorescence meristem itself will eventually become a flower meristem.
  • floral induction for example, a vegetative shoot meristem can be transformed into an inflorescence meristem upon floral induction, and in some species, the inflorescence meristem itself will eventually become a flower meristem.
  • the ovule is the primary female sexual reproductive organ of flowering plants. At maturity it contains the egg cell and one large central cell containing two polar nuclei encased by two integuments that, after fertilization, develops into the embryo, endosperm, and seed coat of the mature seed, respectively. As the ovule develops into the seed, the ovary matures into the fruit or silique. As such, seed and fruit development requires the orchestrated transcription of numerous polynucleotides, some of which are ubiquitous, others that are embryo-specific and still others that are expressed only in the endosperm, seed coat, or fruit. Such genes are termed fruit development responsive genes and can be used to modulate seed and fruit growth and development such as seed size, seed yield, seed composition and seed dormancy.
  • the relative levels of mRNA product in the siliques relative to the plant as a whole was measured.
  • the levels of mRNA product in the seeds relative to those in a leaf and floral stems was measured.
  • Seeds are a vital component of the world's diet. Cereal grains alone, which comprise ⁇ 90% of all cultivated seeds, contribute up to half of the global per capita energy intake.
  • the primary organ system for seed production in flowering plants is the ovule.
  • the ovule consists of a haploid female gametophyte or embryo sac surrounded by several layers of maternal tissue including the nucleus and the integuments.
  • the embryo sac typically contains seven cells including the egg cell, two synergids, a large central cell containing two polar nuclei, and three antipodal cells. That pollination results in the fertilization of both egg and central cell.
  • the fertilized egg develops into the embryo.
  • the fertilized central cell develops into the endosperm.
  • seed dormancy is generally an undesirable characteristic in agricultural crops, where rapid germination and growth are required. However, some degree of dormancy is advantageous, at least during seed development. This is particularly true for cereal crops because it prevents germination of grains while still on the ear of the parent plant (preharvest sprouting), a phenomenon that results in major losses to the agricultural industry.
  • Germination commences with imbibition, the uptake of water by the dry seed, and the activation of the quiescent embryo and endosperm. The result is a burst of intense metabolic activity. At the cellular level, the genome is transformed from an inactive state to one of intense transcriptional activity. Stored lipids, carbohydrates and proteins are catabolized fueling seedling growth and development. DNA and organelles are repaired, replicated and begin functioning. Cell expansion and cell division are triggered. The shoot and root apical meristem are activated and begin growth and organogenesis. Schematic 4 summarizes some of the metabolic and cellular processes that occur during imbibition. Germination is complete when a part of the embryo, the radicle, extends to penetrate the structures that surround it.
  • Imbibition and germination includes those events that commence with the uptake of water by the quiescent dry seed and terminate with the expansion and elongation of the shoots and roots.
  • the germination period exists from imbibition to when part of the embryo, usually the radicle, extends to penetrate the seed coat that surrounds it.
  • Imbibition and germination genes are defined as genes, gene components and products capable of modulating one or more processes of imbibition and germination described above. They are useful to modulate many plant traits from early vigor to yield to stress tolerance.
  • the levels of mRNA product in the seeds versus the plant as a whole was measured.
  • ABA Abscisic acid
  • Plant hormones are naturally occurring substances, effective in very small amounts, which act as signals to stimulate or inhibit growth or regulate developmental processes in plants. Abscisic acid (ABA) is a ubiquitous hormone in vascular plants that has been detected in every major organ or living tissue from the root to the apical bud. The major physiological responses affected by ABA are dormancy, stress stomatal closure, water uptake, abscission and senescence. In contrast to Auxins, cytokinins and gibberellins, which are principally growth promoters, ABA primarily acts as an inhibitor of growth and metabolic processes.
  • ABA responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different ABA responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants.
  • the combination of an ABA responsive polynucleotide and/or gene product with another environmentally responsive polynucleotide is also useful because of the interactions that exist between hormone-regulated pathways, stress and defense induced pathways, nutritional pathways and development.
  • BRs Brassinosteroids
  • Plant hormones are naturally occurring substances, effective in very small amounts, which act as signals to stimulate or inhibit growth or regulate developmental processes in plants.
  • Brassinosteroids are the most recently discovered, and least studied, class of plant hormones.
  • the major physiological response affected by BRs is the longitudinal growth of young tissue via cell elongation and possibly cell division. Consequently, disruptions in BR metabolism, perception and activity frequently result in a dwarf phenotype.
  • any perturbations to the sterol pathway can affect the BR pathway. In the same way, perturbations in the BR pathway can have effects on the later part of the sterol pathway and thus the sterol composition of membranes.
  • BR concentration in the surrounding environment or in contact with a plant result in modulation of many genes and gene products. These genes and/or products are responsible for effects on traits such as plant biomass and seed yield. These genes were discovered and characterized from a much larger set of genes by experiments designed to find genes whose mRNA abundance changed in response to application of BRs to plants.
  • BR responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development.
  • Useful combinations include different BR responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factors and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants.
  • the combination of a BR responsive polynucleotide and/or gene product with another environmentally responsive polynucleotide is useful because of the interactions that exist between hormone-regulated pathways, stress pathways, nutritional pathways and development.
  • useful combinations include polynucleotides that may have different transcription profiles but which participate in common or overlapping pathways.
  • Nitrogen is often the rate-limiting element in plant growth, and all field crops have a fundamental dependence on exogenous nitrogen sources.
  • Nitrogenous fertilizer which is usually supplied as ammonium nitrate, potassium nitrate, or urea, typically accounts for 40% of the costs associated with crops, such as corn and wheat in intensive agriculture. Increased efficiency of nitrogen use by plants should enable the production of higher yields with existing fertilizer inputs and/or enable existing yields of crops to be obtained with lower fertilizer input, or better yields on soils of poorer quality. Also, higher amounts of proteins in the crops could also be produced more cost-effectively. “Nitrogen responsive” genes and gene products can be used to alter or modulate plant growth and development.
  • Plants contain many proteins and pathways that when blocked or induced lead to cell, organ or whole plant death. Gene variants that influence these pathways can have profound effects on plant survival, vigor and performance.
  • the critical pathways include those concerned with metabolism and development or protection against stresses, diseases and pests. They also include those involved in apoptosis and necrosis. Viability genes can be modulated to affect cell or plant death.
  • Herbicides are, by definition, chemicals that cause death of tissues, organs and whole plants.
  • the genes and pathways that are activated or inactivated by herbicides include those that cause cell death as well as those that function to provide protection.
  • Plants are continuously subjected to various forms of wounding from physical attacks including the damage created by pathogens and pests, wind, and contact with other objects. Therefore, survival and agricultural yields depend on constraining the damage created by the wounding process and inducing defense mechanisms against future damage.
  • Plants have evolved complex systems to minimize and/or repair local damage and to minimize subsequent attacks by pathogens or pests or their effects. These involve stimulation of cell division and cell elongation to repair tissues, induction of programmed cell death to isolate the damage caused mechanically and by invading pests and pathogens, and induction of long-range signaling systems to induce protecting molecules, in case of future attack.
  • the genetic and biochemical systems associated with responses to wounding are connected with those associated with other stresses such as pathogen attack and drought.
  • Wounding responsive genes and gene products can be used to alter or modulate traits such as growth rate; whole plant height, width, or flowering time; organ development (such as coleoptile elongation, young leaves, roots, lateral roots, tuber formation, flowers, fruit, and seeds); biomass; fresh and dry weight during any time in plant life, such as at maturation; number of flowers; number of seeds; seed yield, number, size, weight, harvest index (such as content and composition, e.g., amino acid, nitrogen, oil, protein, and carbohydrate); fruit yield, number, size, weight, harvest index, post harvest quality, content and composition (e.g., amino acid, carotenoid, jasmonate, protein, and starch); seed and fruit development; germination of dormant and non-dormant seeds; seed viability, seed reserve mobilization, fruit ripening, initiation of the reproductive cycle from a vegetative state, flower development time, insect attraction for fertilization, time to fruit maturity, senescence; fruits, fruit drop; leaves; stress
  • Manipulation of one or more cold responsive gene activities is useful to modulate growth and development.
  • Drought conditions in the surrounding environment or within a plant results in modulation of many genes and gene products.
  • Jasmonic acid and its derivatives are naturally occurring derivatives of plant lipids. These substances are synthesized from linolenic acid in a lipoxygenase-dependent biosynthetic pathway. Jasmonates are signalling molecules which have been shown to be growth regulators as well as regulators of defense and stress responses. As such, jasmonates represent a separate class of plant hormones. Jasmonate responsive genes can be used to modulate plant growth and development.
  • Salicylic acid is a signaling molecule necessary for activation of the plant induced defense system known as systemic acquired resistance or SAR. This response, which is triggered by prior exposure to avirulent pathogens, is long lasting and provides protection against a broad spectrum of pathogens.
  • Another induced defense system is the hypersensitive response (HR). HR is far more rapid, occurs at the sites of pathogen (avirulent pathogens) entry and precedes SAR.
  • SA is also the key signaling molecule for this defense pathway.
  • Osmotic stress is a major component of stress imposed by saline soil and water deficit. Decreases in yield and crop failure frequently occur as a result of aberrant or transient environmental stress conditions even in areas considered suitable for the cultivation of a given species or cultivar. Only modest increases in the osmotic and salt tolerance of a crop species would have a dramatic impact on agricultural productivity. The development of genotypes with increased osmotic tolerance would provide a more reliable means to minimize crop losses and diminish the use of energy-costly practices to modify the soil environment. Thus, osmotic stress responsive genes can be used to modulate plant growth and development.
  • Plants sense the ratio of Red (R):Far Red (FR) light in their environment and respond differently to particular ratios.
  • a low R:FR ratio for example, enhances cell elongation and favors flowering over leaf production.
  • the changes in R:FR ratios mimic and cause the shading response effects in plants.
  • the response of a plant to shade in the canopy structures of agricultural crop fields influences crop yields significantly. Therefore manipulation of genes regulating the shade avoidance responses can improve crop yields.
  • phytochromes mediate the shade avoidance response, the down-stream factors participating in this pathway are largely unknown.
  • One potential downstream participant, ATHB-2 is a member of the HD-Zip class of transcription factors and shows a strong and rapid response to changes in the R:FR ratio.
  • ATHB-2 overexpressors have a thinner root mass, smaller and fewer leaves and longer hypocotyls and petioles. This elongation arises from longer epidermal and cortical cells, and a decrease in secondary vascular tissues, paralleling the changes observed in wild-type seedlings grown under conditions simulating canopy shade.
  • plants with reduced ATHB-2 expression have a thick root mass and many larger leaves and shorter hypocotyls and petioles.
  • the changes in the hypocotyl result from shorter epidermal and cortical cells and increased proliferation of vascular tissue.
  • application of Auxin is able to reverse the root phenotypic consequences of high ATHB-2 levels, restoring the wild-type phenotype. Consequently, given that ATHB-2 is tightly regulated by phytochrome, these data suggest that ATHB-2 may link the Auxin and phytochrome pathways in the shade avoidance response pathway.
  • Shade responsive genes can be used to modulate plant growth and development.
  • Plants contain many proteins and pathways that when blocked or induced lead to cell, organ or whole plant death. Gene variants that influence these pathways can have profound effects on plant survival, vigor and performance.
  • the critical pathways include those concerned with metabolism and development or protection against stresses, diseases and pests. They also include those involved in apoptosis and necrosis. The applicants have elucidated many such genes and pathways by discovering genes that when inactivated lead to cell or plant death.
  • Herbicides are, by definition, chemicals that cause death of tissues, organs and whole plants.
  • the genes and pathways that are activated or inactivated by herbicides include those that cause cell death as well as those that function to provide protection. The applicants have elucidated these genes.
  • the genes defined in this section have many uses including manipulating which cells, tissues and organs are selectively killed, which are protected, making plants resistant to herbicides, discovering new herbicides and making plants resistant to various stresses.
  • Viability genes were also identified from a much larger set of genes by experiments designed to find genes whose mRNA products changed in concentration in response to applications of different herbicides to plants. Viability genes are characteristically differentially transcribed in response to fluctuating herbicide levels or concentrations, whether internal or external to an organism or cell.
  • the MA_diff Table reports the changes in transcript levels of various viability genes.
  • One of the more active stages of the plant life cycle is a few days after germination is complete, also referred to as the early seedling phase. During this period the plant begins development and growth of the first leaves, roots, and other organs not found in the embryo. Generally this stage begins when germination ends. The first sign that germination has been completed is usually that there is an increase in length and fresh weight of the radicle.
  • Such genes and gene products can regulate a number of plant traits to modulate yield. For example, these genes are active or potentially active to a greater extent in developing and rapidly growing cells, tissues and organs, as exemplified by development and growth of a seedling 3 or 4 days after planting a seed.
  • Rapid, efficient establishment of a seedling is very important in commercial agriculture and horticulture. It is also vital that resources are approximately partitioned between shoot and root to facilitate adaptive growth. Phototropism and geotropism need to be established. All these require post-germination process to be sustained to ensure that vigorous seedlings are produced. Early seedling phase genes, gene components and products are useful to manipulate these and other processes.
  • stomata Scattered throughout the epidermis of the shoot are minute pores called stomata. Each stomal pore is surrounded by two guard cells.
  • the guard cells control the size of the stomal pore, which is critical since the stomata control the exchange of carbon dioxide, oxygen, and water vapor between the interior of the plant and the outside atmosphere. Stomata open and close through turgor changes driven by ion fluxes, which occur mainly through the guard cell plasma membrane and tonoplast.
  • Guard cells are known to respond to a number of external stimuli such as changes in light intensity, carbon dioxide and water vapor, for example. Guard cells can also sense and rapidly respond to internal stimuli including changes in ABA, auxin and calcium ion flux.
  • genes, gene products, and fragments thereof differentially transcribed and/or translated in guard cells can be useful to modulate ABA responses, drought tolerance, respiration, water potential, and water management as examples. All of which can in turn affect plant yield including seed yield, harvest index, fruit yield, etc.
  • guard cell genes To identify such guard cell genes, gene products, and fragments thereof, Applicants have performed a microarray experiment comparing the transcript levels of genes in guard cells versus leaves. Experimental data is shown below.
  • NO nitric oxide
  • ROS reactive oxygen intermediates
  • SA salicylic acid
  • a nitric oxide responsive polynucleotide and/or gene product with other environmentally responsive polynucleotides is also useful because of the interactions that exist between hormone regulated pathways, stress pathways, pathogen stimulated pathways, nutritional pathways and development.
  • Nitric oxide responsive genes and gene products can function either to increase or dampen the above phenotypes or activities either in response to changes in nitric oxide concentration or in the absence of nitric oxide fluctuations. More specifically, these genes and gene products can modulate stress responses in an organism. In plants, these genes and gene products are useful for modulating yield under stress conditions. Measurements of yield include seed yield, seed size, fruit yield, fruit size, etc.
  • SAM stem apical meristem
  • SAM genes of the instant invention are useful for modulating one or more processes of SAM structure and/or function including (I) cell size and division; (II) cell differentiation and organ primordia.
  • the genes and gene components of this invention are useful for modulating any one or all of these cell division processes generally, as in timing and rate, for example.
  • the polynucleotides and polypeptides of the invention can control the response of these processes to the internal plant programs associated with embryogenesis, and hormone responses, for example.
  • SAMs determine the architecture of the plant, modified plants will be useful in many agricultural, horticultural, forestry and other industrial sectors. Plants with a different shape, numbers of flowers and seed and fruits will have altered yields of plant parts. For example, plants with more branches can produce more flowers, seed or fruits. Trees without lateral branches will produce long lengths of clean timber. Plants with greater yields of specific plant parts will be useful sources of constituent chemicals.
  • the polynucleotide sequences of the present invention were tested for promoter activity using Green Fluorescent Protein (GFP) assays in the following manner.
  • GFP Green Fluorescent Protein
  • genomic sequence occurring immediately upstream of the ATG translational start site of the gene of interest was isolated using appropriate primers tailed with BstXI restriction sites. Standard PCR reactions using these primers and genomic DNA were conducted. The resulting product was isolated, cleaved with BstXI and cloned into the BstXI site of an appropriate vector, such as pNewBin4-HAP1-GFP (see FIG. 1 ).
  • Tissues are dissected by eye or under magnification using INOX 5 grade forceps and placed on a slide with water and coverslipped. An attempt is made to record images of observed expression patterns at earliest and latest stages of development of tissues listed below. Specific tissues will be preceded with High (H), Medium (M), Low (L) designations.
  • T1 Mature These are the T1 plants resulting from independent transformation events. These are screened between stage 6.50-6.90 (means the plant is flowering and that 50-90% of the flowers that the plant will make have developed) which is 4-6 weeks of age. At this stage the mature plant possesses flowers, siliques at all stages of development, and fully expanded leaves. We do not generally differentiate between 6.50 and 6.90 in the report but rather just indicate 6.50.
  • the plants are initially imaged under UV with a Leica Confocal microscope. This allows examination of the plants on a global level. If expression is present, they are imaged using scanning laser confocal microscopy.
  • T2 Seedling Progeny are collected from the T1 plants giving the same expression pattern and the progeny (T2) are sterilized and plated on agar-solidified medium containing M&S salts. In the event that there was no expression in the T1 plants, T2 seeds are planted from all lines. The seedlings are grown in Percival incubators under continuous light at 22° C. for 10-12 days. Cotyledons, roots, hypocotyls, petioles, leaves, and the shoot meristem region of individual seedlings were screened until two seedlings were observed to have the same pattern. Generally found the same expression pattern was found in the first two seedlings. However, up to 6 seedlings were screened before “no expression pattern” was recorded. All constructs are screened as T2 seedlings even if they did not have an expression pattern in the T1 generation.
  • T2 Mature The T2 mature plants were screened in a similar manner to the T1 plants. The T2 seeds were planted in the greenhouse, exposed to selection and at least one plant screened to confirm the T1 expression pattern. In instances where there were any subtle changes in expression, multiple plants were examined and the changes noted in the tables.
  • T3 Seedling This was done similar to the T2 seedlings except that only the plants for which we are trying to confirm the pattern are planted.
  • Images are collected by scanning laser confocal microscopy. Scanned images are taken as 2-D optical sections or 3-D images generated by stacking the 2-D optical sections collected in series. All scanned images are saved as TIFF files by imaging software, edited in Adobe Photoshop, and labeled in Powerpoint specifying organ and specific expressing tissues.
  • One channel for transmitted light detector One channel for transmitted light detector.
  • the section in Table 1 entitled “The spatial expression of the promoter-marker-vector” presents the results of the GFP assays as reported by their corresponding cDNA ID number, construct number and line number. Unlike the microarray results, which measure the difference in expression of the endogenous cDNA under various conditions, the GFP data gives the location of expression that is visible under the imaging parameters. Table 3 summarizes the results of the spatial expression results for each promoter.
  • Table 1 includes various information about each promoter or promoter control element of the invention including the nucleotid sequence, the spatial expression promoted by each promoter, and the corresponding results from different expression experiments.
  • Promoter YP0396 Modulates the gene: PAR-related protein
  • promoter information Bidirectionality: Pass Exons: Pass Repeats: No The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12646726 cDNA nucleotide sequence: ACTACACCCAAAAGAACATCTTTCCTTCGAATTTTCTTTCAATTAACATTTCTTTTACTTGTCTC CTTGTGTCTTCACTTCACATCACAACATGGCTTTGAAGACAGTTTTCGTAGCTTTTATGATTCT CCTTGCGATCTATTCGCAAACGACGTTTGGGGACGATGTGAAGTGCGAGAATCTGGATGAAAA CACGTGTGCCUCGCGGTCTCGTCCACTGGAAAACGTTGCGTTTTGGAGAAGAGCATGAAGAG GAGCGGGATCGAGGTGTACACATGTCGATCATCGGAGATAGAAGCTAACAAGGTCACAAACA TTATTGAATCGGACGAGTGCATTAAAGCGTGTGGTCTAGACCGGAAAGCTTTAGGTATATCTT CGGACGCATTGTTGGAATCTCAGTATATCTT CGGAC
  • thaliana 12646726 At_42deg_Heat 20000173 Tissue Aerial 12646726 At_42deg-Heat 20000173 Plant Line WS 12646726 At_Shoots 20000164 Age (day) 7 vs. 21 12646726 At_Shoots 20000184 Organism A. thaliana 12646726 At_Shoots 20000184 Tissue Shoots vs. Whole Plant 12646726 At_Shoots 20000184 Plant Line WS 12646726 At_Roots 20000185 Age (day) 7 vs. 21 12646726 At_Roots 20000185 Organism A. thaliana 12646726 At_Roots 20000185 Tissue Roots vs.
  • thaliana 12646726 At_Shoots 20000438 Tissue Shoots vs. Whole Plant 12646726 At_Shoots 20000438 Plant Line WS 12646726 At_1uM_BR-BRZ 20000441 Treatment 1uM BR vs. No Treatment 12646726 At_1uM_BR-BRZ 20000441 Tissue Shoot Apices 12646726 At_1uM_BR-BRZ 20000443 Treatment 1uM BRZ vs.
  • thaliana 12646726 At_42deg_Heat 20000458 Tissue Aerial 12646726 At_42deg_Heat 20000458 Plant Line WS 12646726 At_Guard_Cells 20000495 Harvest Date Aug. 2, 2002 12646726 At_Guard_Cells 20000495 Organism A. thaliana 12646726 At_Guard_Cells 20000495 Tissue Guard Cells vs. Leaves 12646726 At_10percent_PEG 20000527 Age (day) 20 12646726 At_10percent_PEG 20000527 Timepoint (day) 20 12646726 At_10percent_PEG 20000527 Treatment 10percent PEG vs.
  • Promoter YP0388 Modulates the gene: protein phosphatase 2C (PP2C), putative The GenBank description of the gene: NM_125312 Arabidopsis thaliana protein phosphatase 2C (PP2C), putative (At5g59220) mRNA, complete cds gi
  • the promoter sequence 5′tatttgtagtgacatattctacaattatcacatttttctcttatgtttcgtagtcgcagatggtca attttttctataataatttgtccttgaacacaccaaactttagaaacgatgatatataccgtattgtc acgctcacaatg
  • thaliana 13593066 At_2mM_SA 20000182 Tissue Aerial 13593066 At_2mM_SA 20000182 Plant Line WS 13593066 At_20%_PEG 20000233 Timepoint (hr) 6 13593066 At_20%_PEG 20000233 Treatment 20% PEG vs. No Treatment 13593066 At_20%_PEG 20000233 Tissue Aerial 13593066 At_Open_Flower 20000264 Age (day) 21 13593066 At_Open_Flower 20000264 Organism A. thaliana 13593066 At_Open_Flower 20000264 Tissue Open Flower vs.
  • thaliana 13593066 At_100mM_NaCl 20000268 Tissue Whole Plant 13593066 At_100mM_NaCl 20000268 Plant Line WS 13593066 At_Pollen 20000326 Age (day) 0 vs. 21 13593066 At_Pollen 20000326 Organism A. thaliana 13593066 At_Pollen 20000326 Tissue Pollen vs. Whole Plant 13593066 At_Pollen 20000326 Plant Line WS 13593066 At_Drought 20000436 Age (day) 7 13593066 At_Drought 20000436 Timepoint (hr) 12 13593066 At_Drought 20000436 Organism A.
  • thaliana 13593066 At_Far-red-enriched-adult 20001771 Tissue Aerial 13593066 At_Far-red-enriched-adult 20001771 Plant Line Columbia 13593066 At_Far-red-enriched-adult 20001771 Light Far-red enriched vs. White 13593066 At_Drought_Reproduction 20001904 Timepoint (day) 7 13593066 At_Drought_Reproduction 20001904 Age (day) 37 13593066 At_Drought_Reproduction 20001904 Organism A. thaliana 13593066 At_Drought_Reproduction 20001904 Treatment Drought vs.
  • Neoxanthin cleavage enzyme The GenBank description of the gene: NM_112304 Arabidopsis thaliana 9-cis-epoxycarotenoid dioxygenase [neoxanthin cleavage enzyme](NC1)(NCED1), putative (At3g14440) mRNA, complete cds gi
  • T2 seedling Expression in root epidermal cells. Expression rapidly decreases from root transition zone to mid root. Misc. promoter information: Bidirectionality: Pass Exons: Pass Repeats: No Optional Promoter Fragments: 5′UTR region at base pairs 880-999.
  • the Ceres cDNA ID of the endogenous coding sequence to the promoter 12658348 cDNA nucleotide sequence: AAACCAACTCTCTCTTCTCTCTTCTCTGCTCTCTTCTACAAGAAGAAAAAAAACAGAGCCTTTA CACATCTCAAAATCGAACTTACTTTAACCACCAAATACTGATTGAACACACTTGAAAAATGGC TTCTTTCAGGGCAACGGCTGCGGTTTCTGGGAGATGGCTTGGTGGCAATCATACTCAGCCGCC ATTATCGTCTTGTCAAAGCTGCGACTTGAGTTATTGTAGCTCCTTACCTATGGCCAGTCGTGTC ACACGTAAGCTCAATGTTTCATCTGCGCTTCAGACTCCTCCAGCTCTTCATTTCCCTAAGCAAT CATCAAACTCTCCCGCCATTGTTGTTAAGCCCAAAGCCAAAGAATCCAACACTAAACAGATGA ATTTGTTCCAGAGCGCGGGCGGCAGCGTTGGACGCGGCGTTGGACGTTTCCTTGTCAGCCACG AGAAG
  • thaliana 12658348 At_100mM_NaCl 20000268 Tissue Whole Plant 12658348 At_100mM_NaCl 20000268 Plant Line WS 12658348 At_Open_Flower 20000286 Age (day) 21 12658348 At_Open_Flower 20000286 Organism A.
  • thaliana 12658348 At_Open_Flower 20000286 Tissue Half Open vs. Whole Plant 12658348 At_Open_Flower 20000286 Plant Line WS 12658348 At_Drought 20000436 Age (day) 7 12658348 At_Drought 20000436 Timepoint (hr) 12 12658348 At_Drought 20000436 Organism A.
  • WS 12658348 At_Line_Comparisons 20002010 Plant Line ME02031 vs. WS 12658348 At_8deg_Cold 20002105 Age (day) 7 12658348 At_8deg_Cold 20002105 Timepoint (hr) 8 12658348 At_8deg_Cold 20002105 Temperature (deg C.) 8 vs. 22 12658348 At_8deg_Cold 20002105 Organism A.
  • GenBank description of the gene NM_113182 Arabidopsis thaliana heat shock transcription factor family (At3g22830) mRNA, complete cds gi
  • the promoter sequence 5′ataaaaattcacatttgcaaattttattcagtcggaatatatatttgaaacaagttttgaaatccattg gacgattaaaattcattgttgagaggataaatatggattttgttcatctgaaccatgtcgttgattagtgat tgactaccatgaaaaatatgttatgaaaagtataacaacttttgataaatcacatttattaacaataaatc aagacaaaatatgtcaacaataatagtagtagaagatattaattcaaattcatccgtaa
  • T2 seedling High expression throughout root epidermal cells. Misc. promoter information: Bidirectionality: Pass Exons: Pass Repeats: No Optional Promoter Fragments: 5′UTR region at base pairs 839-999.
  • the Ceres cDNA ID of the endogenous coding sequence to the promoter 12730108 cDNA nucleotide sequence: ACAAAATATCTCTCCCTCTATCTGCAAATTTTCCAAAGTTGCATCCTTTCAATTTCCACTCCTCT CTAATATAATTCACATTTTCCCACTATTGCTGATTCATTTTTTTTTGTGAATTATTTCAAACCCA CATAAAAAAATCTTTGTTTAAATTTAAAACCATGGATCCTTCATTTAGGTTCATTAAAGAGGA GTTTCCTGCTGGATTCAGTGATTCTCCATCACCACCATCTTCTTCTTCATACCTTTATTCATCTT CCATGGCTGAAGCAGCCATAAATGATCCAACAACATTGAGCTATCCACAACCATTAGAAGGTC TCCATGAATCAGGGCCACCTCCAT
  • thaliana 12730108 At_100mM_NaCl 20000268 Tissue Whole Plant 12730108 At_100mM_NaCl 20000268 Plant Line WS 12730108 At_Drought 20000288 Timepoint (hr) 1 12730108 At_Drought 20000288 Age (day) 7 12730108 At_Drought 20000288 Organism A. thaliana 12730108 At_Drought 20000288 Treatment Drought vs.
  • Organism A thaliana 12735575 At_42deg_Heat 20000171 Tissue Aerial 12735575 At_42deg_Heat 20000171 Plant Line WS 12735575 At_42deg_Heat 20000173 Timepoint (hr) 6 12735575 At_42deg_Heat 20000173 Age (day) 14 12735575 At_42deg_Heat 20000173 Temperature (deg C.) 42 vs. 22 12735575 At_42deg_Heat 2000017171 Organism A.
  • thaliana 12735575 At_2mM_SA 20000181 Tissue Aerial 12735575 At_2mM_SA 20000181 Plant Line WS 12735575 At_2mM_SA 20000182 Timepoint (hr) 6 12735575 At_2mM_SA 20000182 Age (day) 14 12735575 At_2mM_SA 20000182 Treatment 2mM SA vs. No Treatment 12735575 At_2mM_SA 20000182 Organism A. thaliana 12735575 At_2mM_SA 20000182 Tissue Aerial 12735575 At_2mM_SA 20000182 Plant Line WS 12735575 At_Shoots 20000184 Age (day) 7 vs.
  • thaliana 12735575 At_100mM_NaCl 20000268 Tissue Whole Plant 12735575 At_100mM_NaCl 20000268 Plant Line WS 12735575 At_Open_Flower 20000286 Age (day) 21 12735575 At_Open_Flower 20000286 Organism A. thaliana 12735575 At_Open_Flower 20000286 Tissue Half Open vs. Whole Plant 12735575 At_Open_Flower 20000286 Plant Line WS 12735575 At_Pollen 20000326 Age (day) 0 vs. 21 12735575 At_Pollen 20000326 Organism A. thaliana 12735575 At_Pollen 20000326 Tissue Pollen vs.
  • thaliana 12735575 At_10percent_PEG 20000527 Tissue Whole Plant 12735575 At_10percent_PEG 20000527 Plant Line WS 12735575 At_100uM_ABA_Mutants 20000573 Organism A. thaliana 12735575 At_100uM_ABA_Mutants 20000573 Plant Line CS22 vs.
  • thaliana 12735575 At_Far-red-induction 20001247 Plant Line Columbia 12735575 At_Far-red-induction 20001247 Light Far-red vs. White 12735575 At_Far-red-induction 20001247 Tissue Whole Plant 12735575 At_Far-red-induction 20001248 Timepoint (hr) 4 12735575 At_Far-red-induction 20001248 Age (day) 7 12735575 At_Far-red-induction 20001248 Organism A. thaliana 12735575 At_Far-red-induction 20001248 Plant Line Columbia 12735575 At_Far-red-induction 20001248 Light Far-red vs.
  • thaliana 12735575 At_Far-red-induction 20001450 Plant Line Columbia 12735575 At_Far-red-induction 20001450 Light Far-red vs. White 12735575 At_Far-red-induction 20001450 Tissue Whole Plant 12735575 At_Drought_Soil_Dry 20001557 Post Timepoint (hr) 3 12735575 At_Drought_Soil_Dry 20001557 Timepoint (day) 13 12735575 At_Drought_Soil_Dry 20001557 Age (day) 27 12735575 At_Drought_Soil_Dry 20001557 Organism A. thaliana 12735575 At_Drought_Soil_Dry 20001557 Treatment Drought vs.
  • T2 seedling GFP expressed in root and hypocotyl vasculature.
  • Misc. promoter information Bidirectionality: Pass Exons: Pass Repeats: No Optional Promoter Fragments: 5′UTR region at base pairs 671-975.
  • Organism A thaliana 12736859 At_100uM_ABA 20000166 Tissue Aerial 12736859 At_100uM_ABA 20000166 Plant Line WS 12736859 At_100uM_ABA 20000169 Timepoint (hr) 6 12736859 At_100uM_ABA 20000169 Age (day) 14 12736859 At_100uM_ABA 20000169 Treatment 100uM ABA vs. No Treatment 12736859 At_100uM_ABA 20000169 Organism A.
  • thaliana 12736859 At_100uM_ABA 20000169 Tissue Aerial 12736859 At_100uM_ABA 20000169 Plant Line WS 12736859 At_Germinating_Seeds 20000179 Age (hr) 6 vs. 0 12736859 At_Germinating_Seeds 20000179 Organism A. thaliana 12736859 At_Germinating_Seeds 20000179 Tissue Germinating Seeds 12736859 At_Germinating_Seeds 20000179 Plant Line WS 12736859 At_Germinating_Seeds 20000180 Age (hr) 24 vs. 0 12736859 At_Germinating_Seeds 20000180 Organism A.
  • thaliana 12736859 At_2mM_SA 20000182 Tissue Aerial 12736859 At_2mM_SA 20000182 Plant Line WS 12736859 At_Root-Tips-vs-Tops 20000227 Age (day) 7, 10, 14 12736859 At_Root-Tips-vs-Tops 20000227 Organism A. thaliana 12736859 At_Root-Tips-vs-Tops 20000227 Tissue Root Tips vs. Root Tops 12736859 At_Root-Tips-vs-Tops 20000227 Plant Line WS 12736859 At_Siliques 20000234 Age (day) 21 12736859 At_Siliques 20000234 Tissue ⁇ 5mm Siliques vs.
  • thaliana 12736859 At_100mM_NaCl 20000268 Tissue Whole Plant 12736859 At_100mM_NaCl 20000268 Plant Line WS 12736859 At_Open_Flower 20000286 Age (day) 21 12736859 At_Open_Flower 20000286 Organism A. thaliana 12736859 At_Open_Flower 20000286 Tissue Half Open vs. Whole Plant 12736859 At_Open_Flower 20000286 Plant Line WS 12736859 At_Drought 20000436 Age (day) 7 12736859 At_Drought 20000436 Timepoint (hr) 12 12736859 At_Drought 20000436 Organism A.
  • thaliana 12736859 At_42deg_Heat 20000458 Tissue Aerial 12736859 At_42deg_Heat 20000458 Plant Line WS 12736859 At_10percent_PEG 20000460 Age (day) 12 12736859 At_10percent_PEG 20000460 Timepoint (day) 12 12736859 At_10percent_PEG 20000460 Treatment 10percent PEG vs. No Treatment 12736859 At_10percent_PEG 20000460 Organism A. thaliana 12736859 At_10percent_PEG 20000460 Tissue Whole Plant 12736859 At_10percent_PEG 20000460 Plant Line WS 12736859 At_100uM_ABA Mutants 20000574 Organism A.
  • thaliana 12736859 At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial 12736859 At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS 12736859 At_Petals 20000794 Age (day) 23-25 days 12736859 At_Petals 20000794 Organism A. thaliana 12736859 At_Petals 20000794 Tissue Petals vs. Whole plant 12736859 At_Petals 20000794 Plant Line WS 12736859 At_Line_Comparisons 20001151 Plant Line ME01339-01 vs. WS 12736859 At_Line_Comparisons 20001184 Plant Line ME01848-01 vs.
  • thaliana 12736859 At_Far-red-induction 20001450 Plant Line Columbia 12736859 At_Far-red-induction 20001450 Light Far-red vs. White 12736859 At_Far-red-induction 20001450 Tissue Whole Plant 12736859 At_Far-red-induction 20001451 Age (day) 8 12736859 At_Far-red-induction 20001451 Timepoint (hr) 24 12736859 At_Far-red-induction 20001451 Organism A. thaliana 12736859 At_Far-red-induction 20001451 Plant Line Columbia 12736859 At_Far-red-induction 20001451 Light Far-red vs.
  • thaliana 12736859 At_8deg_Cold 20002108 Tissue Whole Plant 12736859 At_8deg_Cold 20002108 Plant Line WS 12736859 At_Drought-Air-Dry 20002254 Timepoint (hr) 4 12736859 At_Drought-Air-Dry 20002254 Age (day) 35 12736859 At_Drought-Air-Dry 20002254 Organism A. thaliana 12736859 At_Drought-Air-Dry 20002254 Treatment Drought vs.
  • promoter information Bidirectionality: Pass Exons: Pass Repeats: No The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12462179 cDNA nucleotide sequence: AATGTGTACGTCTTTTGCATAAGAAGAAACAGAGAGCATTATGAATTATTAACAATTACACAA GACAGCGAGATTGTAAAAGAGTAAGAGAGAGAATGGCAGGAGAGGCAGAGGCTTTGGCC ACGACGGCACCGTTAGCTCCGGTCACCAGTCAGCGAAAAGTACGGAACGATTTGGAGGAAAC ATTACCAAAACCATACATGGCAAGAGCATTAGCAGCTGCAGATACAGAGCATCCGAATGGAA CAGAAGGTCACGATAGCAAAGGAATGAGTGTTATGCAACAACATGTTGCTTTCTTCGACCAAA ACGACGATGGAATCGTCTATCCTTGGGAGACTTATAAGGGATTTCGTGACCTTGGTTTCAACC CAATTTCCTCTATCTTTTGGAGCTTACTCATAAACTTAGCGTTCAGC
  • Organism A thaliana 12462179 At_100uM_ABA 20000166 Tissue Aerial 12462179 At_100uM_ABA 20000166 Plant Line WS 12462179 At_100uM_ABA 20000169 Timepoint (hr) 6 12462179 At_100uM_ABA 20000169 Age (day) 14 12462179 At_100uM_ABA 20000169 Treatment 100uM ABA vs. No Treatment 12462179 At_100uM_ABA 20000169 Organism A.
  • thaliana 12462179 At_100uM_ABA 20000169 Tissue Aerial 12462179 At_100uM_ABA 20000169 Plant Line WS 12462179 At_2mM_SA 20000182 Timepoint (hr) 6 12462179 At_2mM_SA 20000182 Age (day) 14 12462179 At_2mM_SA 20000182 Treatment 2mM SA vs. No Treatment 12462179 At_2mM_SA 20000182 Organism A. thaliana 12462179 At_2mM_SA 20000182 Tissue Aerial 12462179 At_2mM_SA 20000182 Plant Line WS 12462179 At_Shoots 20000184 Age (day) 7 vs.
  • thaliana 12462179 At_0.001percent_MeJA 20000211 Tissue Aerial 12462179 At_0.001percent_MeJA 20000211 Plant Line WS 12462179 At_Open_Flower 20000264 Age (day) 21 12462179 At_Open_Flower 20000264 Organism A. thaliana 12462179 At_Open_Flower 20000264 Tissue Open Flower vs. Whole Plant 12462179 At_Open_Flower 20000264 Plant Line WS 12462179 At_Open_Flower 20000265 Age (day) 21 12462179 At_Open_Flower 20000265 Organism A. thaliana 12462179 At_Open_Flower 20000265 Tissue Closed Flower vs.
  • thaliana 12462179 At_100mM_NaCl 20000308 Tissue Whole Plant 12462179 At_100mM_NaCl 20000308 Plant Line WS 12462179 At_Pollen 20000326 Age (day) 0 vs. 21 12462179 At_Pollen 20000326 Organism A. thaliana 12462179 At_Pollen 20000326 Tissue Pollen vs. Whole Plant 12462179 At_Pollen 20000326 Plant Line WS 12462179 At_Drought 20000436 Age (day) 7 12462179 At_Drought 20000436 Timepoint (hr) 12 12462179 At_Drought 20000436 Organism A.
  • thaliana 12462179 At_100uM_NAA 20000445 Tissue Aerial 12462179 At_100uM_NAA 20000445 Plant Line WS 12462179 At_100uM_ABA 20000453 Age (day) 15 12462179 At_100uM_ABA 20000453 Timepoint (hr) 24 12462179 At_100uM_ABA 20000453 Treatment 100uM ABA vs. No Treatment 12462179 At_100uM ABA 20000453 Organism A.
  • thaliana 12462179 At_100uM_ABA 20000453 Tissue Aerial 12462179 At_100uM_ABA 20000453 Plant Line WS 12462179 At_100uM_ABA 20000455 Age (day) 16 12462179 At_100uM_ABA 20000455 Timepoint (hr) 48 12462179 At_100uM_ABA 20000455 Treatment 100uM ABA vs. No Treatment 12462179 At_100uM_ABA 20000455 Organism A.
  • thaliana 12462179 At_100uM_ABA 20000455 Tissue Aerial 12462179 At_100uM_ABA 20000455 Plant Line WS 12462179 At_42deg_Heat 20000458 Timepoint (hr) 8 12462179 At_42deg_Heat 20000458 Age (day) 14 12462179 At_42deg_Heat 20000458 Temperature (deg C.) 42 vs. 22 12462179 At_42deg_Heat 20000458 Organism A.
  • thaliana 12462179 At_42deg_Heat 20000458 Tissue Aerial 12462179 At_42deg_Heat 20000458 Plant Line WS 12462179 At_Wounding 20000506 Timepoint (hr) 6 12462179 At_Wounding 20000506 Age (day) 14 12462179 At_Wounding 20000506 Organism A. thaliana 12462179 At_Wounding 20000506 Tissue Aerial 12462179 At_Wounding 20000506 Treatment Wounding vs.
  • thaliana 12462179 At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial 12462179 At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS 12462179 At_Petals 20000794 Age (day) 23-25 days 12462179 At_Petals 20000794 Organism A. thaliana 12462179 At_Petals 20000794 Tissue Petals vs. Whole plant 12462179 At_Petals 20000794 Plant Line WS 12462179 At_Line_Comparisons 20001151 Plant Line ME01339-01 vs. WS 12462179 At_Line_Comparisons 20001184 Plant Line ME01848-01 vs.
  • WS 12462179 At_Far-red-induction 20001248 Timepoint (hr) 4 12462179 At_Far-red-induction 20001246 Age (day) 7 12462179 At_Far-red-induction 20001248 Organism A. thaliana 12462179 At_Far-red-induction 20001248 Plant Line Columbia 12462179 At_Far-red-induction 20001248 Light Far-red vs. White 12462179 At_Far-red-induction 20001248 Tissue Whole Plant 12462179 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs.
  • thaliana 12462179 At_Far-red-enriched-adult 20001771 Tissue Aerial 12462179 At_Far-red-enriched-adult 20001771 Plant Line Columbia 12462179 At_Far-red-enriched-adult 20001771 Light Far-red enriched vs. White 12462179 At_Far-red-enriched-adult 20001774 Age (day) 31 12462179 At_Far-red-enriched-adult 20001774 Timepoint (hr) 72 12462179 At_Far-red-enriched-adult 20001774 Organism A.
  • thaliana 12462179 At_Far-red-enriched-adult 20001774 Tissue Aerial 12462179 At_Far-red-enriched-adult 20001774 Plant Line Columbia 12462179 At_Far-red-enriched-adult 20001774 Light Far-red enriched vs. White 12462179 At_Drought_Reproduction 20001904 Timepoint (day) 7 12462179 At_Drought_Reproduction 20001904 Age (day) 37 12462179 At_Drought_Reproduction 20001904 Organism A. thaliana 12462179 At_Drought_Reproduction 20001904 Treatment Drought vs.
  • thaliana 12462179 At_8deg_Cold 20002109 Tissue Whole Plant 12462179 At_8deg_Cold 20002109 Plant Line WS CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE 13613778 At_Root_Tips 108434 Tissue Root Tips 13613778 At_20uM_KNO3_H-to-L 108455 Timepoint (hr) 1 13613778 At_20uM_KNO3_H-to-L 108455 Treatment 20uM KNO3 vs.
  • Organism A thaliana 13613778 At_42deg_Heat 20000171 Tissue Aerial 13613778 At_42deg_Heat 20000171 Plant Line WS 13613778 At_42deg_Heat 20000173 Timepoint (hr) 6 13613778 At_42deg_Heat 20000173 Age (day) 14 13613778 At_42deg_Heat 20000173 Temperature 42 vs.22 (deg C.) 13613778 At_42deg_Heat 20000173 Organism A.
  • thaliana 13613778 At_42deg_Heat 20000173 Tissue Aerial 13613778 At_42deg_Heat 20000173 Plant Line WS 13613778 At_2mM_SA 20000181 Timepoint (hr) 1 13613778 At_2mM_SA 20000181 Age (day) 14 13613778 At_2mM_SA 20000181 Treatment 2mM SA vs. No Treatment 13613778 At_2mM_SA 20000181 Organism A.
  • thaliana 13613778 At_2mM_SA 20000181 Tissue Aerial 13613778 At_2mM_SA 20000181 Plant Line WS 13613778 At_Shoots 20000184 Age (day) 7 vs.21 13613778 At_Shoots 20000184 Organism A. thaliana 13613778 At_Shoots 20000184 Tissue Shoots vs. Whole Plant 13613778 At_Shoots 20000184 Plant Line WS 13613778 At_Roots 20000185 Age (day) 7 vs. 21 13613778 At_Roots 20000185 Organism A. thaliana 13613778 At_Roots 20000185 Tissue Roots vs.
  • thaliana 13613778 At_Pollen 20000326 Tissue Pollen vs. Whole Plant 13613778 At_Pollen 20000326 Plant Line WS 13613778 At_Shoots 20000438 Age (day) 14 vs. 21 13613778 At_Shoots 20000438 Organism A. thaliana 13613778 At_Shoots 20000438 Tissue Shoots vs. Whole Plant 13613778 At_Shoots 20000438 Plant Line WS 13613778 At_Roots 20000439 Age (day) 14 vs. 21 13613778 At_Roots 20000439 Organism A. thaliana 13613778 At_Roots 20000439 Tissue Roots vs.
  • thaliana 13613778 At_10percent_PEG 20000460 Tissue Whole Plant 13613778 At_10percent_PEG 20000460 Plant Line WS 13613778 At_Guard_Cells 20000495 Harvest Date Aug. 2, 2002 13613778 At_Guard_Cells 20000495 Organism A. thaliana 13613778 At_Guard_Cells 20000495 Tissue Guard Cells vs. Leaves 13613778 At_10percent_PEG 20000527 Age (day) 20 13613778 At_10percent_PEG 20000527 Timepoint (day) 20 13613778 At_10percent_PEG 20000527 Treatment 10percent PEG vs.
  • thaliana 13613778 At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial 13613778 At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS 13613778 At_Petals 20000794 Age (day) 23-25 days 13613778 At_Petals 20000794 Organism A. thaliana 13613778 At_Petals 20000794 Tissue Petals vs. Whole plant 13613778 At_Petals 20000794 Plant Line WS 13613778 At_Line_Comparisons 20001151 Plant Line ME01339-01 vs. WS 13613778 At_Line_Comparisons 20001184 Plant Line ME01848-01 vs.
  • WS 13613778 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS 13613778 At_Line_Comparisons 20001308 Plant Line WBin4-WX49-C vs. WS 13613778 At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS 13613778 At_Line_Comparisons 20001310 Plant Line WBin4-WX1 7-A vs. WS 13613778 At_Line_Comparisons 20001318 Plant Line WBin4-WX14R-A vs.
  • thaliana 13613778 At_Far-red-enriched-adult 20001773 Tissue Aerial 13613778 At_Far-red-enriched-adult 20001773 Plant Line Columbia 13613778 At_Far-red-enriched-adult 20001773 Light Far-red enriched vs. White 13613778 At_Far-red-enriched-adult 20001774 Age (day) 31 13613778 At_Far-red-enriched-adult 20001774 Timepoint (hr) 72 13613778 At_Far-red-enriched-adult 20001774 Organism A.
  • thaliana 13613778 At_Far-red-enriched-adult 20001774 Tissue Aerial 13613778 At_Far-red-enriched-adult 20001774 Plant Line Columbia 13613778 At_Far-red-enriched-adult 20001774 Light Far-red enriched vs. White 13613778 At_Drought_Reproduction 20001904 Timepoint (day) 7 13613778 At_Drought_Reproduction 20001904 Age (day) 37 13613778 At_Drought_Reproduction 20001904 Organism A. thaliana 13613778 At_Drought_Reproduction 20001904 Treatment Drought vs.
  • thaliana 13613778 At_8deg_Cold 20002108 Tissue Whole Plant 13613778 At_8deg_Cold 20002108 Plant Line WS 13613778 At_8deg_Cold 20002109 Age (day) 16 13613778 At_8deg_Cold 20002109 Timepoint (hr) 216 13613778 At_8deg_Cold 20002109 Temperature 8 vs. 22 (deg C.) 13613778 At_8deg_Cold 20002109 Organism A.
  • Organism A thaliana 12370888 At_100uM_ABA 20000166 Tissue Aerial 12370888 At_100uM_ABA 20000166 Plant Line WS 12370888 At_100uM_ABA 20000169 Timepoint (hr) 6 12370888 At_100uM ABA 20000169 Age (day) 14 12370888 At_100uM_ABA 20000169 Treatment 100uM ABA vs. No Treatment 12370888 At_100uM_ABA 20000169 Organism A.
  • thaliana 12370888 At_42deg_Heat 20000173 Tissue Aerial 12370888 At_42deg_Heat 20000173 Plant Line WS 12370888 At_2mM_SA 20000182 Timepoint (hr) 6 12370888 At_2mM_SA 20000182 Age (day) 14 12370888 At_2mM_SA 20000182 Treatment 2mM SA vs. No Treatment 12370888 At_2mM_SA 20000182 Organism A. thaliana 12370888 At_2mM_SA 20000182 Tissue Aerial 12370888 At_2mM_SA 20000182 Plant Line WS 12370888 At_Open_Flower 20000264 Age (day) 21 12370888 At_Open_Flower 20000264 Organism A.
  • thaliana 12370888 At_Open_Flower 20000264 Tissue Open Flower vs. Whole Plant 12370888 At_Open_Flower 20000264 Plant Line WS 12370888 At_Shoots 20000438 Age (day) 14 vs. 21 12370888 At_Shoots 20000438 Organism A. thaliana 12370888 At_Shoots 20000438 Tissue Shoots vs. Whole Plant 12370888 At_Shoots 20000438 Plant Line WS 12370888 At_100uM_ABA 20000453 Age (day) 15 12370888 At_100uM_ABA 20000453 Timepoint (hr) 24 12370888 At_100uM_ABA 20000453 Treatment 100uM ABA vs.
  • thaliana 12370888 At_42deg_Heat 20000457 Tissue Aerial 12370888 At_42deg_Heat 20000457 Plant Line WS 12370888 At_42deg_Heat 20000458 Timepoint (hr) 8 12370888 At_42deg_Heat 20000458 Age (day) 14 12370888 At_42deg_Heat 20000458 Temperature (deg C.) 42 vs. 22 12370888 At_42deg_Heat 20000458 Organism A. thaliana 12370888 At_42deg_Heat 20000458 Tissue Aerial 12370888 At_42deg_Heat 20000458 Plant Line WS 12370888 At_Guard_Cells 20000495 Harvest Date Aug.
  • thaliana 12370888 At_10percent_PEG 20000527 Tissue Whole Plant 12370888 At_10percent_PEG 20000527 Plant Line WS 12370888 At_Petals 20000794 Age (day) 23-25 days 12370888 At_Petals 20000794 Organism A.
  • thaliana 12370888 At_Petals 20000794 Tissue Petals vs. Whole plant 12370888 At_Petals 20000794 Plant Line WS 12370888 At_Far-red-induction 20001248 Timepoint (hr) 4 12370888 At_Far-red-induction 20001248 Age (day) 7 12370888 At_Far-red-induction 20001248 Organism A.
  • thaliana 12370888 At_Far-red-induction 20001248 Plant Line Columbia 12370888 At_Far-red-induction 20001248 Light Far-red vs. White 12370888 At_Far-red-induction 20001248 Tissue Whole Plant 12370888 At_Far-red-enriched 20001504 Timepoint (day) 6 12370888 At_Far-red-enriched 20001504 Age (day) 10 12370888 At_Far-red-enriched 20001504 Organism A. thaliana 12370888 At_Far-red-enriched 20001504 Plant Line Columbia 12370888 At_Far-red-enriched 20001504 Light Far-red enriched vs.
  • AAA family proteins Contains putative conserved domains: [ATPase family associated with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes].
  • GenBank description of the gene NM_179511 Arabidopsis thaliana AAA-type ATPase family protein (At1g64110) mRNA, complete cds gi
  • T2 seedling Weak root epidermal expression. Misc. promoter information: Bidirectionality: Pass Exons: Pass Repeats: No An overlap in an exon with the endogenous coding sequence to the promoter occurs at base pairs 537-754
  • the Ceres cDNA ID of the endogenous coding sequence to the promoter 12657397 cDNA nucleotide sequence: AGCGATCAAAAAAATCTTCATTAAAAGAACCCTAAATCTCTCATATCCGCCGCCGTCTTTGCCT CATTTTCAACACCGGTGATGACGTGTAAATAGATCTGGTTTTCACGGTTCTCACTACTCTCTGT GATTTTTCAGACTATTGAATCGTTAGGACCAAAACAAGTACAAAGAAACTGCAGAAGAAAAG ATTTGAGAGATATCTTACGAAACAAGCAAACAGATGTTGTTGTCGGCGCTTGGCGTCGGAG TTGGAGTAGGTGTGGGTTTAGGCTTGGCTTCTGGTCAAGCCGTCGGAAAATGGGCCGGCGGGA ACTCGTC

Abstract

The present invention is directed to promoter sequences and promoter control elements, polynucleotide constructs comprising the promoters and control elements, and methods of identifying the promoters, control elements, or fragments thereof. The invention further relates to the use of the present promoters or promoter control elements to modulate transcript levels.

Description

    CROSS REFERENCES TO RELATED APPLICATIONS
  • This nonprovisional application claims priority under 35 U.S.C. § 119(e) on U.S. application Ser. No. 10/950,321, filed Sep. 23, 2004, and Provisional Application No. 60,505,689 filed on Sep. 23, 2003; Application No. 60,511,460 filed on Oct. 14, 2003; Application No. 60/518,075 filed on Nov. 6, 2003; Application No. 60/527,611 filed on Dec. 4, 2003; Application No. 60,529,352 filed on Dec. 12, 2003; and Application No. 60/544,771 filed on Feb. 13, 2004, which are herein incorporated by reference.
    • FIELD OF THE INVENTION
  • The present invention relates to promoters and promoter control elements that are useful for modulating transcription of a desired polynucleotide. Such promoters and promoter control elements can be included in polynucleotide constructs, expression cassettes, vectors, or inserted into the chromosome or as an exogenous element, to modulate in vivo and in vitro transcription of a polynucleotide. Host cells, including plant cells, and organisms, such as regenerated plants therefrom, with desired traits or characteristics using polynucleotides comprising the promoters and promoter control elements of the present invention are also a part of the invention.
    • BACKGROUND OF THE INVENTION
  • This invention relates to the field of biotechnology and, in particular, to specific promoter sequences and promoter control element sequences which are useful for the transcription of polynucleotides in a host cell or transformed host organism.
  • One of the primary goals of biotechnology is to obtain organisms, such as plants, mammals, yeast, and prokaryotes having particular desired characteristics or traits. Examples of these characteristic or traits abound and may include, for example, in plants, virus resistance, insect resistance, herbicide resistance, enhanced stability or additional nutritional value. Recent advances in genetic engineering have enabled researchers in the field to incorporate polynucleotide sequences into host cells to obtain the desired qualities in the organism of choice. This technology permits one or more polynucleotides from a source different than the organism of choice to be transcribed by the organism of choice. If desired, the transcription and/or translation of these new polynucleotides can be modulated in the organism to exhibit a desired characteristic or trait. Alternatively, new patterns of transcription and/or translation of polynucleotides endogenous to the organism can be produced. Both approaches can be used at the same time.
    • SUMMARY OF THE INVENTION
  • The present invention is directed to isolated polynucleotide sequences that comprise promoters and promoter control elements from plants, especially Arabidopsis thaliana, Glycine max, Oryza sativa, and Zea mays, and other promoters and promoter control elements functional in plants.
  • It is an object of the present invention to provide isolated polynucleotides that are promoter sequences. These promoter sequences comprise, for example,
      • (1) a polynucleotide having a nucleotide sequence as set forth in Table 1, in the section entitled “The predicted promoter sequence” or fragment thereof;
      • (2) a polynucleotide having a nucleotide sequence having at least 80% sequence identity to a sequence as set forth in Table 1, in the section entitled “The predicted promoter sequence” or fragment thereof; and
      • (3) a polynucleotide having a nucleotide sequence which hybridizes to a sequence as set forth in Table 1, in the section entitled “The predicted promoter sequence” under a condition establishing a Tm −20° C.
  • It is another object of the present invention to provide isolated polynucleotides that are promoter control element sequences. These promoter control element sequences comprise, for example,
      • (1) a polynucleotide having a nucleotide sequence as set forth in Table 1, in the section entitled “The predicted promoter sequence” or fragment thereof;
      • (2) a polynucleotide having a nucleotide sequence having at least 80% sequence identity to a sequence as set forth in Table 1, in the section entitled “The predicted promoter sequence” or fragment thereof; and
      • (3) a polynucleotide having a nucleotide sequence which hybridizes to a sequence as set forth in Table 1, in the section entitled “The predicted promoter sequence” under a condition establishing a Tm −20° C.
  • Promoter or promoter control element sequences of the present invention are capable of modulating preferential transcription.
  • In another embodiment, the present promoter control elements are capable of serving as or fulfilling the function, for example, as a core promoter, a TATA box, a polymerase binding site, an initiator site, a transcription binding site, an enhancer, an inverted repeat, a locus control region, or a scaffold/matrix attachment region.
  • It is yet another object of the present invention to provide a polynucleotide that includes at least a first and a second promoter control element. The first promoter control element is a promoter control element sequence as discussed above, and the second promoter control element is heterologous to the first control element. Moreover, the first and second control elements are operably linked. Such promoters may modulate transcript levels preferentially in a tissue or under particular conditions.
  • In another embodiment, the present isolated polynucleotide comprises a promoter or a promoter control element as described above, wherein the promoter or promoter control element is operably linked to a polynucleotide to be transcribed.
  • In another embodiment of the present vector, the promoter and promoter control elements of the instant invention are operably linked to a heterologous polynucleotide that is a regulatory sequence.
  • It is another object of the present invention to provide a host cell comprising an isolated polynucleotide or vector as described above or fragment thereof. Host cells include, for instance, bacterial, yeast, insect, mammalian, and plant. The host cell can comprise a promoter or promoter control element exogenous to the genome. Such a promoter can modulate transcription in cis- and in trans-.
  • In yet another embodiment, the present host cell is a plant cell capable of regenerating into a plant.
  • It is yet another embodiment of the present invention to provide a plant comprising an isolated polynucleotide or vector described above.
  • It is another object of the present invention to provide a method of modulating transcription in a sample that contains either a cell-free system of transcription or host cell. This method comprises providing a polynucleotide or vector according to the present invention as described above, and contacting the sample of the polynucleotide or vector with conditions that permit transcription.
  • In another embodiment of the present method, the polynucleotide or vector preferentially modulates
  • (a) constitutive transcription,
  • (b) stress induced transcription,
  • (c) light induced transcription,
  • (d) dark induced transcription,
  • (e) leaf transcription,
  • (f) root transcription,
  • (g) stem or shoot transcription,
  • (h) silique transcription,
  • (i) callus transcription,
  • (j) flower transcription,
  • (k) immature bud and inflorescence specific transcription, or
  • (l) senescing induced transcription
  • (m) germination transcription.
  • Other and further objects of the present invention will be made clear or become apparent from the following description.
    • BRIEF DESCRIPTION OF THE TABLES AND FIGURES
  • Table 1
  • Table 1 consists of the Expression Reports for each promoter of the invention providing the nucleotide sequence for each promoter and details for expression driven by each of the nucleic acid promoter sequences as observed in transgenic plants. The results are presented as summaries of the spatial expression, which provides information as to gross and/or specific expression in various plant organs and tissues. The observed expression pattern is also presented, which gives details of expression during different generations or different developmental stages within a generation. Additional information is provided regarding the associated gene, the GenBank reference, the source organism of the promoter, and the vector and marker genes used for the construct. The following symbols are used consistently throughout the Table:
  • T1: First generation transformant
  • T2: Second generation transformant
  • T3: Third generation transformant
  • (L): low expression level
  • (M): medium expression level
  • (H): high expression level
  • Each row of the table begins with heading of the data to be found in the section. The following provides a description of the data to be found in each section:
    Heading in Table 1 Description
    Promoter Identifies the particular promoter by its construct
    ID.
    Modulates the gene: This row states the name of the gene modulated by
    the promoter
    The GenBank description of the gene: This field gives the Locus Number of the gene as
    well as the accession number.
    The predicted promoter sequence: Identifies the nucleic acid promoter sequence in
    question.
    The promoter was cloned from the organism: Identifies the source of the DNA template used to
    clone the promoter.
    The experimental promoter sequence: Identifies the nucleic acid sequence in planta driving
    expression of the reporter gene.
    The promoter was cloned in the vector: Identifies the vector used into which a promoter was
    cloned.
    When cloned into the vector the promoter was Identifies the type of marker linked to the promoter.
    operably linked to a marker, which was the type: The marker is used to determine patterns of gene
    expression in plant tissue.
    Promoter-marker vector was tested in: Identifies the organism in which the promoter-
    marker vector was tested.
    Generation screened: T1 Mature T2 Identifies the plant generation(s) used in the
    Seedling T2 Mature T3 Seedling screening process. T1 plants are those plants
    subjected to the transformation event while the T2
    generation plants are from the seeds collected from
    the T1 plants and T3 plants are from the seeds of T2
    plants.
    The spatial expression of the promoter-marker Identifies the specific parts of the plant where
    vector was found observed in and would be useful in various levels of GFP expression are observed.
    expression in any or all of the following: Expression levels are noted as either low (L),
    medium (M), or high (H).
    Observed expression pattern of the promoter-marker Identifies a general explanation of where GFP
    vector was in: expression in different generations of plants was
    T1 mature: observed.
    T2 seedling:
    The promoter can be of use in the following trait Identifies which traits and subtraits the promoter
    and sub-trait areas: (search for the trait and sub-trait cDNA can modulate
    table)
    The promoter has utility in: Identifies a specific function or functions that can be
    modulated using the promoter cDNA.
    Misc. promoter information: “Bidirectionality” is determined by the number of
    Bidirectionality: base pairs between the promoter and the start codon
    Exons: of a neighboring gene. A promoter is considered
    Repeats: bidirectional if it is closer than 200 bp to a start
    codon of a gene 5′ or 3′ to the promoter. “Exons”
    (or any coding sequence) identifies if the promoter
    has overlapped with either the modulating gene's or
    other neighboring gene's coding sequence. A “fail”
    for exons means that this overlap has occurred.
    ”Repeats” identifies the presence of normally
    occurring sequence repeats that randomly exist
    throughout the genome. A “pass” for repeats
    indicates a lack of repeats in the promoter.
    An overlap in an exon with the endogenous coding Identifies the specific nucleotides overlapping the
    sequence to the promoter occurs at base pairs: UTR region or exon of a neighboring gene. The
    orientation relative to the promoter is designated
    with a 5′ or 3′.
    The Ceres cDNA ID of the endogenous coding Identifies the number associated with the Ceres
    sequence to the promoter: cDNA that corresponds to the endogenous cDNA
    sequence of the promoter.
    cDNA nucleotide sequence: The nucleic acid sequence of the Ceres cDNA
    matching the endogenous cDNA region of the
    promoter.
    Coding sequence: A translated protein sequence of the gene modulated
    by a protein encoded by a cDNA
    Microarray Data shows that the coding sequence Microarray data is identified along with the
    was expressed in the following experiments, which corresponding experiments along with the
    shows that the promoter would useful to modulate corresponding gene expression. Gene expression is
    expression in situations similar to the following: identified by a “+” or a “−” in the
    “SIGN(LOG_RATIO)” column. A “+” notation
    indicates the cDNA is upregulated while a “−”
    indicates that the cDNA is downregulated. The
    “SHORT_NAME” field describes the experimental
    conditions.
    The parameters for the microarray experiments Parameters for microarray experiments include age,
    listed above by EXPT_REP_ID and Short_Name organism, specific tissues, age, treatments and other
    are as follow below: distinguishing characteristics or features.

    Table 2
  • Table 1 provides the results of differential expression experiments indicating if the expression levels were increased (“+”) or decreased (“−”). Such increase or decrease expression levels indicates the utility of the corresponding promoter. The following Table 2 correlates the various differential expression experiments with the utility for the promoter that would be understood from an increased or decreased expression. Table 2 includes three columns, the first column (“EXPT_REP_ID”) lists the microarray experiments by their experimental prep ID number and correspond to the same number listings in Table 1 in the “Microarray data” section. The second column lists the Short_Name of the experiment that corresponds to the EXPT_REP_ID. When a cDNA is differentially expressed in an experiment, identified by its EXPT_REP_ID, the cDNA and its endogenous promoter can be used to modulate the traits and subtraits listed in the third column.
  • FIG. 1
  • FIG. 1 is a schematic representation of the vector pNewBin4-HAP1-GFP. The definitions of the abbreviations used in the vector map are as follows:
    • Ori—the origin of replication used by an E. coli host
    • RB—sequence for the right border of the T-DNA from pMOG800
    • BstXI—restriction enzyme cleavage site used for cloning
    • HAP1VPI16—coding sequence for a fusion protein of the HAP1 and VP16 activation domains
    • NOS—terminator region from the nopaline synthase gene
    • HAP1UAS—the upstream activating sequence for HAP1
    • 5ERGFP—the green fluorescent protein gene that has been optimized for localization to the endoplasmic reticulum
    • OCS2—the terminator sequence from the octopine synthase 2 gene
    • OCS—the terminator sequence from the octopine synthase gene
    • p28716 (a.k.a 28716 short)—promoter used to drive expression of the PAT (BAR) gene
    • PAT (BAR)—a marker gene conferring herbicide resistance
    • LB—sequence for the left border of the T-DNA from pMOG800
    • Spec—a marker gene conferring spectinomycin resistance
    • TrfA—transcription repression factor gene
    • RK2-OriV—origin of replication for Agrobacterium
    DETAILED DESCRIPTION OF THE INVENTION
  • 1. Definitions
  • Chimeric: The term “chimeric” is used to describe polynucleotides or genes, as defined supra, or constructs wherein at least two of the elements of the polynucleotide or gene or construct, such as the promoter and the polynucleotide to be transcribed and/or other regulatory sequences and/or filler sequences and/or complements thereof, are heterologous to each other.
  • Constitutive Promoter: Promoters referred to herein as “constitutive promoters” actively promote transcription under most, but not necessarily all, environmental conditions and states of development or cell differentiation. Examples of constitutive promoters include the cauliflower mosaic virus (CaMV) 35S transcript initiation region and the 1′ or 2′ promoter derived from T-DNA of Agrobacterium tumefaciens, and other transcription initiation regions from various plant genes, such as the maize ubiquitin-1 promoter, known to those of skill.
  • Core Promoter: This is the minimal stretch of contiguous DNA sequence that is sufficient to direct accurate initiation of transcription by the RNA polymerase II machinery (for review see: Struhl, 1987, Cell 49: 295-297; Smale, 1994, In Transcription: Mechanisms and Regulation (eds R. C. Conaway and J. W. Conaway), pp 63-81/Raven Press, Ltd., New York; Smale, 1997, Biochim. Biophys. Acta 1351: 73-88; Smale et al., 1998, Cold Spring Harb. Symp. Quant. Biol. 58: 21-31; Smale, 2001, Genes & Dev. 15: 2503-2508; Weis and Reinberg, 1992, FASEB J. 6: 3300-3309; Burke et al., 1998, Cold Spring Harb. Symp. Quant. Biol 63: 75-82). There are several sequence motifs, including the TATA box, initiator (Inr), TFIIB recognition element (BRE) and downstream core promoter element (DPE), that are commonly found in core promoters, however not all of these elements occur in all promoters and there are no universal core promoter elements (Butler and Kadonaga, 2002, Genes & Dev. 16: 2583-2592).
  • Domain: Domains are fingerprints or signatures that can be used to characterize protein families and/or parts of proteins. Such fingerprints or signatures can comprise conserved (1) primary sequence, (2) secondary structure, and/or (3) three-dimensional conformation. A similar analysis can be applied to polynucleotides. Generally, each domain has been associated with either a conserved primary sequence or a sequence motif. Generally these conserved primary sequence motifs have been correlated with specific in vitro and/or in vivo activities. A domain can be any length, including the entirety of the polynucleotide to be transcribed. Examples of domains include, without limitation, AP2, helicase, homeobox, zinc finger, etc.
  • Endogenous: The term “endogenous,” within the context of the current invention refers to any polynucleotide, polypeptide or protein sequence which is a natural part of a cell or organisms regenerated from said cell. In the context of promoter, the term “endogenous coding region” or “endogenous cDNA” refers to the coding region that is naturally operably linked to the promoter.
  • Enhancer/Suppressor: An “enhancer” is a DNA regulatory element that can increase the steady state level of a transcript, usually by increasing the rate of transcription initiation. Enhancers usually exert their effect regardless of the distance, upstream or downstream location, or orientation of the enhancer relative to the start site of transcription. In contrast, a “suppressor” is a corresponding DNA regulatory element that decreases the steady state level of a transcript, again usually by affecting the rate of transcription initiation. The essential activity of enhancer and suppressor elements is to bind a protein factor(s). Such binding can be assayed, for example, by methods described below. The binding is typically in a manner that influences the steady state level of a transcript in a cell or in an in vitro transcription extract.
  • Exogenous: As referred to within, “exogenous” is any polynucleotide, polypeptide or protein sequence, whether chimeric or not, that is introduced into the genome of a host cell or organism regenerated from said host cell by any means other than by a sexual cross. Examples of means by which this can be accomplished are described below, and include Agrobacterium-mediated transformation (of dicots—e.g. Salomon et al. EMBO J. 3:141 (1984); Herrera-Estrella et al. EMBO J. 2:987 (1983); of monocots, representative papers are those by Escudero et al., Plant J. 10:355 (1996), Ishida et al., Nature Biotechnology 14:745 (1996), May et al., Bio/Technology 13:486 (1995)), biolistic methods (Armaleo et al., Current Genetics 17:97 1990)), electroporation, in planta techniques, and the like. Such a plant containing the exogenous nucleic acid is referred to here as a T0 for the primary transgenic plant and T1 for the first generation. The term “exogenous” as used herein is also intended to encompass inserting a naturally found element into a non-naturally found location.
  • Gene: The term “gene,” as used in the context of the current invention, encompasses all regulatory and coding sequence contiguously associated with a single hereditary unit with a genetic function. Genes can include non-coding sequences that modulate the genetic function that include, but are not limited to, those that specify polyadenylation, transcriptional regulation, DNA conformation, chromatin conformation, extent and position of base methylation and binding sites of proteins that control all of these. Genes encoding proteins are comprised of “exons” (coding sequences), which may be interrupted by “introns” (non-coding sequences). In some instances complexes of a plurality of protein or nucleic acids or other molecules, or of any two of the above, may be required for a gene's function. On the other hand a gene's genetic function may require only RNA expression or protein production, or may only require binding of proteins and/or nucleic acids without associated expression. In certain cases, genes adjacent to one another may share sequence in such a way that one gene will overlap the other. A gene can be found within the genome of an organism, in an artificial chromosome, in a plasmid, in any other sort of vector, or as a separate isolated entity.
  • Heterologous sequences: “Heterologous sequences” are those that are not operatively linked or are not contiguous to each other in nature. For example, a promoter from corn is considered heterologous to an Arabidopsis coding region sequence. Also, a promoter from a gene encoding a growth factor from corn is considered heterologous to a sequence encoding the corn receptor for the growth factor. Regulatory element sequences, such as UTRs or 3′ end termination sequences that do not originate in nature from the same gene as the coding sequence originates from, are considered heterologous to said coding sequence. Elements operatively linked in nature and contiguous to each other are not heterologous to each other.
  • Homologous: In the current invention, a “homologous” gene or polynucleotide or polypeptide refers to a gene or polynucleotide or polypeptide that shares sequence similarity with the gene or polynucleotide or polypeptide of interest. This similarity may be in only a fragment of the sequence and often represents a functional domain such as, examples including without limitation a DNA binding domain or a domain with tyrosine kinase activity. The functional activities of homologous polynucleotide are not necessarily the same.
  • Inducible Promoter: An “inducible promoter” in the context of the current invention refers to a promoter, the activity of which is influenced by certain conditions, such as light, temperature, chemical concentration, protein concentration, conditions in an organism, cell, or organelle, etc. A typical example of an inducible promoter, which can be utilized with the polynucleotides of the present invention, is PARSK1, the promoter from an Arabidopsis gene encoding a serine-threonine kinase enzyme, and which promoter is induced by dehydration, abscissic acid and sodium chloride (Wang and Goodman, Plant J. 8:37 (1995)). Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions, elevated temperature, the presence or absence of a nutrient or other chemical compound or the presence of light.
  • Modulate Transcription Level: As used herein, the phrase “modulate transcription” describes the biological activity of a promoter sequence or promoter control element. Such modulation includes, without limitation, includes up- and down-regulation of initiation of transcription, rate of transcription, and/or transcription levels.
  • Mutant: In the current invention, “mutant” refers to a heritable change in nucleotide sequence at a specific location. Mutant genes of the current invention may or may not have an associated identifiable phenotype.
  • Operable Linkage: An “operable linkage” is a linkage in which a promoter sequence or promoter control element is connected to a polynucleotide sequence (or sequences) in such a way as to place transcription of the polynucleotide sequence under the influence or control of the promoter or promoter control element. Two DNA sequences (such as a polynucleotide to be transcribed and a promoter sequence linked to the 5′ end of the polynucleotide to be transcribed) are said to be operably linked if induction of promoter function results in the transcription of mRNA encoding the polynucleotide and if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter sequence to direct the expression of the protein, antisense RNA or ribozyme, or (3) interfere with the ability of the DNA template to be transcribed. Thus, a promoter sequence would be operably linked to a polynucleotide sequence if the promoter was capable of effecting transcription of that polynucleotide sequence.
  • Optional Promoter Fragments: The phrase “optional promoter fragments” is used to refer to any sub-sequence of the promoter that is not required for driving transcription of an operationally linked coding region. These fragments comprise the 5′ UTR and any exon(s) of the endogenous coding region. The optional promoter fragments may also comprise any exon(s) and the 3′ or 5′ UTR of the gene residing upstream of the promoter (that is, 5′ to the promoter). Optional promoter fragments also include any intervening sequences that are introns or sequence that occurs between exons or an exon and the UTR.
  • Orthologous: “Orthologous” is a term used herein to describe a relationship between two or more polynucleotides or proteins. Two polynucleotides or proteins are “orthologous” to one another if they serve a similar function in different organisms. In general, orthologous polynucleotides or proteins will have similar catalytic functions (when they encode enzymes) or will serve similar structural functions (when they encode proteins or RNA that form part of the ultrastructure of a cell).
  • Percentage of sequence identity: “Percentage of sequence identity,” as used herein, is determined by comparing two optimally aligned sequences over a comparison window, where the fragment of the polynucleotide or amino acid sequence in the comparison window may comprise additions or deletions (e.g., gaps or overhangs) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Add. APL. Math. 2:482 (1981), by the homology alignment algorithm of Needleman and Wunsch J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson and Lipman Proc. Natl. Acad. Sci. (USA) 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, PASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection. Given that two sequences have been identified for comparison, GAP and BESTFIT are preferably employed to determine their optimal alignment. Typically, the default values of 5.00 for gap weight and 0.30 for gap weight length are used.
  • Plant Promoter: A “plant promoter” is a promoter capable of initiating transcription in plant cells and can modulate transcription of a polynucleotide. Such promoters need not be of plant origin. For example, promoters derived from plant viruses, such as the CaMV35S promoter or from Agrobacterium tumefaciens such as the T-DNA promoters, can be plant promoters. A typical example of a plant promoter of plant origin is the maize ubiquitin-1 (ubi-1) promoter known to those of skill.
  • Plant Tissue: The term “plant tissue” includes differentiated and undifferentiated tissues or plants, including but not limited to roots, stems, shoots, cotyledons, epicotyl, hypocotyl, leaves, pollen, seeds, tumor tissue and various forms of cells in culture such as single cells, protoplast, embryos, and callus tissue. The plant tissue may be in plants or in organ, tissue or cell culture.
  • Preferential Transcription: “Preferential transcription” is defined as transcription that occurs in a particular pattern of cell types or developmental times or in response to specific stimuli or combination thereof. Non-limitive examples of preferential transcription include: high transcript levels of a desired sequence in root tissues; detectable transcript levels of a desired sequence in certain cell types during embryogenesis; and low transcript levels of a desired sequence under drought conditions. Such preferential transcription can be determined by measuring initiation, rate, and/or levels of transcription.
  • Promoter: A “promoter” is a DNA sequence that directs the transcription of a polynucleotide. Typically a promoter is located in the 5′ region of a polynucleotide to be transcribed, proximal to the transcriptional start site of such polynucleotide. More typically, promoters are defined as the region upstream of the first exon; more typically, as a region upstream of the first of multiple transcription start sites; more typically, as the region downstream of the preceding gene and upstream of the first of multiple transcription start sites; more typically, the region downstream of the polyA signal and upstream of the first of multiple transcription start sites; even more typically, about 3,000 nucleotides upstream of the ATG of the first exon; even more typically, 2,000 nucleotides upstream of the first of multiple transcription start sites. The promoters of the invention comprise at least a core promoter as defined above. Frequently promoters are capable of directing transcription of genes located on each of the complementary DNA strands that are 3′ to the promoter. Stated differently, many promoters exhibit bidirectionality and can direct transcription of a downstream gene when present in either orientation (i.e. 5′ to 3′ or 3′ to 5′ relative to the coding region of the gene). Additionally, the promoter may also include at least one control element such as an upstream element. Such elements include UARs and optionally, other DNA sequences that affect transcription of a polynucleotide such as a synthetic upstream element.
  • Promoter Control Element: The term “promoter control element” as used herein describes elements that influence the activity of the promoter. Promoter control elements include transcriptional regulatory sequence determinants such as, but not limited to, enhancers, scaffold/matrix attachment regions, TATA boxes, transcription start locus control regions, UARs, URRs, other transcription factor binding sites and inverted repeats.
  • Public sequence: The term “public sequence,” as used in the context of the instant application, refers to any sequence that has been deposited in a publicly accessible database prior to the filing date of the present application. This term encompasses both amino acid and nucleotide sequences. Such sequences are publicly accessible, for example, on the BLAST databases on the NCBI FTP web site (accessible at ncbi.nlm.nih.gov/ftp). The database at the NCBI FTP site utilizes “gi” numbers assigned by NCBI as a unique identifier for each sequence in the databases, thereby providing a non-redundant database for sequence from various databases, including GenBank, EMBL, DBBJ, (DNA Database of Japan) and PDB (Brookhaven Protein Data Bank).
  • Regulatory Sequence: The term “regulatory sequence,” as used in the current invention, refers to any nucleotide sequence that influences transcription or translation initiation and rate, or stability and/or mobility of a transcript or polypeptide product. Regulatory sequences include, but are not limited to, promoters, promoter control elements, protein binding sequences, 5′ and 3′ UTRs, transcriptional start sites, termination sequences, polyadenylation sequences, introns, certain sequences within amino acid coding sequences such as secretory signals, protease cleavage sites, etc.
  • Related Sequences: “Related sequences” refer to either a polypeptide or a nucleotide sequence that exhibits some degree of sequence similarity with a reference sequence.
  • Specific Promoters: In the context of the current invention, “specific promoters” refers to a subset of promoters that have a high preference for modulating transcript levels in a specific tissue or organ or cell and/or at a specific time during development of an organism. By “high preference” is meant at least 3-fold, preferably 5-fold, more preferably at least 10-fold still more preferably at least 20-fold, 50-fold or 100-fold increase in transcript levels under the specific condition over the transcription under any other reference condition considered. Typical examples of temporal and/or tissue or organ specific promoters of plant origin that can be used with the polynucleotides of the present invention, are: PTA29, a promoter which is capable of driving gene transcription specifically in tapetum and only during anther development (Koltonow et al., Plant Cell 2:1201 (1990); RCc2 and RCc3, promoters that direct root-specific gene transcription in rice (Xu et al., Plant Mol. Biol. 27:237 (1995); TobRB27, a root-specific promoter from tobacco (Yamamoto et al., Plant Cell 3:371 (1991)). Examples of tissue-specific promoters under developmental control include promoters that initiate transcription only in certain tissues or organs, such as root, ovule, fruit, seeds, or flowers. Other specific promoters include those from genes encoding seed storage proteins or the lipid body membrane protein, oleosin. A few root-specific promoters are noted above. See also “Preferential transcription”.
  • Stringency: “Stringency” as used herein is a function of probe length, probe composition (G+C content), and salt concentration, organic solvent concentration, and temperature of hybridization or wash conditions. Stringency is typically compared by the parameter Tm, which is the temperature at which 50% of the complementary molecules in the hybridization are hybridized, in terms of a temperature differential from Tm. High stringency conditions are those providing a condition of Tm −5° C. to Tm −10° C. Medium or moderate stringency conditions are those providing Tm −20° C. to Tm −29° C. Low stringency conditions are those providing a condition of Tm −40° C. to Tm −48° C. The relationship of hybridization conditions to Tm (in ° C.) is expressed in the mathematical equation
    T m=81.5−16.6(log10[Na+])+0.41(%G+C)−(600/N)  (1)
    where N is the length of the probe. This equation works well for probes 14 to 70 nucleotides in length that are identical to the target sequence. The equation below for Tm of DNA-DNA hybrids is useful for probes in the range of 50 to greater than 500 nucleotides, and for conditions that include an organic solvent (formamide).
    T m=81.5+16.6log {[Na+]/(1+0.7[Na+])}+0.41(%G+C)−500/L0.63(% formamide)  (2)
    where L is the length of the probe in the hybrid. (P. Tijessen, “Hybridization with Nucleic Acid Probes” in Laboratory Techniques in Biochemistry and Molecular Biology, P. C. vand der Vliet, ed., c. 1993 by Elsevier, Amsterdam.) The Tm of equation (2) is affected by the nature of the hybrid; for DNA-RNA hybrids Tm is 10-15° C. higher than calculated, for RNA-RNA hybrids Tm is 20-25° C. higher. Because the Tm decreases about 1° C. for each 1% decrease in homology when a long probe is used (Bonner et al., J. Mol. Biol. 81:123 (1973)), stringency conditions can be adjusted to favor detection of identical genes or related family members.
  • Equation (2) is derived assuming equilibrium and therefore, hybridizations according to the present invention are most preferably performed under conditions of probe excess and for sufficient time to achieve equilibrium. The time required to reach equilibrium can be shortened by inclusion of a hybridization accelerator such as dextran sulfate or another high volume polymer in the hybridization buffer.
  • Stringency can be controlled during the hybridization reaction or after hybridization has occurred by altering the salt and temperature conditions of the wash solutions used. The formulas shown above are equally valid when used to compute the stringency of a wash solution. Preferred wash solution stringencies lie within the ranges stated above; high stringency is 5-8° C. below Tm, medium or moderate stringency is 26-29° C. below Tm and low stringency is 45-48° C. below Tm.
  • Substantially free of: A composition containing A is “substantially free of” B when at least 85% by weight of the total A+B in the composition is A. Preferably, A comprises at least about 90% by weight of the total of A+B in the composition, more preferably at least about 95% or even 99% by weight. For example, a plant gene can be substantially free of other plant genes. Other examples include, but are not limited to, ligands substantially free of receptors (and vice versa), a growth factor substantially free of other growth factors and a transcription binding factor substantially free of nucleic acids.
  • Suppressor: See “Enhancer/Suppressor”
  • TATA to start: “TATA to start” shall mean the distance, in number of nucleotides, between the primary TATA motif and the start of transcription.
  • Transgenic plant: A “transgenic plant” is a plant having one or more plant cells that contain at least one exogenous polynucleotide introduced by recombinant nucleic acid methods.
  • Translational start site: In the context of the present invention, a “translational start site” is usually an ATG or AUG in a transcript, often the first ATG or AUG. A single protein encoding transcript, however, may have multiple translational start sites.
  • Transcription start site: “Transcription start site” is used in the current invention to describe the point at which transcription is initiated. This point is typically located about 25 nucleotides downstream from a TFIID binding site, such as a TATA box. Transcription can initiate at one or more sites within the gene, and a single polynucleotide to be transcribed may have multiple transcriptional start sites, some of which may be specific for transcription in a particular cell-type or tissue or organ. “+1” is stated relative to the transcription start site and indicates the first nucleotide in a transcript.
  • Upstream Activating Region (UAR): An “Upstream Activating Region” or “UAR” is a position or orientation dependent nucleic acid element that primarily directs tissue, organ, cell type, or environmental regulation of transcript level, usually by affecting the rate of transcription initiation. Corresponding DNA elements that have a transcription inhibitory effect are called herein “Upstream Repressor Regions” or “URR”s. The essential activity of these elements is to bind a protein factor. Such binding can be assayed by methods described below. The binding is typically in a manner that influences the steady state level of a transcript in a cell or in vitro transcription extract.
  • Untranslated region (UTR): A “UTR” is any contiguous series of nucleotide bases that is transcribed, but is not translated. A 5′ UTR lies between the start site of the transcript and the translation initiation codon and includes the +1 nucleotide. A 3′ UTR lies between the translation termination codon and the end of the transcript. UTRs can have particular functions such as increasing mRNA message stability or translation attenuation. Examples of 3′ UTRs include, but are not limited to polyadenylation signals and transcription termination sequences.
  • Variant: The term “variant” is used herein to denote a polypeptide or protein or polynucleotide molecule that differs from others of its kind in some way. For example, polypeptide and protein variants can consist of changes in amino acid sequence and/or charge and/or post-translational modifications (such as glycosylation, etc). Likewise, polynucleotide variants can consist of changes that add or delete a specific UTR or exon sequence. It will be understood that there may be sequence variations within sequence or fragments used or disclosed in this application. Preferably, variants will be such that the sequences have at least 80%, preferably at least 90%, 95, 97, 98, or 99% sequence identity. Variants preferably measure the primary biological function of the native polypeptide or protein or polynucleotide.
  • 2. Introduction
  • The polynucleotides of the invention comprise promoters and promoter control elements that are capable of modulating transcription.
  • Such promoters and promoter control elements can be used in combination with native or heterologous promoter fragments, control elements or other regulatory sequences to modulate transcription and/or translation.
  • Specifically, promoters and control elements of the invention can be used to modulate transcription of a desired polynucleotide, which includes without limitation:
      • (a) antisense;
      • (b) ribozymes;
      • (c) coding sequences; or
      • (d) fragments thereof.
        The promoter also can modulate transcription in a host genome in cis- or in trans-.
  • In an organism, such as a plant, the promoters and promoter control elements of the instant invention are useful to produce preferential transcription which results in a desired pattern of transcript levels in a particular cells, tissues, or organs, or under particular conditions.
  • 3. Table of Contents
  • The following description of the present invention is outlined in the following table of contents.
  • A. Identifying and Isolating Promoter Sequences of the Invention
      • (1) Cloning Methods
      • (2) Chemical Synthesis
  • B. Generating a “core” promoter sequence
  • C. Isolating Related Promoter Sequences
      • (1) Relatives Based on Nucleotide Sequence Identity
      • (2) Relatives Based on Coding Sequence Identity
      • (3) Relatives based on Common Function
  • D. Identifying Control Elements
      • (1) Types of Transcription Control Elements
      • (2) Those Described by the Examples
      • (3) Those Identifiable by Bioinformatics
      • (4) Those Identifiable by In Vitro and In Vivo Assays
      • (5) Non-Natural Control Elements
  • E. Constructing Promoters and Control Elements
      • (1) Combining Promoters and Promoter Control Elements
      • (2) Number of Promoter Control Elements
      • (3) Spacing Between Control Elements
  • F. Vectors
      • (1) Modification of Transcription by Promoters and Promoter Control Elements
      • (2) Polynucleotide to be Transcribed
      • (3) Other Regulatory Elements
      • (4) Other Components of Vectors
  • G. Insertion of Polynucleotides and Vectors Into a Host Cell
      • (1) Autonomous of the Host Genome
      • (2) Integrated into the Host Genome
  • H. Utility
  • A. Identifying and Isolating Promoter Sequences of the Invention
  • The promoters and promoter control elements of the present invention are presented in Table 1 in the section entitled “The predicted promoter” sequence and were identified from Arabidopsis thaliana or Oryza sativa. Additional promoter sequences encompassed by the invention can be identified as described below.
  • (1) Cloning Methods
  • Isolation from genomic libraries of polynucleotides comprising the sequences of the promoters and promoter control elements of the present invention is possible using known techniques.
  • For example, polymerase chain reaction (PCR) can amplify the desired polynucleotides utilizing primers designed from sequences in the row titled “The spatial expression of the promoter-marker-vector”. Polynucleotide libraries comprising genomic sequences can be constructed according to Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed. (1989) Cold Spring Harbor Press, Cold Spring Harbor, N.Y.), for example.
  • Other procedures for isolating polynucleotides comprising the promoter sequences of the invention include, without limitation, tail-PCR, and 5′ rapid amplification of cDNA ends (RACE). See, for tail-PCR, for example, Liu et al., Plant J 8(3): 457-463 (September, 1995); Liu et al., Genomics 25: 674-681 (1995); Liu et al., Nucl. Acids Res. 21(14): 3333-3334 (1993); and Zoe et al., BioTechniques 27(2): 240-248 (1999); for RACE, see, for example, PCR Protocols: A Guide to Methods and Applications, (1990) Academic Press, Inc.
  • (2) Chemical Synthesis
  • In addition, the promoters and promoter control elements described in Table 1 in the section entitled “The predicted promoter” sequence can be chemically synthesized according to techniques in common use. See, for example, Beaucage et al., Tet. Lett. (1981) 22: 1859 and U.S. Pat. No. 4,668,777.
  • Such chemical oligonucleotide synthesis can be carried out using commercially available devices, such as, Biosearch 4600 or 8600 DNA synthesizer, by Applied Biosystems, a division of Perkin-Elmer Corp., Foster City, Calif., USA; and Expedite by Perceptive Biosystems, Framingham, Mass., USA.
  • Synthetic RNA, including natural and/or analog building blocks, can be synthesized on the Biosearch 8600 machines, see above.
  • Oligonucleotides can be synthesized and then ligated together to construct the desired polynucleotide.
  • B. Generating Reduced and “Core” Promoter Sequences
  • Included in the present invention are reduced and “core” promoter sequences. The reduced promoters can be isolated from the promoters of the invention by deleting at least one 5′ UTR, exon or 3′ UTR sequence present in the promoter sequence that is associated with a gene or coding region located 5′ to the promoter sequence or in the promoter's endogenous coding region.
  • Similarly, the “core” promoter sequences can be generated by deleting all 5′ UTRs, exons and 3′ UTRs present in the promoter sequence and the associated intervening sequences that are related to the gene or coding region 5′ to the promoter region and the promoter's endogenous coding region.
  • This data is presented in the row titled “Optional Promoter Fragments”.
  • C. Isolating Related Promoter Sequences
  • Included in the present invention are promoter and promoter control elements that are related to those described in Table 1 in the section entitled “The predicted promoter sequence”. Such related sequence can be isolated utilizing
  • (a) nucleotide sequence identity;
  • (b) coding sequence identity; or
  • (c) common function or gene products.
  • Relatives can include both naturally occurring promoters and non-natural promoter sequences. Non-natural related promoters include nucleotide substitutions, insertions or deletions of naturally-occurring promoter sequences that do not substantially affect transcription modulation activity. For example, the binding of relevant DNA binding proteins can still occur with the non-natural promoter sequences and promoter control elements of the present invention.
  • According to current knowledge, promoter sequences and promoter control elements exist as functionally important regions, such as protein binding sites, and spacer regions. These spacer regions are apparently required for proper positioning of the protein binding sites. Thus, nucleotide substitutions, insertions and deletions can be tolerated in these spacer regions to a certain degree without loss of function.
  • In contrast, less variation is permissible in the functionally important regions, since changes in the sequence can interfere with protein binding. Nonetheless, some variation in the functionally important regions is permissible so long as function is conserved.
  • The effects of substitutions, insertions and deletions to the promoter sequences or promoter control elements may be to increase or decrease the binding of relevant DNA binding proteins to modulate transcript levels of a polynucleotide to be transcribed. Effects may include tissue-specific or condition-specific modulation of transcript levels of the polypeptide to be transcribed. Polynucleotides representing changes to the nucleotide sequence of the DNA-protein contact region by insertion of additional nucleotides, changes to identity of relevant nucleotides, including use of chemically-modified bases, or deletion of one or more nucleotides are considered encompassed by the present invention.
  • (1) Relatives Based on Nucleotide Sequence Identity
  • Included in the present invention are promoters exhibiting nucleotide sequence identity to those described in Table 1 in the section entitled “The predicted promoter sequence”.
  • Definition
  • Typically, such related promoters exhibit at least 80% sequence identity, preferably at least 85%, more preferably at least 90%, and most preferably at least 95%, even more preferably, at least 96%, 97%, 98% or 99% sequence identity compared to those shown in Table 1 in the section entitled “The predicted promoter” sequence. Such sequence identity can be calculated by the algorithms and computers programs described above.
  • Usually, such sequence identity is exhibited in an alignment region that is at least 75% of the length of a sequence shown in Table 1 in the section entitled “The predicted promoter” sequence or corresponding full-length sequence; more usually at least 80%; more usually, at least 85%, more usually at least 90%, and most usually at least 95%, even more usually, at least 96%, 97%, 98% or 99% of the length of a sequence shown in Table 1 in the section entitled “The predicted promoter sequence”.
  • The percentage of the alignment length is calculated by counting the number of residues of the sequence in region of strongest alignment, e.g., a continuous region of the sequence that contains the greatest number of residues that are identical to the residues between two sequences that are being aligned. The number of residues in the region of strongest alignment is divided by the total residue length of a sequence in Table 1 in the section entitled “The predicted promoter sequence”.
  • These related promoters may exhibit similar preferential transcription as those promoters described in Table 1 in the section entitled “The predicted promoter sequence”.
  • Construction of Polynucleotides
  • Naturally occurring promoters that exhibit nucleotide sequence identity to those shown in Table 1 in the section entitled “The predicted promoter sequence” can be isolated using the techniques as described above. More specifically, such related promoters can be identified by varying stringencies, as defined above, in typical hybridization procedures such as Southern blots or probing of polynucleotide libraries, for example.
  • Non-natural promoter variants of those shown in Table 1 can be constructed using cloning methods that incorporate the desired nucleotide variation. See, for example, Ho, S. N., et al. Gene 77:51-59 1989, describing a procedure site directed mutagenesis using PCR.
  • Any related promoter showing sequence identity to those shown in Table can be chemically synthesized as described above.
  • Also, the present invention includes non-natural promoters that exhibit the above-sequence identity to those in Table 1.
  • The promoters and promoter control elements of the present invention may also be synthesized with 5′ or 3′ extensions, to facilitate additional manipulation, for instance.
  • The present invention also includes reduced promoter sequences. These sequences have at least one of the optional promoter fragments deleted.
  • Core promoter sequences are another embodiment of the present invention. The core promoter sequences have all of the optional promoter fragments deleted.
  • Testing of Polynucleotides
  • Polynucleotides of the invention were tested for activity by cloning the sequence into an appropriate vector, transforming plants with the construct and assaying for marker gene expression. Recombinant DNA constructs were prepared which comprise the polynucleotide sequences of the invention inserted into a vector suitable for transformation of plant cells. The construct can be made using standard recombinant DNA techniques (Sambrook et al. 1989) and can be introduced to the species of interest by Agrobacterium-mediated transformation or by other means of transformation as referenced below.
  • The vector backbone can be any of those typical in the art such as plasmids, viruses, artificial chromosomes, BACs, YACs and PACs and vectors of the sort described by
    • (a) BAC: Shizuya et al., Proc. Natl. Acad. Sci. USA 89: 8794-8797 (1992); Hamilton et al., Proc. Natl. Acad. Sci. USA 93: 9975-9979 (1996);
    • (b) YAC: Burke et al., Science 236:806-812 (1987);
    • (c) PAC: Sternberg N. et al., Proc Natl Acad Sci USA. January; 87 (1):103-7 (1990);
    • (d) Bacteria-Yeast Shuttle Vectors: Bradshaw et al., Nucl Acids Res 23: 4850-4856 (1995);
    • (e) Lambda Phage Vectors: Replacement Vector, e.g., Frischauf et al., J. Mol. Biol 170: 827-842 (1983); or Insertion vector, e.g., Huynh et al., In: Glover NM (ed) DNA Cloning: A practical Approach, Vol. 1 Oxford: IRL Press (1985); T-DNA gene fusion vectors: Walden et al., Mol Cell Biol 1: 175-194 (1990); and
    • (g) Plasmid vectors: Sambrook et al., infra.
  • Typically, the construct comprises a vector containing a sequence of the present invention operationally linked to any marker gene. The polynucleotide was identified as a promoter by the expression of the marker gene. Although many marker genes can be used, Green Fluorescent Protein (GFP) is preferred. The vector may also comprise a marker gene that confers a selectable phenotype on plant cells. The marker may encode biocide resistance, particularly antibiotic resistance, such as resistance to kanamycin, G418, bleomycin, hygromycin, or herbicide resistance, such as resistance to chlorosulfuron or phosphinotricin. Vectors can also include origins of replication, scaffold attachment regions (SARs), markers, homologous sequences, introns, etc.
  • Promoter Control Elements of the Invention
  • The promoter control elements of the present invention include those that comprise a sequence shown in Table 1 in the section entitled “The predicted promoter sequence” and fragments thereof. The size of the fragments of the row titled “The predicted promoter sequence” can range from 5 bases to 10 kilobases (kb). Typically, the fragment size is no smaller than 8 bases; more typically, no smaller than 12; more typically, no smaller than 15 bases; more typically, no smaller than 20 bases; more typically, no smaller than 25 bases; even more typically, no more than 30, 35, 40 or 50 bases.
  • Usually, the fragment size in no larger than 5 kb bases; more usually, no larger than 2 kb; more usually, no larger than 1 kb; more usually, no larger than 800 bases; more usually, no larger than 500 bases; even more usually, no more than 250, 200, 150 or 100 bases.
  • Relatives Based on Nucleotide Sequence Identity
  • Included in the present invention are promoter control elements exhibiting nucleotide sequence identity to those described in Table 1 in the section entitled “The predicted promoter sequence” of fragments thereof.
  • Typically, such related promoters exhibit at least 80% sequence identity, preferably at least 85%, more preferably at least 90%, and most preferably at least 95%, even more preferably, at least 96%, 97%, 98% or 99% sequence identity compared to those shown in Table 1 in the section entitled “The predicted promoter sequence”. Such sequence identity can be calculated by the algorithms and computers programs described above.
  • Promoter Control Element Configuration
  • A common configuration of the promoter control elements in RNA polymerase II promoters is shown below:
  • For more description, see, for example, “Models for prediction and recognition of eukaryotic promoters”, T. Werner, Mammalian Genome, 10, 168-175 (1999).
  • Promoters are generally modular in nature. Promoters can consist of a basal promoter which functions as a site for assembly of a transcription complex comprising an RNA polymerase, for example RNA polymerase II. A typical transcription complex will include additional factors such as TFIIB, TFIID, and TFIIE. Of these, TFIID appears to be the only one to bind DNA directly. The promoter might also contain one or more promoter control elements such as the elements discussed above. These additional control elements may function as binding sites for additional transcription factors that have the function of modulating the level of transcription with respect to tissue specificity and of transcriptional responses to particular environmental or nutritional factors, and the like.
  • One type of promoter control element is a polynucleotide sequence representing a binding site for proteins. Typically, within a particular functional module, protein binding sites constitute regions of 5 to 60, preferably 10 to 30, more preferably 10 to 20 nucleotides. Within such binding sites, there are typically 2 to 6 nucleotides which specifically contact amino acids of the nucleic acid binding protein.
  • The protein binding sites are usually separated from each other by 10 to several hundred nucleotides, typically by 15 to 150 nucleotides, often by 20 to 50 nucleotides.
  • Further, protein binding sites in promoter control elements often display dyad symmetry in their sequence. Such elements can bind several different proteins, and/or a plurality of sites can bind the same protein. Both types of elements may be combined in a region of 50 to 1,000 base pairs.
  • Binding sites for any specific factor have been known to occur almost anywhere in a promoter. For example, functional AP-1 binding sites can be located far upstream, as in the rat bone sialoprotein gene, where an AP-1 site located about 900 nucleotides upstream of the transcription start site suppresses expression. Yamauchi et al., Matrix Biol., 15, 119-130 (1996). Alternatively, an AP-1 site located close to the transcription start site plays an important role in the expression of Moloney murine leukemia virus. Sap et al., Nature, 340, 242-244, (1989).
  • (2) Those Identifiable by Bioinformatics
  • Promoter control elements from the promoters of the instant invention can be identified utilizing bioinformatic or computer driven techniques.
  • One method uses a computer program AlignACE to identify regulatory motifs in genes that exhibit common preferential transcription across a number of time points. The program identifies common sequence motifs in such genes. See, Roth et al., Nature Biotechnol. 16: 949-945 (1998); Tavazoie et al., Nat Genet 1999 July; 22(3):281-5;
  • Genomatix, also makes available a GEMS Launcher program and other programs to identify promoter control elements and configuration of such elements. Genomatix is located in Munich, Germany.
  • Other references also describe detection of promoter modules by models independent of overall nucleotide sequence similarity. See, for instance, Klingenhoff et al., Bioinformatics 15, 180-186 (1999).
  • Protein binding sites of promoters can be identified as reported in “Computer-assisted prediction, classification, and delimination of protein binding sites in nucleic acids”, Frech, et al., Nucleic Acids Research, Vol. 21, No. 7, 1655-1664, 1993.
  • Other programs used to identify protein binding sites include, for example, Signal Scan, Prestridge et al., Comput. Appl. Biosci. 12: 157-160 (1996); Matrix Search, Chen et al., Comput. Appl. Biosci. 11: 563-566 (1995), available as part of Signal Scan 4.0; MatInspector, Ghosh et al., Nucl. Acid Res. 21: 3117-3118 (1993) available http://ww.gsf.de/cgi-bin/matsearch.pl; ConsInspector, Frech et al., Nucl. Acids Res. 21: 1655-1664 (1993), available at ftp://ariane.gsf.de/pub/dos; TFSearch; and TESS.
  • Frech et al., “Software for the analysis of DNA sequence elements of transcription”, Bioinformatics & Sequence Analysis, Vol. 13, no. 1, 89-97 (1997) is a review of different software for analysis of promoter control elements. This paper also reports the usefulness of matrix-based approaches to yield more specific results.
  • For other procedures, see, Fickett et al., Curr. Op. Biotechnol. 11: 19-24 (2000); and Quandt et al., Nucleic Acids Res., 23, 4878-4884 (1995).
  • (3) Those Identifiable by In-Vitro and In-Vivo Assays
  • Promoter control elements also can be identified with in-vitro assays, such as transcription detection methods; and with in-vivo assays, such as enhancer trapping protocols.
  • In-Vitro Assays
  • Examples of in-vitro assays include detection of binding of protein factors that bind promoter control elements. Fragments of the instant promoters can be used to identify the location of promoter control elements. Another option for obtaining a promoter control element with desired properties is to modify known promoter sequences. This is based on the fact that the function of a promoter is dependent on the interplay of regulatory proteins that bind to specific, discrete nucleotide sequences in the promoter, termed motifs. Such interplay subsequently affects the general transcription machinery and regulates transcription efficiency. These proteins are positive regulators or negative regulators (repressors), and one protein can have a dual role depending on the context (Johnson, P. F. and McKnight, S. L. Annu. Rev. Biochem. 58:799-839 (1989)).
  • One type of in-vitro assay utilizes a known DNA binding factor to isolate DNA fragments that bind. If a fragment or promoter variant does not bind, then a promoter control element has been removed or disrupted. For specific assays, see, for instance, B. Luo et al., J. Mol. Biol. 266:470 (1997), S. Chusacultanachai et al., J. Biol. Chem. 274:23591 (1999), D. Fabbro et al., Biochem. Biophys. Res. Comm. 213:781 (1995)).
  • Alternatively, a fragment of DNA suspected of conferring a particular pattern of specificity can be examined for activity in binding transcription factors involved in that specificity by methods such as DNA footprinting (e.g. D. J. Cousins et al., Immunology 99:101 (2000); V. Kolla et al., Biochem. Biophys. Res. Comm. 266:5 (1999)) or “mobility-shift” assays (E. D. Fabiani et al., J. Biochem. 347:147 (2000); N. Sugiura et al., J. Biochem 347:155 (2000)) or fluorescence polarization (e.g. Royer et al., U.S. Pat. No. 5,445,935). Both mobility shift and DNA footprinting assays can also be used to identify portions of large DNA fragments that are bound by proteins in unpurified transcription extracts prepared from tissues or organs of interest.
  • Cell-free transcription extracts can be prepared and used to directly assay in a reconstitutable system (Narayan et al., Biochemistry 39:818 (2000)).
  • In-Vivo Assays
  • Promoter control elements can be identified with reporter genes in in-vivo assays with the use of fragments of the instant promoters or variants of the instant promoter polynucleotides.
  • For example, various fragments can be inserted into a vector, comprising a basal or “core” promoter, for example, operably linked to a reporter sequence, which, when transcribed, can produce a detectable label. Examples of reporter genes include those encoding luciferase, green fluorescent protein, GUS, neo, cat and bar. Alternatively, reporter sequence can be detected utilizing AFLP and microarray techniques.
  • In promoter probe vector systems, genomic DNA fragments are inserted upstream of the coding sequence of a reporter gene that is expressed only when the cloned fragment contains DNA having transcription modulation activity (Neve, R. L. et al., Nature 277:324-325 (1979)). Control elements are disrupted when fragments or variants lacking any transcription modulation activity. Probe vectors have been designed for assaying transcription modulation in E. coli (An, G. et al., J. Bact. 140:400-407 (1979)) and other bacterial hosts (Band, L. et al., Gene 26:313-315 (1983); Achen, M. G., Gene 45:45-49 (1986)), yeast (Goodey, A. R. et al., Mol. Gen. Genet. 204:505-511 (1986)) and mammalian cells (Pater, M. M. et al., J. Mol. App. Gen. 2:363-371 (1984)).
  • A different design of a promoter/control element trap includes packaging into retroviruses for more efficient delivery into cells. One type of retroviral enhancer trap was described by von Melchner et al. (Genes Dev. 1992; U.S. Pat. No. 5,364,783). The basic design of this vector includes a reporter protein coding sequence engineered into the U3 portion of the 3′ LTR. No splice acceptor consensus sequences are included, limiting its utility to work as an enhancer trap only. A different approach to a gene trap using retroviral vectors was pursued by Friedrich and Soriano (Genes Dev. 1991), who engineered a lacZ-neo fusion protein linked to a splicing acceptor. LacZ-neo fusion protein expression from trapped loci allows not only for drug selection, but also for visualization of β-galatactosidase expression using the chromogenic substrate, X-gal.
  • A general review of tools for identifying transcriptional regulatory regions of genomic DNA is provided by J. W. Fickett et al. (Curr. Opn. Biotechnol. 11: 19 (2000).
  • (4) Non-Natural Control Elements
  • Non-natural control elements can be constructed by inserting, deleting or substituting nucleotides into the promoter control elements described above. Such control elements are capable of transcription modulation that can be determined using any of the assays described above.
  • D. Constructing Promoters with Control Elements
  • (1) Combining Promoters and Promoter Control Elements
  • The promoter polynucleotides and promoter control elements of the present invention, both naturally occurring and synthetic, can be combined with each other to produce the desired preferential transcription. Also, the polynucleotides of the invention can be combined with other known sequences to obtain other useful promoters to modulate, for example, tissue transcription specific or transcription specific to certain conditions. Such preferential transcription can be determined using the techniques or assays described above.
  • Fragments, variants, as well as full-length sequences those shown in Table 1 in the section entitled “The predicted promoter sequence” and relatives are useful alone or in combination.
  • The location and relation of promoter control elements within a promoter can affect the ability of the promoter to modulate transcription. The order and spacing of control elements is a factor when constructing promoters.
  • (2) Number of Promoter Control Elements
  • Promoters can contain any number of control elements. For example, a promoter can contain multiple transcription binding sites or other control elements. One element may confer tissue or organ specificity; another element may limit transcription to specific time periods, etc. Typically, promoters will contain at least a basal or core promoter as described above. Any additional element can be included as desired. For example, a fragment comprising a basal or “core” promoter can be fused with another fragment with any number of additional control elements.
  • (3) Spacing Between Control Elements
  • Spacing between control elements or the configuration or control elements can be determined or optimized to permit the desired protein-polynucleotide or polynucleotide interactions to occur.
  • For example, if two transcription factors bind to a promoter simultaneously or relatively close in time, the binding sites are spaced to allow each factor to bind without steric hinderance. The spacing between two such hybridizing control elements can be as small as a profile of a protein bound to a control element. In some cases, two protein binding sites can be adjacent to each other when the proteins bind at different times during the transcription process.
  • Further, when two control elements hybridize the spacing between such elements will be sufficient to allow the promoter polynucleotide to hairpin or loop to permit the two elements to bind. The spacing between two such hybridizing control elements can be as small as a t-RNA loop, to as large as 10 kb.
  • Typically, the spacing is no smaller than 5 bases; more typically, no smaller than 8;
  • more typically, no smaller than 15 bases; more typically, no smaller than 20 bases; more typically, no smaller than 25 bases; even more typically, no more than 30, 35, 40 or 50 bases.
  • Usually, the fragment size in no larger than 5 kb bases; more usually, no larger than 2 kb; more usually, no larger than 1 kb; more usually, no larger than 800 bases; more usually, no larger than 500 bases; even more usually, no more than 250, 200, 150 or 100 bases.
  • Such spacing between promoter control elements can be determined using the techniques and assays described above.
  • (4) Other Promoters
  • The following are promoters that are induced under stress conditions and can be combined with those of the present invention: ldh1 (oxygen stress; tomato; see Germain and Ricard. 1997. Plant Mol Biol 35:949-54), GPx and CAT (oxygen stress; mouse; see Franco et al. 1999. Free Radic Biol Med 27:1122-32), ci7 (cold stress; potato; see Kirch et al. 1997. Plant Mol. Biol. 33:897-909), Bz2 (heavy metals; maize; see Marrs and Walbot. 1997. Plant Physiol 113:93-102), HSP32 (hyperthermia; rat; see Raju and Maines. 1994. Biochim Biophys Acta 1217:273-80); MAPKAPK-2 (heat shock; Drosophila; see Larochelle and Suter. 1995. Gene 163:209-14).
  • In addition, the following examples of promoters are induced by the presence or absence of light can be used in combination with those of the present invention: Topoisomerase II (pea; see Reddy et al. 1999. Plant Mol Biol 41:125-37), chalcone synthase (soybean; see Wingender et al. 1989. Mol Gen Genet 218:315-22) mdm2 gene (human tumor; see Saucedo et al. 1998. Cell Growth Differ 9:119-30), Clock and BMAL1 (rat; see Namihira et al. 1999. Neurosci Lett 271:1-4, PHYA (Arabidopsis; see Canton and Quail 1999. Plant Physiol 121:1207-16), PRB-1b (tobacco; see Sessa et al. 1995. Plant Mol Biol 28:537-47) and Ypr10 (common bean; see Walter et al. 1996. Eur J Biochem 239:281-93).
  • The promoters and control elements of the following genes can be used in combination with the present invention to confer tissue specificity: MipB (iceplant; Yamada et al. 1995. Plant Cell 7:1129-42) and SUCS (root nodules; broadbean; Kuster et al. 1993. Mol Plant Microbe Interact 6:507-14) for roots, OsSUTI (rice; Hirose et al. 1997. Plant Cell Physiol 38:1389-96) for leaves, Msg (soybean; Stomvik et al. 1999. Plant Mol Biol 41:217-31) for siliques, cell (Arabidopsis; Shani et al. 1997. Plant Mol Biol 34(6):837-42) and ACT11 (Arabidopsis; Huang et al. 1997. Plant Mol Biol 33:125-39) for inflorescence.
  • Still other promoters are affected by hormones or participate in specific physiological processes, which can be used in combination with those of present invention. Some examples are the ACC synthase gene that is induced differently by ethylene and brassinosteroids (mung bean; Yi et al. 1999. Plant Mol Biol 41:443-54), the TAPG1 gene that is active during abscission (tomato; Kalaitzis et al. 1995. Plant Mol Biol 28:647-56), and the 1-aminocyclopropane-1-carboxylate synthase gene (carnation; Jones et al. 19951 Plant Mol Biol 28:505-12) and the CP-2/cathepsin L gene (rat; Kim and Wright. 1997. Biol Reprod 57:1467-77), both active during senescence.
  • E. Vectors
  • Vectors are a useful component of the present invention. In particular, the present promoters and/or promoter control elements may be delivered to a system such as a cell by way of a vector. For the purposes of this invention, such delivery may range from simply introducing the promoter or promoter control element by itself randomly into a cell to integration of a cloning vector containing the present promoter or promoter control element. Thus, a vector need not be limited to a DNA molecule such as a plasmid, cosmid or bacterial phage that has the capability of replicating autonomously in a host cell. All other manner of delivery of the promoters and promoter control elements of the invention are envisioned. The various T-DNA vector types are a preferred vector for use with the present invention. Many useful vectors are commercially available.
  • It may also be useful to attach a marker sequence to the present promoter and promoter control element in order to determine activity of such sequences. Marker sequences typically include genes that provide antibiotic resistance, such as tetracycline resistance, hygromycin resistance or ampicillin resistance, or provide herbicide resistance. Specific selectable marker genes may be used to confer resistance to herbicides such as glyphosate, glufosinate or broxynil (Comai et al., Nature 317: 741-744 (1985); Gordon-Kamm et al., Plant Cell 2: 603-618 (1990); and Stalker et al., Science 242: 419-423 (1988)). Other marker genes exist which provide hormone responsiveness.
  • (1) Modification of Transcription by Promoters and Promoter Control Elements
  • The promoter or promoter control element of the present invention may be operably linked to a polynucleotide to be transcribed. In this manner, the promoter or promoter control element may modify transcription by modulate transcript levels of that polynucleotide when inserted into a genome.
  • However, prior to insertion into a genome, the promoter or promoter control element need not be linked, operably or otherwise, to a polynucleotide to be transcribed. For example, the promoter or promoter control element may be inserted alone into the genome in front of a polynucleotide already present in the genome. In this manner, the promoter or promoter control element may modulate the transcription of a polynucleotide that was already present in the genome. This polynucleotide may be native to the genome or inserted at an earlier time.
  • Alternatively, the promoter or promoter control element may be inserted into a genome alone to modulate transcription. See, for example. Vaucheret, H et al. (1998) Plant J 16: 651-659. Rather, the promoter or promoter control element may be simply inserted into a genome or maintained extrachromosomally as a way to divert transcription resources of the system to itself. This approach may be used to downregulate the transcript levels of a group of polynucleotide(s).
  • (2) Polynucleotide to be Transcribed
  • The nature of the polynucleotide to be transcribed is not limited. Specifically, the polynucleotide may include sequences that will have activity as RNA as well as sequences that result in a polypeptide product. These sequences may include, but are not limited to antisense sequences, ribozyme sequences, spliceosomes, amino acid coding sequences, and fragments thereof.
  • Specific coding sequences may include, but are not limited to endogenous proteins or fragments thereof, or heterologous proteins including marker genes or fragments thereof.
  • Promoters and control elements of the present invention are useful for modulating metabolic or catabolic processes. Such processes include, but are not limited to, secondary product metabolism, amino acid synthesis, seed protein storage, oil development, pest defense and nitrogen usage. Some examples of genes, transcripts and peptides or polypeptides participating in these processes, which can be modulated by the present invention: are tryptophan decarboxylase (tdc) and strictosidine synthase (str1), dihydrodipicolinate synthase (DHDPS) and aspartate kinase (AK), 2S albumin and alpha-, beta-, and gamma-zeins, ricinoleate and 3-ketoacyl-ACP synthase (KAS), Bacillus thuringiensis (Bt) insecticidal protein, cowpea trypsin inhibitor (CpTI), asparagine synthetase and nitrite reductase. Alternatively, expression constructs can be used to inhibit expression of these peptides and polypeptides by incorporating the promoters in constructs for antisense use, co-suppression use or for the production of dominant negative mutations.
  • (3) Other Regulatory Elements
  • As explained above, several types of regulatory elements exist concerning transcription regulation. Each of these regulatory elements may be combined with the present vector if desired.
  • (4) Other Components of Vectors
  • Translation of eukaryotic mRNA is often initiated at the codon that encodes the first methionine. Thus, when constructing a recombinant polynucleotide according to the present invention for expressing a protein product, it is preferable to ensure that the linkage between the 3′ portion, preferably including the TATA box, of the promoter and the polynucleotide to be transcribed, or a functional derivative thereof, does not contain any intervening codons which are capable of encoding a methionine.
  • The vector of the present invention may contain additional components. For example, an origin of replication allows for replication of the vector in a host cell. Additionally, homologous sequences flanking a specific sequence allows for specific recombination of the specific sequence at a desired location in the target genome. T-DNA sequences also allow for insertion of a specific sequence randomly into a target genome.
  • The vector may also be provided with a plurality of restriction sites for insertion of a polynucleotide to be transcribed as well as the promoter and/or promoter control elements of the present invention. The vector may additionally contain selectable marker genes. The vector may also contain a transcriptional and translational initiation region, and a transcriptional and translational termination region functional in the host cell. The termination region may be native with the transcriptional initiation region, may be native with the polynucleotide to be transcribed, or may be derived from another source. Convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also, Guerineau et al., (1991) Mol. Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev. 5:141-149; Mogen et al. (1990) Plant Cell 2:1261-1272; Munroe et al. (1990) Gene 91:151-158; Ballas et al. 1989) Nucleic Acids Res. 17:7891-7903; Joshi et al. (1987) Nucleic Acid Res. 15:9627-9639.
  • Where appropriate, the polynucleotide to be transcribed may be optimized for increased expression in a certain host cell. For example, the polynucleotide can be synthesized using preferred codons for improved transcription and translation. See U.S. Pat. Nos. 5,380,831, 5,436, 391; see also and Murray et al., (1989) Nucleic Acids Res. 17:477-498.
  • Additional sequence modifications include elimination of sequences encoding spurious polyadenylation signals, exon intron splice site signals, transposon-like repeats, and other such sequences well characterized as deleterious to expression. The G-C content of the polynucleotide may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. The polynucleotide sequence may be modified to avoid hairpin secondary mRNA structures.
  • A general description of expression vectors and reporter genes can be found in Gruber, et al., “Vectors for Plant Transformation, in Methods in Plant Molecular Biology & Biotechnology” in Glich et al., (Eds. pp. 89-119, CRC Press, 1993). Moreover GUS expression vectors and GUS gene cassettes are available from Clonetech Laboratories, Inc., Palo Alto, Calif. while luciferase expression vectors and luciferase gene cassettes are available from Promega Corp. (Madison, Wis.). GFP vectors are available from Aurora Biosciences.
  • F. Polynucleotide Insertion Into A Host Cell
  • The polynucleotides according to the present invention can be inserted into a host cell. A host cell includes but is not limited to a plant, mammalian, insect, yeast, and prokaryotic cell, preferably a plant cell.
  • The method of insertion into the host cell genome is chosen based on convenience. For example, the insertion into the host cell genome may either be accomplished by vectors that integrate into the host cell genome or by vectors which exist independent of the host cell genome.
  • (1) Polynucleotides Autonomous of the Host Genome
  • The polynucleotides of the present invention can exist autonomously or independent of the host cell genome. Vectors of these types are known in the art and include, for example, certain type of non-integrating viral vectors, autonomously replicating plasmids, artificial chromosomes, and the like.
  • Additionally, in some cases transient expression of a polynucleotide may be desired.
  • (2) Polynucleotides Integrated into the Host Genome
  • The promoter sequences, promoter control elements or vectors of the present invention may be transformed into host cells. These transformations may be into protoplasts or intact tissues or isolated cells. Preferably expression vectors are introduced into intact tissue. General methods of culturing plant tissues are provided for example by Maki et al. “Procedures for Introducing Foreign DNA into Plants” in Methods in Plant Molecular Biology & Biotechnology, Glich et al. (Eds. pp. 67-88 CRC Press, 1993); and by Phillips et al. “Cell-Tissue Culture and In-Vitro Manipulation” in Corn & Corn Improvement, 3rd Edition 10Sprague et al. (Eds. pp. 345-387) American Society of Agronomy Inc. et al. 1988.
  • Methods of introducing polynucleotides into plant tissue include the direct infection or co-cultivation of plant cell with Agrobacterium tumefaciens, Horsch et al., Science, 227:1229 (1985). Descriptions of Agrobacterium vector systems and methods for Agrobacterium-mediated gene transfer provided by Gruber et al. supra.
  • Alternatively, polynucleotides are introduced into plant cells or other plant tissues using a direct gene transfer method such as microprojectile-mediated delivery, DNA injection, electroporation and the like. More preferably polynucleotides are introduced into plant tissues using the microprojectile media delivery with the biolistic device. See, for example, Tomes et al., “Direct DNA transfer into intact plant cells via microprojectile bombardment” In: Gamborg and Phillips (Eds.) Plant Cell, Tissue and Organ Culture: Fundamental Methods, Springer Verlag, Berlin (1995).
  • In another embodiment of the current invention, expression constructs can be used for gene expression in callus culture for the purpose of expressing marker genes encoding peptides or polypeptides that allow identification of transformed plants. Here, a promoter that is operatively linked to a polynucleotide to be transcribed is transformed into plant cells and the transformed tissue is then placed-on callus-inducing media. If the transformation is conducted with leaf discs, for example, callus will initiate along the cut edges. Once callus growth has initiated, callus cells can be transferred to callus shoot-inducing or callus root-inducing media. Gene expression will occur in the callus cells developing on the appropriate media: callus root-inducing promoters will be activated on callus root-inducing media, etc. Examples of such peptides or polypeptides useful as transformation markers include, but are not limited to barstar, glyphosate, chloramphenicol acetyltransferase (CAT), kanamycin, spectinomycin, streptomycin or other antibiotic resistance enzymes, green fluorescent protein (GFP), and β-glucuronidase (GUS), etc. Some of the exemplary promoters of the row titled “The predicted promoter sequence” will also be capable of sustaining expression in some tissues or organs after the initiation or completion of regeneration. Examples of these tissues or organs are somatic embryos, cotyledon, hypocotyl, epicotyl, leaf, stems, roots, flowers and seed.
  • Integration into the host cell genome also can be accomplished by methods known in the art, for example, by the homologous sequences or T-DNA discussed above or using the cre-lox system (A. C. Vergunst et al., Plant Mol. Biol. 38:393 (1998)).
  • G. Utility
  • Common Uses
  • In yet another embodiment, the promoters of the present invention can be used to further understand developmental mechanisms. For example, promoters that are specifically induced during callus formation, somatic embryo formation, shoot formation or root formation can be used to explore the effects of overexpression, repression or ectopic expression of target genes, or for isolation of trans-acting factors.
  • The vectors of the invention can be used not only for expression of coding regions but may also be used in exon-trap cloning, or promoter trap procedures to detect differential gene expression in various tissues, K. Lindsey et al., 1993 “Tagging Genomic Sequences That Direct Transgene Expression by Activation of a Promoter Trap in Plants”, Transgenic Research 2:3347. D. Auch & Reth, et al., “Exon Trap Cloning: Using PCR to Rapidly Detect and Clone Exons from Genomic DNA Fragments”, Nucleic Acids Research, Vol. 18, No. 22, p. 674.
  • Entrapment vectors, first described for use in bacteria (Casadaban and Cohen, 1979, Proc. Nat. Aca. Sci. U.S.A., 76: 4530; Casadaban et al., 1980, J. Bacteriol., 143: 971) permit selection of insertional events that lie within coding sequences. Entrapment vectors can be introduced into pluripotent ES cells in culture and then passed into the germline via chimeras (Gossler et al., 1989, Science, 244: 463; Skarnes, 1990, Biotechnology, 8: 827). Promoter or gene trap vectors often contain a reporter gene, e.g., lacZ, lacking its own promoter and/or splice acceptor sequence upstream. That is, promoter gene traps contain a reporter gene with a splice site but no promoter. If the vector lands in a gene and is spliced into the gene product, then the reporter gene is expressed.
  • Recently, the isolation of preferentially-induced genes has been made possible with the use of sophisticated promoter traps (e.g. IVET) that are based on conditional auxotrophy complementation or drug resistance. In one IVET approach, various bacterial genome fragments are placed in front of a necessary metabolic gene coupled to a reporter gene. The DNA constructs are inserted into a bacterial strain otherwise lacking the metabolic gene, and the resulting bacteria are used to infect the host organism. Only bacteria expressing the metabolic gene survive in the host organism; consequently, inactive constructs can be eliminated by harvesting only bacteria that survive for some minimum period in the host. At the same time, constitutively active constructs can be eliminated by screening only bacteria that do not express the reporter gene under laboratory conditions. The bacteria selected by such a method contain constructs that are selectively induced only during infection of the host. The IVET approach can be modified for use in plants to identify genes induced in either the bacteria or the plant cells upon pathogen infection or root colonization. For information on IVET see the articles by Mahan et al. in Science 259:686-688 (1993), Mahan et al. in PNAS USA 92:669-673 (1995), Heithoff et al. in PNAS USA 94:934-939 (1997), and Wang et al. in PNAS USA. 93:10434 (1996).
  • Constitutive Transcription
  • Use of promoters and control elements providing constitutive transcription is desired for modulation of transcription in most cells of an organism under most environmental conditions. In a plant, for example, constitutive transcription is useful for modulating genes involved in defense, pest resistance, herbicide resistance, etc.
  • Constitutive up-regulation and transcription down-regulation is useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase defense, pest and herbicide resistance may require constitutive up-regulation of transcription. In contrast, constitutive transcriptional down-regulation may be desired to inhibit those genes, transcripts, and/or polypeptides that lower defense, pest and herbicide resistance.
  • Typically, promoter or control elements that provide constitutive transcription produce transcription levels that are statistically similar in many tissues and environmental conditions observed.
  • Calculation of P-value from the different observed transcript levels is one means of determining whether a promoter or control element is providing constitutive up-regulation. P-value is the probability that the difference of transcript levels is not statistically significant. The higher the P-value, the more likely the difference of transcript levels is not significant. One formula used to calculate P-value is as follows:
    ∫φ(x) dx, integrated from a to ∞,
  • where φ(x) is a normal distribution;
  • where a=|Sx−μ|
      • δ(all Samples except Sx);
  • where Sx=the intensity of the sample of interest
  • where μ=is the average of the intensities of all samples except Sx, = ( Σ ⁢   ⁢ S ⁢   ⁢ 1 ⁢   ⁢ … ⁢   ⁢ Sn ) - Sx n - 1
  • where δ(S1 . . . S11, not including Sx)=the standard deviation of all sample intensities except Sx.
  • The P-value from the formula ranges from 1.0 to 0.0.
  • Usually, each P-value of the transcript levels observed in a majority of cells, tissues, or organs under various environmental conditions produced by the promoter or control element is greater than 10−8; more usually, greater than 10−7; even more usually, greater than 10−6; even more usually, greater than 10−5 or 10−4.
  • For up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Stress Induced Preferential Transcription
  • Promoters and control elements providing modulation of transcription under oxidative, drought, oxygen, wound, and methyl jasmonate stress are particularly useful for producing host cells or organisms that are more resistant to biotic and abiotic stresses. In a plant, for example, modulation of genes, transcripts, and/or polypeptides in response to oxidative stress can protect cells against damage caused by oxidative agents, such as hydrogen peroxide and other free radicals.
  • Drought induction of genes, transcripts, and/or polypeptides are useful to increase the viability of a plant, for example, when water is a limiting factor. In contrast, genes, transcripts, and/or polypeptides induced during oxygen stress can help the flood tolerance of a plant.
  • The promoters and control elements of the present invention can modulate stresses similar to those described in, for example, stress conditions are VuPLD1 (drought stress; Cowpea; see Pham-Thi et al. 1999. Plant molecular Biology. 1257-65), pyruvate decarboxylase (oxygen stress; rice; see Rivosal et al. 1997. Plant Physiol. 114(3): 1021-29), chromoplast specific carotenoid gene (oxidative stress; capsicum; see Bouvier et al. 1998. Journal of Biological Chemistry 273: 30651-59).
  • Promoters and control elements providing preferential transcription during wounding or induced by methyl jasmonate can produce a defense response in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptides under such conditions is useful to induce a defense response to mechanical wounding, pest or pathogen attack or treatment with certain chemicals.
  • Promoters and control elements of the present invention also can trigger a response similar to those described for cf9 (viral pathogen; tomato; see O'Donnell et al. 1998. The Plant journal: for cell and molecular biology 14(1): 137-42), hepatocyte growth factor activator inhibitor type 1 (HAI-1), which enhances tissue regeneration (tissue injury; human; Koono et al. 1999. Journal of Histochemistry and Cytochemistry 47: 673-82), copper amine oxidase (CuAO), induced during ontogenesis and wound healing (wounding; chick-pea; Rea et al. 1998. FEBS Letters 437: 177-82), proteinase inhibitor II (wounding; potato; see Pena-Cortes et al. 1988. Planta 174: 84-89), protease inhibitor II (methyl jasmonate; tomato; see Farmer and Ryan. 1990. Proc Natl Acad Sci USA 87: 7713-7716), two vegetative storage protein genes VspA and VspB (wounding, jasmonic acid, and water deficit; soybean; see Mason and Mullet. 1990. Plant Cell 2: 569-579).
  • Up-regulation and transcription down-regulation are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase oxidative, flood, or drought tolerance may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to inhibit those genes, transcripts, and/or polypeptides that lower such tolerance.
  • Typically, promoter or control elements, which provide preferential transcription in wounding or under methyl jasmonate induction, produce transcript levels that are statistically significant as compared to cell types, organs or tissues under other conditions.
  • For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Light Induced Preferential Transcription
  • Promoters and control elements providing preferential transcription when induced by light exposure can be utilized to modulate growth, metabolism, and development; to increase drought tolerance; and decrease damage from light stress for host cells or organisms. In a plant, for example, modulation of genes, transcripts, and/or polypeptides in response to light is useful
      • (1) to increase the photosynthetic rate;
      • (2) to increase storage of certain molecules in leaves or green parts only, e.g., silage with high protein or starch content;
      • (3) to modulate production of exogenous compositions in green tissue, e.g., certain feed enzymes;
      • (4) to induce growth or development, such as fruit development and maturity, during extended exposure to light;
      • (5) to modulate guard cells to control the size of stomata in leaves to prevent water loss, or
      • (6) to induce accumulation of beta-carotene to help plants cope with light induced stress.
        The promoters and control elements of the present invention also can trigger responses similar to those described in: abscisic acid insensitive3 (ABI3) (dark-grown Arabidopsis seedlings, see Rohde et al. 2000. The Plant Cell 12: 35-52), asparagine synthetase (pea root nodules, see Tsai, F. Y.; Coruzzi, G. M. 1990. EMBO J 9: 323-32), mdm2 gene (human tumor; see Saucedo et al. 1998. Cell Growth Differ 9: 119-30).
  • Up-regulation and transcription down-regulation are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase drought or light tolerance may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to inhibit those genes, transcripts, and/or polypeptides that lower such tolerance.
  • Typically, promoter or control elements, which provide preferential transcription in cells, tissues or organs exposed to light, produce transcript levels that are statistically significant as compared to cells, tissues, or organs under decreased light exposure (intensity or length of time).
  • For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Dark Induced Preferential Transcription
  • Promoters and control elements providing preferential transcription when induced by dark or decreased light intensity or decreased light exposure time can be utilized to time growth, metabolism, and development, to modulate photosynthesis capabilities for host cells or organisms. In a plant, for example, modulation of genes, transcripts, and/or polypeptides in response to dark is useful, for example,
      • (1) to induce growth or development, such as fruit development and maturity, despite lack of light;
      • (2) to modulate genes, transcripts, and/or polypeptide active at night or on cloudy days; or
      • (3) to preserve the plastid ultra structure present at the onset of darkness.
        The present promoters and control elements can also trigger response similar to those described in the section above.
  • Up-regulation and transcription down-regulation is useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase growth and development may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to inhibit those genes, transcripts, and/or polypeptides that modulate photosynthesis capabilities.
  • Typically, promoter or control elements, which provide preferential transcription under exposure to dark or decrease light intensity or decrease exposure time, produce transcript levels that are statistically significant.
  • For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Leaf Preferential Transcription
  • Promoters and control elements providing preferential transcription in a leaf can modulate growth, metabolism, and development or modulate energy and nutrient utilization in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptide in a leaf, is useful, for example,
      • (1) to modulate leaf size, shape, and development;
      • (2) to modulate the number of leaves; or
      • (3) to modulate energy or nutrient usage in relation to other organs and tissues
  • Up-regulation and transcription down-regulation is useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase growth, for example, may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to inhibit energy usage in a leaf to be directed to the fruit instead, for instance.
  • Typically, promoter or control elements, which provide preferential transcription in the cells, tissues, or organs of a leaf, produce transcript levels that are statistically significant as compared to other cells, organs or tissues.
  • For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Root Preferential Transcription
  • Promoters and control elements providing preferential transcription in a root can modulate growth, metabolism, development, nutrient uptake, nitrogen fixation, or modulate energy and nutrient utilization in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or in a leaf, is useful
      • (1) to modulate root size, shape, and development;
      • (2) to modulate the number of roots, or root hairs;
      • (3) to modulate mineral, fertilizer, or water uptake;
      • (4) to modulate transport of nutrients; or
      • (4) to modulate energy or nutrient usage in relation to other organs and tissues.
  • Up-regulation and transcription down-regulation is useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase growth, for example, may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to inhibit nutrient usage in a root to be directed to the leaf instead, for instance.
  • Typically, promoter or control elements, which provide preferential transcription in cells, tissues, or organs of a root, produce transcript levels that are statistically significant as compared to other cells, organs or tissues.
  • For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Stem/Shoot Preferential Transcription
  • Promoters and control elements providing preferential transcription in a stem or shoot can modulate growth, metabolism, and development or modulate energy and nutrient utilization in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptide in a stem or shoot, is useful, for example,
      • (1) to modulate stem/shoot size, shape, and development; or
      • (2) to modulate energy or nutrient usage in relation to other organs and tissues
  • Up-regulation and transcription down-regulation is useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase growth, for example, may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to inhibit energy usage in a stem/shoot to be directed to the fruit instead, for instance.
  • Typically, promoter or control elements, which provide preferential transcription in the cells, tissues, or organs of a stem or shoot, produce transcript levels that are statistically significant as compared to other cells, organs or tissues.
  • For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Fruit and Seed Preferential Transcription
  • Promoters and control elements providing preferential transcription in a silique or fruit can time growth, development, or maturity; or modulate fertility; or modulate energy and nutrient utilization in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptides in a fruit, is useful
      • (1) to modulate fruit size, shape, development, and maturity;
      • (2) to modulate the number of fruit or seeds;
      • (3) to modulate seed shattering;
      • (4) to modulate components of seeds, such as, storage molecules, starch, protein, oil, vitamins, anti-nutritional components, such as phytic acid;
      • (5) to modulate seed and/or seedling vigor or viability;
      • (6) to incorporate exogenous compositions into a seed, such as lysine rich proteins;
      • (7) to permit similar fruit maturity timing for early and late blooming flowers; or
      • (8) to modulate energy or nutrient usage in relation to other organs and tissues.
  • Up-regulation and transcription down-regulation is useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase growth, for example, may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to inhibit late fruit maturity, for instance.
  • Typically, promoter or control elements, which provide preferential transcription in the cells, tissues, or organs of siliques or fruits, produce transcript levels that are statistically significant as compared to other cells, organs or tissues.
  • For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Callus Preferential Transcription
  • Promoters and control elements providing preferential transcription in a callus can be useful to modulating transcription in dedifferentiated host cells. In a plant transformation, for example, preferential modulation of genes, transcripts, in callus is useful to modulate transcription of a marker gene, which can facilitate selection of cells that are transformed with exogenous polynucleotides.
  • Up-regulation and transcription down-regulation is useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase marker gene detectability, for example, may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to increase the ability of the calluses to later differentiate, for instance.
  • Typically, promoter or control elements, which provide preferential transcription in callus, produce transcript levels that are statistically significant as compared to other cell types, tissues, or organs. Calculation of P-value from the different observed transcript levels is one means of determining whether a promoter or control element is providing such preferential transcription.
  • Usually, each P-value of the transcript levels observed in callus as compared to, at least one other cell type, tissue or organ, is less than 10−4; more usually, less than 10−5; even more usually, less than 10−6; even more usually, less than 10−7 or 10−8.
  • For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Flower Specific Transcription
  • Promoters and control elements providing preferential transcription in flowers can modulate pigmentation; or modulate fertility in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptides in a flower, is useful,
      • (1) to modulate petal color; or
      • (2) to modulate the fertility of pistil and/or stamen.
  • Up-regulation and transcription down-regulation is useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase pigmentation, for example, may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to inhibit fertility, for instance.
  • Typically, promoter or control elements, which provide preferential transcription in flowers, produce transcript levels that are statistically significant as compared to other cells, organs or tissues.
  • For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Immature Bud and Inflorescence Preferential Transcription
  • Promoters and control elements providing preferential transcription in a immature bud or inflorescence can time growth, development, or maturity; or modulate fertility or viability in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptide in a fruit, is useful,
      • (1) to modulate embryo development, size, and maturity;
      • (2) to modulate endosperm development, size, and composition;
      • (3) to modulate the number of seeds and fruits; or
      • (4) to modulate seed development and viability.
  • Up-regulation and transcription down-regulation is useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase growth, for example, may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to decrease endosperm size, for instance.
  • Typically, promoter or control elements, which provide preferential transcription in immature buds and inflorescences, produce transcript levels that are statistically significant as compared to other cell types, organs or tissues.
  • For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Senescence Preferential Transcription
  • Promoters and control elements providing preferential transcription during senescence can be used to modulate cell degeneration, nutrient mobilization, and scavenging of free radicals in host cells or organisms. Other types of responses that can be modulated include, for example, senescence associated genes (SAG) that encode enzymes thought to be involved in cell degeneration and nutrient mobilization (Arabidopsis; see Hensel et al. 1993. Plant Cell 5: 553-64), and the CP-2/cathepsin L gene (rat; Kim and Wright. 1997. Biol Reprod 57: 1467-77), both induced during senescence.
  • In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptides during senescencing is useful to modulate fruit ripening.
  • Up-regulation and transcription down-regulation is useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase scavenging of free radicals, for example, may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to inhibit cell degeneration, for instance.
  • Typically, promoter or control elements, which provide preferential transcription in cells, tissues, or organs during senescence, produce transcript levels that are statistically significant as compared to other conditions.
  • For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Germination Preferential Transcription
  • Promoters and control elements providing preferential transcription in a germinating seed can time growth, development, or maturity; or modulate viability in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptide in a germinating seed, is useful,
      • (1) to modulate the emergence of they hypocotyls, cotyledons and radical; or
      • (2) to modulate shoot and primary root growth and development;
  • Up-regulation and transcription down-regulation is useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase growth, for example, may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to decrease endosperm size, for instance.
  • Typically, promoter or control elements, which provide preferential transcription in a germinating seed, produce transcript levels that are statistically significant as compared to other cell types, organs or tissues.
  • For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
  • Microarray Analysis
  • A major way that a cell controls its response to internal or external stimuli is by regulating the rate of transcription of specific genes. For example, the differentiation of cells during organogenensis into forms characteristic of the organ is associated with the selective activation and repression of large numbers of genes. Thus, specific organs, tissues and cells are functionally distinct due to the different populations of mRNAs and protein products they possess. Internal signals program the selective activation and repression programs. For example, internally synthesized hormones produce such signals. The level of hormone can be raised by increasing the level of transcription of genes encoding proteins concerned with hormone synthesis.
  • To measure how a cell reacts to internal and/or external stimuli, individual mRNA levels can be measured and used as an indicator for the extent of transcription of the gene. Cells can be exposed to a stimulus, and mRNA can be isolated and assayed at different time points after stimulation. The mRNA from the stimulated cells can be compared to control cells that were not stimulated. The mRNA levels that are higher in the stimulated cell versus the control indicate a stimulus-specific response of the cell. The same is true of mRNA levels that are lower in stimulated cells versus the control condition.
  • Similar studies can be performed with cells taken from an organism with a defined mutation in their genome as compared with cells without the mutation. Altered mRNA levels in the mutated cells indicate how the mutation causes transcriptional changes. These transcriptional changes are associated with the phenotype that the mutated cells exhibit that is different from the phenotype exhibited by the control cells.
  • Applicants have utilized microarray techniques to measure the levels of mRNAs in cells from plants transformed with a construct containing the promoter or control elements of the present invention together with their endogenous cDNA sequences. In general, transformants with the constructs were grown to an appropriate stage, and tissue samples were prepared for the microarray differential expression analysis. In this manner it is possible to determine the differential expression for the cDNAs under the control of the endogenous promoter under various conditions.
  • Microarray Experimental Procedures and Results
  • Procedures
  • 1. Sample Tissue Preparation
  • Tissue samples for each of the expression analysis experiments were prepared as follows:
  • (a) Roots
  • Seeds of Arabidopsis thaliana (Ws) were sterilized in full strength bleach for less than 5 min., washed more than 3 times in sterile distilled deionized water and plated on MS agar plates. The plates were placed at 4° C. for 3 nights and then placed vertically into a growth chamber having 16 hr light/8 hr dark cycles, 23° C., 70% relative humidity and ˜11,000 LUX. After 2 weeks, the roots were cut from the agar, flash frozen in liquid nitrogen and stored at −80° C.
  • (b) Rosette Leaves, Stems, and Siliques
  • Arabidopsis thaliana (Ws) seed was vernalized at 4° C. for 3 days before sowing in Metro-mix soil type 350. Flats were placed in a growth chamber having 16 hr light/8 hr dark, 80% relative humidity, 23° C. and 13,000 LUX for germination and growth. After 3 weeks, rosette leaves, stems, and siliques were harvested, flash frozen in liquid nitrogen and stored at −80° C. until use. After 4 weeks, siliques (<5 mm, 5-10 mm and >10 mm) were harvested, flash frozen in liquid nitrogen and stored at −80° C. until use. 5 week old whole plants (used as controls) were harvested, flash frozen in liquid nitrogen and kept at −80° C. until RNA was isolated.
  • (c) Germination
  • Arabidopsis thaliana seeds (ecotype Ws) were sterilized in bleach and rinsed with sterile water. The seeds were placed in 100 mm petri plates containing soaked autoclaved filter paper. Plates were foil-wrapped and left at 4° C. for 3 nights to vernalize. After cold treatment, the foil was removed and plates were placed into a growth chamber having 16 hr light/8 hr dark cycles, 23° C., 70% relative humidity and ˜11,000 lux. Seeds were collected 1 d, 2 d, 3 d and 4 d later, flash frozen in liquid nitrogen and stored at −80° C. until RNA was isolated.
  • (d) Abscissic Acid (ABA)
  • Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in trays and left at 4° C. for 4 days to vernalize. They were then transferred to a growth chamber having grown 16 hr light/8 hr dark, 13,000 LUX, 70% humidity, and 20° C. and watered twice a week with 1 L of 1× Hoagland's solution. Approximately 1,000 14 day old plants were spayed with 200-250 mls of 100 μM ABA in a 0.02% solution of the detergent Silwet L-77. Whole seedlings, including roots, were harvested within a 15 to 20 minute time period at 1 hr and 6 hr after treatment, flash-frozen in liquid nitrogen and stored at −80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 100 μM ABA for treatment. Control plants were treated with water. After 6 hr and 24 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C.
  • (e) Brassinosteroid Responsive
  • Two separate experiments were performed, one with epi-brassinolide and one with the brassinosteroid biosynthetic inhibitor brassinazole. In the epi-brassinolide experiments, seeds of wild-type Arabidopsis thaliana (ecotype Wassilewskija) and the brassinosteroid biosynthetic mutant dwf4-1 were sown in trays and left at 4° C. for 4 days to vernalize. They were then transferred to a growth chamber having 16 hr light/8 hr dark, 11,000 LUX, 70% humidity and 22° C. temperature. Four week old plants were spayed with a 1 μM solution of epi-brassinolide and shoot parts (unopened floral primordia and shoot apical meristems) harvested three hours later. Tissue was flash-frozen in liquid nitrogen and stored at −80° C. In the brassinazole experiments, seeds of wild-type Arabidopsis thaliana (ecotype Wassilewskija) were grown as described above. Four week old plants were spayed with a 1 μM solution of brassinazole and shoot parts (unopened floral primordia and shoot apical meristems) harvested three hours later. Tissue was flash-frozen in liquid nitrogen and stored at −80° C.
  • In addition to the spray experiments, tissue was prepared from two different mutants; (1) a dwf4-1 knock out mutant and (2) a mutant overexpressing the dwf4-1 gene.
  • Seeds of wild-type Arabidopsis thaliana (ecotype Wassilewskija) and of the dwf4-1 knock out and overexpressor mutants were sown in trays and left at 4° C. for 4 days to vernalize. They were then transferred to a growth chamber having 16 hr light/8 hr dark, 11,000 LUX, 70% humidity and 22° C. temperature. Tissue from shoot parts (unopened floral primordia and shoot apical meristems) was flash-frozen in liquid nitrogen and stored at −80° C.
  • Another experiment was completed with seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in trays and left at 4° C. for 4 days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr. dark) conditions, 13,000 LUX light intensity, 70% humidity, 20° C. temperature and watered twice a week with 1 L 1× Hoagland's solution (recipe recited in Feldmann et al., (1987) Mol. Gen. Genet. 208: 1-9 and described as complete nutrient solution). Approximately 1,000 14 day old plants were spayed with 200-250 mls of 0.1 μM Epi-Brassinolite in 0.02% solution of the detergent Silwet L-77. At 1 hr. and 6 hrs. after treatment aerial tissues were harvested within a 15 to 20 minute time period and flash-frozen in liquid nitrogen.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in I-liter beakers with 0.1 μM epi-brassinolide for treatment. Control plants were treated with distilled deionized water. After 24 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C.
  • (f) Nitrogen: High to Low
  • Wild type Arabidopsis thaliana seeds (ecotpye Ws) were surface sterilized with 30% Clorox, 0.1% Triton X-100 for 5 minutes. Seeds were then rinsed with 4-5 exchanges of sterile double distilled deionized water. Seeds were vernalized at 4° C. for 2-4 days in darkness. After cold treatment, seeds were plated on modified 1×MS media (without NH4NO3 or KNO3), 0.5% sucrose, 0.5 g/L MES pH5.7, 1% phytagar and supplemented with KNO3 to a final concentration of 60 mM (high nitrate modified 1×MS media). Plates were then grown for 7 days in a Percival growth chamber at 22° C. with 16 hr. light/8 hr dark.
  • Germinated seedlings were then transferred to a sterile flask containing 50 mL of high nitrate modified 1×MS liquid media. Seedlings were grown with mild shaking for 3 additional days at 22° C. in 16 hr. light/8 hr dark (in a Percival growth chamber) on the high nitrate modified 1×MS liquid media.
  • After three days of growth on high nitrate modified 1×MS liquid media, seedlings were transferred either to a new sterile flask containing 50 mL of high nitrate modified 1×MS liquid media or to low nitrate modified 1×MS liquid media (containing 20 □M KNO3). Seedlings were grown in these media conditions with mild shaking at 22° C. in 16 hr light/8 hr dark for the appropriate time points and whole seedlings harvested for total RNA isolation via the Trizol method (LifeTech.). The time points used for the microarray experiments were 10 min. and 1 hour time points for both the high and low nitrate modified 1×MS media.
  • Alternatively, seeds that were surface sterilized in 30% bleach containing 0.1% Triton X-100 and further rinsed in sterile water, were planted on MS agar, (0.5% sucrose) plates containing 50 mM KNO3 (potassium nitrate). The seedlings were grown under constant light (3500 LUX) at 22° C. After 12 days, seedlings were transferred to MS agar plates containing either 1 mM KNO3 or 50 mM KNO3. Seedlings transferred to agar plates containing 50 mM KNO3 were treated as controls in the experiment. Seedlings transferred to plates with 1 mM KNO3 were rinsed thoroughly with sterile MS solution containing 1 mM KNO3. There were ten plates per transfer. Root tissue was collected and frozen in 15 mL Falcon tubes at various time points which included 1 hour, 2 hours, 3 hours, 4 hours, 6 hours, 9 hours, 12 hours, 16 hours, and 24 hours.
  • Maize 35A19 Pioneer hybrid seeds were sown on flats containing sand and grown in a Conviron growth chamber at 25° C., 16 hr light/8 hr dark, ˜13,000 LUX and 80% relative humidity. Plants were watered every three days with double distilled deionized water. Germinated seedlings are allowed to grow for 10 days and were watered with high nitrate modified 1×MS liquid media (see above). On day 11, young corn seedlings were removed from the sand (with their roots intact) and rinsed briefly in high nitrate modified 1×MS liquid media. The equivalent of half a flat of seedlings were then submerged (up to their roots) in a beaker containing either 500 mL of high or low nitrate modified 1×MS liquid media (see above for details).
  • At appropriate time points, seedlings were removed from their respective liquid media, the roots separated from the shoots and each tissue type flash frozen in liquid nitrogen and stored at −80° C. This was repeated for each time point. Total RNA was isolated using the Trizol method (see above) with root tissues only.
  • Corn root tissues isolated at the 4 hr and 16 hr time points were used for the microarray experiments. Both the high and low nitrate modified 1×MS media were used.
  • (g) Nitrogen: Low to High
  • Arabidopsis thaliana ecotype Ws seeds were sown on flats containing 4 L of a 1:2 mixture of Grace Zonolite vermiculite and soil. Flats were watered with 3 L of water and vernalized at 4° C. for five days. Flats were placed in a Conviron growth chamber having 16 hr light/8 hr dark at 20° C., 80% humidity and 17,450 LUX. Flats were watered with approximately 1.5 L of water every four days. Mature, bolting plants (24 days after germination) were bottom treated with 2 L of either a control (100 mM mannitol pH 5.5) or an experimental (50 mM ammonium nitrate, pH 5.5) solution. Roots, leaves and siliques were harvested separately 30, 120 and 240 minutes after treatment, flash frozen in liquid nitrogen and stored at −80° C.
  • Hybrid maize seed (Pioneer hybrid 35A19) were aerated overnight in deionized water. Thirty seeds were plated in each flat, which contained 4 liters of Grace zonolite vermiculite. Two liters of water were bottom fed and flats were kept in a Conviron growth chamber with 16 hr light/8 hr dark at 20° C. and 80% humidity. Flats were watered with 1 L of tap water every three days. Five day old seedlings were treated as described above with 2 L of either a control (100 mM mannitol pH 6.5) solution or 1 L of an experimental (50 mM ammonium nitrate, pH 6.8) solution. Fifteen shoots per time point per treatment were harvested 10, 90 and 180 minutes after treatment, flash frozen in liquid nitrogen and stored at −80° C.
  • Alternatively, seeds of Arabidopsis thaliana (ecotype Wassilewskija) were left at 4° C. for 3 days to vernalize. They were then sown on vermiculite in a growth chamber having 16 hours light/8 hours dark, 12,000-14,000 LUX, 70% humidity, and 20° C. They were bottom-watered with tap water, twice weekly. Twenty-four days old plants were sprayed with either water (control) or 0.6% ammonium nitrate at 4 μL/cm2 of tray surface. Total shoots and some primary roots were cleaned of vermiculite, flash-frozen in liquid nitrogen and stored at −80° C.
  • (h) Methyl Jasmonate
  • Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in trays and left at 4° C. for 4 days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr. dark, 13,000 LUX, 70% humidity, 20° C. temperature and watered twice a week with 1 L of a 1× Hoagland's solution. Approximately 1,000 14 day old plants were spayed with 200-250 mls of 0.001% methyl jasmonate in a 0.02% solution of the detergent Silwet L-77. At 1 hr and 6 hrs after treatment, whole seedlings, including roots, were harvested within a 15 to 20 minute time period, flash-frozen in liquid nitrogen and stored at −80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 0.001% methyl jasmonate for treatment. Control plants were treated with water. After 24 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C.
  • (i) Salicylic Acid
  • Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in trays and left at 4° C. for 4 days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr. dark, 13,000 LUX, 70% humidity, 20° C. temperature and watered twice a week with 1 L of a 1× Hoagland's solution. Approximately 1,000 14 day old plants were spayed with 200-250 mls of 5 mM salicylic acid (solubilized in 70% ethanol) in a 0.02% solution of the detergent Silwet L-77. At 1 hr and 6 hrs after treatment, whole seedlings, including roots, were harvested within a 15 to 20 minute time period flash-frozen in liquid nitrogen and stored at −80° C.
  • Alternatively, seeds of wild-type Arabidopsis thaliana (ecotype Columbia) and mutant CS3726 were sown in soil type 200 mixed with osmocote fertilizer and Marathon insecticide and left at 4° C. for 3 days to vernalize. Flats were incubated at room temperature with continuous light. Sixteen days post germination plants were sprayed with 2 mM SA, 0.02% SilwettL-77 or control solution (0.02% SilwettL-77. Aerial parts or flowers were harvested 1 hr, 4 hr, 6 hr, 24 hr and 3 weeks post-treatment flash frozen and stored at −80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 2 mM SA for treatment. Control plants were treated with water. After 12 hr and 24 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C.
  • (j) Drought Stress
  • Seeds of Arabidopsis thaliana (Wassilewskija) were sown in pots and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 150,000-160,000 LUX, 20° C. and 70% humidity. After 14 days, aerial tissues were cut and left to dry on 3 MM Whatman paper in a Petri-plate for 1 hour and 6 hours. Aerial tissues exposed for 1 hour and 6 hours to 3 MM Whatman paper wetted with 1× Hoagland's solution served as controls. Tissues were harvested, flash-frozen in liquid nitrogen and stored at −80° C.
  • Alternatively, Arabidopsis thaliana (Ws) seed was vernalized at 4° C. for 3 days before sowing in Metromix soil type 350. Flats were placed in a growth chamber with 23° C., 16 hr light/8 hr. dark, 80% relative humidity, ˜13,000 LUX for germination and growth. Plants were watered with 1-1.5 L of water every four days. Watering was stopped 16 days after germination for the treated samples, but continued for the control samples. Rosette leaves and stems, flowers and siliques were harvested 2 d, 3 d, 4 d, 5 d, 6 d and 7 d after watering was stopped. Tissue was flash frozen in liquid nitrogen and kept at −80° C. until RNA was isolated. Flowers and siliques were also harvested on day 8 from plants that had undergone a 7 d drought treatment followed by 1 day of watering. Control plants (whole plants) were harvested after 5 weeks, flash frozen in liquid nitrogen and stored as above.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in empty 1-liter beakers at room temperature for treatment. Control plants were placed in water. After 1 hr, 6 hr, 12 hr and 24 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C.
  • (k) Osmotic Stress
  • Seeds of Arabidopsis thaliana (Wassilewskija) were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C., and 70% humidity. After 14 days, the aerial tissues were cut and placed on 3 MM Whatman paper in a petri-plate wetted with 20% PEG (polyethylene glycol-Mr 8,000) in 1× Hoagland's solution. Aerial tissues on 3 MM Whatman paper containing 1× Hoagland's solution alone served as the control. Aerial tissues were harvested at 1 hour and 6 hours after treatment, flash-frozen in liquid nitrogen and stored at −80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 10% PEG (polyethylene glycol-Mr 8,000) for treatment. Control plants were treated with water. After 1 hr and 6 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 150 mM NaCl for treatment. Control plants were treated with water. After 1 hr, 6 hr, and 24 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C.
  • (l) Heat Shock Treatment
  • Seeds of Arabidopsis Thaliana (Wassilewskija) were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber with 16 hr light/8 hr dark, 12,000-14,000 Lux, 70% humidity and 20° C., fourteen day old plants were transferred to a 42° C. growth chamber and aerial tissues were harvested 1 hr and 6 hr after transfer. Control plants were left at 20° C. and aerial tissues were harvested. Tissues were flash-frozen in liquid nitrogen and stored at −80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers containing 42° C. water for treatment. Control plants were treated with water at 25° C. After 1 hr and 6 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C.
  • (m) Cold Shock Treatment
  • Seeds of Arabidopsis thaliana (Wassilewskija) were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C. and 70% humidity. Fourteen day old plants were transferred to a 4° C. dark growth chamber and aerial tissues were harvested 1 hour and 6 hours later. Control plants were maintained at 20° C. and covered with foil to avoid exposure to light. Tissues were flash-frozen in liquid nitrogen and stored at −80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers containing 4° C. water for treatment. Control plants were treated with water at 25° C. After 1 hr and 6 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C.
  • (n) Arabidopsis Seeds
  • Fruits (Pod+Seed) 0-5 mm
  • Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of Arabidopsis embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Siliques 0-5 mm in length containing post fertilization through pre-heart stage [0-72 hours after fertilization (HAF)] embryos were harvested and flash frozen in liquid nitrogen.
  • Fruits (Pod+Seed) 5-10 mm
  • Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of Arabidopsis embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Siliques 5-10 mm in length containing heart- through early upturned-U-stage [72-120 hours after fertilization (HAF)] embryos were harvested and flash frozen in liquid nitrogen.
  • Fruits (Pod+Seed)>10 mm
  • Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of Arabidopsis embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Siliques>10 mm in length containing green, late upturned-U-stage [>120 hours after fertilization (HAF)-9 days after flowering (DAF)] embryos were harvested and flash frozen in liquid nitrogen.
  • Green Pods 5-10 mm (Control Tissue for Samples 72-74)
  • Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of Arabidopsis embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Green siliques 5-10 mm in length containing developing seeds 72-120 hours after fertilization (HAF)] were opened and the seeds removed. The remaining tissues (green pods minus seed) were harvested and flash frozen in liquid nitrogen.
  • Green Seeds from Fruits>10 mm
  • Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of Arabidopsis embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Green siliques>10 mm in length containing developing seeds up to 9 days after flowering (DAF)] were opened and the seeds removed and harvested and flash frozen in liquid nitrogen.
  • Brown Seeds from Fruits>10 mm
  • Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of Arabidopsis embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Yellowing siliques>10 mm in length containing brown, dessicating seeds>11 days after flowering (DAF)] were opened and the seeds removed and harvested and flash frozen in liquid nitrogen.
  • Green/Brown Seeds from Fruits>10 mm
  • Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of Arabidopsis embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Green siliques>10 mm in length containing both green and brown seeds>9 days after flowering (DAF)] were opened and the seeds removed and harvested and flash frozen in liquid nitrogen.
  • Mature Seeds (24 Hours After Imbibition)
  • Mature dry seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown onto moistened filter paper and left at 4° C. for two to three days to vernalize. Imbibed seeds were then transferred to a growth chamber [16 hr light: 8 hr dark conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature], the emerging seedlings harvested after 48 hours and flash frozen in liquid nitrogen.
  • Mature Seeds (Dry)
  • Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature and taken to maturity. Mature dry seeds are collected, dried for one week at 28° C., and vernalized for one week at 4° C. before used as a source of RNA.
  • (o) Herbicide Treatment
  • Arabidopsis thaliana (Ws) seeds were sterilized for 5 min. with 30% bleach, 50 μl Triton in a total volume of 50 ml. Seeds were vernalized at 4° C. for 3 days before being plated onto GM agar plates at a density of about 144 seeds per plate. Plates were incubated in a Percival growth chamber having 16 hr light/8 hr dark, 80% relative humidity, 22° C. and 11,000 LUX for 14 days.
  • Plates were sprayed (˜0.5 mls/plate) with water, Finale (1.128 g/L), Glean (1.88 g/L), RoundUp (0.01 g/L) or Trimec (0.08 g/L). Tissue was collected and flash frozen in liquid nitrogen at the following time points: 0, 1, 2, 4, 8, 12 and 24 hours. Frozen tissue was stored at −80° C. prior to RNA isolation.
  • (p) Root Tips
  • Seeds of Arabidopsis thaliana (ecotype Ws) were placed on MS plates and vernalized at 4° C. for 3 days before being placed in a 25° C. growth chamber having 16 hr light/8 hr dark, 70% relative humidity and about 3 W/m2. After 6 days, young seedlings were transferred to flasks containing B5 liquid medium, 1% sucrose and 0.05 mg/l indole-3-butyric acid. Flasks were incubated at room temperature with 100 rpm agitation. Media was replaced weekly. After three weeks, roots were harvested and incubated for 1 hr with 2% pectinase, 0.2% cellulase, pH 7 before straining through a #80 (Sigma) sieve. The root body material remaining on the sieve (used as the control) was flash frozen and stored at −80° C. until use. The material that passed through the #80 sieve was strained through a #200 (Sigma) sieve and the material remaining on the sieve (root tips) was flash frozen and stored at −80° C. until use. Approximately 10 mg of root tips were collected from one flask of root culture.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 8 days. Seedlings were carefully removed from the sand and the root tips (˜2 mm long) were removed and flash frozen in liquid nitrogen prior to storage at −80° C. The tissues above the root tips (˜1 cm long) were cut, treated as above and used as control tissue.
  • (q) Imbibed Seed
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in covered flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. One day after sowing, whole seeds were flash frozen in liquid nitrogen prior to storage at −80° C. Two days after sowing, embryos and endosperm were isolated and flash frozen in liquid nitrogen prior to storage at −80° C. On days 3-6, aerial tissues, roots and endosperm were isolated and flash frozen in liquid nitrogen prior to storage at −80° C.
  • (r) Flowers (Green, White or Buds)
  • Approximately 10 μl of Arabidopsis thaliana seeds (ecotype Ws) were sown on 350 soil (containing 0.03% marathon) and vernalized at 4 C for 3 days. Plants were then grown at room temperature under fluorescent lighting until flowering. Flowers were harvested after 28 days in three different categories. Buds that had not opened at all and were completely green were categorized as “flower buds” (also referred to as green buds by the investigator). Buds that had started to open, with white petals emerging slightly were categorized as “green flowers” (also referred to as white buds by the investigator). Flowers that had opened mostly (with no silique elongation) with white petals completely visible were categorized as “white flowers” (also referred to as open flowers by the investigator). Buds and flowers were harvested with forceps, flash frozen in liquid nitrogen and stored at −80 C until RNA was isolated.
  • s) Ovules
  • Seeds of Arabidopsis thaliana heterozygous for pistillata (pi) [ecotype Landsberg erecta (Ler)] were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 76% humidity, and 24° C. temperature. Inflorescences were harvested from seedlings about 40 days old. The inflorescences were cut into small pieces and incubated in the following enzyme solution (pH 5) at room temperature for 0.5-1 hr.: 0.2% pectolyase Y-23, 0.04% pectinase, 5 mM MES, 3% Sucrose and MS salts (1900 mg/l KNO3, 1650 mg/l NH4NO3, 370 mg/l MgSO4.7H2O, 170 mg/l KH2PO4, 440 mg/l CaCl2.2H2O, 6.2 mg/l H2BO3, 15.6 mg/l MnSO4.4H2O, 8.6 mg/l ZnSO4.7H2O, 0.25 mg/l NaMoO4.2H2O, 0.025 mg/l CuCO4.5H2O, 0.025 mg/l CoCl2.6H2O, 0.83 mg/l KI, 27.8 mg/l FeSO4.7H2O, 37.3 mg/l Disodium EDTA, pH 5.8). At the end of the incubation the mixture of inflorescence material and enzyme solution was passed through a size 60 sieve and then through a sieve with a pore size of 125 μm. Ovules greater than 125 μm in diameter were collected, rinsed twice in B5 liquid medium (2500 mg/l KNO3, 250 mg/l MgSO4.7H2O, 150 mg/l NaH2PO4.H2O, 150 mg/l CaCl2.2H2O, 134 mg/l (NH4)2CaCl2.SO4, 3 mg/l H2BO3, 10 mg/l MnSO4.4H2O, 2ZnSO4.7H2O, 0.25 mg/l NaMoO4.2H2O, 0.025 mg/l CuCO4.5H2O, 0.025 mg/l CoCl2.6H2O, 0.75 mg/l KI, 40 mg/l EDTA sodium ferric salt, 20 g/l sucrose, 10 mg/l Thiamine hydrochloride, 1 mg/l Pyridoxine hydrochloride, 1 mg/l Nicotinic acid, 100 mg/l myo-inositol, pH 5.5)), rinsed once in deionized water and flash frozen in liquid nitrogen. The supernatant from the 125 μm sieving was passed through subsequent sieves of 50 μm and 32 μm. The tissue retained in the 32 μm sieve was collected and mRNA prepared for use as a control.
  • t) Wounding
  • Seeds of Arabidopsis thaliana (Wassilewskija) were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 70% humidity and 20° C. After 14 days, the leaves were wounded with forceps. Aerial tissues were harvested 1 hour and 6 hours after wounding. Aerial tissues from unwounded plants served as controls. Tissues were flash-frozen in liquid nitrogen and stored at −80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were wounded (one leaf nicked by scissors) and placed in 1-liter beakers of water for treatment. Control plants were treated not wounded. After 1 hr and 6 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C.
  • u) Nitric Oxide Treatment
  • Seeds of Arabidopsis thaliana (Wassilewskija) were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C. and 70% humidity. Fourteen day old plants were sprayed with 5 mM sodium nitroprusside in a 0.02% Silwett L-77 solution. Control plants were sprayed with a 0.02% Silwett L-77 solution. Aerial tissues were harvested 1 hour and 6 hours after spraying, flash-frozen in liquid nitrogen and stored at −80° C.
  • Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in I-liter beakers with 5 mM nitroprusside for treatment. Control plants were treated with water. After 1 hr, 6 hr and 12 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C.
  • v) Root Hairless Mutants
  • Plants mutant at the rhl gene locus lack root hairs. This mutation is maintained as a heterozygote.
  • Seeds of Arabidopsis thaliana (Landsberg erecta) mutated at the rhl gene locus were sterilized using 30% bleach with 1 ul/ml 20% Triton-X 100 and then vernalized at 4° C. for 3 days before being plated onto GM agar plates. Plates were placed in growth chamber with 16 hr light/8 hr. dark, 23° C., 14,500-15,900 LUX, and 70% relative humidity for germination and growth.
  • After 7 days, seedlings were inspected for root hairs using a dissecting microscope. Mutants were harvested and the cotyledons removed so that only root tissue remained. Tissue was then flash frozen in liquid nitrogen and stored at −80 C.
  • Arabidopsis thaliana (Landsberg erecta) seedlings grown and prepared as above were used as controls.
  • Alternatively, seeds of Arabidopsis thaliana (Landsberg erecta), heterozygous for the rhl1 (root hairless) mutation, were surface-sterilized in 30% bleach containing 0.1% Triton X-100 and further rinsed in sterile water. They were then vernalized at 4° C. for 4 days before being plated onto MS agar plates. The plates were maintained in a growth chamber at 24° C. with 16 hr light/8 hr dark for germination and growth. After 10 days, seedling roots that expressed the phenotype (i.e. lacking root hairs) were cut below the hypocotyl junction, frozen in liquid nitrogen and stored at −80° C. Those seedlings with the normal root phenotype (heterozygous or wt) were collected as described for the mutant and used as controls.
  • w) Ap2
  • Seeds of Arabidopsis thaliana (ecotype Landesberg erecta) and floral mutant apetala2 (Jofuku et al., 1994, Plant Cell 6:1211-1225) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light, 8 hr dark) conditions 7000-8000 LUX light intensity, 70% humidity and 22° C. temperature. Inflorescences containing immature floral buds (stages 1-7; Bowman, 1994) as well as the inflorescence meristem were harvested and flashfrozen. Polysomal polyA+ RNA was isolated from tissue according to Cox and Goldberg, 1988).
  • x) Salt
  • Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing in flats containing vermiculite soil. Flats were placed at 20° C. in a Conviron growth chamber having 16 hr light/8 hr dark. Whole plants (used as controls) received water. Other plants were treated with 100 mM NaCl. After 6 hr and 72 hr, aerial and root tissues were harvested and flash frozen in liquid nitrogen prior to storage at −80° C.
  • y) Petals
  • Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing in flats containing vermiculite soil. Flats were watered placed at 20° C. in a Conviron growth chamber having 16 hr light/8 hr dark. Whole plants (used as the control) and petals from inflorescences 23-25 days after germination were harvested, flash frozen in liquid nitrogen and stored at −80° C.
  • z) Pollen
  • Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing in flats containing vermiculite soil. Flats were watered and placed at 20° C. in a Conviron growth chamber having 16 hr light/8 hr dark. Whole plants (used as controls) and pollen from plants 38 dap was harvested, flash frozen in liquid nitrogen and stored at −80° C.
  • aa) Interploidy Crosses
  • Interploidy crosses involving a 6× parent are lethal. Crosses involving a 4× parent are complete and analyzed. The imbalance in the maternal/paternal ratio produced from the cross can lead to big seeds. Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing. Small siliques were harvested at 5 days after pollination, flash frozen in liquid nitrogen and stored at −80° C.
  • bb) Line Comparisons
  • Alkaloid 35S over-expressing lines were used to monitor the expression levels of terpenoid/alkaloid biosynthetic and P450 genes to identify the transcriptional regulatory points I the biosynthesis pathway and the related P450 genes. Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing in vermiculite soil (Zonolite) supplemented by Hoagland solution. Flats were placed in Conviron growth chambers under long day conditions (16 hr light, 23° C./8 hr dark, 20° C.) Basta spray and selection of the overexpressing lines was conducted about 2 weeks after germination. Approximately 2-3 weeks after bolting (approximately 5-6 weeks after germination), stem and siliques from the over-expressing lines and from wild-type plants were harvested, flash frozen in liquid nitrogen and stored at −80° C.
  • cc) DMT-II
  • Demeter (dmt) is a mutant of a methyl transferase gene and is similar to fie. Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing. Cauline leaves and closed flowers were isolated from 35S::DMT and dmt−/− plant lines, flash frozen in liquid nitrogen and stored at −80° C.
  • dd) CS6630 Roots and Shoots
  • Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing on MS media (1%) sucrose on bactor-agar. Roots and shoots were separated 14 days after germination, flash frozen in liquid nitrogen and stored at −80° C.
  • ee) CS237
  • CS237 is an ethylene triple response mutant that is insensitive to ethylene and which has an etr1-1 phenotype. Arabidopsis thaliana CS237 seeds were vernalized at 4° C. for 3 days before sowing. Aerial tissue was collected from mutants and wild-type Columbia ecotype plants, flash frozen in liquid nitrogen and stored at −80° C.
  • ff) Guard Cells
  • Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3 days before sowing. Leaves were harvested, homogenized and centrifuged to isolate the guard cell containing fraction. Homogenate from leaves served as the control. Samples were flash frozen in liquid nitrogen and stored at −80° C. Identical experiments using leaf tissue from canola were performed.
  • gg) 3642-1
  • 3642-1 is a T-DNA mutant that affects leaf development. This mutant segregates 3:1, wild-type:mutant. Arabidopsis thaliana 3642-1 mutant seeds were vernalized at 4° C. for 3 days before sowing in flats of MetroMix 200. Flats were placed in the greenhouse, watered and grown to the 8 leaf, pre-flower stage. Stems and rosette leaves were harvested from the mutants and the wild-type segregants, flash frozen and stored at −80° C.
  • hh) Caf
  • Carple factory (Caf) is a double-stranded RNAse protein that is hypothesized to process small RNAs in Arabidopsis. The protein is closely related to a Drosophila protein named DICER that functions in the RNA degradation steps of RNA interference. Arabidopsis thaliana Caf mutant seeds were vernalized at 4° C. for 3 days before sowing in flats of MetroMix 200. Flats were placed in the greenhouse, watered and grown to the 8 leaf, pre-flower stage. Stems and rosette leaves were harvested from the mutants and the wild-type segregants, flash frozen and stored at −80° C.
  • 2. Microarray Hybridization Procedures
  • Microarray technology provides the ability to monitor mRNA transcript levels of thousands of genes in a single experiment. These experiments simultaneously hybridize two differentially labeled fluorescent cDNA pools to glass slides that have been previously spotted with cDNA clones of the same species. Each arrayed cDNA spot will have a corresponding ratio of fluorescence that represents the level of disparity between the respective mRNA species in the two sample pools. Thousands of polynucleotides can be spotted on one slide, and each experiment generates a global expression pattern.
  • Coating Slides
  • The microarray consists of a chemically coated microscope slide, referred herein as a “chip” with numerous polynucleotide samples arrayed at a high density. The poly-L-lysine coating allows for this spotting at high density by providing a hydrophobic surface, reducing the spreading of spots of DNA solution arrayed on the slides. Glass microscope slides (Gold Seal #3010 manufactured by Gold Seal Products, Portsmouth, N.H., USA) were coated with a 0.1% W/V solution of Poly-L-lysine (Sigma, St. Louis, Mo.) using the following protocol:
    • 1. Slides were placed in slide racks (Shandon Lipshaw #121). The racks were then put in chambers (Shandon Lipshaw #121).
    • 2. Cleaning solution was prepared:
      • 70 g NaOH was dissolved in 280 mL ddH2O.
      • 420 mL 95% ethanol was added. The total volume was 700 mL (=2×350 mL); it was stirred until completely mixed. If the solution remained cloudy, ddH2O was added until clear.
    • 3. The solution was poured into chambers with slides; the chambers were covered with glass lids. The solution was mixed on an orbital shaker for 2 hr.
    • 4. The racks were quickly transferred to fresh chambers filled with ddH2O. They were rinsed vigorously by plunging racks up and down. Rinses were repeated 4× with fresh ddH2O each time, to remove all traces of NaOH-ethanol.
    • 5. Polylysine solution was prepared:
      • 0 mL poly-L-lysine+70 mL tissue culture PBS in 560 mL water, using plastic graduated cylinder and beaker.
    • 6. Slides were transferred to polylysine solution and shaken for 1 hr.
    • 7. The rack was transferred to a fresh chambers filled with ddH2O. It was plunged up and down 5× to rinse.
    • 8. The slides were centrifuged on microtiter plate carriers (paper towels were placed below the rack to absorb liquid) for 5 min. @ 500 rpm. The slide racks were transferred to empty chambers with covers.
    • 9. Slide racks were dried in a 45 C oven for 10 min.
    • 10. The slides were stored in a closed plastic slide box.
    • 11. Normally, the surface of lysine coated slides was not very hydrophobic immediately after this process, but became increasingly hydrophobic with storage. A hydrophobic surface helped ensure that spots didn't run together while printing at high densities. After they aged for 10 days to a month the slides were ready to use. However, coated slides that have been sitting around for long periods of time were usually too old to be used. This was because they developed opaque patches, visible when held to the light, and these resulted in high background hybridization from the fluorescent probe. Alternatively, pre-coated glass slides were purchased from TeleChem International, Inc. (Sunnyvale, Calif., 94089; catalog number SMM-25, Superamine substrates).
      PCR Amplification of cDNA Clone Inserts
  • Polynucleotides were amplified from Arabidopsis cDNA clones using insert specific probes. The resulting 100 uL PCR reactions were purified with Qiaquick 96 PCR purification columns (Qiagen, Valencia, Calif., USA) and eluted in 30 uL of 5 mM Tris. 8.5 uL of the elution were mixed with 1.5 uL of 20×SSC to give a final spotting solution of DNA in 3×SSC. The concentrations of DNA generated from each clone varied between 10-100 ng/ul, but were usually about 50 ng/ul.
  • Arraying of PCR Products on Glass Slides
  • PCR products from cDNA clones were spotted onto the poly-L-Lysine coated glass slides using an arrangement of quill-tip pins (ChipMaker 3 spotting pins; Telechem, International, Inc., Sunnyvale, Calif., USA) and a robotic arrayer (PixSys 3500, Cartesian Technologies, Irvine, Calif., USA). Around 0.5 nl of a prepared PCR product was spotted at each location to produce spots with approximately 100 um diameters. Spot center-to-center spacing was from 180 um to 210 um depending on the array. Printing was conducted in a chamber with relative humidity set at 50%.
  • Slides containing maize sequences were purchased from Agilent Technology (Palo Alto, Calif. 94304).
  • Post-Processing of Slides
  • After arraying, slides were processed through a series of steps—rehydration, UV cross-linking, blocking and denaturation—required prior to hybridization. Slides were rehydrated by placing them over a beaker of warm water (DNA face down), for 2-3 sec, to distribute the DNA more evenly within the spots, and then snap dried on a hot plate (DNA side, face up). The DNA was then cross-linked to the slides by UV irradiation (60-65 mJ; 2400 Stratalinker, Stratagene, La Jolla, Calif., USA).
  • Following this a blocking step was performed to modify remaining free lysine groups, and hence minimize their ability to bind labeled probe DNA. To achieve this the arrays were placed in a slide rack. An empty slide chamber was left ready on an orbital shaker. The rack was bent slightly inwards in the middle, to ensure the slides would not run into each other while shaking. The blocking solution was prepared as follows:
  • 3×350-ml glass chambers (with metal tops) were set to one side, and a large round Pyrex dish with dH2O was placed ready in the microwave. At this time, 15 ml sodium borate was prepared in a 50 ml conical tube.
  • 6-g succinic anhydride was dissolved in approx. 325-350 mL 1-methyl-2-pyrrolidinone. Rapid addition of reagent was crucial.
  • a. Immediately after the last flake of the succinic anhydride dissolved, the 15-mL sodium borate was added.
  • b. Immediately after the sodium borate solution mixed in, the solution was poured into an empty slide chamber.
  • c. The slide rack was plunged rapidly and evenly in the solution. It was vigorously shaken up and down for a few seconds, making sure slides never left the solution.
  • d. It was mixed on an orbital shaker for 15-20 min. Meanwhile, the water in the Pyrex dish (enough to cover slide rack) was heated to boiling.
  • Following this, the slide rack was gently plunge in the 95 C water (just stopped boiling) for 2 min. Then the slide rack was plunged 5×in 95% ethanol. The slides and rack were centrifuged for 5 min. @ 500 rpm. The slides were loaded quickly and evenly onto the carriers to avoid streaking. The arrays were used immediately or store in slide box.
  • The Hybridization process began with the isolation of mRNA from the two tissues (see “Isolation of total RNA ” and “Isolation of mRNA ”, below) in question followed by their conversion to single stranded cDNA (see “Generation of probes for hybridization ”, below). The cDNA from each tissue was independently labeled with a different fluorescent dye and then both samples were pooled together. This final differentially labeled cDNA pool was then placed on a processed microarray and allowed to hybridize (see “Hybridization and wash conditions”, below).
  • Isolation of Total RNA
  • Approximately 1 g of plant tissue was ground in liquid nitrogen to a fine powder and transferred into a 50-ml centrifuge tube containing 10 ml of Trizol reagent. The tube was vigorously vortexed for 1 min and then incubated at room temperature for 10-20 min. on an orbital shaker at 220 rpm. Two ml of chloroform was added to the tube and the solution vortexed vigorously for at least 30-sec before again incubating at room temperature with shaking. The sample was then centrifuged at 12,000×g (10,000 rpm) for 15-20 min at 4° C. The aqueous layer was removed and mixed by inversion with 2.5 ml of 1.2 M NaCl/0.8 M Sodium Citrate and 2.5 ml of isopropyl alcohol added. After a 10 min. incubation at room temperature, the sample was centrifuged at 12,000×g (10,000 rpm) for 15 min at 4° C. The pellet was washed with 70% ethanol, re-centrifuged at 8,000 rpm for 5 min and then air dried at room temperature for 10 min. The resulting total RNA was dissolved in either TE (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) or DEPC (diethylpyrocarbonate) treated deionized water (RNAse-free water). For subsequent isolation of mRNA using the Qiagen kit, the total RNA pellet was dissolved in RNAse-free water.
  • Isolation of mRNA
  • mRNA was isolated using the Qiagen Oligotex mRNA Spin-Column protocol (Qiagen, Valencia, Calif.). Briefly, 500 μl OBB buffer (20 mM Tris-Cl, pH 7.5, 1 M NaCl, 2 mM EDTA, 0.2% SDS) was added to 500 μl of total RNA (0.5-0.75 mg) and mixed thoroughly. The sample was first incubated at 70° C. for 3 min, then at room temperature for 10 minutes and finally centrifuged for 2 min at 14,000-18,000×g. The pellet was resuspended in 400 μl OW2 buffer (10 mM Tris-Cl, pH 7.5, 150 mM NaCl, 1 mM EDTA) by vortexing, the resulting solution placed on a small spin column in a 1.5 ml RNase-free microcentrifuge tube and centrifuged for 1 min at 14,000-18,000×g. The spin column was transferred to a new 1.5 ml RNase-free microcentrifuge tube and washed with 400 μl of OW2 buffer. To release the isolated mRNA from the resin, the spin column was again transferred to a new RNase-free 1.5 ml microcentrifuge tube, 20-100 μl 70° C. OEB buffer (5 mM Tris-Cl, pH 7.5) added and the resin resuspended in the resulting solution via pipeting. The mRNA solution was collected after centrifuging for 1 min at 14,000-18,000×g.
  • Alternatively, mRNA was isolated using the Stratagene Poly(A) Quik mRNA Isolation Kit (Startagene, La Jolla, Calif.). Here, up to 0.5 mg of total RNA (maximum volume of 1 ml) was incubated at 65° C. for 5 minutes, snap cooled on ice and 0.1× volumes of 10× sample buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA (pH 8.0) 5 M NaCl) added. The RNA sample was applied to a prepared push column and passed through the column at a rate of ˜1 drop every 2 sec. The solution collected was reapplied to the column and collected as above. 200 μl of high salt buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.5 NaCl) was applied to the column and passed through the column at a rate of ˜1 drop every 2 sec. This step was repeated and followed by three low salt buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.1 M NaCl) washes preformed in a similar manner. mRNA was eluted by applying to the column four separate 200 μl aliquots of elution buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA) preheated to 65° C. Here, the elution buffer was passed through the column at a rate of 1 drop/sec. The resulting mRNA solution was precipitated by adding 0.1× volumes of 10× sample buffer, 2,5 volumes of ice-cold 100% ethanol, incubating overnight at −20° C. and centrifuging at 14,000-18,000×g for 20-30 min at 4° C. The pellet was washed with 70% ethanol and air dried for 10 min. at room temperature before resuspension in RNase-free deionized water.
  • Preparation of Yeast Controls
  • Plasmid DNA was isolated from the following yeast clones using Qiagen filtered maxiprep kits (Qiagen, Valencia, Calif.): YAL022c(Fun26), YAL031c(Fun21), YBR032w, YDL131w, YDL182w, YDL194w, YDL196w, YDR050c and YDR116c. Plasmid DNA was linearized with either BsrBI (YAL022c(Fun26), YAL031c(Fun21), YDL131w, YDL182w, YDL194w, YDL196w, YDR050c) or AflIII (YBR032w, YDR116c) and isolated.
  • In Vitro Transcription of Yeast Clones
  • The following solution was incubated at 37° C. for 2 hours: 17 μl of isolated yeast insert DNA (1 μg), 20 μl 5× buffer, 10 μl 100 mM DTT, 2.5 μl (100 U) RNasin, 20 μl 2.5 mM (ea.) rNTPs, 2.7 μl (40 U) SP6 polymerase and 27.8 μl RNase-free deionized water. 2 μl (2 U) Ampli DNase I was added and the incubation continued for another 15 min. 10 μl 5M NH4OAC and 100 μl phenol:chloroform:isoamyl alcohol (25:24:1) were added, the solution vortexed and then centrifuged to separate the phases. To precipitate the RNA, 250 μl ethanol was added and the solution incubated at −20° C. for at least one hour. The sample was then centrifuged for 20 min at 4° C. at 14,000-18,000×g, the pellet washed with 500 μl of 70% ethanol, air dried at room temperature for 10 min and resuspended in 100 μl of RNase-free deionized water. The precipitation procedure was then repeated.
  • Alternatively, after the two-hour incubation, the solution was extracted with phenol/chloroform once before adding 0.1 volume 3M sodium acetate and 2.5 volumes of 100% ethanol. The solution was centrifuged at 15,000 rpm, 4° C. for 20 minutes and the pellet resuspended in RNase-free deionized water. The DNase I treatment was carried out at 37° C. for 30 minutes using 2 U of Ampli DNase I in the following reaction condition: 50 mM Tris-HCl (pH 7.5), 10 mM MgCl2. The DNase I reaction was then stopped with the addition of NH4OAC and phenol:chloroform:isoamyl alcohol (25:24:1), and RNA isolated as described above.
  • 0.15-2.5 ng of the in vitro transcript RNA from each yeast clone were added to each plant mRNA sample prior to labeling to serve as positive (internal) probe controls.
  • Generation of Probes for Hybridization
  • Generation of Labeled Probes for Hybridization from First-Strand cDNA
  • Hybridization probes were generated from isolated mRNA using an Atlas™ Glass Fluorescent Labeling Kit (Clontech Laboratories, Inc., Palo Alto, Calif., USA). This entails a two step labeling procedure that first incorporates primary aliphatic amino groups during cDNA synthesis and then couples fluorescent dye to the cDNA by reaction with the amino functional groups. Briefly, 5 μg of oligo(dT)18 primer d(TTTTTTTTTTTTTTTTTTV) was mixed with Poly A+ mRNA (1.5-2 μg mRNA isolated using the Qiagen Oligotex mRNA Spin-Column protocol or-the Stratagene Poly(A) Quik mRNA Isolation protocol (Stratagene, La Jolla, Calif., USA)) in a total volume of 25 μl. The sample was incubated in a thermocycler at 70° C. for 5 min, cooled to 48° C. and 10 μl of 5×cDNA Synthesis Buffer (kit supplied), 5 μl 10×dNTP mix (dATP, dCTP, dGTP, dTTP and aminoallyl-dUTP; kit supplied), 7.5 μl deionized water and 2.5 μl MMLV Reverse Transcriptase (500 U) added. The reaction was then incubated at 48° C. for 30 minutes, followed by 1 hr incubation at 42° C. At the end of the incubation the reaction was heated to 70° C. for 10 min, cooled to 37° C. and 0.5 μl (5 U) RNase H added, before incubating for 15 min at 37° C. The solution was vortexed for 1 min after the addition of 0.5 μl 0.5 M EDTA and 5 μl of QuickClean Resin (kit supplied) then centrifuged at 14,000-18,000×g for 1 min. After removing the supernatant to a 0.45 μm spin filter (kit supplied), the sample was again centrifuged at 14,000-18,000×g for 1 min, and 5.5 μl 3 M sodium acetate and 137.5 μl of 100% ethanol added to the sample before incubating at −20° C. for at least 1 hr. The sample was then centrifuged at 14,000-18,000×g at 4° C. for 20 min, the resulting pellet washed with 500 μl 70% ethanol, air-dried at room temperature for 10 min and resuspended in 10 μl of 2× fluorescent labeling buffer (kit provided). 10 μl each of the fluorescent dyes Cy3 and Cy5 (Amersham Pharmacia (Piscataway, N.J., USA); prepared according to Atlas™ kit directions of Clontech) were added and the sample incubated in the dark at room temperature for 30 min.
  • The fluorescently labeled first strand cDNA was precipitated by adding 2 μl 3M sodium acetate and 50 μl 100% ethanol, incubated at −20° C. for at least 2 hrs, centrifuged at 14,000-18,000×g for 20 min, washed with 70% ethanol, air-dried for 10 min and dissolved in 100 μl of water.
  • Alternatively, 3-4 μg mRNA, 2.5 (˜8.9 ng of in vitro translated mRNA) μl yeast control and 3 μg oligo dTV (TTTTTTTTTTTTTTTTTT(A/C/G) were mixed in a total volume of 24.7 μl. The sample was incubated in a thermocycler at 70° C. for 10 min. before chilling on ice. To this, 8 μl of 5× first strand buffer (SuperScript II RNase H—Reverse Transcriptase kit from Invitrogen (Carlsbad, Calif. 92008); cat no. 18064022), 0.8° C. of aa-dUTP/dNTP mix (50×; 25 mM dATP, 25 mM dGTP, 25 mM dCTP, 15 mM dTTP, 10 mM aminoallyl-dUTP), 4 μl of 0.1 M DTT and 2.5 μl (500 units) of Superscript R.T.II enzyme (Stratagene) were added. The sample was incubated at 42° C. for 2 hours before a mixture of 10° C. of 1 M NaOH and 10° C. of 0.5 M EDTA were added. After a 15 minute incubation at 65° C., 25 μl of 1 M Tris pH 7.4 was added. This was mixed with 450 μl of water in a Microcon 30 column before centrifugation at 11,000×g for 12 min. The column was washed twice with 450 μl (centrifugation at 11,000 g, 12 min.) before eluting the sample by inverting the Microcon column and centrifuging at 11,000×g for 20 seconds. Sample was dehydrated by centrifugation under vacuum and stored at −20° C.
  • Each reaction pellet was dissolved in 9 μl of 0.1 M carbonate buffer (0.1 M sodium carbonate and sodium bicarbonate, pH=8.5-9) and 4.5 μl of this placed in two microfuge tubes. 4.5 μl of each dye (in DMSO) were added and the mixture incubated in the dark for 1 hour. 4.5 μl of 4 M hydroxylamine was added and again incubated in the dark for 15 minutes.
  • Regardless of the method used for probe generation, the probe was purified using a Qiagen PCR cleanup kit (Qiagen, Valencia, Calif., USA), and eluted with 100 ul EB (kit provided). The sample was loaded on a Microcon YM-30 (Millipore, Bedford, Mass., USA) spin column and concentrated to 4-5 ul in volume. Probes for the maize microarrays were generated using the Fluorescent Linear Amplification Kit (cat. No. G2556A) from Agilent Technologies (Palo Alto, Calif.).
  • Hybridization and Wash Conditions
  • The following Hybridization and Washing Condition were developed:
  • Hybridization Conditions:
  • Labeled probe was heated at 95° C. for 3 min and chilled on ice. Then 25□L of the hybridization buffer which was warmed at 42 C was added to the probe, mixing by pipeting, to give a final concentration of:
  • 50% formamide
  • 4×SSC
  • 0.03% SDS
  • 5× Denhardt's solution
  • 0.1 μg/ml single-stranded salmon sperm DNA
  • The probe was kept at 42 C. Prior to the hybridization, the probe was heated for 1 more min., added to the array, and then covered with a glass cover slip. Slides were placed in hybridization chambers (Telechem, Sunnyvale, Calif.) and incubated at 42° C. overnight.
  • Washing Conditions:
    • A. Slides were washed in 1×SSC+0.03% SDS solution at room temperature for 5 minutes,
    • B. Slides were washed in 0.2×SSC at room temperature for 5 minutes,
    • C. Slides were washed in 0.05×SSC at room temperature for 5 minutes.
  • After A, B, and C, slides were spun at 800×g for 2 min. to dry. They were then scanned.
  • Maize microarrays were hybridized according to the instructions included Fluorescent Linear Amplification Kit (cat. No. G2556A) from Agilent Technologies (Palo Alto, Calif.).
  • Scanning of Slides
  • The chips were scanned using a ScanArray 3000 or 5000 (General Scanning, Watertown, Mass., USA). The chips were scanned at 543 and 633 nm, at 10 um resolution to measure the intensity of the two fluorescent dyes incorporated into the samples hybridized to the chips.
  • Data Extraction and Analysis
  • The images generated by scanning slides consisted of two 16-bit TIFF images representing the fluorescent emissions of the two samples at each arrayed spot. These images were then quantified and processed for expression analysis using the data extraction software Imagene™ (Biodiscovery, Los Angeles, Calif., USA). Imagene output was subsequently analyzed using the analysis program Genespring™ (Silicon Genetics, San Carlos, Calif., USA). In Genespring, the data was imported using median pixel intensity measurements derived from Imagene output. Background subtraction, ratio calculation and normalization were all conducted in Genespring. Normalization was achieved by breaking the data in to 32 groups, each of which represented one of the 32 pin printing regions on the microarray. Groups consist of 360 to 550 spots. Each group was independently normalized by setting the median of ratios to one and multiplying ratios by the appropriate factor.
  • Results
  • The results of the microaray experiments are set forth in Table 1 in the section entitled “Microarray Data” which shows the results of the differential expression experiments for the mRNAs, as reported by their corresponding cDNA ID number, that were differentially transcribed under a particular set of conditions as compared to a control sample. The cDNA ID numbers correspond to those utilized. Increases in mRNA abundance levels in experimental plants versus the controls are denoted with the plus sign (+). Likewise, reductions in mRNA abundance levels in the experimental plants are denoted with the minus (−) sign.
  • The Table 1 section entitled “Microarray Data” is organized according to the clone number with each set of experimental conditions being denoted by the term “Expt Rep ID:” followed by a “short name”. The row titled “Microarray Experiment Parameters” links each “short name” with a short description of the experiment and the parameters.
  • The sequences showing differential expression in a particular experiment (denoted by either a “+” or “−” in the column in Table 1 entitled “SIGNCLOG_RATIO”) thereby show utility for a function in a plant, and these functions/utilities are described in detail below, where the title of each section (i.e. a “utility section”) is correlated with the particular differential expression experiment in the section of Table 1 entitled “Microarray Experiment Parameters”.
  • Organ-Affecting Genes, Gene Components, Products (Including Differentiation and Function)
  • Root Genes
  • The economic values of roots arise not only from harvested adventitious roots or tubers, but also from the ability of roots to funnel nutrients to support growth of all plants and increase their vegetative material, seeds, fruits, etc. Roots have four main functions. First, they anchor the plant in the soil. Second, they facilitate and regulate the molecular signals and molecular traffic between the plant, soil, and soil fauna. Third, the root provides a plant with nutrients gained from the soil or growth medium. Fourth, they condition local soil chemical and physical properties.
  • Root genes are active or potentially active to a greater extent in roots than in most other organs of the plant. These genes and gene products can regulate many plant traits from yield to stress tolerance. Root genes can be used to modulate root growth and development.
  • Differential Expression of the Sequences in Roots
  • The relative levels of mRNA product in the root versus the aerial portion of the plant was measured. Specifically, mRNA was isolated from roots and root tips of Arabidopsis plants and compared to mRNA isolated from the aerial portion of the plants utilizing microarray procedures.
  • Root Hair Genes, Gene Components And Products
  • Root hairs are specialized outgrowths of single epidermal cells termed trichoblasts. In many and perhaps all species of plants, the trichoblasts are regularly arranged around the perimeter of the root. In Arabidopsis, for example, trichoblasts tend to alternate with non-hair cells or atrichoblasts. This spatial patterning of the root epidermis is under genetic control, and a variety of mutants have been isolated in which this spacing is altered or in which root hairs are completely absent.
  • The root hair development genes of the instant invention are useful to modulate one or more processes of root hair structure and/or function including (1) development; (2) interaction with the soil and soil contents; (3) uptake and transport in the plant; and (4) interaction with microorganisms.
  • 1.) Development
  • The surface cells of roots can develop into single epidermal cells termed trichoblasts or root hairs. Some of the root hairs will persist for the life of the plant; others will gradually die back; some may cease to function due to external influences. These genes and gene products can be used to modulate root hair density or root hair growth; including rate, timing, direction, and size, for example. These genes and gene products can also be used to modulate cell properties such as cell size, cell division, rate and direction and number, cell elongation, cell differentiation, lignified cell walls, epidermal cells (including trichoblasts) and root apical meristem cells (growth and initiation); and root hair architecture such as leaf cells under the trichome, cells forming the base of the trichome, trichome cells, and root hair responses. In addition these genes and gene products can be used to modulate one or more of the growth and development processes in response to internal plant programs or environmental stimuli in, for example, the seminal system, nodal system, hormone responses, Auxin, root cap abscission, root senescence, gravitropism, coordination of root growth and development with that of other organs (including leaves, flowers, seeds, fruits, and stems), and changes in soil environment (including water, minerals, Ph, and microfauna and flora).
  • 2.) Interaction With Soil And Soil Contents
  • Root hairs are sites of intense chemical and biological activity and as a result can strongly modify the soil they contact. Roots hairs can be coated with surfactants and mucilage to facilitate these activities. Specifically, roots hairs are responsible for nutrient uptake by mobilizing and assimilating water, reluctant ions, organic and inorganic compounds and chemicals. In addition, they attract and interact with beneficial microfauna and flora. Root hairs also help to mitigate the effects of toxic ions, pathogens and stress. Thus, root hair genes and gene products can be used to modulate traits such as root hair surfactant and mucilage (including composition and secretion rate and time); nutrient uptake (including water, nitrate and other sources of nitrogen, phosphate, potassium, and micronutrients (e.g. iron, copper, etc.); microbe and nematode associations (such as bacteria including nitrogen-fixing bacteria, mycorrhizae, nodule-forming and other nematodes, and nitrogen fixation); oxygen transpiration; detoxification effects of iron, aluminum, cadium, mercury, salt, and other soil constituents; pathogens (including chemical repellents) glucosinolates (GSLI), which release pathogen-controlling isothiocyanates; and changes in soil (such as Ph, mineral excess and depletion), and rhizosheath.
  • 3.) Transport of Materials in Plants
  • Uptake of the nutrients by the root and root hairs contributes a source-sink effect in a plant. The greater source of nutrients, the more sinks, such as stems, leaves, flowers, seeds, fruits, etc. can draw sustenance to grow. Thus, root hair development genes and gene products can be used to modulate the vigor and yield of the overall plant as well as distinct cells, organs, or tissues of a plant. The genes and gene products, therefore, can modulate plant nutrition, growth rate (such as whole plant, including height, flowering time, etc., seedling, coleoptile elongation, young leaves, stems, flowers, seeds and fruit) and yield, including biomass (fresh and dry weight during any time in plant life, including maturation and senescence), number of flowers, number of seeds, seed yield, number, size, weight and harvest index (content and composition, e.g. amino acid, jasmonate, oil, protein and starch) and fruit yield (number, size, weight, harvest index, and post harvest quality).
  • Reproduction Genes, Gene Components and Products
  • Reproduction genes are defined as genes or components of genes capable of modulating any aspect of sexual reproduction from flowering time and inflorescence development to fertilization and finally seed and fruit development. These genes are of great economic interest as well as biological importance. The fruit and vegetable industry grosses over $1 billion USD a year. The seed market, valued at approximately $15 billion USD annually, is even more lucrative.
  • Inflorescence and Floral Development Genes, Gene Components And Products
  • During reproductive growth the plant enters a program of floral development that culminates in fertilization, followed by the production of seeds. Senescence may or may not follow. The flower formation is a precondition for the sexual propagation of plants and is therefore essential for the propagation of plants that cannot be propagated vegetatively as well as for the formation of seeds and fruits. The point of time at which the merely vegetative growth of plants changes into flower formation is of vital importance for example in agriculture, horticulture and plant breeding. Also the number of flowers is often of economic importance, for example in the case of various useful plants (tomato, cucumber, zucchini, cotton etc.) with which an increased number of flowers may lead to an increased yield, or in the case of growing ornamental plants and cut flowers.
  • Flowering plants exhibit one of two types of inflorescence architecture: indeterminate, in which the inflorescence grows indefinitely, or determinate, in which a terminal flower is produced. Adult organs of flowering plants develop from groups of stem cells called meristems. The identity of a meristem is inferred from structures it produces: vegetative meristems give rise to roots and leaves, inflorescence meristems give rise to flower meristems, and flower meristems give rise to floral organs such as sepals and petals. Not only are meristems capable of generating new meristems of different identity, but their own identity can change during development. For example, a vegetative shoot meristem can be transformed into an inflorescence meristem upon floral induction, and in some species, the inflorescence meristem itself will eventually become a flower meristem. Despite the importance of meristem transitions in plant development, little is known about the underlying mechanisms.
  • Following germination, the shoot meristem produces a series of leaf meristems on its flanks. However, once floral induction has occurred, the shoot meristem switches to the production of flower meristems. Flower meristems produce floral organ primordia, which develop individually into sepals, petals, stamens or carpels. Thus, flower formation can be thought of as a series of distinct developmental steps, i.e. floral induction, the formation of flower primordia and the production of flower organs. Mutations disrupting each of the steps have been isolated in a variety of species, suggesting that a genetic hierarchy directs the flowering process (see for review, Weigel and Meyerowitz, In Molecular Basis of Morphogenesis (ed. M. Bernfield). 51st Annual Symposium of the Society for Developmental Biology, pp. 93-107, New York, 1993).
  • Expression of many reproduction genes and gene products is orchestrated by internal programs or the surrounding environment of a plant. These genes can be used to modulate traits such as fruit and seed yield
  • Seed And Fruit Development Genes, Gene Components And Products
  • The ovule is the primary female sexual reproductive organ of flowering plants. At maturity it contains the egg cell and one large central cell containing two polar nuclei encased by two integuments that, after fertilization, develops into the embryo, endosperm, and seed coat of the mature seed, respectively. As the ovule develops into the seed, the ovary matures into the fruit or silique. As such, seed and fruit development requires the orchestrated transcription of numerous polynucleotides, some of which are ubiquitous, others that are embryo-specific and still others that are expressed only in the endosperm, seed coat, or fruit. Such genes are termed fruit development responsive genes and can be used to modulate seed and fruit growth and development such as seed size, seed yield, seed composition and seed dormancy.
  • Differential Expression of the Sequences in Siliques, Inflorescences and Flowers
  • The relative levels of mRNA product in the siliques relative to the plant as a whole was measured.
  • Differential Expression of the Sequences in Hybrid Seed Development
  • The levels of mRNA product in the seeds relative to those in a leaf and floral stems was measured.
  • Development Genes, Gene Components and Products
  • Imbibition And Germination Responsive Genes, Gene Components And Products
  • Seeds are a vital component of the world's diet. Cereal grains alone, which comprise ˜90% of all cultivated seeds, contribute up to half of the global per capita energy intake. The primary organ system for seed production in flowering plants is the ovule. At maturity, the ovule consists of a haploid female gametophyte or embryo sac surrounded by several layers of maternal tissue including the nucleus and the integuments. The embryo sac typically contains seven cells including the egg cell, two synergids, a large central cell containing two polar nuclei, and three antipodal cells. That pollination results in the fertilization of both egg and central cell. The fertilized egg develops into the embryo. The fertilized central cell develops into the endosperm. And the integuments mature into the seed coat. As the ovule develops into the seed, the ovary matures into the fruit or silique. Late in development, the developing seed ends a period of extensive biosynthetic and cellular activity and begins to desiccate to complete its development and enter a dormant, metabolically quiescent state. Seed dormancy is generally an undesirable characteristic in agricultural crops, where rapid germination and growth are required. However, some degree of dormancy is advantageous, at least during seed development. This is particularly true for cereal crops because it prevents germination of grains while still on the ear of the parent plant (preharvest sprouting), a phenomenon that results in major losses to the agricultural industry. Extensive domestication and breeding of crop species have ostensibly reduced the level of dormancy mechanisms present in the seeds of their wild ancestors, although under some adverse environmental conditions, dormancy may reappear. By contrast, weed seeds frequently mature with inherent dormancy mechanisms that allow some seeds to persist in the soil for many years before completing germination.
  • Germination commences with imbibition, the uptake of water by the dry seed, and the activation of the quiescent embryo and endosperm. The result is a burst of intense metabolic activity. At the cellular level, the genome is transformed from an inactive state to one of intense transcriptional activity. Stored lipids, carbohydrates and proteins are catabolized fueling seedling growth and development. DNA and organelles are repaired, replicated and begin functioning. Cell expansion and cell division are triggered. The shoot and root apical meristem are activated and begin growth and organogenesis. Schematic 4 summarizes some of the metabolic and cellular processes that occur during imbibition. Germination is complete when a part of the embryo, the radicle, extends to penetrate the structures that surround it. In Arabidopsis, seed germination takes place within twenty-four (24) hours after imbibition. As such, germination requires the rapid and orchestrated transcription of numerous polynucleotides. Germination is followed by expansion of the hypocotyl and opening of the cotyledons. Meristem development continues to promote root growth and shoot growth, which is followed by early leaf formation.
  • Imbibition and Germination Genes
  • Imbibition and germination includes those events that commence with the uptake of water by the quiescent dry seed and terminate with the expansion and elongation of the shoots and roots. The germination period exists from imbibition to when part of the embryo, usually the radicle, extends to penetrate the seed coat that surrounds it. Imbibition and germination genes are defined as genes, gene components and products capable of modulating one or more processes of imbibition and germination described above. They are useful to modulate many plant traits from early vigor to yield to stress tolerance.
  • Differential Expression of the Sequences in Germinating Seeds and Imbibed Embryos
  • The levels of mRNA product in the seeds versus the plant as a whole was measured.
  • Hormone Responsive Genes, Gene Components and Products
  • Abscissic Acid Responsive Genes, Gene Components And Products
  • Plant hormones are naturally occurring substances, effective in very small amounts, which act as signals to stimulate or inhibit growth or regulate developmental processes in plants. Abscisic acid (ABA) is a ubiquitous hormone in vascular plants that has been detected in every major organ or living tissue from the root to the apical bud. The major physiological responses affected by ABA are dormancy, stress stomatal closure, water uptake, abscission and senescence. In contrast to Auxins, cytokinins and gibberellins, which are principally growth promoters, ABA primarily acts as an inhibitor of growth and metabolic processes.
  • Changes in ABA concentration internally or in the surrounding environment in contact with a plant results in modulation of many genes and gene products. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. While ABA responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different ABA responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. In addition, the combination of an ABA responsive polynucleotide and/or gene product with another environmentally responsive polynucleotide is also useful because of the interactions that exist between hormone-regulated pathways, stress and defense induced pathways, nutritional pathways and development.
  • Differential Expression of the Sequences in ABA Treated Plants
  • The relative levels of mRNA product in plants treated with ABA versus controls treated with water were measured.
  • Brassinosteroid Responsive Genes Gene Components and Products
  • Plant hormones are naturally occurring substances, effective in very small amounts, which act as signals to stimulate or inhibit growth or regulate developmental processes in plants. Brassinosteroids (BRs) are the most recently discovered, and least studied, class of plant hormones. The major physiological response affected by BRs is the longitudinal growth of young tissue via cell elongation and possibly cell division. Consequently, disruptions in BR metabolism, perception and activity frequently result in a dwarf phenotype. In addition, because BRs are derived from the sterol metabolic pathway, any perturbations to the sterol pathway can affect the BR pathway. In the same way, perturbations in the BR pathway can have effects on the later part of the sterol pathway and thus the sterol composition of membranes.
  • Changes in BR concentration in the surrounding environment or in contact with a plant result in modulation of many genes and gene products. These genes and/or products are responsible for effects on traits such as plant biomass and seed yield. These genes were discovered and characterized from a much larger set of genes by experiments designed to find genes whose mRNA abundance changed in response to application of BRs to plants.
  • While BR responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different BR responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factors and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. In addition, the combination of a BR responsive polynucleotide and/or gene product with another environmentally responsive polynucleotide is useful because of the interactions that exist between hormone-regulated pathways, stress pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common or overlapping pathways.
  • Differential Expression of the Sequences in Epi-brassinolide Or Brassinozole Plants
  • The relative levels of mRNA product in plants treated with either epi-brassinolide or brassinozole were measured.
  • Metabolism Affecting Genes, Gene Components and Products
  • Nitrogen Responsive Genes, Gene Components And Products
  • Nitrogen is often the rate-limiting element in plant growth, and all field crops have a fundamental dependence on exogenous nitrogen sources. Nitrogenous fertilizer, which is usually supplied as ammonium nitrate, potassium nitrate, or urea, typically accounts for 40% of the costs associated with crops, such as corn and wheat in intensive agriculture. Increased efficiency of nitrogen use by plants should enable the production of higher yields with existing fertilizer inputs and/or enable existing yields of crops to be obtained with lower fertilizer input, or better yields on soils of poorer quality. Also, higher amounts of proteins in the crops could also be produced more cost-effectively. “Nitrogen responsive” genes and gene products can be used to alter or modulate plant growth and development.
  • Differential Expression of the Sequences in Whole Seedlings, Shoots and Roots
  • The relative levels of mRNA product in whole seedlings, shoots and roots treated with either high or low nitrogen media were compared to controls.
  • Viability Genes, Gene Components and Products
  • Plants contain many proteins and pathways that when blocked or induced lead to cell, organ or whole plant death. Gene variants that influence these pathways can have profound effects on plant survival, vigor and performance. The critical pathways include those concerned with metabolism and development or protection against stresses, diseases and pests. They also include those involved in apoptosis and necrosis. Viability genes can be modulated to affect cell or plant death.
  • Herbicides are, by definition, chemicals that cause death of tissues, organs and whole plants. The genes and pathways that are activated or inactivated by herbicides include those that cause cell death as well as those that function to provide protection.
  • Differential Expression of the Sequences in Herbicide Treated Plants and Herbicide Resistant Mutants
  • The relative levels of mRNA product in plants treated with heribicide and mutants resistant to heribicides were compared to control plants.
  • Stress Responsive Genes, Gene Components and Products
  • Wounding Responsive Genes, Gene Components And Products
  • Plants are continuously subjected to various forms of wounding from physical attacks including the damage created by pathogens and pests, wind, and contact with other objects. Therefore, survival and agricultural yields depend on constraining the damage created by the wounding process and inducing defense mechanisms against future damage.
  • Plants have evolved complex systems to minimize and/or repair local damage and to minimize subsequent attacks by pathogens or pests or their effects. These involve stimulation of cell division and cell elongation to repair tissues, induction of programmed cell death to isolate the damage caused mechanically and by invading pests and pathogens, and induction of long-range signaling systems to induce protecting molecules, in case of future attack. The genetic and biochemical systems associated with responses to wounding are connected with those associated with other stresses such as pathogen attack and drought.
  • Wounding responsive genes and gene products can be used to alter or modulate traits such as growth rate; whole plant height, width, or flowering time; organ development (such as coleoptile elongation, young leaves, roots, lateral roots, tuber formation, flowers, fruit, and seeds); biomass; fresh and dry weight during any time in plant life, such as at maturation; number of flowers; number of seeds; seed yield, number, size, weight, harvest index (such as content and composition, e.g., amino acid, nitrogen, oil, protein, and carbohydrate); fruit yield, number, size, weight, harvest index, post harvest quality, content and composition (e.g., amino acid, carotenoid, jasmonate, protein, and starch); seed and fruit development; germination of dormant and non-dormant seeds; seed viability, seed reserve mobilization, fruit ripening, initiation of the reproductive cycle from a vegetative state, flower development time, insect attraction for fertilization, time to fruit maturity, senescence; fruits, fruit drop; leaves; stress and disease responses; drought; heat and cold; wounding by any source, including wind, objects, pests and pathogens; uv and high light damage (insect, fungus, virus, worm, nematode damage).
  • Cold Responsive Genes, Gene Components and Products
  • The ability to endure low temperatures and freezing is a major determinant of the geographical distribution and productivity of agricultural crops. Even in areas considered suitable for the cultivation of a given species or cultivar, can give rise to yield decreases and crop failures as a result of aberrant, freezing temperatures. Even modest increases (1-2° C.) in the freezing tolerance of certain crop species would have a dramatic impact on agricultural productivity in some areas. The development of genotypes with increased freezing tolerance would provide a more reliable means to minimize crop losses and diminish the use of energy-costly practices to modify the microclimate.
  • Sudden cold temperatures result in modulation of many genes and gene products, including promoters. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield.
  • Manipulation of one or more cold responsive gene activities is useful to modulate growth and development.
  • Differential Expression of the Sequences in Cold Treated Plants
  • The relative levels of mRNA product in cold treated plants were compared to control plants.
  • Heat Responsive Genes, Gene Components and Products
  • The ability to endure high temperatures is a major determinant of the geographical distribution and productivity of agricultural crops. Decreases in yield and crop failure frequently occur as a result of aberrant, hot conditions even in areas considered suitable for the cultivation of a given species or cultivar. Only modest increases in the heat tolerance of crop species would have a dramatic impact on agricultural productivity. The development of genotypes with increased heat tolerance would provide a more reliable means to minimize crop losses and diminish the use of energy-costly practices to modify the microclimate.
  • Changes in temperature in the surrounding environment or in a plant microclimate results in modulation of many genes and gene products.
  • Differential Expression of the Sequences in Heat Treated Plants
  • The relative levels of mRNA product in heat treated plants were compared to control plants.
  • Drought Responsive Genes, Gene Components and Products
  • The ability to endure drought conditions is a major determinant of the geographical distribution and productivity of agricultural crops. Decreases in yield and crop failure frequently occur as a result of aberrant, drought conditions even in areas considered suitable for the cultivation of a given species or cultivar. Only modest increases in the drought tolerance of crop species would have a dramatic impact on agricultural productivity. The development of genotypes with increased drought tolerance would provide a more reliable means to minimize crop losses and diminish the use of energy-costly practices to modify the microclimate.
  • Drought conditions in the surrounding environment or within a plant, results in modulation of many genes and gene products.
  • Differential Expression of the Sequences in Drought Treated Plants and Drought Mutants
  • The relative levels of mRNA product in drought treated plants and drought mutants were compared to control plants.
  • Methyl Jasmonate (Jasmonate) Responsive Genes, Gene Components and Products
  • Jasmonic acid and its derivatives, collectively referred to as jasmonates, are naturally occurring derivatives of plant lipids. These substances are synthesized from linolenic acid in a lipoxygenase-dependent biosynthetic pathway. Jasmonates are signalling molecules which have been shown to be growth regulators as well as regulators of defense and stress responses. As such, jasmonates represent a separate class of plant hormones. Jasmonate responsive genes can be used to modulate plant growth and development.
  • Differential Expression of the Sequences in Methyl Jasmonate Treated Plants
  • The relative levels of mRNA product in methyl jasmonate treated plants were compared to control plants.
  • Salicylic Acid Responsive Genes, Gene Components and Products
  • Plant defense responses can be divided into two groups: constitutive and induced. Salicylic acid (SA) is a signaling molecule necessary for activation of the plant induced defense system known as systemic acquired resistance or SAR. This response, which is triggered by prior exposure to avirulent pathogens, is long lasting and provides protection against a broad spectrum of pathogens. Another induced defense system is the hypersensitive response (HR). HR is far more rapid, occurs at the sites of pathogen (avirulent pathogens) entry and precedes SAR. SA is also the key signaling molecule for this defense pathway.
  • Differential Expression of the Sequences in Salicylic Acid Treated Plants
  • The relative levels of mRNA product in salicylic acid treated plants were compared to control plants.
  • Osmotic Stress Responsive Genes, Gene Components and Products
  • The ability to endure and recover from osmotic and salt related stress is a major determinant of the geographical distribution and productivity of agricultural crops. Osmotic stress is a major component of stress imposed by saline soil and water deficit. Decreases in yield and crop failure frequently occur as a result of aberrant or transient environmental stress conditions even in areas considered suitable for the cultivation of a given species or cultivar. Only modest increases in the osmotic and salt tolerance of a crop species would have a dramatic impact on agricultural productivity. The development of genotypes with increased osmotic tolerance would provide a more reliable means to minimize crop losses and diminish the use of energy-costly practices to modify the soil environment. Thus, osmotic stress responsive genes can be used to modulate plant growth and development.
  • Differential Expression of the Sequences in PEG Treated Plants
  • The relative levels of mRNA product in PEG treated plants were compared to control plants.
  • Shade Responsive Genes, Gene Components and Products
  • Plants sense the ratio of Red (R):Far Red (FR) light in their environment and respond differently to particular ratios. A low R:FR ratio, for example, enhances cell elongation and favors flowering over leaf production. The changes in R:FR ratios mimic and cause the shading response effects in plants. The response of a plant to shade in the canopy structures of agricultural crop fields influences crop yields significantly. Therefore manipulation of genes regulating the shade avoidance responses can improve crop yields. While phytochromes mediate the shade avoidance response, the down-stream factors participating in this pathway are largely unknown. One potential downstream participant, ATHB-2, is a member of the HD-Zip class of transcription factors and shows a strong and rapid response to changes in the R:FR ratio. ATHB-2 overexpressors have a thinner root mass, smaller and fewer leaves and longer hypocotyls and petioles. This elongation arises from longer epidermal and cortical cells, and a decrease in secondary vascular tissues, paralleling the changes observed in wild-type seedlings grown under conditions simulating canopy shade. On the other hand, plants with reduced ATHB-2 expression have a thick root mass and many larger leaves and shorter hypocotyls and petioles. Here, the changes in the hypocotyl result from shorter epidermal and cortical cells and increased proliferation of vascular tissue. Interestingly, application of Auxin is able to reverse the root phenotypic consequences of high ATHB-2 levels, restoring the wild-type phenotype. Consequently, given that ATHB-2 is tightly regulated by phytochrome, these data suggest that ATHB-2 may link the Auxin and phytochrome pathways in the shade avoidance response pathway.
  • Shade responsive genes can be used to modulate plant growth and development.
  • Differential Expression of the Sequences in Far-red Light Treated Plants
  • The relative levels of mRNA product in far-red light treated plants were compared to control plants.
  • Viability Genes, Gene Components and Products
  • Plants contain many proteins and pathways that when blocked or induced lead to cell, organ or whole plant death. Gene variants that influence these pathways can have profound effects on plant survival, vigor and performance. The critical pathways include those concerned with metabolism and development or protection against stresses, diseases and pests. They also include those involved in apoptosis and necrosis. The applicants have elucidated many such genes and pathways by discovering genes that when inactivated lead to cell or plant death.
  • Herbicides are, by definition, chemicals that cause death of tissues, organs and whole plants. The genes and pathways that are activated or inactivated by herbicides include those that cause cell death as well as those that function to provide protection. The applicants have elucidated these genes.
  • The genes defined in this section have many uses including manipulating which cells, tissues and organs are selectively killed, which are protected, making plants resistant to herbicides, discovering new herbicides and making plants resistant to various stresses.
  • Viability genes were also identified from a much larger set of genes by experiments designed to find genes whose mRNA products changed in concentration in response to applications of different herbicides to plants. Viability genes are characteristically differentially transcribed in response to fluctuating herbicide levels or concentrations, whether internal or external to an organism or cell. The MA_diff Table reports the changes in transcript levels of various viability genes.
  • Early Seedling-Phase Specific Responsive Genes, Gene Components and Products
  • One of the more active stages of the plant life cycle is a few days after germination is complete, also referred to as the early seedling phase. During this period the plant begins development and growth of the first leaves, roots, and other organs not found in the embryo. Generally this stage begins when germination ends. The first sign that germination has been completed is usually that there is an increase in length and fresh weight of the radicle. Such genes and gene products can regulate a number of plant traits to modulate yield. For example, these genes are active or potentially active to a greater extent in developing and rapidly growing cells, tissues and organs, as exemplified by development and growth of a seedling 3 or 4 days after planting a seed.
  • Rapid, efficient establishment of a seedling is very important in commercial agriculture and horticulture. It is also vital that resources are approximately partitioned between shoot and root to facilitate adaptive growth. Phototropism and geotropism need to be established. All these require post-germination process to be sustained to ensure that vigorous seedlings are produced. Early seedling phase genes, gene components and products are useful to manipulate these and other processes.
  • Guard Cell Genes, Gene Components and Products
  • Scattered throughout the epidermis of the shoot are minute pores called stomata. Each stomal pore is surrounded by two guard cells. The guard cells control the size of the stomal pore, which is critical since the stomata control the exchange of carbon dioxide, oxygen, and water vapor between the interior of the plant and the outside atmosphere. Stomata open and close through turgor changes driven by ion fluxes, which occur mainly through the guard cell plasma membrane and tonoplast. Guard cells are known to respond to a number of external stimuli such as changes in light intensity, carbon dioxide and water vapor, for example. Guard cells can also sense and rapidly respond to internal stimuli including changes in ABA, auxin and calcium ion flux.
  • Thus, genes, gene products, and fragments thereof differentially transcribed and/or translated in guard cells can be useful to modulate ABA responses, drought tolerance, respiration, water potential, and water management as examples. All of which can in turn affect plant yield including seed yield, harvest index, fruit yield, etc.
  • To identify such guard cell genes, gene products, and fragments thereof, Applicants have performed a microarray experiment comparing the transcript levels of genes in guard cells versus leaves. Experimental data is shown below.
  • Nitric Oxide Responsive Genes, Gene Components and Products
  • The rate-limiting element in plant growth and yield is often its ability to tolerate suboptimal or stress conditions, including pathogen attack conditions, wounding and the presence of various other factors. To combat such conditions, plant cells deploy a battery of inducible defense responses, including synergistic interactions between nitric oxide (NO), reactive oxygen intermediates (ROS), and salicylic acid (SA). NO has been shown to play a critical role in the activation of innate immune and inflammatory responses in animals. At least part of this mammalian signaling pathway is present in plants, where NO is known to potentiate the hypersensitive response (HR). In addition, NO is a stimulator molecule in plant photomorphogenesis.
  • Changes in nitric oxide concentration in the internal or surrounding environment, or in contact with a plant, results in modulation of many genes and gene products.
  • In addition, the combination of a nitric oxide responsive polynucleotide and/or gene product with other environmentally responsive polynucleotides is also useful because of the interactions that exist between hormone regulated pathways, stress pathways, pathogen stimulated pathways, nutritional pathways and development.
  • Nitric oxide responsive genes and gene products can function either to increase or dampen the above phenotypes or activities either in response to changes in nitric oxide concentration or in the absence of nitric oxide fluctuations. More specifically, these genes and gene products can modulate stress responses in an organism. In plants, these genes and gene products are useful for modulating yield under stress conditions. Measurements of yield include seed yield, seed size, fruit yield, fruit size, etc.
  • Shoot-Apical Meristem Genes, Gene Components and Products
  • New organs, stems, leaves, branches and inflorescences develop from the stem apical meristem (SAM). The growth structure and architecture of the plant therefore depends on the behavior of SAMs. Shoot apical meristems (SAMs) are comprised of a number of morphologically undifferentiated, dividing cells located at the tips of shoots. SAM genes elucidated here are capable of modifying the activity of SAMs and thereby many traits of economic interest from ornamental leaf shape to organ number to responses to plant density.
  • In addition, a key attribute of the SAM is its capacity for self-renewal. Thus, SAM genes of the instant invention are useful for modulating one or more processes of SAM structure and/or function including (I) cell size and division; (II) cell differentiation and organ primordia. The genes and gene components of this invention are useful for modulating any one or all of these cell division processes generally, as in timing and rate, for example. In addition, the polynucleotides and polypeptides of the invention can control the response of these processes to the internal plant programs associated with embryogenesis, and hormone responses, for example.
  • Because SAMs determine the architecture of the plant, modified plants will be useful in many agricultural, horticultural, forestry and other industrial sectors. Plants with a different shape, numbers of flowers and seed and fruits will have altered yields of plant parts. For example, plants with more branches can produce more flowers, seed or fruits. Trees without lateral branches will produce long lengths of clean timber. Plants with greater yields of specific plant parts will be useful sources of constituent chemicals.
  • GFP Experimental Procedures and Results
  • Procedures
  • The polynucleotide sequences of the present invention were tested for promoter activity using Green Fluorescent Protein (GFP) assays in the following manner.
  • Approximately 1-2 kb of genomic sequence occurring immediately upstream of the ATG translational start site of the gene of interest was isolated using appropriate primers tailed with BstXI restriction sites. Standard PCR reactions using these primers and genomic DNA were conducted. The resulting product was isolated, cleaved with BstXI and cloned into the BstXI site of an appropriate vector, such as pNewBin4-HAP1-GFP (see FIG. 1).
  • Transformation
  • The following procedure was used for transformation of plants
  • 1. Stratification of WS-2 Seed.
      • Add 0.5 ml WS-2 (CS2360) seed to 50 ml of 0.2% Phytagar in a 50 ml Corning tube and vortex until seeds and Phytagar form a homogenous mixture.
      • Cover tube with foil and stratify at 4° C. for 3 days.
        2. Preparation of Seed Mixture.
      • Obtain stratified seed from cooler.
      • Add seed mixture to a 1000 ml beaker.
      • Add an additional 950 ml of 0.2% Phytagar and mix to homogenize.
        3. Preparation of Soil Mixture.
      • Mix 24 L SunshineMix #5 soil with 16 L Therm-O-Rock vermiculite in cement mixer to make a 60:40 soil mixture.
      • Amend soil mixture by adding 2 Tbsp Marathon and 3 Tbsp Osmocote and mix contents thoroughly.
      • Add 1 Tbsp Peters fertilizer to 3 gallons of water and add to soil mixture and mix thoroughly.
      • Fill 4-inch pots with soil mixture and round the surface to create a slight dome.
      • Cover pots with 8-inch squares of nylon netting and fasten using rubber bands.
      • Place 14 4-inch pots into each no-hole utility flat.
        4. Planting.
      • Using a 60 ml syringe, aspirate 35 ml of the seed mixture.
      • Exude 25 drops of the seed mixture onto each pot.
      • Repeat until all pots have been seeded.
      • Place flats on greenhouse bench, cover flat with clear propagation domes, place 55% shade cloth on top of flats and subirrigate by adding 1 inch of water to bottom of each flat.
        5. Plant Maintenance.
      • 3 to 4 days after planting, remove clear lids and shade cloth.
      • Subirrigate flats with water as needed.
      • After 7-10 days, thin pots to 20 plants per pot using forceps.
      • After 2 weeks, subirrigate all plants with Peters fertilizer at a rate of 1 Tsp per gallon water.
      • When bolts are about 5-10 cm long, clip them between the first node and the base of stem to induce secondary bolts.
      • 6 to 7 days after clipping, perform dipping infiltration.
        6. Preparation of Agrobacterium
      • Add 150 ml fresh YEB to 250 ml centrifuge bottles and cap each with a foam plug (Identi-Plug).
      • Autoclave for 40 min at 121° C.
      • After cooling to room temperature, uncap and add 0.1 ml each of carbenicillin, spectinomycin and rifampicin stock solutions to each culture vessel.
      • Obtain Agrobacterium starter block (96-well block with Agrobacterium cultures grown to an OD600 of approximately 1.0) and inoculate one culture vessel per construct by transferring 1 ml from appropriate well in the starter block.
      • Cap culture vessels and place on Lab-Line incubator shaker set at 27° C. and 250 RPM.
      • Remove after Agrobacterium cultures reach an OD600 of approximately 1.0 (about 24 hours), cap culture vessels with plastic caps, place in Sorvall SLA 1500 rotor and centrifuge at 8000 RPM for 8 min at 4° C.
      • Pour out supernatant and put bottles on ice until ready to use.
      • Add 200 ml Infiltration Media (IM) to each bottle, resuspend Agrobacterium pellets and store on ice.
        7. Dipping Infiltration.
      • Pour resuspended Agrobacterium into 16 oz polypropylene containers.
      • Invert 4-inch pots and submerge the aerial portion of the plants into the Agrobacterium suspension and let stand for 5 min.
      • Pour out Agrobacterium suspension into waste bucket while keeping polypropylene container in place and return the plants to the upright position.
      • Place 10 covered pots per flat.
      • Fill each flat with 1-inch of water and cover with shade cloth.
      • Keep covered for 24 hr and then remove shade cloth and polypropylene containers.
      • Resume normal plant maintenance.
      • When plants have finished flowering cover each pot with a ciber plant sleeve.
      • After plants are completely dry, collect seed and place into 2.0 ml micro tubes and store in 100-place cryogenic boxes.
        Recipes:
        0.2% Phytagar
  • 2 g Phytagar
  • 1 L nanopure water
      • Shake until Phytagar suspended
      • Autoclave 20 min
        YEB (for 1 L)
  • 5 g extract of meat
  • 5 g Bacto peptone
  • 1 g yeast extract
  • 5 g sucrose
  • 0.24 g magnesium sulfate
      • While stirring, add ingredients, in order, to 900 ml nanopure water
      • When dissolved, adjust pH to 7.2
      • Fill to 1 L with nanopure water
      • Autoclave 35 min
        Infiltration Medium (IM) (for 1 L)
  • 2.2 g MS salts
  • 50 g sucrose
  • 5 ul solution (stock is 2 mg/ml)
      • While stirring, add ingredients in order listed to 900 ml nanopure water
      • When dissolved, adjust pH to 5.8.
      • Volume up to 1 L with nanopure water.
      • Add 0.02% Silwet L-77 just prior to resuspending Agrobacterium
  • High Throughput Screening—T1 Generation
  • 1. Soil Preparation. Wear Gloves at all Times.
      • In a large container, mix 60% autoclaved SunshineMix #5 with 40% vermiculite.
      • Add 2.5 Tbsp of Osmocote, and 2.5 Tbsp of 1% granular Marathon per 25 L of soil.
      • Mix thoroughly.
        2. Fill Com-Packs With Soil.
      • Loosely fill D601 Com-Packs level to the rim with the prepared soil.
      • Place filled pot into utility flat with holes, within a no-hole utility flat.
      • Repeat as necessary for planting. One flat set should contain 6 pots.
        3. Saturate Soil.
      • Evenly water all pots until the soil is saturated and water is collecting in the bottom of the flats.
      • After the soil is completely saturated, dump out the excess water.
        4. Plant the Seed.
        5. Stratify the Seeds.
      • After sowing the seed for all the flats, place them into a dark 4° C. cooler.
      • Keep the flats in the cooler for 2 nights for WS seed. Other ecotypes may take longer. This cold treatment will help promote uniform germination of the seed.
        6. Remove Flats From Cooler and Cover With Shade Cloth. (Shade Cloth is Only Needed in the Greenhouse)
      • After the appropriate time, remove the flats from the cooler and place onto growth racks or benches.
      • Cover the entire set of flats with 55% shade cloth. The cloth is necessary to cut down the light intensity during the delicate germination period.
      • The cloth and domes should remain on the flats until the cotyledons have fully expanded. This usually takes about 4-5 days under standard greenhouse conditions.
        7. Remove 55% Shade Cloth and Propagation Domes.
      • After the cotyledons have fully expanded, remove both the 55% shade cloth and propagation domes.
        8. Spray Plants With Finale Mixture. Wear Gloves and Protective Clothing at all Times.
      • Prepare working Finale mixture by mixing 3 ml concentrated Finale in 48 oz of water in the Poly-TEK sprayer.
      • Completely and evenly spray plants with a fine mist of the Finale mixture.
      • Repeat Finale spraying every 3-4 days until only transformants remain. (Approximately 3 applications are necessary.)
      • When satisfied that only transformants remain, discontinue Finale spraying.
        9. Weed Out Excess Transformants.
        Weed out excess transformants such that a maximum number of five plants per pot exist evenly spaced throughout the pot.
  • GFP Assay
  • Tissues are dissected by eye or under magnification using INOX 5 grade forceps and placed on a slide with water and coverslipped. An attempt is made to record images of observed expression patterns at earliest and latest stages of development of tissues listed below. Specific tissues will be preceded with High (H), Medium (M), Low (L) designations.
    Flower pedicel receptacle nectary sepal petal filament
    anther pollen carpel style papillae
    vascular epidermis stomata trichome
    Silique stigma style carpel septum placentae transmitting
    tissue vascular epidermis stomata abscission zone
    ovule
    Ovule Pre-fertilization: inner integument outer integument
    embryo sac funiculus chalaza micropyle
    gametophyte
    Post-fertilization: zygote inner integument outer
    integument seed coat primordia chalaza micropyle
    early endosperm mature endosperm embryo
    Embryo suspensor preglobular globular heart torpedo
    late mature provascular hhypophysis radicle
    cotyledons hypocotyl
    Stem epidermis cortex vascular xylem phloem pith
    stomata trichome
    Leaf petiole mesophyll vascular epidermis trichome
    primordia stomata stipule margin
  • T1 Mature: These are the T1 plants resulting from independent transformation events. These are screened between stage 6.50-6.90 (means the plant is flowering and that 50-90% of the flowers that the plant will make have developed) which is 4-6 weeks of age. At this stage the mature plant possesses flowers, siliques at all stages of development, and fully expanded leaves. We do not generally differentiate between 6.50 and 6.90 in the report but rather just indicate 6.50. The plants are initially imaged under UV with a Leica Confocal microscope. This allows examination of the plants on a global level. If expression is present, they are imaged using scanning laser confocal microscopy.
  • T2 Seedling: Progeny are collected from the T1 plants giving the same expression pattern and the progeny (T2) are sterilized and plated on agar-solidified medium containing M&S salts. In the event that there was no expression in the T1 plants, T2 seeds are planted from all lines. The seedlings are grown in Percival incubators under continuous light at 22° C. for 10-12 days. Cotyledons, roots, hypocotyls, petioles, leaves, and the shoot meristem region of individual seedlings were screened until two seedlings were observed to have the same pattern. Generally found the same expression pattern was found in the first two seedlings. However, up to 6 seedlings were screened before “no expression pattern” was recorded. All constructs are screened as T2 seedlings even if they did not have an expression pattern in the T1 generation.
  • T2 Mature: The T2 mature plants were screened in a similar manner to the T1 plants. The T2 seeds were planted in the greenhouse, exposed to selection and at least one plant screened to confirm the T1 expression pattern. In instances where there were any subtle changes in expression, multiple plants were examined and the changes noted in the tables.
  • T3 Seedling: This was done similar to the T2 seedlings except that only the plants for which we are trying to confirm the pattern are planted.
  • Image Data:
  • Images are collected by scanning laser confocal microscopy. Scanned images are taken as 2-D optical sections or 3-D images generated by stacking the 2-D optical sections collected in series. All scanned images are saved as TIFF files by imaging software, edited in Adobe Photoshop, and labeled in Powerpoint specifying organ and specific expressing tissues.
  • Instrumentation:
  • Microscope
  • Inverted Leica DM IRB
  • Fluorescence filter blocks:
  • Blue excitation BP 450-490; long pass emission LP 515.
  • Green excitation BP 515-560; long pass emission LP 590
  • Objectives
  • HCPL FLUOTAR 5×/0.5
  • HCPL APO 10×/0.4 IMM water/glycerol/oil
  • HCPL APO 20×/0.7 IMM water/glycerol/oil
  • HCXL APO 63×/1.2 IMM water/glycerol/oil
  • Leica TCS SP2 Confocal Scanner
  • Spectral range of detector optics 400-850 nm.
  • Variable computer controlled pinhole diameter.
  • Optical zoom 1-32×.
  • Four simultaneous detectors:
  • Three channels for collection of fluorescence or reflected light.
  • One channel for transmitted light detector.
  • Laser sources:
  • Blue Ar 458/5 mW, 476 nm/5 mW, 488 nm/20 mW, 514 nm/20 mW.
  • Green HeNe 543 nm/1.2 mW
  • Red HeNe 633 nm/10 mW
  • Results
  • The section in Table 1 entitled “The spatial expression of the promoter-marker-vector” presents the results of the GFP assays as reported by their corresponding cDNA ID number, construct number and line number. Unlike the microarray results, which measure the difference in expression of the endogenous cDNA under various conditions, the GFP data gives the location of expression that is visible under the imaging parameters. Table 3 summarizes the results of the spatial expression results for each promoter.
  • Explanation of Table 1
  • Table 1 includes various information about each promoter or promoter control element of the invention including the nucleotid sequence, the spatial expression promoted by each promoter, and the corresponding results from different expression experiments.
    TABLE 1
    Promoter Sequences and Related Information
    Promoter YP0396
    Modulates the gene: PAR-related protein
    The GenBank description of the gene: : NM_124618 Arabidopsis thaliana photoassimilate-responsive
    protein PAR-related protein (At5g52390) mRNA, complete cds gi|30696178|ref|NM_124618.2|[30696178]
    The promoter sequence:
    5′ctaagtaaaataagataaaacatgttatttgaatttgaatatcgtgggatgcgtatttcggtatttgat
    taaaggtctggaaaccggagctcctataacccgaataaaaatgcataacatgttcttccccaacgaggcga
    gcgggtcagggcactagggtcattgcaggcagctcataaagtcatgatcatctaggagatcaaattgtatg
    tcggccttctcaaaattacctctaagaatctcaaacccaatcatagaacctctaaaaagacaaagtcgtcg
    ctttagaatgggttcggtttttggaaccatatttcacgtcaatttaatgtttagtataatttctgaacaac
    agaattttggatttatttgcacgtatacaaatatctaattaataaggacgactcgtgactatccttacatt
    aagtttcactgtcgaaataacatagtacaatacttgtcgttaatttccacgtctcaagtctataccgtcat
    ttacggagaaagaacatctctgtttttcatccaaactactattctcactttgtctatatatttaaaattaa
    gtaaaaaagactcaatagtccaataaaatgatgaccaaatgagaagatggttttgtgccagattttaggaa
    aagtgagtcaaggtttcacatctcaaatttgactgcataatcttcgccattaacaacggcattatatatgt
    caagccaattttccatgttgcgtacttttctattgaggtgaaaatatgggtttgttgattaatcaaagagt
    ttgcctaactaatataactacgactttttcagtgaccattccatgtaaactctgcttagtgtttcatttgt
    caacaatattgtcgttactcattaaatcaaggaaaaatatacaattgtataattttcttatattttaaaat
    taattttga 3′
    ccaaaagaacatctttccttcgaattttctttcattaacatttcttttacttgtctccttgtgtcttcact
    tcacatcacaacATG
    The promoter was cloned from the organism: Arabidopsis thaliana, Columbia ecotype
    Alternative nucleotides:
    Predicted Position (bp) Mismatch Predicted/Experimental
    1-1000 None Identities = 1000/1000 (100%)
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature  XT2 Seedling  T2 Mature  T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower H sepal H petal H anther H style
    Silique H style H ovule
    Ovule H outer integument H outer integument L seed coat
    Leaf H vascular
    Primary Root H epidermis
    Observed expression pattern:
    T1 mature: High GFP expression in the style, sepals, petals, and anthers in flowers.
    Expressed in outer integuments of ovule primordia through developing seed stages and in remnants of
    aborted ovules. High vasculature expression in leaf
    T2 seedling: Medium to low root epidermal expression at root transition zone decreasing toward root tip.
    Specific to epidermal cells flanking lateral roots.
    Misc. promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12646726
    cDNA nucleotide sequence:
    ACTACACCCAAAAGAACATCTTTCCTTCGAATTTTCTTTCAATTAACATTTCTTTTACTTGTCTC
    CTTGTGTCTTCACTTCACATCACAACATGGCTTTGAAGACAGTTTTCGTAGCTTTTATGATTCT
    CCTTGCGATCTATTCGCAAACGACGTTTGGGGACGATGTGAAGTGCGAGAATCTGGATGAAAA
    CACGTGTGCCUCGCGGTCTCGTCCACTGGAAAACGTTGCGTTTTGGAGAAGAGCATGAAGAG
    GAGCGGGATCGAGGTGTACACATGTCGATCATCGGAGATAGAAGCTAACAAGGTCACAAACA
    TTATTGAATCGGACGAGTGCATTAAAGCGTGTGGTCTAGACCGGAAAGCTTTAGGTATATCTT
    CGGACGCATTGTTGGAATCTCAGTTCACACATAAACTCTGCTCGGTTAAATGCTTAAACCAAT
    GTCCTAACGTAGTCGATCTCTACTTCAACCTTGCTGCTGGTGAAGGAGTGTATTTACCAAAGCT
    ATGTGAATCACAAGAAGGGAAGTCAAGAAGAGCAATGTCGGAAATTAGGAGCTCGGGAATTG
    CAATGGACACTCTTGCACCGGTTGGACCAGTCATGTTGGGCGAGATAGCACCTGAGCCGGCTA
    CTTCAATGGACAACATGCCTTACGTGCCGGCACCTTCACCGTATTAATTAAGGCAAGGGAAAA
    TGGAGAGGACACGTATGATATCATGAGTTTTCGACGAGAATAATTAAGAGATTTATGTTTAGT
    TCGACGGTTTTAGTATTACATCGTTTATTGCGTCCTTATATATATGTACTTCATAAAAACACAC
    CACGACACATTAAGAGATGGTGAAAGTAGGCTGCGTTCTGGTGTAACTTTTACACAAGTAACG
    TCTTATAATATATATGATTCGAATAAAATGTTGAGTTTTGGTGAAAATATATAATATGTTTCTG
    Coding sequence:
    MALKTVFVAFMILLAIYSQTTFGDDVKCENLDENTCAFAVSSTGKRCVLEKSMKRSGIEVYTCRSS
    EIEANKVTNIIESDECIKACGLDRKALGISSDALLESQFTHKLCSVKCLNQCPNVVDLYFNLAAGEG
    VYLPKLCESQEGKSRRAMSEIRSSGIAMDTLAPVGPVMLGEIAPEPATSMDNMPYVPAPSPY*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12646726 At_Root_Tips 108434 −
    12646726 At_Drought_Flowers 108473 +
    12646726 At_Drought_Flowers 108474 +
    12646726 At_Shoot_Apices 108479 +
    12646726 At_Shoot_Apices 108480 −
    12646726 At_15mM_NH4NO3_L-to-H_Rosette 108489 +
    12646726 At_ap2-floral_buds 108501 −
    12646726 At_Ler-rhl_Root 108594 −
    12646726 At-Ler-pi_Ovule 108595 +
    12646726 At_100uM_ABA 108609 +
    12646726 At_100uM_ABA_Mutants 20000069 +
    12646726 At_100uM_ABA_Mutants 20000070 +
    12646726 At_100uM_ABA_Mutants 20000071 +
    12646726 At_100uM_ABA_Mutants 20000072 +
    12646726 At_100uM_ABA_Mutants 20000117 +
    12646726 At_42deg_Heat 20000173 −
    12646726 At_Shoots 20000184 −
    12646726 At_Roots 20000185 −
    12646726 At_Root-Tips-vs-Tops 20000227 −
    12646726 At_Siliques 20000234 +
    12646726 At_Open_Flower 20000265 +
    12646726 At_Drought 20000267 +
    12646726 At_100mM-NaCl 20000268 +
    12646726 At_100mM NaCl 20000308 +
    12646726 At_Drought 20000436 +
    12646726 At_Drought 20000437 +
    12646726 At_Shoots 20000438 −
    12646726 At_1uM_BR-BRZ 20000441 −
    12646726 At_1uM_BR-BRZ 20000443 −
    12646726 At_100uM_ABA 20000453 +
    12646726 At_42deg_Heat 20000457 +
    12646726 At_42deg_Heat 20000458 −
    12646726 At_Guard_Cells 20000495 −
    12646726 At_10percent_PEG 20000527 −
    12646726 At_100uM_ABA_Mutants 20000573 −
    12646726 At_100uM_ABA_Mutants 20000574 −
    12646726 At_15mM_NH4NO3_L-to-H 20000709 −
    12646726 At_Line_Comparisons 20001151 +
    12646726 At_Line_Comparisons 20001300 +
    12646726 At_Line_Comparisons 20001307 +
    12646726 At_Line_Comparisons 20001309 −
    12646726 At_Line_Comparisons 20001310 −
    12646726 At_interploidy_Crosses 20001316 −
    12646726 At_Line_Comparisons 20001448 +
    12646726 At_Drought_Soil_Dry 20001554 +
    12646726 At_Drought_Soil_Dry 20001555 +
    12646726 At_Drought_Soil_Dry 20001556 +
    12646726 At_Interploidy_Crosses 20001654 +
    12646726 At_Interploidy_Crosses 20001704 +
    12646726 At_Interploidy_Crosses 20001853 +
    12646726 At_Drought_Reproduction 20001905 +
    12646726 At_Drought_Reproduction 20001906 +
    12646726 At_Drought_Reproduction 20001910 +
    12646726 At_Drought_Reproduction 20001911 +
    12646726 At_8deg_Cold 20002108 −
    12646726 At_8deg_Cold 20002109 −
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12646726 At_Root_Tips 108434 Tissue Root Tips
    12646726 At_Drought_Flowers 108473 Timepoint (hr) 7 d
    12646726 At_Drought_Flowers 108473 Treatment Drought vs. No Drought
    12646726 At_Drought_Flowers 108473 Tissue Flower
    12646726 At_Drought_Flowers 108474 Timepoint (hr) 8 d (1d-post_re-watering)
    12646726 At_Drought_Flowers 108474 Treatment Drought vs. No Drought
    12646726 At_Drought_Flowers 108474 Tissue Flower
    12646726 At_Shoot_Apices 108479 Plant Line AOD4-4
    12646726 At_Shoot_Apices 108479 Treatment None
    12646726 At_Shoot_Apices 108480 Treatment 1uM BR vs. No Treatment
    12646726 At_Shoot_Apices 108480 Plant Line Ws-2
    12646726 At_15mM_NH4NO3_L-to- 108489 Timepoint (hr) 4
    H-Rosette
    12646726 At_15mM_NH4NO3_L-to- 108489 Treatment 15mM NH4NO3 vs. 30mM
    H-Rosette Mannitol
    12646726 At_15mM_NH4NO3_L-to- 108489 Tissue Rosette
    H-Rosette
    12646726 At_ap2_floral_buds 108501 Plant Line ap2 (Ler.)
    12646726 At_ap2_floral_buds 108501 Tissue Closed Flower
    12646726 At_Ler-rhi_Root 108594 Plant Line Ler_rhl
    12646726 At_Ler-rhi_Root 108594 Tissue Roots
    12646726 At_Ler-pi_Ovule 108595 Plant Line Ler_pi
    12646726 At_Ler-pi_Ovule 108595 Tissue Ovules
    12646726 At_100uM_ABA 108609 Timepoint (hr) 24
    12646726 At_100uM_ABA 108609 Treatment 100uM ABA vs. No
    Treatment
    12646726 At_100uM_ABA 108609 Tissue Aerial
    12646726 At_100uM_ABA_Mutants 20000069 Timepoint (hr) 6
    12646726 At_100uM_ABA_Mutants 20000069 Treatment 100uM ABA vs. No
    Treatment
    12646726 At_100uM_ABA_Mutants 20000069 Tissue Aerial
    12646726 At_100uM_ABA_Mutants 20000069 Plant Line CS23
    12646726 At_100uM_ABA_Mutants 20000070 Timepoint (hr) 6
    12646726 At_100uM_ABA_Mutants 20000070 Treatment 100uM ABA vs. No
    Treatment
    12646726 At_100uM_ABA_Mutants 20000070 Tissue Aerial
    12646726 At_100uM_ABA_Mutants 20000070 Plant Line CS24
    12646726 At_100uM_ABA_Mutants 20000071 Timepoint (hr) 6
    12646726 At_100uM_ABA_Mutants 20000071 Treatment 100uM ABA vs. No
    Treatment
    12646726 At_100uM_ABA_Mutants 20000071 Tissue Aerial
    12646726 At_100uM_ABA_Mutants 20000071 Plant Line CS8104
    12646726 At_100uM_ABA_Mutants 20000072 Timepoint (hr) 6
    12646726 At_100uM_ABA_Mutants 20000072 Treatment 100uM ABA vs. No
    Treatment
    12646726 At_100uM_ABA_Mutants 20000072 Tissue Aerial
    12646726 At_100uM_ABA_Mutants 20000072 Plant Line CS8105
    12646726 At_100uM_ABA_Mutants 20000117 Timepoint (hr) 6
    12646726 At_100uM_ABA_Mutants 20000117 Treatment 100uM ABA vs. No
    Treatment
    12646726 At_100uM_ABA_Mutants 20000117 Tissue Aerial
    12646726 At_100uM_ABA_Mutants 20000117 Plant Line Columbia
    12646726 At_42deg_Heat 20000173 Timepoint (hr) 6
    12646726 At_42deg_Heat 20000173 Age (day) 14
    12646726 At_42deg_Heat 20000173 Temperature (deg 42 vs. 22
    C.)
    12646726 At_42deg_Heat 20000173 Organism A. thaliana
    12646726 At_42deg_Heat 20000173 Tissue Aerial
    12646726 At_42deg-Heat 20000173 Plant Line WS
    12646726 At_Shoots 20000164 Age (day) 7 vs. 21
    12646726 At_Shoots 20000184 Organism A. thaliana
    12646726 At_Shoots 20000184 Tissue Shoots vs. Whole Plant
    12646726 At_Shoots 20000184 Plant Line WS
    12646726 At_Roots 20000185 Age (day) 7 vs. 21
    12646726 At_Roots 20000185 Organism A. thaliana
    12646726 At_Roots 20000185 Tissue Roots vs. Whole Plant
    12646726 At_Roots 20000185 Plant Line WS
    12646726 At_Root-Tips-vs-Tops 20000227 Age (day) 7, 10, 14
    12646726 At_Root-Tips-vs-Tops 20000227 Organism A. thaliana
    12646726 At_Root-Tips-vs-Tops 20000227 Tissue Root Tips vs. Root Tops
    12646726 At_Root-Tips-vs-Tops 20000227 Plant Line WS
    12646726 At_Siliques 20000234 Age (day) 21
    12646726 At_Siliques 20000234 Tissue <5 mm Siliques vs. Whole
    Plant
    12646726 At_Siliques 20000234 Organism A. thaliana
    12646726 At_Siliques 20000234 Plant Line WS
    12646726 At_Open_Flower 20000265 Age (day) 21
    12646726 At_Open_Flower 20000265 Organism A. thaliana
    12646726 At_Open-Flower 20000265 Tissue Closed Flower vs. Whole
    Plant
    12646726 At_Open_Flower 20000265 Plant Line WS
    12646726 At_Drought 20000267 Timepoint (hr) 6
    12646726 At_Drought 20000267 Age (day) 7
    12646726 At_Drought 20000267 Organism A. thaliana
    12646726 At_Drought 20000267 Treatment Drought vs. No Drought
    12646726 At_Drought 20000267 Tissue Whole Plant
    12646726 At_Drought 20000267 Plant Line WS
    12646726 At_100mM_NaCl 20000268 Timepoint (hr) 6
    12646726 At_100mM_NaCl 20000268 Age (day) 14
    12646726 At_100mM_NaCl 20000268 Treatment 100mM NaCl vs. No
    Treatment
    12646726 At_100mM_NaCl 20000268 Organism A. thaliana
    12646726 At_100mM_NaCl 20000268 Tissue Whole Plant
    12646726 At_100mM_NaCl 20000268 Plant Line WS
    12646726 At_100mM_NaCl 20000308 Age (day) 17
    12646726 At_100mM_NaCl 20000308 Timepoint (hr) 72
    12646726 At_100mM_NaCl 20000308 Treatment 100mM NaCl vs. No
    Treatment
    12646726 At_100mM_NaCl 20000308 Organism A. thaliana
    12646726 At_100mM_NaCl 20000308 Tissue Whole Plant
    12646726 At_100mM_NaCl 20000308 Plant Line WS
    12646726 At_Drought 20000436 Age (day) 7
    12646726 At_Drought 20000436 Timepoint (hr) 12
    12646726 At_Drought 20000436 Organism A. thaliana
    12646726 At_Drought 20000436 Treatment Drought vs. No Drought
    12646726 At_Drought 20000436 Tissue Whole Plant
    12646726 At_Drought 20000436 Plant Line WS
    12646726 At_Drought 20000437 Age (day) 8
    12646726 At_Drought 20000437 Timepoint (hr) 24
    12646726 At_Drought 20000437 Organism A. thaliana
    12646726 At_Drought 20000437 Treatment Drought vs. No Drought
    12646726 At_Drought 20000437 Tissue Whole Plant
    12646726 At_Drought 20000437 Plant Line WS
    12646726 At_Shoots 20000438 Age (day) 14 vs. 21
    12646726 At_Shoots 20000438 Organism A. thaliana
    12646726 At_Shoots 20000438 Tissue Shoots vs. Whole Plant
    12646726 At_Shoots 20000438 Plant Line WS
    12646726 At_1uM_BR-BRZ 20000441 Treatment 1uM BR vs. No Treatment
    12646726 At_1uM_BR-BRZ 20000441 Tissue Shoot Apices
    12646726 At_1uM_BR-BRZ 20000443 Treatment 1uM BRZ vs. No Treatment
    12646726 At_1uM_BR-BRZ 20000443 Tissue Shoot Apices
    12646726 At_100uM_ABA 20000453 Age (day) 15
    12646726 At_100uM_ABA 20000453 Timepoint (hr) 24
    12646726 At_100uM_ABA 20000453 Treatment 100uM ABA vs. No
    Treatment
    12646726 At_100uM_ABA 20000453 Organism A. thaliana
    12646726 At_100uM_ABA 20000453 Tissue Aerial
    12646726 At_100uM_ABA 20000453 Plant Line WS
    12646726 At_42deg_Heat 20000457 Timepoint (hr) 0.166
    12646726 At_42deg_Heat 20000457 Age (day) 14
    12646726 At_42deg_Heat 20000457 Temperature (deg 42 vs. 22
    C.)
    12646726 At_42deg_Heat 20000457 Organism A. thaliana
    12646726 At_42deg_Heat 20000457 Tissue Aerial
    12646726 At_42deg_Heat 20000457 Plant Line WS
    12646726 At_42deg_Heat 20000458 Timepoint (hr) 8
    12646726 At_42deg_Heat 20000458 Age (day) 14
    12646726 At_42deg_Heat 20000458 Temperature (deg 42 vs. 22
    C.)
    12646726 At_42deg_Heat 20000458 Organism A. thaliana
    12646726 At_42deg_Heat 20000458 Tissue Aerial
    12646726 At_42deg_Heat 20000458 Plant Line WS
    12646726 At_Guard_Cells 20000495 Harvest Date Aug. 2, 2002
    12646726 At_Guard_Cells 20000495 Organism A. thaliana
    12646726 At_Guard_Cells 20000495 Tissue Guard Cells vs. Leaves
    12646726 At_10percent_PEG 20000527 Age (day) 20
    12646726 At_10percent_PEG 20000527 Timepoint (day) 20
    12646726 At_10percent_PEG 20000527 Treatment 10percent PEG vs. No
    Treatment
    12646726 At_10percent_PEG 20000527 Organism A. thaliana
    12646726 At_10percent_PEG 20000527 Tissue Whole Plant
    12646726 At_10percent_PEG 20000527 Plant Line WS
    12646726 At_100uM_ABA_Mutants 20000573 Organism A. thaliana
    12646726 At_100uM_ABA_Mutants 20000573 Plant Line CS22 vs. Lerwt
    12646726 At_100uM_ABA_Mutants 20000573 Timepoint (hr) N/A
    12646726 At_100uM_ABA_Mutants 20000573 Treatment None
    12646726 At_100uM_ABA_Mutants 20000573 Tissue Whole Plant
    12646726 At_100uM_ABA_Mutants 20000574 Organism A. thaliana
    12646726 At_100uM_ABA_Mutants 20000574 Plant Line C523 vs. Ler wt
    12646726 At_100uM_ABA_Mutants 20000574 Timepoint (hr) N/A
    12646726 At_100uM_ABA_Mutants 20000574 Treatment None
    12646726 At_100uM_ABA_Mutants 20000574 Tissue Whole Plant
    12646726 At_15mM_NH4NO3_L-to-H 20000709 Timepoint (hr) 4
    12646726 At_15mM_NH4NO3_L-to-H 20000709 Age (hr) 14
    12646726 At_15mM_NH4NO3_L-to-H 20000709 Treatment 15mM NH4NO3 vs. 30mM
    Mannitol
    12646726 At_15mM_NH4NO3_L-to-H 20000709 Organism A. thaliana
    12646726 At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial
    12646726 At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS
    12646726 At_Line_Comparisons 20001151 Plant Line ME01339-01 vs. WS
    12646726 At_Line_Comparisons 20001300 Plant Line ME01338-05 vs. WS
    12646726 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS
    12646726 At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS
    12646726 At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS
    12646726 At_interploidy_Crosses 20001316 Age (day) 5
    12646726 At_Interploidy_Crosses 20001316 Organism A. thaliana
    12646726 At_Interploidy_Crosses 20001316 Plant Line Columbia
    12646726 At_Interploidy_Crosses 20001316 Cross hemi × 2X vs. 2X × 2X
    12646726 At_lnterploidy_Crosses 20001316 Tissue Siliques
    12646726 At_Line_Comparisons 20001448 Plant Line ME01323-01 vs. WS
    12646726 At_Drought_Soil_Dry 20001554 Timepoint (day) 7
    12646726 At_Drought_Soil_Dry 20001554 Age (day) 21
    12646726 At_Drought_Soil_Dry 20001554 Organism A. thaliana
    12646726 At_Drought_Soil_Dry 20001554 Treatment Drought vs. No Drought
    12646726 At_Drought_Soil_Dry 20001554 Post Timepoint (hr) None
    12646726 At_Drought_Soil_Dry 20001554 Post-Treatment None
    12646726 At_Drought_Soil_Dry 20001554 Plant Line WS
    12646726 At_Drought_Soil_Dry 20001555 Timepoint (day) 10
    12646726 At_Drought_Soil_Dry 20001555 Age (day) 24
    12646726 At_Drought_Soil_Dry 20001555 Organism A. thaliana
    12646726 At_Drought_Soil_Dry 20001555 Treatment Drought vs. No Drought
    12646726 At_Drought_Soil_Dry 20001555 Post Timepoint (hr) None
    12646726 At_Drought_Soil_Dry 20001555 Post-Treatment None
    12646726 At_Drought_Soil_Dry 20001555 Plant Line WS
    12646726 At_Drought_Soil_Dry 20001556 Timepoint (day) 12
    12646726 At_Drought_Soil_Dry 20001556 Age (day) 26
    12646726 At_Drought_Soil_Dry 20001556 Organism A. thaliana
    12646726 At_Drought_Soil_Dry 20001556 Treatment Drought vs. No Drought
    12646726 At_Drought_Soil_Dry 20001556 Post Timepoint (hr) None
    12646726 At_Drought_Soil_Dry 20001556 Post-Treatment None
    12646726 At_Drought_Soil_Dry 20001556 Plant Line WS
    12646726 At_Interploidy_Crosses 20001654 Age (day) 5
    12646726 At_Interploidy_Crosses 20001654 Cross 6X × 2X vs. 2X × 2X
    12646726 At_Interploidy_Crosses 20001654 Organism A. thaliana
    12646726 At_Interploidy_Crosses 20001654 Plant Line Columbia
    12646726 At_Interploidy_Crosses 20001654 Tissue Siliques
    12646726 At_Interploidy_Crosses 20001704 Age (day) 5
    12646726 At_Interploidy_Crosses 20001704 Cross 4X × 2X vs. 2X × 2X
    12646726 At_Interploidy_Crosses 20001704 Organism A. thaliana
    12646726 At_Interploidy_Crosses 20001704 Plant Line Columbia
    12646726 At_Interploidy_Crosses 20001704 Tissue Siliques
    12646726 At_Interploidy_Crosses 20001853 Age (day) 5
    12646726 At_Interploidy_Crosses 20001853 Organism A. thaliana
    12646726 At_Interploidy_Crosses 20001853 Plant Line Columbia
    12646726 At_Interploidy_Crosses 20001853 Cross Fis1 vs. 2X × 2X
    12646726 At_Interploidy_Crosses 20001853 Tissue Siliques
    12646726 At_Drought_Reproduction 20001905 Timepoint (day) 10
    12646726 At_Drought_Reproduction 20001905 Age (day) 40
    12646726 At_Drought_Reproduction 20001905 Organism A. thaliana
    12646726 At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought
    12646726 At_Drought_Reproduction 20001905 Tissue Rosettes
    12646726 At_Drought_Reproduction 20001905 Plant Line WS
    12646726 At_Drought_Reproduction 20001906 Timepoint (day) 5
    12646726 At_Drought_Reproduction 20001906 Age (day) 35
    12646726 At_Drought_Reproduction 20001906 Organism A. thaliana
    12646726 At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought
    12646726 At_Drought_Reproduction 20001906 Tissue Siliques
    12646726 At_Drought_Reproduction 20001906 Plant Line WS
    12646726 At_Drought_Reproduction 20001910 Timepoint (day) 7
    12646726 At_Drought_Reproduction 20001910 Age (day) 37
    12646726 At_Drought_Reproduction 20001910 Organism A. thaliana
    12646726 At_Drought_Reproduction 20001910 Treatment Drought vs. No Drought
    12646726 At_Drought_Reproduction 20001910 Tissue Flowers
    12646726 At_Drought_Reproduction 20001910 Plant Line WS
    12646726 At_Drought_Reproduction 20001911 Timepoint (day) 10
    12646726 At_Drought_Reproduction 20001911 Age (day) 40
    12646726 At_Drought_Reproduction 20001911 Organism A. thaliana
    12646726 At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought
    12646726 At_Drought_Reproduction 20001911 Tissue Flowers
    12646726 At_Drought_Reproduction 20001911 Plant Line WS
    12646726 At_8deg_Cold 20002108 Age (day) 14
    12646726 At_8deg_Cold 20002108 Timepoint (hr) 168
    12646726 At_8deg_Cold 20002108 Temperature (deg 8 vs. 22
    C.)
    12646726 At_8deg_Cold 20002108 Organism A. thaliana
    12646726 At_8deg_Cold 20002108 Tissue Whole Plant
    12646726 At_8deg_Cold 20002108 Plant Line WS
    12646726 At_8deg_Cold 20002109 Age (day) 16
    12646726 At_8deg_Cold 20002109 Timepoint (hr) 216
    12646726 At_8deg_Cold 20002109 Temperature (deg 8 vs. 22
    C.)
    12646726 At_8deg_Cold 20002109 Organism A. thaliana
    12646726 At_8deg_Cold 20002109 Tissue Whole Plant
    12646726 At_8deg_Cold 20002109 Plant Line WS
    Promoter YP0388
    Modulates the gene: protein phosphatase 2C (PP2C), putative
    The GenBank description of the gene: NM_125312 Arabidopsis thaliana protein phosphatase 2C (PP2C),
    putative (At5g59220) mRNA, complete cds gi|3069719|ref|NM 125312.2|[30697191]
    The promoter sequence:
    5′tatttgtagtgacatattctacaattatcacatttttctcttatgtttcgtagtcgcagatggtca
    attttttctataataatttgtccttgaacacaccaaactttagaaacgatgatatataccgtattgtc
    acgctcacaatgaaacaaacgcgatgaatcgtcatcaccagctaaaagcctaaaacaccatcttagtt
    ttcactcagataaaaagattatttgtttccaacctttctattgaattgattagcagtgatgacgtaat
    tagtgatagtttatagtaaaacaaatggaagtggtaataaatttacacaacaaaatatggtaagaatc
    tataaaataagaggttaagagatctcatgttatattaaatgattgaaagaaaaacaaactattggttg
    atttccatatgtaatagtaagttgtgatgaaagtgatgacgtaattagttgtatttatagtaaaacaa
    attaaaatggtaaggtaaatttccacaacaaaacttggtaaaaatcttaaaaaaaaaaaaagaggttt
    agagatcgcatgcgtgtcatcaaaggttctttttcactttaggtctgagtagtgttagactttgattg
    gtgcacgtaagtgtttcgtatcgcgatttaggagaagtacgttttacacgtggacacaatcaacggtc
    aagatttcgtcgtccagatagaggagcgatacgtcacgccattcaacaatctcctcttcttcattcct
    tcattttgattttgagttttgatctgcccgttcaaaagtctcggtcatctgcccgtaaatataaagat
    gattatatttatttatatcttctggtgaaagaagctaaTATAaagcttccatggctaatcttgtttaa
    gcttctcttcttcttctctctcctgtgtctcgttcactagttttttttcgggggagagtgatggagtg
    tgtttgttgaata 3′cATG
    The promoter was cloned from the organism: Arabidopsis thaliana, Columbia ecotype
    Alternative nucleotides:
    Predicted Position (bp) Mismatch Predicted/Experimental
    1-1000 None Identities = 1000/1000 (100%)
    The promoter was cloned in the vector: pNewbin4-HAPI-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower H filament H anther H stomata
    Silique H ovule
    Ovule Post-fertilization: H outer H seed coat H chalaza
    Leaf L vascular H stomata
    Primary Root H epidermis
    Observed expression pattern:
    T1 mature: Very high GFP expression levels in stamens of developing flowers. Low expression in
    vasculature of leaves and guard cells throughout plant. High expression in outer integument of ovules and in
    seed coats. High incidence of aborted ovules.
    T2 seedling: Low expression in root epidermal cells.
    Misc. promoter information:  Bidirectionality: Pass  Exons: Pass  Repeats: No
    Optional Promoter Fragments: 5′UTR region at base pairs 880-987.
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 13593066
    cDNA nucleotide sequence:
    AAAGCTTGCATGGGTAATCTTGTTTAAGCTTCTCTTCTTCTTCTCTCTCCTGTGTCTCGTTCACT
    AGTTTTTTTTCGGGGGAGAGTGATGGAGTGTGYFTGTTGAATAGTTTTGACGATCACATGGCT
    GAGATTTGTTACGAGAACGAGACTATGATGATTGAAACGACGGCGACGGTGGTGAAGAAGGC
    AACGACGACAAGGAGGAGACGAGAACGGAGCTCGTCTCAAGCAGCGAGAAGAAGGAGAATG
    GAGATCCGGAGGTTTAAGTTTGTTTCCGGCGAACAAGAACCTGTCTTCGTCGACGGTGACTTA
    CAGAGGCGGAGGAGAAGAGAATCCACCGTCGCAGGCTCCACCTCCACCGTGTTTTACGAAACG
    GCGAAGGAAGTTGTCGTCCTATGCGAGTCTCTTAGTTCAACGGTTGTGGCATTGCCTGATCCT
    GAAGCTTATCCTAAATACGGCGTCGCTTCAGTCTGTGGAAGAAGACGTGAAATGGAAGACGCC
    GTCGCTGTGCATCCGTTTTTTTCCCGTCATCAGACGGAATATTCATCCACCGGATTTCACTATT
    GCGGCGTTTACGATGGCCATGGCTGTTCCCATGTAGCGATGAAATGTAGAGAAAGACTACACG
    AGCTAGTCCGTGAAGAGTTTGAAGCTGATGCTGACTGGGAAAAGTCAATGGCGCGTAGCTTCA
    CGCGCATGGACATGGAGGTTGTTGCGTTGAACGCCGATGGTGCGGCAAAATGCCGGTGCGAG
    CTTCAGAGGCCGGACTGCGACGCGGTGGGATGCACTGCGGTTGTGTCTGTCCTTACGCCGGAG
    AAAATCATCGTGGCGAATTGCGGTGACTCACGTGCCGTTCTCTGTCGTAACGGCAAAGCCATT
    GCTTTATCCTCCGATCATAAGCCAGACCGTGCGGACGAGCTAGACCGGATTCAAGCAGCGGGT
    GGTCGTGTTATCTACTGGGATGGCCCACGTGTCCTTGGAGTACTTGCAATGTCACGAGCCATT
    GGAGATAATTACTTGAAGCCGTATGTAATCAGCAGACCGGAGGTAACCGTGACGGACCGGGC
    CAACGGAGACGATTTTCTTATTCTCGCAAGTGACGGTCTTTGGGACGTTGTTTCAAACGAAAC
    TGCATGTAGCGTCGTTCGAATGTGTTTGAGAGGAAAAGTCAATGGTCAAGTATCATCATCACC
    GGAAAGGGAAATGACAGGTGTCGGCGCCGGGAATGTGGTGGTTGGAGGAGGAGATTTGCCAG
    ATAAAGCGTGTGAGGAGGCGTCGCTGTTGCTGACGAGGCTTGCGTTGGCTAGACAAAGTTCGG
    ACAACGTAAGTGTTGTGGTGGTTGATCTACGACGAGACAGGTAGTTGTATTTGTCTCTCTCGT
    AATGTTTGTTGTTTTTTGTCCTGAGTCATCGACTTTTGGGCTTTTTCTTTTAACCTTTTTTGCTC
    TTCGGTGTAAGACAACGAAGGGTTTTTAATTTAGCTTGACTATGGGTTATGTCAGTCACTGTGT
    TGAATGGCGGTTTAGATCTACAAAGATTTTCACCAGTAGTGAAAATGGTAAAAAGCGGTGAAA
    TGTGAAAGACTTGAGTTCAATTTAATTTTAAATTTAATAGAATCAGTTGATC
    Coding sequence:
    MAEICYENETMMIETTATVVKKATTTTRRRERSSSQAARRRRMEIRRFKFVSGEQEPVFVDGDLQ
    RRRRRESTVAASTSTVFYETAKEVVVLCESLSSTVVALPDPEAYPKYGVASVCGRRREMEDAVAV
    HPFFSRHQTEYSSTGFHYCGVYDGHGCSHVAMKCRERLHELVREEFEADADWEKSMARSFTRMD
    MEVVALNADGAAKCRCELQRPDCDAVGSTAVVSVLTPEKIIVANCGDSRAVLCRNGKAIALSSDH
    KPDRPDELDRIQAAGGRVIYWDGPRVLGVLAMSRAIGDNYLKPYVISRPEVTVTDRANGDDFLILA
    SDGLWDVVSNETACSVVRMCLRGKVNGQVSSSPEREMTGVGAGNVVVGGGDLPDKACEEASLL
    LTRLALARQSSDNVSVVVVDLRRDT*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    13593066 At_100uM_ABA 20000166 +
    13593066 At_100uM_ABA 20000169 +
    13593066 At_2mM_SA 20000182 +
    13593066 At_20%_PEG 20000233 +
    13593066 At_Open_Flower 20000264 −
    13593066 At_Drought 20000267 +
    13593066 At_100mM_NaCI 20000268 +
    13593066 At_Pollen 20000326 −
    13593066 At_Drought 20000436 +
    13593066 At_Drought 20000437 +
    13593066 At_Shoots 20000438 −
    13593066 At_100uM_ABA 20000453 +
    13593066 At_100uM_ABA 20000455 +
    13593066 At_100uM_ABA_Mutants 20000576 +
    13593066 At_Herbicide_Mutants 20000642 −
    13593066 At_Line_Comparisons 20001151 +
    13593066 At_Line_Comparisons 20001184 +
    13593066 At_Line_Comparisons 20001307 +
    13593066 At_Line_Comparisons 20001309 −
    13593066 At_Line_Comparisons 20001310 −
    13593066 At_Far-red-induction 20001451 +
    13593066 At_Drought_Soil_Dry 20001554 +
    13593066 At_Drought_Soil_Dry 20001555 +
    13593066 At_Drought_Soil_Dry 20001556 +
    13593066 At_Drought_Soil_Dry 20001557 +
    13593066 At_Drought_Soil_Dry 20001559 +
    13593066 At_Drought_Soil_Dry 20001560 +
    13593066 At_50mM_NH4NO3_L-to-H 20001757 −
    13593066 At_Far-red-enriched-adult 20001771 +
    13593066 At_Drought_Reproduction 20001904 +
    13593066 At_Drought_Reproduction 20001905 +
    13593066 At_Drought_Reproduction 20001906 +
    13593066 At_Drought_Reproduction 20001907 +
    13593066 At_Drought_Reproduction 20001908 +
    13593066 At_Drought_Reproduction 20001911 +
    13593066 At_8deg_Cold 20002107 −
    13593066 At_8deg_Cold 20002108 −
    13593066 At_8deg_Cold 20002109 −
    13593066 At_Drought-Air-Dry 20002256 +
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    13593066 At_100uM_ABA 20000166 Timepoint (hr) 1
    13593066 At_100uM_ABA 20000166 Age (day) 14
    13593066 At_100uM_ABA 20000166 Treatment 100uM ABA vs. No Treatment
    13593066 At_100uM_ABA 20000166 Organism A. thaliana
    13593066 At_100uM_ABA 20000166 Tissue Aerial
    13593066 At_100uM_ABA 20000166 Plant Line WS
    13593066 At_100uM_ABA 20000169 Timepoint (hr) 6
    13593066 At_100uM_ABA 20000169 Age (day) 14
    13593066 At_100uM_ABA 20000169 Treatment 100uM ABA vs. No Treatment
    13593066 At_100uM_ABA 20000169 Organism A. thaliana
    13593066 At_100uM_ABA 20000169 Tissue Aerial
    13593066 At_100uM_ABA 20000169 Plant Line WS
    13593066 At_2mM_SA 20000182 Timepoint (hr) 6
    13593066 At_2mM_SA 20000182 Age (day) 14
    13593066 At_2mM_SA 20000182 Treatment 2mM SA vs. No Treatment
    13593066 At_2mM_SA 20000182 Organism A. thaliana
    13593066 At_2mM_SA 20000182 Tissue Aerial
    13593066 At_2mM_SA 20000182 Plant Line WS
    13593066 At_20%_PEG 20000233 Timepoint (hr) 6
    13593066 At_20%_PEG 20000233 Treatment 20% PEG vs. No Treatment
    13593066 At_20%_PEG 20000233 Tissue Aerial
    13593066 At_Open_Flower 20000264 Age (day) 21
    13593066 At_Open_Flower 20000264 Organism A. thaliana
    13593066 At_Open_Flower 20000264 Tissue Open Flower vs. Whole Plant
    13593066 At_Open_Flower 20000264 Plant Line WS
    13593066 At_Drought 20000267 Timepoint (hr) 6
    13593066 At_Drought 20000267 Age (day) 7
    13593066 At_Drought 20000267 Organism A. thaliana
    13593066 At_Drought 20000267 Treatment Drought vs. No Drought
    13593066 At_Drought 20000267 Tissue Whole Plant
    13593066 At_Drought 20000267 Plant Line WS
    13593066 At_100mM_NaCl 20000268 Timepoint (hr) 6
    13593066 At_100mM_NaCl 20000268 Age (day) 14
    13593066 At_100mM_NaCl 20000268 Treatment 100mM NaCl vs. No Treatment
    13593066 At_100mM_NaCl 20000268 Organism A. thaliana
    13593066 At_100mM_NaCl 20000268 Tissue Whole Plant
    13593066 At_100mM_NaCl 20000268 Plant Line WS
    13593066 At_Pollen 20000326 Age (day) 0 vs. 21
    13593066 At_Pollen 20000326 Organism A. thaliana
    13593066 At_Pollen 20000326 Tissue Pollen vs. Whole Plant
    13593066 At_Pollen 20000326 Plant Line WS
    13593066 At_Drought 20000436 Age (day) 7
    13593066 At_Drought 20000436 Timepoint (hr) 12
    13593066 At_Drought 20000436 Organism A. thaliana
    13593066 At_Drought 20000436 Treatment Drought vs. No Drought
    13593066 At_Drought 20000436 Tissue Whole Plant
    13593066 At_Drought 20000436 Plant Line WS
    13593066 At_Drought 20000437 Age (day) 8
    13593066 At_Drought 20000437 Timepoint (hr) 24
    13593066 At_Drought 20000437 Organism A. thaliana
    13593066 At_Drought 20000437 Treatment Drought vs. No Drought
    13593066 At_Drought 20000437 Tissue Whole Plant
    13593066 At_Drought 20000437 Plant Line WS
    13593066 At_Shoots 20000438 Age (day) 14 vs. 21
    13593066 At_Shoots 20000438 Organism A. thaliana
    13593066 At_Shoots 20000438 Tissue Shoots vs. Whole Plant
    13593066 At_Shoots 20000438 Plant Line WS
    13593066 At_100uM_ABA 20000453 Age (day) 15
    13593066 At_100uM_ABA 20000453 Timepoint (hr) 24
    13593066 At_100uM_ABA 20000453 Treatment 100uM ABA vs. No Treatment
    13593066 At_100uM_ABA 20000453 Organism A. thaliana
    13593066 At_100uM_ABA 20000453 Tissue Aerial
    13593066 At_100uM_ABA 20000453 Plant Line WS
    13593066 At_100uM_ABA 20000455 Age (day) 16
    13593066 At_100uM_ABA 20000455 Timepoint (hr) 48
    13593066 At_100uM_ABA 20000455 Treatment 100uM ABA vs. No Treatment
    13593066 At_100uM_ABA 20000455 Organism A. thaliana
    13593066 At_100uM_ABA 20000455 Tissue Aerial
    13593066 At_100uM_ABA 20000455 Plant Line WS
    13593066 At_100uM_ABA_Mutants 20000576 Timepoint (hr) 6
    13593066 At_100uM_ABA_Mutants 20000576 Treatment 100uM ABA vs. No Treatment
    13593066 At_100uM_ABA_Mutants 20000576 Organism A. thaliana
    13593066 At_100uM_ABA_Mutants 20000576 Plant Line CS23
    13593066 At_100uM_ABA_Mutants 20000576 Tissue Whole Plant
    13593066 At_Herbicide_Mutants 20000642 Timepoint (hr) 12
    13593066 At_Herbicide_Mutants 20000642 Plant Line 3950BR/PCJE10000
    13593066 At_Herbicide_Mutants 20000642 Treatment Finale vs. No Treatment
    13593066 At_Herbicide_Mutants 20000642 Tissue Seedlings
    13593066 At_Line_Comparisons 20001151 Plant Line ME01339-01 vs. WS
    13593066 At_Line_Comparisons 20001184 Plant Line ME01848-01 vs. WS
    13593066 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS
    13593066 At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS
    13593066 At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS
    13593066 At_Far-red-induction 20001451 Age (day) 8
    13593066 At_Far-red-induction 20001451 Timepoint (hr) 24
    13593066 At_Far-red-induction 20001451 Organism A. thaliana
    13593066 At_Far-red-induction 20001451 Plant Line Columbia
    13593066 At_Far-red-induction 20001451 Light Far-red vs. White
    13593066 At Far-red-induction 20001451 Tissue Whole Plant
    13593066 At_Drought_Soil_Dry 20001554 Timepoint (day) 7
    13593066 At_Drought_Soil_Dry 20001554 Age (day) 21
    13593066 At_Drought_Soil_Dry 20001554 Organism A. thaliana
    13593066 At_Drought_Soil_Dry 20001554 Treatment Drought vs. No Drought
    13593066 At_Drought_Soil_Dry 20001554 Post Timepoint (hr) None
    13593066 At_Drought_Soil_Dry 20001554 Post-Treatment None
    13593066 At_Drought_Soil_Dry 20001554 Plant Line WS
    13593066 At_Drought_Soil_Dry 20001555 Timepoint (day) 10
    13593066 At_Drought_Soil_Dry 20001555 Age (day) 24
    13593066 At_Drought_Soil_Dry 20001555 Organism A. thaliana
    13593066 At_Drought_Soil_Dry 20001555 Treatment Drought vs. No Drought
    13593066 At_Drought_Soil_Dry 20001555 Post Timepoint (hr) None
    13593066 At_Drought_Soil_Dry 20001555 Post-Treatment None
    13593066 At_Drought_Soil_Dry 20001555 Plant Line WS
    13593066 At_Drought_Soil_Dry 20001556 Timepoint (day) 12
    13593066 At_Drought_Soil_Dry 20001556 Age (day) 26
    13593066 At_Drought_Soil_Dry 20001556 Organism A. thaliana
    13593066 At_Drought_Soil_Dry 20001556 Treatment Drought vs. No Drought
    13593066 At_Drought_Soil_Dry 20001556 Post Timepoint (hr) None
    13593066 At_Drought_Soil_Dry 20001556 Post-Treatment None
    13593066 At_Drought_Soil_Dry 20001556 Plant Line WS
    13593066 At_Drought_Soil_Dry 20001557 Post Timepoint (hr) 3
    13593066 At_Drought_Soil_Dry 20001557 Timepoint (day) 13
    13593066 At_Drought_Soil_Dry 20001557 Age (day) 27
    13593066 At_Drought_Soil_Dry 20001557 Organism A. thaliana
    13593066 At_Drought_Soil_Dry 20001557 Treatment Drought vs. No Drought
    13593066 At_Drought_Soil_Dry 20001557 Post-Treatment Re-Water vs. No Drought
    13593066 At_Drought_Soil_Dry 20001557 Plant Line WS
    13593066 At_Drought_Soil_Dry 20001559 Timepoint (day) 14
    13593066 At_Drought_Soil_Dry 20001559 Age (day) 28
    13593066 At_Drought_Soil_Dry 20001559 Post Timepoint (hr) 29
    13593066 At_Drought_Soil_Dry 20001559 Organism A. thaliana
    13593066 At_Drought_Soil_Dry 20001559 Treatment Drought vs. No Drought
    13593066 At_Drought_Soil_Dry 20001559 Post-Treatment Re-Water vs. No Drought
    13593066 At_Drought_Soil_Dry 20001559 Plant Line WS
    13593066 At_Drought_Soil_Dry 20001560 Timepoint (day) 14
    13593066 At_Drought_Soil_Dry 20001560 Age (day) 28
    13593066 At_Drought_Soil_Dry 20001560 Organism A. thaliana
    13593066 At_Drought_Soil_Dry 20001560 Treatment Drought vs. No Drought
    13593066 At_Drought_Soil_Dry 20001560 Post Timepoint (hr) None
    13593066 At_Drought_Soil_Dry 20001560 Post-Treatment None
    13593066 At_Drought_Soil_Dry 20001560 Plant Line WS
    13593066 At_50mM_NH4NO3_L-to-H 20001757 Timepoint (hr) 6
    13593066 At_50mM_NH4NO3_L-to-H 20001757 Treatment 50mM NH4NO3 vs 100mM
    Mannitol
    13593066 At_50mM_NH4NO3_L-to-H 20001757 Tissue Leaf
    13593066 At_Far-red-enriched-adult 20001771 Timepoint (hr) 16
    13593066 At_Far-red-enriched-adult 20001771 Age (day) 28
    13593066 At_Far-red-enriched-adult 20001771 Organism A. thaliana
    13593066 At_Far-red-enriched-adult 20001771 Tissue Aerial
    13593066 At_Far-red-enriched-adult 20001771 Plant Line Columbia
    13593066 At_Far-red-enriched-adult 20001771 Light Far-red enriched vs. White
    13593066 At_Drought_Reproduction 20001904 Timepoint (day) 7
    13593066 At_Drought_Reproduction 20001904 Age (day) 37
    13593066 At_Drought_Reproduction 20001904 Organism A. thaliana
    13593066 At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought
    13593066 At_Drought_Reproduction 20001904 Tissue Rosettes
    13593066 At_Drought_Reproduction 20001904 Plant Line WS
    13593066 At_Drought_Reproduction 20001905 Timepoint (day) 10
    13593066 At_Drought_Reproduction 20001905 Age (day) 40
    13593066 At_Drought_Reproduction 20001905 Organism A. thaliana
    13593066 At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought
    13593066 At_Drought_Reproduction 20001905 Tissue Rosettes
    13593066 At_Drought_Reproduction 20001905 Plant Line WS
    13593066 At_Drought_Reproduction 20001906 Timepoint (day) 5
    13593066 At_Drought_Reproduction 20001906 Age (day) 35
    13593066 At_Drought_Reproduction 20001906 Organism A. thaliana
    13593066 At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought
    13593066 At_Drought_Reproduction 20001906 Tissue Siliques
    13593066 At_Drought_Reproduction 20001906 Plant Line WS
    13593066 At_Drought_Reproduction 20001907 Timepoint (day) 7
    13593066 At_Drought_Reproduction 20001907 Age (day) 37
    13593066 At_Drought_Reproduction 20001907 Organism A. thaliana
    13593066 At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought
    13593066 At_Drought_Reproduction 20001907 Tissue Siligues
    13593066 At_Drought_Reproduction 20001907 Plant Line WS
    13593066 At_Drought_Reproduction 20001908 Timepoint (day) 10
    13593066 At_Drought_Reproduction 20001906 Age (day) 40
    13593066 At_Drought_Reproduction 20001908 Organism A. thaliana
    13593066 At_Drought_Reproduction 20001908 Treatment Drought vs. No Drought
    13593066 At_Drought_Reproduction 20001908 Tissue Siligues
    13593066 At_Drought_Reproduction 20001908 Plant Line WS
    13593066 At_Drought_Reproduction 20001911 Timepoint (day) 10
    13593066 At_Drought_Reproduction 20001911 Age (day) 40
    13593066 At_Drought_Reproduction 20001911 Organism A. thaliana
    13593066 At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought
    13593066 At_Drought_Reproduction 20001911 Tissue Flowers
    13593066 At_Drought_Reproduction 20001911 Plant Line WS
    13593066 At_8deg_Cold 20002107 Age (day) 11
    13593066 At_8deg_Cold 20002107 Timepoint (hr) 96
    13593066 At_8deg_Cold 20002107 Temperature (deg C.) 8 vs. 22
    13593066 At_8deg_Cold 20002107 Organism A. thaliana
    13593066 At_8deg_Cold 20002107 Tissue Whole Plant
    13593066 At_8deg_Cold 20002107 Plant Line WS
    13593066 At_8deg_Cold 20002108 Age (day) 14
    13593066 At_8deg_Cold 20002108 Timepoint (hr) 168
    13593066 At_8deg_Cold 20002108 Temperature (deg C.) 8 vs. 22
    13593066 At_8deg_Cold 20002108 Organism A. thaliana
    13593066 At_8deg_Cold 20002108 Tissue Whole Plant
    13593066 At_8deg_Cold 20002108 Plant Line WS
    13593066 At_8deg_Cold 20002109 Age (day) 16
    13593066 At_8deg_Cold 20002109 Timepoint (hr) 216
    13593066 At_8deg_Cold 20002109 Temperature (deg C.) 8 vs. 22
    13593066 At_8deg_Cold 20002109 Organism A. thaliana
    13593066 At_8deg_Cold 20002109 Tissue Whole Plant
    13593066 At_8deg_Cold 20002109 Plant Line WS
    13593066 At_Drought-Air-Dry 20002256 Timepoint (hr) 4
    13593066 At_Drought-Air-Dry 20002256 Age (day) 35
    13593066 At_Drought-Air-Dry 20002256 Organism A. thaliana
    13593066 At_Drought-Air-Dry 20002256 Treatment Drought vs. No Drought
    13593066 At_Drought-Air-Dry 20002256 Tissue Shoots
    13593066 At_Drought-Air-Dry 20002256 Plant Line WS
    Promoter YP0385
    Modulates the gene: Neoxanthin cleavage enzyme.
    The GenBank description of the gene: NM_112304 Arabidopsis thaliana 9-cis-epoxycarotenoid
    dioxygenase [neoxanthin cleavage enzyme](NC1)(NCED1), putative (At3g14440) mRNA, complete cds
    gi|30683162|ref| NM_112304.2|[30683162].
    The promoter sequence:
    5′aaaattccaattattgtgttactctattcttctaaatttgaacactaatagactatgacatatgagtat
    ataatgtgaagtcttaagatattttcatgtgggagatgaataggccaagttggagtctgcaaacaagaagc
    tcttgagccacgacataagccaagttgatgaccgtaattaatgaaactaaatgtgtgtggttatatattag
    ggacccatggccatatacacaatttttgtttctgtcgatagcatgcgtttatatatatttctaaaaaaact
    aacatatttactggatttgagttcgaatattgacactaatataaactacgtaccaaactacatatgtttat
    ctatatttgattgatcgaagaattctgaactgttttagaaaatttcaatacacttaacttcatcttacaac
    ggtaaaagaaatcaccactagacaaacaatgcctcataatgtctcgaaccctcaaactcaagagtatacat
    tttactagattagagaatttgatatcctcaagttgccaaagaattggaagcttttgttaccaaacttagaa
    acagaagaagccacaaaaaaagacaaagggagttaaagattgaagtgatgcatttgtctaagtgtgaaagg
    tctcaagtctcaactttgaaccataataacattactcacactccctttttttttctttttttttcccaaag
    taccctttttaattccctctataacccactcactccattccctctttctgtcactgattcaacacgtggcc
    acactgatgggatccacctttcctcttacccacctcccggttTATAtaaacccttcacaacacttcatcgc
    tctcaaaccaactctctcttctctcttctctcctctcttctacaagaagaaaaaaaacagagcctttacac
    atctcaaaatcgaacttactttaaccacc 3′-aATG
    The promoter was cloned from the organism: Arabidopsis thaliana, Columbia ecotype
    Alternative nucleotides:
    Predicted Position (bp) Mismatch Predicted/Experimental
     7 PCR error or ecotype variant SNP g/−
    28 Read error a/a corrected
    29 PCR error or ecotype variant SNP a/−
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower L receptacle
    Silique L abscission zone
    Primary Root H epidermis
    Observed expression pattern of the promoter-marker vector was in:
    T1 mature: Expression specific to abscission zone of mature flowers.
    T2 seedling: Expression in root epidermal cells. Expression rapidly decreases from root transition zone
    to mid root.
    Misc. promoter information:  Bidirectionality: Pass  Exons: Pass  Repeats: No
    Optional Promoter Fragments: 5′UTR region at base pairs 880-999.
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12658348
    cDNA nucleotide sequence:
    AAACCAACTCTCTCTTCTCTCTTCTCTGCTCTCTTCTACAAGAAGAAAAAAAACAGAGCCTTTA
    CACATCTCAAAATCGAACTTACTTTAACCACCAAATACTGATTGAACACACTTGAAAAATGGC
    TTCTTTCAGGGCAACGGCTGCGGTTTCTGGGAGATGGCTTGGTGGCAATCATACTCAGCCGCC
    ATTATCGTCTTGTCAAAGCTGCGACTTGAGTTATTGTAGCTCCTTACCTATGGCCAGTCGTGTC
    ACACGTAAGCTCAATGTTTCATCTGCGCTTCAGACTCCTCCAGCTCTTCATTTCCCTAAGCAAT
    CATCAAACTCTCCCGCCATTGTTGTTAAGCCCAAAGCCAAAGAATCCAACACTAAACAGATGA
    ATTTGTTCCAGAGAGCGGCGGCGGCAGCGTTGGACGCGGCGGAGGGTTTCCTTGTCAGCCACG
    AGAAGCTACAGCCGCTTCCTAAAACGGCTGATCCTAGTGTTCAGATCGCCGGAAATTTTGCTC
    CGGTGAATGAACAGCCCGTCCGGCGTAATCTTCCGGTGGTCGGAAAACTTCCCGATTCCATCA
    AAGGAGTGTATGTGCGCAACGGAGCTAACCCAGTTCACGAGCCGGTGACAGGTCACGACTTCT
    TCGACGGAGACGGTATGGTTCACGCCGTCAAATTCGAACACGGTTCAGCTAGCTACGCTTGCC
    GGTTTACTCAGACTAACCGGTTTGTTCAGGAACGTCAATTGGGTCGACCGGTTTTCCCCAAAG
    CCATCGGTGAGCTTCACGGCCACACCGGTATTGCCCGACTCATGCTATTCTACGCCAGAGCTG
    CAGCCGGTATAGTCGACCCGGCACACGGAACCGGTGTAGCTAACGCCGGTTTGGTCTATTTCA
    ATGGCCGGTTATTGGCTATGTCGGAGGATGATTTACCTTACCAAGTTCAGATCACTCCCAATG
    GAGATTTAAAAACCGTTGGTCGGTTCGATTTTGATGGACAATTAGAATCCACAATGATTGGCC
    ACCCGAAAGTCGACCCGGAATCCGGTGAACTCTTCGCTTTAAGCTACGACGTCGTTTCAAAGC
    CTTACCTAAAATACTTCCGATTCTCACCGGACGGAACTAAATCACCGGACGTCGAGATTCAGC
    TTGATCAGCCAACGATGATGCACGATTTCGCGATTACAGAGAACTTCGTCGTCGTACCTGACC
    AGCAAGTCGTTTTCAAGCTGCCGGAGATGATCCGCGGTGGGTCTCCGGTGGTTTACGAGAAGA
    ACAAGGTCGCAAGATTCGGGATTTTAGACAAATACGCCGAAGATTCATCGAACATTAAGTGGA
    TTGATGCTCCAGATTGCTTCTGCTTCCATCTCTGGAACGCTTGGGAAGAGCCAGAAACAGATG
    AAGTCGTCGTGATAGGGTCCTGTATGACTCCACCAGACTCAATTTTCAACGAGTCTGACGAGA
    ATCTCAAGAGTGTCCTGTCTGAAATCCGCCTGAATCTCAAAACCGGTGAATCAACTCGCCGTC
    CGATCATCTCCAACGAAGATCAACAAGTCAACCTCGAAGCAGGGATGGTCAACAGAAACATG
    CTCGGCCGTAAAACCAAATTCGCTTACTTGGCTTTAGCCGAGCCGTGGCCTAAAGTCTCAGGA
    TTCGCTAAAGFFGATCTCACTACTGGAGAAGTTAAGAAACATCTTTACGGCGATAACCGTTAC
    GGAGGAGAGCCTCTGTTTCTCCCCGGAGAAGGAGGAGAGGAAGACGAAGGATACATCCTCTG
    TTTCGTTCACGACGAGAAGACATGGAAATCGGAGTTACAGATAGTTAACGCCGTTAGCTTAGA
    GGTTGAAGCAACGGTTAAACTTCCGTCAAGGGTTCCGTACGGATTTCACGGTACATTCATCGG
    AGCCGATGATTTGGCGAAGCAGGTCGTGTGAGTTCTTATGTGTAAATACGCACAAAATACATA
    TACGTGATGAAGAAGCTTCTAGAAGGAAAAGAGAGAGCGAGATTTACCAGTGGGATGCTCTG
    GATATACGTCCCCGGAATCTGCTCCTCTGTTTTTTTTTTTTTGCTCTGTTTCTTGTTTGTTGTTTC
    TTTTGGGGTGCGGTTTGCTAGTTCCCTTTTTTTTGGGGTCAATCTAGAAATCTGAAAGATTTTG
    AGGGACCAGCTTGTAGCTTTTGGGCTGTAGGGTAGCCTAGCCGTTGGAGCTCAGCTGGTTTCT
    GTTATTCTTTCACTTATTGTTCATCGTAATGAGAAGTATATAAAATATTAAACAACAAAGATAT
    GTTTGTATATGTGCATGAATTAAGGAACATTTTTTTT
    Coding sequence:
    MASFTATAAVSGRWLGGNHTQPPLSSSQSSDLSYCSSLPMASRVTRKLNVSSALHTPPALHFPKQS
    SNSPAIVVKPKAKESNTKQMNLFQRAAAAALDAAEGFLVSHEKLHPLPKTADPSVQIAGNFAPVN
    EQPVRRNLPVVGKLPDSIKGVYVRNGANPLHEPVTGHHFFDGDGMVHAVKFEHGSASYACRFTQ
    TNRFVQERQLGRPVFPKAIGELHGHTGIARLMLFYARAAAGIVDPAHGTGVANAGLVYFNGRLLA
    MSEDDLPYQVQITPNGDLKTVGRFDFDGQLESTMIAHPKVDPESGELFALSYDVVSKPYLKYFRFS
    PDGTKSPDVEIQLDQPTMMHDFAITENFVVVPDQQVVFKLPEMIRGGSPVVYDKNKVARFGILDK
    YAEDSSNIKWIDAPDCFCFHLWNAWEEPETDEVVVIGSCMTPPDSIFNESDENLKSVLSEIRLNLKT
    GESTRRPIISNEDQQVNLEAGMVNRNMLGRKTKFAYLALAEPWPKVSGFAKVDLTTGEVKKHLY
    GDNRYGGEPLFLPGEGGEEDEGYILCFVHDEKTWKSELQIVNAVSLEVEATVKLPSRVPYGFHGTF
    IGADDLAKQVV*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12658348 At_2mM_SA 20000182 +
    12658348 At_Siliques 20000235 −
    12658348 At_Siliques 20000236 −
    12658348 At_Open_Flower 20000264 −
    12658348 At_Open_Flower 20000265 −
    12658348 At_Drought 20000267 +
    12658348 At_100mM_NaCl 20000268 +
    12658348 At_Open_Flower 20000286 −
    12658348 At_Drought 20000436 +
    12658348 At_Drought 20000437 +
    12658348 At_100uM_ABA 20000453 +
    12658348 At_Herbicide_Mutants 20000640 −
    12658348 At_Line_Comparisons 20001195 −
    12658348 At_Far-red-induction 20001247 +
    12658348 At_Line_Comparisons 20001309 −
    12658348 At_Line_Comparisons 20001310 −
    12658348 At_Far-red-induction 20001451 +
    12658348 At_Drought_Soil_Dry 20001554 +
    12658348 At_Drought_Soil_Dry 20001555 +
    12658348 At_Drought_Soil_Dry 20001560 −
    12658348 At_50mM_NH4NO3_L-to-H 20001762 +
    12658348 At_Drought_Reproduction 20001904 +
    12658348 At_Drought_Reproduction 20001905 +
    12658348 At_Drought_Reproduction 20001906 +
    12658348 At_Drought_Reproduction 20001907 +
    12658348 At_Drought_Reproduction 20001908 +
    12658348 At_Drought_Reproduction 20001910 +
    12658348 At_Drought_Reproduction 20001911 +
    12658348 At_Line_Comparisons 20002008 +
    12658348 At_Line_Comparisons 20002010 +
    12658348 At_8deg_Cold 20002105 +
    12658348 At_Drought-Air-Dry 20002253 +
    12658348 At_Drought-Air-Dry 20002255 +
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12658348 At_2mM_SA 20000182 Timepoint (hr) 6
    12658348 At_2mM_SA 20000182 Age (day) 14
    12658348 At_2mM_SA 20000182 Treatment 2mM SA vs. No Treatment
    12658348 At_2mM_SA 20000182 Organism A. thaliana
    12658348 At_2mM_SA 20000182 Tissue Aerial
    12658348 At_2mM_SA 20000182 Plant Line WS
    12658348 At_Siliques 20000235 Age (day) 21
    12658348 At_Siliques 20000235 Tissue 5-10 mm Siliques vs. Whole
    Plant
    12658348 At_Siliques 20000235 Organism A. thaliana
    12658348 At_Siliques 20000235 Plant Line WS
    12658348 At_Siliques 20000236 Age (day) 21
    12658348 At_Siliques 20000236 Tissue >10 mm Siliques vs. Whole
    Plant
    12658348 At_Siliques 20000236 Organism A. thaliana
    12658348 At_Siliques 20000236 Plant Line WS
    12658348 At_Open_Flower 20000264 Age (day) A. thaliana
    12658348 At_Open_Flower 20000264 Organism A. thaliana
    12658348 At_Open_Flower 20000264 Tissue Open Flower vs. Whole Plant
    12658348 At_Open_Flower 20000264 Plant Line WS
    12658348 At_Open_Flower 20000265 Age (day) 21
    12658348 At_Open_Flower 20000265 Organism A. thaliana
    12658348 At_Open_Flower 20000265 Tissue Closed Flower vs. Whole Plant
    12658348 At_Open_Flower 20000265 Plant Line WS
    12658348 At_Drought 20000267 Timepoint (hr) 6
    12658348 At_Drought 20000267 Age (day) 7
    12658348 At_Drought 20000267 Organism A. thaliana
    12658348 At_Drought 20000267 Treatment Drought vs. No Drought
    12658348 At_Drought 20000267 Tissue Whole Plant
    12658348 At_Drought 20000267 Plant Line WS
    12658348 At_100mM_NaCl 20000268 Timepoint (hr) 6
    12658348 At_100mM_NaCl 20000268 Age (day) 14
    12658348 At_100mM_NaCl 20000268 Treatment 100mM NaCl vs. No Treatment
    12658348 At_100mM_NaCl 20000268 Organism A. thaliana
    12658348 At_100mM_NaCl 20000268 Tissue Whole Plant
    12658348 At_100mM_NaCl 20000268 Plant Line WS
    12658348 At_Open_Flower 20000286 Age (day) 21
    12658348 At_Open_Flower 20000286 Organism A. thaliana
    12658348 At_Open_Flower 20000286 Tissue Half Open vs. Whole Plant
    12658348 At_Open_Flower 20000286 Plant Line WS
    12658348 At_Drought 20000436 Age (day) 7
    12658348 At_Drought 20000436 Timepoint (hr) 12
    12658348 At_Drought 20000436 Organism A. thaliana
    12658348 At_Drought 20000436 Treatment Drought vs. No Drought
    12658348 At_Drought 20000436 Tissue Whole Plant
    12658348 At_Drought 20000436 Plant Line WS
    12658348 At_Drought 20000437 Age (day) 8
    12658348 At_Drought 20000437 Timepoint (hr) 24
    12658348 At_Drought 20000437 Organism A. thaliana
    12658348 At_Drought 20000437 Treatment Drought vs. No Drought
    12658348 At_Drought 20000437 Tissue Whole Plant
    12658348 At_Drought 20000437 Plant Line WS
    12658348 At_100uM_ABA 20000453 Age (day) 15
    12658348 At_100uM_ABA 20000453 Timepoint (hr) 24
    12658348 At_100uM_ABA 20000453 Treatment 100uM ABA vs. No Treatment
    12658348 At_100uM_ABA 20000453 Organism A. thaliana
    12658348 At_100uM_ABA 20000453 Tissue Aerial
    12658348 At_100uM_ABA 20000453 Plant Line WS
    12658348 At_Herbicide_Mutants 20000640 Timepoint (hr) 12
    12658348 At_Herbicide_Mutants 20000640 Plant Line 05377RR/BR27173
    12658348 At_Herbicide_Mutants 20000640 Treatment Roundup vs. No Treatment
    12658348 At_Herbicide_Mutants 20000640 Tissue Seedlings
    12658348 At_Line_Comparisons 20001195 Plant Line WBin4-WX14-B vs. WS
    12658348 At_Far-red-induction 20001247 Timepoint (hr) 1
    12658348 At_Far-red-induction 20001247 Age (day) 7
    12658348 At_Far-red-induction 20001247 Organism A. thaliana
    12658348 At_Far-red-induction 20001247 Plant Line Columbia
    12658348 At_Far-red-induction 20001247 Light Far-red vs. White
    12658348 At_Far-red-induction 20001247 Tissue Whole Plant
    12658348 At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS
    12658348 At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS
    12658348 At_Far-red-induction 20001451 Age (day) 8
    12658348 At_Far-red-induction 20001451 Timepoint (hr) 24
    12658348 At_Far-red-induction 20001451 Organism A. thaliana
    12658348 At_Far-red-induction 20001451 Plant Line Columbia
    12658348 At_Far-red-induction 20001451 Light Far-red vs. White
    12658348 At_Far-red-induction 20001451 Tissue Whole Plant
    12658348 At_Drought_Soil_Dry 20001554 Timepoint (day) 7
    12658348 At_Drought_Soil_Dry 20001554 Age (day) 21
    12658348 At_Drought_Soil_Dry 20001554 Organism A. thaliana
    12658348 At_Drought_Soil_Dry 20001554 Treatment Drought vs. No Drought
    12658348 At_Drought_Soil_Dry 20001554 Post Timepoint (hr) None
    12658348 At_Drought_Soil_Dry 20001554 Post-Treatment None
    12658348 At_Drought_Soil_Dry 20001554 Plant Line WS
    12658348 At_Drought_Soil_Dry 20001555 Timepoint (day) 10
    12658348 At_Drought_Soil_Dry 20001555 Age (day) 24
    12658348 At_Drought_Soil_Dry 20001555 Organism A. thaliana
    12658348 At_Drought_Soil_Dry 20001555 Treatment Drought vs. No Drought
    12658348 At_Drought_Soil_Dry 20001555 Post Timepoint (hr) None
    12658348 At_Drought_Soil_Dry 20001555 Post-Treatment None
    12658348 At_Drought_Soil_Dry 20001555 Plant Line WS
    12658348 At_Drought_Soil_Dry 20001560 Timepoint (day) 14
    12658348 At_Drought_Soil_Dry 20001560 Age (day) 28
    12658348 At_Drought_Soil_Dry 20001560 Organism A. thaliana
    12658348 At_Drought_Soil_Dry 20001560 Treatment Drought vs. No Drought
    12658348 At_Drought_Soil_Dry 20001560 Post Timepoint (hr) None
    12658348 At_Drought_Soil_Dry 20001560 Post-Treatment None
    12658348 At_Drought_Soil_Dry 20001560 Plant Line WS
    12658348 At_50mM_NH4NO3_L-to-H 20001762 Timepoint (hr) 6
    12658348 At_50mM_NH4NO3_L-to-H 20001762 Treatment 50mM NH4NO3 vs 100mM
    Mannitol
    12658348 At_50mM_NH4NO3_L-to-H 20001762 Tissue Siliques
    12658348 At_Drought_Reproduction 20001904 Timepoint (day) 7
    12658348 At_Drought_Reproduction 20001904 Age (day) 37
    12658348 At_Drought_Reproduction 20001904 Organism A. thaliana
    12658348 At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought
    12658348 At_Drought_Reproduction 20001904 Tissue Rosettes
    12658348 At_Drought_Reproduction 20001904 Plant Line WS
    12658348 At_Drought_Reproduction 20001905 Timepoint (day) 10
    12658348 At_Drought_Reproduction 20001905 Age (day) 40
    12658348 At_Drought_Reproduction 20001905 Organism A. thaliana
    12658348 At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought
    12658348 At_Drought_Reproduction 20001905 Tissue Rosettes
    12658348 At_Drought_Reproduction 20001905 Plant Line WS
    12658348 At_Drought_Reproduction 20001906 Timepoint (day) 5
    12658348 At_Drought_Reproduction 20001906 Age (day) 35
    12658348 At_Drought_Reproduction 20001906 Organism A. thaliana
    12658348 At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought
    12658348 At_Drought_Reproduction 20001906 Tissue Siliques
    12658348 At_Drought_Reproduction 20001906 Plant Line WS
    12658348 At_Drought_Reproduction 20001907 Timepoint (day) 7
    12658348 At_Drought_Reproduction 20001907 Age (day) 37
    12658348 At_Drought_Reproduction 20001907 Organism A. thaliana
    12658348 At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought
    12658348 At_Drought_Reproduction 20001907 Tissue Siliques
    12658348 At_Drought_Reproduction 20001907 Plant Line WS
    12658348 At_Drought_Reproduction 20001908 Timepoint (day) 10
    12658348 At_Drought_Reproduction 20001908 Age (day) 40
    12658348 At_Drought_Reproduction 20001908 Organism A. thaliana
    12658348 At_Drought_Reproduction 20001908 Treatment Drought vs. No Drought
    12658348 At_Drought_Reproduction 20001908 Tissue Siliques
    12658348 At_Drought_Reproduction 20001908 Plant Line WS
    12658348 At_Drought_Reproduction 20001910 Timepoint (day) 7
    12658348 At_Drought_Reproduction 20001910 Age (day) 37
    12658348 At_Drought_Reproduction 20001910 Organism A. thaliana
    12658348 At_Drought_Reproduction 20001910 Treatment Drought vs. No Drought
    12658348 At_Drought_Reproduction 20001910 Tissue Flowers
    12658348 At_Drought_Reproduction 20001910 Plant Line WS
    12658348 At_Drought_Reproduction 20001911 Timepoint (day) 10
    12658348 At_Drought_Reproduction 20001911 Age (day) 40
    12658348 At_Drought_Reproduction 20001911 Organism A. thaliana
    12658348 At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought
    12658348 At_Drought_Reproduction 20001911 Tissue Flowers
    12658348 At_Drought_Reproduction 20001911 Plant Line WS
    12658348 At_Line_Comparisons 20002008 Plant Line ME03766 vs. WS
    12658348 At_Line_Comparisons 20002010 Plant Line ME02031 vs. WS
    12658348 At_8deg_Cold 20002105 Age (day) 7
    12658348 At_8deg_Cold 20002105 Timepoint (hr) 8
    12658348 At_8deg_Cold 20002105 Temperature (deg C.) 8 vs. 22
    12658348 At_8deg_Cold 20002105 Organism A. thaliana
    12658348 At_8deg_Cold 20002105 Tissue Whole Plant
    12658348 At Bdeg Cold 20002105 Plant Line WS
    12658348 At_Drought-Air-Dry 20002253 Timepoint (hr) 1
    12658348 At_Drought-Air-Dry 20002253 Age (day) 35
    12658348 At_Drought-Air-Dry 20002253 Organism A. thaliana
    12658348 At_Drought-Air-Dry 20002253 Treatment Drought vs. No Drought
    12658348 At_Drought-Air-Dry 20002253 Tissue Roots
    12658348 At_Drought-Air-Dry 20002253 Plant Line WS
    12658348 At_Drought-Air-Dry 20002255 Timepoint (hr) 1
    12658348 At_Drought-Air-Dry 20002255 Age (day) 35
    12658348 At_Drought-Air-Dry 20002255 Organism A. thaliana
    12658348 At_Drought-Air-Dry 20002255 Treatment Drought vs. No Drought
    12658348 At_Drought-Air-Dry 20002255 Tissue Shoots
    12658348 At_Drought-Air-Dry 20002255 Plant Line WS
    Promoter YP0384
    Modulates the gene: Heat shock transcription factor family.
    The GenBank description of the gene: NM_113182 Arabidopsis thaliana heat shock transcription factor
    family (At3g22830) mRNA, complete cds gi|18403537|ref|NM_113182.1|[18403537]
    The promoter sequence:
    5′ataaaaattcacatttgcaaattttattcagtcggaatatatatttgaaacaagttttgaaatccattg
    gacgattaaaattcattgttgagaggataaatatggatttgttcatctgaaccatgtcgttgattagtgat
    tgactaccatgaaaaatatgttatgaaaagtataacaacttttgataaatcacatttattaacaataaatc
    aagacaaaatatgtcaacaataatagtagtagaagatattaattcaaattcatccgtaacaacaaaaaatc
    ataccacaattaagtgtacagaaaaaccttttggatatatttattgtcgcttttcaatgattttcgtgaaa
    aggatatatttgtgtaaaataagaaggatcttgacgggtgtaaaaacatgcacaattcttaatttagacca
    atcagaagacaacacgaacacttctttattataagctattaaacaaaatcttgcctattttgcttagaata
    atatgaagagtgactcatcagggagtggaaaatatctcaggatttgcttttagctctaacatgtcaaacta
    tctagatgccaacaacacaaagtgcaaattcttttaatatgaaaacaacaataatatttctaatagaaaat
    taaaaagggaaataaaatatttttttaaaatatacaaaagaagaaggaatccatcatcaaagttttataaa
    attgtaatataatacaaacttgtttgcttccttgtctctccctctgtctctctcatctctcctatcttctc
    catatatacttcatcttcacacccaaaactccacacaaaatatctctccctctatctgcaaattttccaaa
    gttgcatcctttcaatttccactcctctctaaTATAattcacattttcccactattgctgattcatttttt
    tttgtgaattatttcaaacccacataaaa 3′-TG
    The promoter was cloned from the organism: Arabidopsis thaliana, Columbia ecotype
    Alternative nucleotides:
    Predicted Position (bp) Mismatch Predicted/Experimental
    18 SNP C/−
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Primary Root    H epidermis H trichoblast H atrichoblast
    Observed expression pattern of the promoter-marker vector was in:
    T1 mature: No expression.
    T2 seedling: High expression throughout root epidermal cells.
    Misc. promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No
    Optional Promoter Fragments: 5′UTR region at base pairs 839-999.
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12730108
    cDNA nucleotide sequence:
    ACAAAATATCTCTCCCTCTATCTGCAAATTTTCCAAAGTTGCATCCTTTCAATTTCCACTCCTCT
    CTAATATAATTCACATTTTCCCACTATTGCTGATTCATTTTTTTTTGTGAATTATTTCAAACCCA
    CATAAAAAAATCTTTGTTTAAATTTAAAACCATGGATCCTTCATTTAGGTTCATTAAAGAGGA
    GTTTCCTGCTGGATTCAGTGATTCTCCATCACCACCATCTTCTTCTTCATACCTTTATTCATCTT
    CCATGGCTGAAGCAGCCATAAATGATCCAACAACATTGAGCTATCCACAACCATTAGAAGGTC
    TCCATGAATCAGGGCCACCTCCATTTTTGACAAAGACATATGACTTGGTGGAAGATTCAAGAA
    CCAATCATGTCGTGTCTTGGAGCAAATCCAATAACAGCTTCATTGTCTGGGATCCACAGGCCT
    TTTCTGTAACTCTCCTTGCCAGATTCTTCAAGCACAATAACTTCTCCAGTTTTGTCCGCCAGCTC
    AACACATATGGTTTCAGAAAGGTGAATCCGGATCGGTGGGAGTTTGCAAACGAAGGGTTTCYF
    AGAGGGCAAAAGCATCTCCTCAAGAACATAAGGAGAAGAAAAACAAGTAATAATAGTAATCA
    AATGCAACAACCTCAAAGTTCTGAACAACAATCTCTAGACAATTTTTGCATAGAAGTGGGTAG
    GTACGGTCTAGATGGAGAGATGGACAGCCTAAGGCGAGACAAGCAAGTGTTGATGATGGAGC
    TAGTGAGACTAAGACAGCAACAACAAAGCACCAAAATGTATCTCACATTGATTGAAGAGAAG
    CTCAAGAAGACCGAGTCAAAACAAAAACAAATGATGAGCTTCCTTGCCCGCGCAATGCAGAA
    TCCAGATTTTATTCAGGAGCTAGTAGAGCAGAAGGAAAAGAGGAAAGAGATCGAAGAGGCGA
    TCAGCAAGAAGAGACAAAGACCGATCGATCAAGGAAAAAGAAATGTGGAAGATTATGGTGAT
    GAAAGTGGTTATGGGAATGATGTTGCAGCCTCATCCTCAGCATTGATTGGTATGAGTCAGGAA
    TATACATATGGAAACATGTCTGAATTCGAGATGTCGGAGTTGGACAAAGTTGCTATGCACATT
    CAAGGACTTGGAGATAATTCCAGTGCTAGGGAAGAAGTCTTGAATGTGGAAAAAGGAAATGA
    TGAGGAAGAAGTAGAAGATCAACAACAAGGGTACCATAAGGAGAACAATGAGATTTATGGTG
    AAGGTTTTTGGGAAGATTTGTTAAATGAAGGTCAAAATTFTGATTTTGAAGGAGATCAAGAAA
    ATGTTGATGTGTTAATTCAGCAACTTGGTTATTTGGGTTCTAGTTCACACACTAATTAAGAAGA
    AATTGAAATGATGACTACTTTAAGCATTTGAATCAACTTGTTTCCTATTAGTAATTTGGCTTTG
    TTTCAATCAAGTGAGTCGTGGACTAAC1TTATTGAATTTGGGGGTTAAATCCGTTTCTTATTTTT
    GGAAATAAAATTGCTTTTTGTTT
    Coding sequence:
    MDPSFRFIKEEFPAGFSDSPSPPSSSSYLYSSSMAEAAINDPTTLSYPQPLEGLHESGPPPFLTKTYDL
    VEDSRTNHVVSWSKSNNSFIVWDPQAFSVTLLPRFFKHNNFSSFVRQLNTYGFRKVNPDRWEFAN
    EGFLRGQKHLLKNIRRRKTSNNSNQMQQPQSSEQQSLDNFCIEVGRYGLDGEMDSLRRDKQVLM
    MELVRLRQQQQSTKMYLTLIEEKLKKTESKQKQMMSFLARAMQNPDFIQQLVEQKEKRKEIEEAI
    SKKRQRPIDQGKRNVEDYGDESGYGNDVAASSSALIGMSQEYTYGNMSEFEMSELDKLAMHIQG
    LGDNSSAREEVLNVEKGNDEEEVEDQQQGYHKENNEIYGEGFWEDLLNEGQNFDFEGDQENVDV
    LIQQLGYLGSSSHTN*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12730108 At_Drought 20000267 +
    12730108 At_100mM_NaCl 20000268 +
    12730108 At_Drought 20000288 +
    12730108 At_Drought 20000436 +
    12730108 At_Drought 20000437 +
    12730108 At_Guard_Cells 20000495 −
    12730108 At_Herbicide_Mutants 20000639 −
    12730108 At_Herbicide_Mutants 20000641 −
    12730108 At_Drought_Reproduction 20001904 +
    12730108 At_Drought_Reproduction 20001905 +
    12730108 At_Drought_Reproduction 20001911 +
    12730108 At_Drought-Air-Dry 20002254 +
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12730108 At_Drought 20000267 Timepoint (hr) 6
    12730108 At_Drought 20000267 Age (day) 7
    12730108 At_Drought 20000267 Organism A. thaliana
    12730108 At_Drought 20000267 Treatment Drought vs. No Drought
    12730108 At_Drought 20000267 Tissue Whole Plant
    12730108 At_Drought 20000267 Plant Line WS
    12730108 At_100mM_NaCl 20000268 Timepoint (hr) 6
    12730108 At_100mM_NaCl 20000268 Age (day) 14
    12730108 At_100mM_NaCl 20000268 Treatment 100mM NaCl vs. No Treatment
    12730108 At_100mM_NaCl 20000268 Organism A. thaliana
    12730108 At_100mM_NaCl 20000268 Tissue Whole Plant
    12730108 At_100mM_NaCl 20000268 Plant Line WS
    12730108 At_Drought 20000288 Timepoint (hr) 1
    12730108 At_Drought 20000288 Age (day) 7
    12730108 At_Drought 20000288 Organism A. thaliana
    12730108 At_Drought 20000288 Treatment Drought vs. No Drought
    12730108 At_Drought 20000288 Tissue Whole Plant
    12730108 At_Drought 20000288 Plant Line WS
    12730108 At_Drought 20000436 Age (day) 7
    12730108 At_Drought 20000436 Timepoint (hr) 12
    12730108 At_Drought 20000436 Organism A. thaliana
    12730108 At_Drought 20000436 Treatment Drought vs. No Drought
    12730108 At_Drought 20000436 Tissue Whole Plant
    12730108 At_Drought 20000436 Plant Line WS
    12730108 At_Drought 20000437 Age (day) 8
    12730108 At_Drought 20000437 Timepoint (hr) 24
    12730108 At_Drought 20000437 Organism A. thaliana
    12730108 At_Drought 20000437 Treatment Drought vs. No Drought
    12730108 At_Drought 20000437 Tissue Whole Plant
    12730108 At_Drought 20000437 Plant Line WS
    12730108 At_Guard_Cells 20000495 Harvest Date Aug. 2, 2002
    12730108 At_Guard_Cells 20000495 Organism A. thaliana
    12730108 At_Guard_Cells 20000495 Tissue Guard Cells vs. Leaves
    12730108 At_Herbicide_Mutants 20000639 Timepoint (hr) 4
    12730108 At_Herbicide_Mutants 20000639 Plant Line 05377RR/BR27173
    12730108 At_Herbicide_Mutants 20000639 Treatment Roundup vs. No Treatment
    12730108 At_Herbicide_Mutants 20000639 Tissue Seedlings
    12730108 At_Herbicide_Mutants 20000641 Timepoint (hr) 4
    12730108 At_Herbicide_Mutants 20000641 Plant Line 3950BR/PCJE10000
    12730108 At_Herbicide_Mutants 20000641 Treatment Finale vs. No Treatment
    12730108 At_Herbicide_Mutants 20000641 Tissue Seedlings
    12730108 At_Drought_Reproduction 20001904 Timepoint (day) 7
    12730108 At_Drought_Reproduction 20001904 Age (day) 37
    12730108 At_Drought_Reproduction 20001904 Organism A. thaliana
    12730108 At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought
    12730108 At_Drought_Reproduction 20001904 Tissue Rosettes
    12730108 At_Drought_Reproduction 20001904 Plant Line WS
    12730108 At_Drought_Reproduction 20001905 Timepoint (day) 10
    12730108 At_Drought_Reproduction 20001905 Age (day) 40
    12730108 At_Drought_Reproduction 20001905 Organism A. thaliana
    12730108 At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought
    12730108 At_Drought_Reproduction 20001905 Tissue Rosettes
    12730108 At_Drought_Reproduction 20001905 Plant Line WS
    12730108 At_Drought_Reproduction 20001911 Timepoint (day) 10
    12730108 At_Drought_Reproduction 20001911 Age (day) 40
    12730108 At_Drought_Reproduction 20001911 Organism A. thaliana
    12730108 At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought
    12730108 At_Drought_Reproduction 20001911 Tissue Flowers
    12730108 At_Drought_Reproduction 20001911 Plant Line WS
    12730108 At_Drought-Air-Dry 20002254 Timepoint (hr) 4
    12730108 At_Drought-Air-Dry 20002254 Age (day) 35
    12730108 At_Drought-Air-Dry 20002254 Organism A. thaliana
    12730108 At_Drought-Air-Dry 20002254 Treatment Drought vs. No Drought
    12730108 At_Drought-Air-Dry 20002254 Tissue Roots
    12730108 At_Drought-Air-Dry 20002254 Plant Line WS
    Promoter YP0382
    Modulates the gene: product = “expressed protein”
    The GenBank description of the gene: NM_129727 Arabidopsis thaliana expressed protein (At2g4l640)
    mRNA, complete cds gi|30688728|ref|NM 129727.2|[30688728]
    The promoter sequence:
    5′ttttttaaaattcgttggaacttggaagggattttaaatattattttgttttccttcatttttataggt
    taataattgtcaaagatacaactcgatggaccaaaataaaataataaaattcgtcgaatttggtaaagcaa
    aacggtcgaggatagctaatatttatgcgaaacccgttgtcaaagcagatgttcagcgtcacgcacatgcc
    gcaaaaagaatatacatcaacctcttttgaacttcacgccgttttttaggcccacaataatgctacgtcgt
    cttctgggttcaccctcgttttttttttaaacttctaaccgataaaataaatggtccactatttcttttct
    tctctgtgtattgtcgtcagagatggtttaaaagttgaaccgaactataacgattctcttaaaatctgaaa
    accaaactgaccgattttcttaactgaaaaaaaaaaaaaaaaaaactgaatttaggccaacttgttgtaat
    atcacaaagaaaattctacaatttaattcatttaaaaataaagaaaaatttaggtaacaatttaactaagt
    ggtctatctaaatcttgcaaattctttgactttgaccaaacacaacttaagttgacagccgtctcctctct
    gttgtttccgtgttattaccgaaatatcagaggaaagtccactaaaccccaaatattaaaaatagaaacat
    tactttctttacaaaaggaatctaaattgatccctttcattcgtttcactcgtttcatatagttgtatgta
    tatatgcgtatgcatcaaaaagtctcttTATAtcctcagagtcacccaatcttatctctctctccttcgtc
    ctcaagaaaagtaattctctgtttgtgtagttttctttaccggtgaattttctcttcgttttgtgcttcaa
    acgtcacccaaatcaccaagatcgatcaa 3′-TG
    The promoter was cloned from the organism: Arabidopsis thaliana, Columbia ecotype
    Alternative nucleotides:
    Predicted Position (bp) Mismatch Predicted/Experimental
    484 Sequence resolution a/-
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower H nectary M sepal M vascular
    Primary Root H epidermis H root cap
    Observed expression pattern:
    T1 mature: Expressed in nectary glands of flowers and vasculature of sepals (see Report 129. Table 1.B.).
    T2 seedling: High root epidermal expression through to root cap.
    Misc. promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No
    Optional Promoter Fragments: 5′UTR region at base pairs 842-999.
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12735575
    cDNA nucleotide sequence:
    AGAGTCACCCAATCTTATCTCTCTCTCCTTCGTCCTCAAGAAAAGTAATTCTCTGTTTGTGTAG
    TTTTCTTTACCGGTGAATTTTCTCTTCGTTTTGTGCTTCAAACGTCACCCAAATCACCAAGATC
    GATCAAAATCGAAACTTAACGTTTCAGAAGATGGTGCAGTACCAGAGATTAATCATCCACCAT
    GGAAGAAAAGAAGATAAGTTTAGAGTTTCTTCAGCAGAGGAAAGTGGTGGAGGTGGTTGTTG
    CTACTCCAAGAGAGCTAAACAAAAGTTTCGTTGTCTTCTCTTTCTCTCTATCCTCTCTTGCTGTT
    TCGTCTTGTCTCCTTATTACCTCTTCGGCTTCTCTACTCTCTCCCTCCTAGATTCGTTTCGCAGA
    GAAATCGAAGGTCTTAGCTCTTATGAGCCAGTTATTACCCCTCTGTGCTCAGAAATCTCCAATG
    GAACCATTTGTTGTGACAGAACCGGTTTGAGATCTGATATTTGTGTAATGAAAGGTGATGTTC
    GAACAAACTCTGCTTCTTCCTCAATCTTCCTCTTCACCTCGTCCAGCAATAAGAACACAAAACC
    GGAAAAGATCAAACCTTACACTAGAAAATGGGAGACTAGTGTGATGGACAGCGTTGAAGAAC
    TCAACCTCATCACCAAAGATTCGAACAAATCTTCAGATCGTGTATGCGATGTGTACGATGATG
    TTCCTGCTGTGTTCTTCTCCACTGGTGGATACACCGGTAACGTATACCACGAGTTTAACGACGG
    GATTATCCCTTTGTTTATAACTTCACAGCATTACAACAAAAAAGTTGTGTTTGTGATGGTCGAG
    TATGATGACTGGTGGGAGATGAAGTATGGAGATGTCGTTTCGCAGCTCTCGGATTATCCTCTG
    GTTGATTTCAATGGAGATACGAGAACACATTGTTTCAAAGAAGCAACCGTTGGATTACGTATT
    CACGACGAGTTAACTGTGAATTCTTCTTTGGTCATTGGGAATCAAACCATTGTTGACTTCAGAA
    ACGTTTTGGATAGGGGTTACTCGCATCGTATCCAAAGCTTGACTCAGGAGGAAACAGAGGCGA
    ACGTGACCGCACTCGATTTCAAGAAGAAGCCAAAACTGGTGATTCTTTCAAGAAACGGGTCAT
    CAAGGGCGATATTAAACGAGAATCTTCTCGTGGAGCTAGCAGAGAAAACAGGGTTCAATGTG
    GAGGTTCTAAGACCACAAAAGACAACGGAAATGGCCAAGATTTATCGTTCGTTGAACACGAG
    CGATGTAATGATCGGTGTACATGGAGCAGCAATGACTCATTTCCTTTTCTTGAAACCGAAAAC
    CGTTTTCATTCAGATCATCCCATTAGGGACGGACTGGGCGGCAGAGACATATTATGGAGAACC
    GGCGAAGAAGCTAGGATTGAAGTACGTTGGTTACAAGATTGCGCCGAAAGAGAGCTCTTTGT
    ATGAAGAATATGGGAAAGATGACCCTGTAATCCGAGATCCGGATAGTCTAAACGACAAAGGA
    TGGGAATATACGAAGAAAATCTATCTACAAGGACAGAACGTGAAGCTTGACTTGAGAAGATT
    CAGAGAAACGTTAACTCGTTCGTATGATTTCTCCATTAGAAGGAGATTTAGAGAAGATTACTT
    GTTACATAGAGAAGATTAAGAATCGTGTGATATTTTTTTTGTAAAGTTTTGAATGACAATTAA
    ATTTATTTATTTTAT
    Coding sequence:
    MVQYQRLIIHHGRKEDKFRVSSAEESGGGGCCYSKRAKQKFRCLLFLSILSCCFVLSPYYLFGFSTL
    SLLDSFRREIEGLSSYEPVITPLCSETSNGTICCDRTGLRSDICVMKGDVRTNSASSSIFLFTSSTNNNT
    KPEKIKPYTRKWETSVMDTVQELNLITKDSNKSSDRVCDVYHDVPAVFFSTGGYTGNVYHEFND
    GIIPLFITSQHYNKKVVFVIVEYHDWWEMKYGDVVSQLSDYPLVDFNGDTRTHCFKEATVGLRIH
    DELTVNSSLVIGNQTIVDFRNVLDRGYSHRIQSLTQEETEANVTALDFKKKPKLVILSRNGSSRAIL
    NENLLVELAEKTGFNVEVLRPQKTTEMAKIYRSLNTSDVMIGVHGAAMTHFLFLKPKTVFIQIIPLG
    TDWAAETYYGEPAKKLGLKYVGYKIAPKESSLYEEYGKDDPVIRDPDSLNDKGWEYTKKIYLQG
    QNVKLDLRRFRETLTRSYDFSIRRRFREDYLLHRED*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12735575 At_42deg_Heat 20000171 −
    12735575 At_42deg_Heat 20000173 −
    12735575 At_2mM_SA 20000181 +
    12735575 At_2mM_SA 20000182 +
    12735575 At_Shoots 20000184 −
    12735575 At_Roots 20000185 −
    12735575 At_Siliques 20000234 −
    12735575 At_Siliques 20000235 −
    12735575 At_Siliques 20000236 −
    12735575 At_Open_Flower 20000264 −
    12735575 At_Open_Flower 20000265 −
    12735575 At_100mM_NaCl 20000268 −
    12735575 At_Open_Flower 20000286 −
    12735575 At_Pollen 20000326 −
    12735575 At_Shoots 20000438 −
    12735575 At_1uM_BR-BRZ 20000441 +
    12735575 At_10percent_PEG 20000460 +
    12735575 At_Guard_Cells 20000495 −
    12735575 At_10percent_PEG 20000527 +
    12735575 At_100uM_ABA_Mutants 20000573 −
    12735575 At_100uM_ABA_Mutants 20000574 −
    12735575 At_Herbicide_Mutants 20000640 −
    12735575 At_15mM_NH4NO3_L-to-H 20000709 +
    12735575 At_Line_Comparisons 20001192 −
    12735575 At_Line_Comparisons 20001195 −
    12735575 At_Far-red-induction 20001247 +
    12735575 At_Far-red-induction 20001248 +
    12735575 At_Line_Comparisons 20001308 +
    12735575 At_Interploidy_Crosses 20001316 −
    12735575 At_Line_Comparisons 20001319 −
    12735575 At_Line_Comparisons 20001347 −
    12735575 At_Far-red-induction 20001450 +
    12735575 At_Drought_Soil_Dry 20001557 +
    12735575 At_Interploidy_Crosses 20001653 +
    12735575 At_Interploidy_Crosses 20001654 +
    12735575 At_Interploidy_Crosses 20001703 −
    12735575 At_Interploidy_Crosses 20001704 −
    12735575 At_50mM_NH4NO3_L-to-H 20001757 −
    12735575 At_Interploidy_Crosses 20001853 −
    12735575 At_Drought_Reproduction 20001905 +
    12735575 At_Drought_Reproduction 20001911 +
    12735575 At_Line_Comparisons 20002007 +
    12735575 At_Line_Comparisons 20002008 +
    12735575 At_Line_Comparisons 20002009 +
    12735575 At_Line_Comparisons 20002010 +
    12735575 At_Line_Comparisons 20002012 +
    12735575 At_8deg_Cold 20002103 −
    12735575 At_8deg_Cold 20002105 −
    12735575 At_8deg_Cold 20002108 −
    12735575 At_8deg_Cold 20002109 −
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12735575 At_42deg_Heat 20000171 Timepoint (hr) 1
    12735575 At_42deg_Heat 20000171 Age (day) 14
    12735575 At_42deg_Heat 20000171 Temperature (deg C.) 42 vs. 22
    12735575 At_42deg_Heat 20000171 Organism A. thaliana
    12735575 At_42deg_Heat 20000171 Tissue Aerial
    12735575 At_42deg_Heat 20000171 Plant Line WS
    12735575 At_42deg_Heat 20000173 Timepoint (hr) 6
    12735575 At_42deg_Heat 20000173 Age (day) 14
    12735575 At_42deg_Heat 20000173 Temperature (deg C.) 42 vs. 22
    12735575 At_42deg_Heat 20000173 Organism A. thaliana
    12735575 At_42deg_Heat 20000173 Tissue Aerial
    12735575 At_42deg_Heat 20000173 Plant Line WS
    12735575 At_2mM_SA 20000181 Timepoint (hr) 1
    12735575 At_2mM_SA 20000181 Age (day) 14
    12735575 At_2mM_SA 20000181 Treatment 2mM SA vs. No Treatment
    12735575 At_2mM_SA 20000181 Organism A. thaliana
    12735575 At_2mM_SA 20000181 Tissue Aerial
    12735575 At_2mM_SA 20000181 Plant Line WS
    12735575 At_2mM_SA 20000182 Timepoint (hr) 6
    12735575 At_2mM_SA 20000182 Age (day) 14
    12735575 At_2mM_SA 20000182 Treatment 2mM SA vs. No Treatment
    12735575 At_2mM_SA 20000182 Organism A. thaliana
    12735575 At_2mM_SA 20000182 Tissue Aerial
    12735575 At_2mM_SA 20000182 Plant Line WS
    12735575 At_Shoots 20000184 Age (day) 7 vs. 21
    12735575 At_Shoots 20000184 Organism A. thaliana
    12735575 At_Shoots 20000184 Tissue Shoots vs. Whole Plant
    12735575 At_Shoots 20000184 Plant Line WS
    12735575 At_Roots 20000185 Age (day) 7 vs. 21
    12735575 At_Roots 20000185 Organism A. thaliana
    12735575 At_Roots 20000185 Tissue Roots vs. Whole Plant
    12735575 At_Roots 20000185 Plant Line WS
    12735575 At_Siliques 20000234 Age (day) 21
    12735575 At_Siliques 20000234 Tissue <5 mm Siliques vs. Whole Plant
    12735575 At_Siliques 20000234 Organism A. thaliana
    12735575 At_Siliques 20000234 Plant Line WS
    12735575 At_Siliques 20000235 Age (day) 21
    5-10 mm Siliques vs. Whole
    12735575 At_Siliques 20000235 Tissue Plant
    12735575 At_Siliques 20000235 Organism A. thaliana
    12735575 At_Siliques 20000235 Plant Line WS
    12735575 At_Siliques 20000236 Age (day) 21
    12735575 At_Siliques 20000236 Tissue >10 mm Siliques vs. Whole
    Plant
    12735575 At_Siliques 20000236 Organism A. thaliana
    12735575 At_Siliques 20000236 Plant Line WS
    12735575 At_Open_Flower 20000264 Age (day) 21
    12735575 At_Open_Flower 20000264 Organism A. thaliana
    12735575 At_Open_Flower 20000264 Tissue Open Flower vs. Whole Plant
    12735575 At_Open_Flower 20000264 Plant Line WS
    12735575 At_Open_Flower 20000265 Age (day) 21
    12735575 At_Open_Flower 20000265 Organism A. thaliana
    12735575 At_Open_Flower 20000265 Tissue Closed Flower vs. Whole Plant
    12735575 At_Open_Flower 20000265 Plant Line WS
    12735575 At_100mM_NaCl 20000268 Timepoint (hr) 6
    12735575 At_100mM_NaCl 20000268 Age (day) 14
    12735575 At_100mM_NaCl 20000268 Treatment 100mM NaCl vs. No Treatment
    12735575 At_100mM_NaCl 20000268 Organism A. thaliana
    12735575 At_100mM_NaCl 20000268 Tissue Whole Plant
    12735575 At_100mM_NaCl 20000268 Plant Line WS
    12735575 At_Open_Flower 20000286 Age (day) 21
    12735575 At_Open_Flower 20000286 Organism A. thaliana
    12735575 At_Open_Flower 20000286 Tissue Half Open vs. Whole Plant
    12735575 At_Open_Flower 20000286 Plant Line WS
    12735575 At_Pollen 20000326 Age (day) 0 vs. 21
    12735575 At_Pollen 20000326 Organism A. thaliana
    12735575 At_Pollen 20000326 Tissue Pollen vs. Whole Plant
    12735575 At_Pollen 20000326 Plant Line WS
    12735575 At_Shoots 20000438 Age (day) 14 vs. 21
    12735575 At_Shoots 20000438 Organism A. thaliana
    12735575 At_Shoots 20000438 Tissue Shoots vs. Whole Plant
    12735575 At_Shoots 20000438 Plant Line WS
    12735575 At_1uM_BR-BRZ 20000441 Treatment 1uM BR vs. No Treatment
    12735575 At_1uM_BR-BRZ 20000441 Tissue Shoot Apices
    12735575 At_10percent_PEG 20000460 Age (day) 12
    12735575 At_10percent_PEG 20000460 Timepoint (day) 12
    12735575 At_10percent_PEG 20000460 Treatment 10percent PEG vs. No
    Treatment
    12735575 At_10percent_PEG 20000460 Organism A. thaliana
    12735575 At_10percent_PEG 20000460 Tissue Whole Plant
    12735575 At_10percent_PEG 20000460 Plant Line WS
    12735575 At_Guard_Cells 20000495 Harvest Date Aug. 2, 2002
    12735575 At_Guard_Cells 20000495 Organism A. thaliana
    12735575 At_Guard_Cells 20000495 Tissue Guard Cells vs. Leaves
    12735575 At_10percent_PEG 20000527 Age (day) 20
    12735575 At_10percent_PEG 20000527 Timepoint (day) 20
    12735575 At_10percent_PEG 20000527 Treatment 10percent PEG vs. No
    Treatment
    12735575 At_10percent_PEG 20000527 Organism A. thaliana
    12735575 At_10percent_PEG 20000527 Tissue Whole Plant
    12735575 At_10percent_PEG 20000527 Plant Line WS
    12735575 At_100uM_ABA_Mutants 20000573 Organism A. thaliana
    12735575 At_100uM_ABA_Mutants 20000573 Plant Line CS22 vs. Ler wt
    12735575 At_100uM_ABA_Mutants 20000573 Timepoint (hr) N/A
    12735575 At_100uM_ABA_Mutants 20000573 Treatment None
    12735575 At_100uM_ABA_Mutants 20000573 Tissue Whole Plant
    12735575 At_100uM_ABA_Mutants 20000574 Organism A. thaliana
    12735575 At_100uM_ABA_Mutants 20000574 Plant Line CS23 vs. Ler wt
    12735575 At_100uM_ABA_Mutants 20000574 Timepoint (hr) N/A
    12735575 At_100uM_ABA_Mutants 20000574 Treatment None
    12735575 At_100uM_ABA_Mutants 20000574 Tissue Whole Plant
    12735575 At_Herbicide_Mutants 20000640 Timepoint (hr) 12
    12735575 At_Herbicide_Mutants 20000640 Plant Line 05377RR/BR27173
    12735575 At_Herbicide_Mutants 20000640 Treatment Roundup vs. No Treatment
    12735575 At_Herbicide_Mutants 20000640 Tissue Seedlings
    12735575 At_15mM_NH4NO3_L-to-H 20000709 Timepoint (hr) 4
    12735575 At_15mM_NH4NO3_L-to-H 20000709 Age (hr) 14
    12735575 At_15mM_NH4NO3_L-to-H 20000709 Treatment 15mM NH4NO3 vs. 30mM
    Mannitol
    12735575 At_15mM_NH4NO3_L-to-H 20000709 Organism A. thaliana
    12735575 At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial
    12735575 At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS
    12735575 At_Line_Comparisons 20001192 Plant Line WBin4-WX13R-A vs. WS
    12735575 At_Line_Comparisons 20001195 Plant Line WBin4-WX14-B vs. WS
    12735575 At_Far-red-induction 20001247 Timepoint (hr) 1
    12735575 At_Far-red-induction 20001247 Age (day) 7
    12735575 At_Far-red-induction 20001247 Organism A. thaliana
    12735575 At_Far-red-induction 20001247 Plant Line Columbia
    12735575 At_Far-red-induction 20001247 Light Far-red vs. White
    12735575 At_Far-red-induction 20001247 Tissue Whole Plant
    12735575 At_Far-red-induction 20001248 Timepoint (hr) 4
    12735575 At_Far-red-induction 20001248 Age (day) 7
    12735575 At_Far-red-induction 20001248 Organism A. thaliana
    12735575 At_Far-red-induction 20001248 Plant Line Columbia
    12735575 At_Far-red-induction 20001248 Light Far-red vs. White
    12735575 At_Far-red-induction 20001248 Tissue Whole Plant
    12735575 At_Line_Comparisons 20001308 Plant Line WBin4-WX49-C vs. WS
    12735575 At_Interploidy_Crosses 20001316 Age (day) 5
    12735575 At_Interploidy_Crosses 20001316 Organism A. thaliana
    12735575 At_Interploidy_Crosses 20001316 Plant Line Columbia
    12735575 At_Interploidy_Crosses 20001316 Cross hemi × 2X vs. 2X × 2X
    12735575 At_Interploidy_Crosses 20001316 Tissue Siliques
    12735575 At_Line_Comparisons 20001319 Plant Line WBin4-WX24-A vs. WS
    12735575 At_Line_Comparisons 20001347 Plant Line ME01604-01 vs. WS
    12735575 At_Far-red-induction 20001450 Age (day) 7
    12735575 At_Far-red-induction 20001450 Timepoint (hr) 8
    12735575 At_Far-red-induction 20001450 Organism A. thaliana
    12735575 At_Far-red-induction 20001450 Plant Line Columbia
    12735575 At_Far-red-induction 20001450 Light Far-red vs. White
    12735575 At_Far-red-induction 20001450 Tissue Whole Plant
    12735575 At_Drought_Soil_Dry 20001557 Post Timepoint (hr) 3
    12735575 At_Drought_Soil_Dry 20001557 Timepoint (day) 13
    12735575 At_Drought_Soil_Dry 20001557 Age (day) 27
    12735575 At_Drought_Soil_Dry 20001557 Organism A. thaliana
    12735575 At_Drought_Soil_Dry 20001557 Treatment Drought vs. No Drought
    12735575 At_Drought_Soil_Dry 20001557 Post-Treatment Re-Water vs. No Drought
    12735575 At_Drought_Soil_Dry 20001557 Plant Line WS
    12735575 At_Interploidy_Crosses 20001653 Age (day) 5
    12735575 At_Interploidy_Crosses 20001653 Cross 2X × 6X vs. 2X × 2X
    12735575 At_Interploidy_Crosses 20001653 Organism A. thaliana
    12735575 At_Interploidy_Crosses 20001653 Plant Line Columbia
    12735575 At_Interploidy_Crosses 20001653 Tissue Siliques
    12735575 At_Interploidy_Crosses 20001654 Age (day) 5
    12735575 At_Interploidy_Crosses 20001654 Cross 6X × 2X vs. 2X × 2X
    12735575 At_Interploidy_Crosses 20001654 Organism A. thaliana
    12735575 At_Interploidy_Crosses 20001654 Plant Line Columbia
    12735575 At_Interploidy_Crosses 20001654 Tissue Siliques
    12735575 At_Interploidy_Crosses 20001703 Age (day) 5
    12735575 At_Interploidy_Crosses 20001703 Cross 2X × 4X vs. 2X × 2X
    12735575 At_Interploidy_Crosses 20001703 Organism A. thaliana
    12735575 At_Interploidy_Crosses 20001703 Plant Line Columbia
    12735575 At_Interploidy_Crosses 20001703 Tissue Siliques
    12735575 At_Interploidy_Crosses 20001704 Age (day) 5
    12735575 At_Interploidy_Crosses 20001704 Cross 4X × 2X vs. 2X × 2X
    12735575 At_Interploidy_Crosses 20001704 Organism A. thaliana
    12735575 At_Interploidy_Crosses 20001704 Plant Line Columbia
    12735575 At_Interploidy_Crosses 20001704 Tissue Siliques
    12735575 At_50mM_NH4NO3_L-to-H 20001757 Timepoint (hr) 6
    12735575 At_50mM_NH4NO3_L-to-H 20001757 Treatment 50mM NH4NO3 vs 100mM
    Mannitol
    12735575 At_50mM_NH4NO3_L-to-H 20001757 Tissue Leaf
    12735575 At_Interploidy_Crosses 20001853 Age (day) 5
    12735575 At_Interploidy_Crosses 20001853 Organism A. thaliana
    12735575 At_Interploidy_Crosses 20001853 Plant Line Columbia
    12735575 At_Interploidy_Crosses 20001853 Cross Fis1 vs. 2X × 2X
    12735575 At_Interploidy_Crosses 20001853 Tissue Siliques
    12735575 At_Drought_Reproduction 20001905 Timepoint (day) 10
    12735575 At_Drought_Reproduction 20001905 Age (day) 40
    12735575 At_Drought_Reproduction 20001905 Organism A. thaliana
    12735575 At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought
    12735575 At_Drought_Reproduction 20001905 Tissue Rosettes
    12735575 At_Drought_Reproduction 20001905 Plant Line WS
    12735575 At_Drought_Reproduction 20001911 Timepoint (day) 10
    12735575 At_Drought_Reproduction 20001911 Age (day) 40
    12735575 At_Drought_Reproduction 20001911 Organism A. thaliana
    12735575 At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought
    12735575 At_Drought_Reproduction 20001911 Tissue Flowers
    12735575 At_Drought_Reproduction 20001911 Plant Line WS
    12735575 At_Line_Comparisons 20002007 Plant Line ME03793 vs. WS
    12735575 At_Line_Comparisons 20002008 Plant Line ME03766 vs. WS
    12735575 At_Line_Comparisons 20002009 Plant Line ME01642 vs. WS
    12735575 At_Line_Comparisons 20002010 Plant Line ME02031 vs. WS
    12735575 At_Line_Comparisons 20002012 Plant Line SALK_073455 vs. Columbia
    12735575 At_8deg_Cold 20002103 Timepoint (hr) 2
    12735575 At_8deg_Cold 20002103 Age (day) 7
    12735575 At_8deg_Cold 20002103 Temperature (deg C.) 8 vs. 22
    12735575 At_8deg_Cold 20002103 Organism A. thaliana
    12735575 At_8deg_Cold 20002103 Tissue Whole Plant
    12735575 At_8deg_Cold 20002103 Plant Line WS
    12735575 At_8deg_Cold 20002105 Age (day) 7
    12735575 At_8deg_Cold 20002105 Timepoint (hr) 8
    12735575 At_8deg_Cold 20002105 Temperature (deg C.) 8 vs. 22
    12735575 At_8deg_Cold 20002105 Organism A. thaliana
    12735575 At_8deg_Cold 20002105 Tissue Whole Plant
    12735575 At_8deg_Cold 20002105 Plant Line WS
    12735575 At_8deg_Cold 20002108 Age (day) 14
    12735575 At_8deg_Cold 20002108 Timepoint (hr) 168
    12735575 At_8deg_Cold 20002108 Temperature (deg C.) 8 vs. 22
    12735575 At_8deg_Cold 20002108 Organism A. thaliana
    12735575 At_8deg_Cold 20002108 Tissue Whole Plant
    12735575 At_8deg_Cold 20002108 Plant Line WS
    12735575 At_8deg_Cold 20002109 Age (day) 16
    12735575 At_8deg_Cold 20002109 Timepoint (hr) 216
    12735575 At_8deg_Cold 20002109 Temperature (deg C.) 8 vs. 22
    12735575 At_8deg_Cold 20002109 Organism A. thaliana
    12735575 At_8deg_Cold 20002109 Tissue Whole Plant
    12735575 At_8deg_Cold 20002109 Plant Line WS
    Promoter YP0381
    Modulates the gene: Unknown expressed protein
    The GenBank description of the gene: NM_113878 Arabidopsis thaliana expressed protein (At3g29575)
    mRNA, complete cds gi|30689672|ref|NM_113878.3|[30689672]
    The promoter sequence:
    5′tcattacattgaaaaagaaaattaattgtctttactcatgtttattctatacaaataaaaatatta
    accaaccatcgcactaacaaaatagaaatcttattctaatcacttaattgttgacaattaaatcattg
    aaaaatacacttaaatgtcaaatattcgttttgcatacttttcaatttaaatacatttaaagttcgac
    aagttgcgtttactatcatagaaaactaaatctcctaccaaagcgaaatgaaactactaaagcgacag
    gcaggttacataacctaacaaatctccacgtgtcaattaccaagagaaaaaaagagaagataagcgga
    acacgtggtagcacaaaaaagataatgtgatttaaattaaaaaacaaaaacaaagacacgtgacgacc
    tgacgctgcaacatcccaccttacaacgtaataaccactgaacataagacacgtgtacgatcttgtct
    ttgttttctcgatgaaaaccacgtgggtgctcaaagtccttgggtcagagtcttccatgattccacgt
    gtcgttaatgcaccaaacaagggtactttcggtattttggcttccgcaaattagacaaaacagctttt
    tgtttgattgatttttctcttctctttttccatctaaattctctttgggctcttaatttctttttgag
    tgttcgttcgagatttgtcggagattttttcggtaaatgttgaaattttgtgggatttttttttattt
    ctttattaaacttttttttattgaattTATAaaaagggaaggtcgtcattaatcgaagaaatggaatc
    ttccaaaatttgatattttgctgttttcttgggatttgaattgctctttatcatcaagaatctgttaa
    aatttctaatctaaaatctaagttgagaaaaagagagatctctzaatttaaccggaattaatattctcc
    3′-cATG
    The promoter was cloned from the organism: Arabidopsis thaliana, Columbia ecotype
    Alternative nucleotides:
    Predicted (Columbia)
    Experimental (Columbia)
    Predicted Position (bp) Mismatch Predicted/Experimental+TZ,1/64
    966 Sequence read error -/a+TZ,1/64
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, Columbia ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower L pedicel H nectary L epidermis
    Hypocotyl L vascular
    Primary Root H vascular
    Observed expression pattern:
    T1 mature: High expression in nectary glands of flowers. Low expression in epidermis of pedicles
    developing flowers.
    T2 seedling: GFP expressed in root and hypocotyl vasculature.
    Misc. promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No
    Optional Promoter Fragments: 5′UTR region at base pairs 671-975.
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12736859
    cDNA nucleotide sequence:
    AAATTGTC1TTGGGCTCTTAATTTCTTTTTGAGTGTTCGTTCGAGATTTGTCGGAGATTTTTTCG
    GTAAATGTTGAAATTTTGTGGGATTTTTTTTTATTTGTTTATTAAACTTTTTTTTATTGAATTTA
    TAAAAAGGGAAGGTCGTGATTAATCGAAGAAATGGAATCTTCCAAAATTTGATATTTTGCTGT
    TTTCTTGGGATTTGAATTGCTCTTTATCATCAAGAATCTGTTAAAATTTCTAATCTAAAATCTA
    AGTTGAGAAAAAGAGAGATCTCTAATTTAACCGGAATTAATATTCTCCGACCGAAGTTATTAT
    GTTGCAGGCTCATGTCGAAGAAACAGAGATTGTCTGAAGAAGATGGAGAGGTAGAGATTGAG
    TTAGACTTAGGTCTATCTCTAAATGGAAGATTTGGTGTTGACCCACTTGCGAAAACAAGGCTT
    ATGAGGTCTACGTCGGTTCTTGATTTGGTGGTCAACGATAGGTCAGGGCTGAGTAGGACTTGT
    TCGTTACCCGTGGAGACGGAGGAAGAGTGGAGGAAGAGGAAGGAGTTGCAGAGTTTGAGGAG
    GCTTGAGGCTAAGAGAAAGAGATCAGAGAAGCAGAGGAAACATAAAGCTTGTGGTGGTGAAG
    AGAAGGTTGTGGAAGAAGGATCTATTGGTTCTTCTGGTAGTGGTTCCTCTGGTTTGTCTGAAG
    TTGATACTCTTCTTCCTCCTGTTCAAGCAACAACGAACAAGTCCGTGGAAACAAGCCCTTCAA
    GTGCCCAATCTCAGCCCGAGAATTTGGGCAAAGAAGCGAGCCAAAACATTATAGAGGACATG
    CCATTCGTGTCAACAACAGGCGATGGACCGAACGGGAAAAAGATTAATGGGTTTCTGTATCGG
    TACCGCAAAGGTGAGGAGGTGAGGATTGTCTGTGTGTGTCATGGAAGCTTCCTCTCACCGGCA
    GAATTCGTTAAGCATGCTGGTGGTGGTGACGTTGCACATCCCTTAAAGCACATCGTTGTAAAT
    CCATCTCCCTTCTTGTGACCCTTTGGGTCTCTTTTGAGGGGTTTGTTGTATCGGAACCATGTTA
    CAAATGCTCATTATCTCCGAGGTGTATAAACATAAATTTATCGAACTCGCAATTTTCAGATTTT
    GTACTTAAAAGAATGGTTTCATTCGTTGAGATTAATTTTAGACCTTTTTCTTGTAC
    Coding sequence:
    MSKKQRLSEEDGEVEIELDLGLSLNGRFGVDPLAKTRLMRSTSVLDLVVNDRSGLSRTCSLPVETE
    EEWRKRKELQSLRRLEAKRKRSEKQRKHKACGGEEKVVEEGSIGSSGSGSSGLSEVDTLLPPVQAT
    TNKSVETSPSSAQSQPENLGKEASQNIIEDMPFVSTTGDGPNGKKINGFLYRYRKGEEVRIVCVCH
    GSFLSPAEFVKHAGGGDVAHPLKHIVVNPPSPFL*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12736859 At_100uM_ABA 20000166 +
    12736859 At_100uM_ABA 20000169 +
    12736859 At_Germinating_Seeds 20000179 +
    12736859 At_Germinating_Seeds 20000180 +
    12736859 At_2mM_SA 20000182 +
    12736859 At_Root-Tips-vs-Tops 20000227 +
    12736859 At_Siliques 20000234 −
    12736859 At_Siliques 20000236 −
    12736859 At_Open_Flower 20000264 −
    12736859 At_Open_Flower 20000265 −
    12736859 At_Drought 20000267 +
    12736859 At_100mM_NaCl 20000268 +
    12736859 At_Open_Flower 20000286 −
    12736859 At_Drought 20000436 +
    12736859 At_Drought 20000437 +
    12736859 At_CS6879_Shoots-Roots 20000451 +
    12736859 At_100uM_ABA 20000453 +
    12736859 At_100uM_ABA 20000455 +
    12736859 At_42deg_Heat 20000458 +
    12736859 At_10percent_PEG 20000460 +
    12736859 At_100uM_ABA_Mutants 20000574 −
    12736859 At_C58548_Mutant 20000606 −
    12736859 At_Herbicide_Mutants 20000639 +
    12736859 At_15mM_NH4NO3_L-to-H 20000709 −
    12736859 At_Petals 20000794 −
    12736859 At_Line_Comparisons 20001151 +
    12736859 At_Line_Comparisons 20001184 +
    12736859 At_Far-red-induction 20001247 +
    12736859 At_Far-red-induction 20001248 +
    12736859 At_Line_Comparisons 20001307 +
    12736859 At_Line_Comparisons 20001309 −
    12736859 At_Line_Comparisons 20001310 −
    12736859 At_Line_Comparisons 20001347 +
    12736859 At_Far-red-induction 20001450 +
    12736859 At_Far-red-induction 20001451 +
    12736859 At Far-red-enriched 20001504 +
    12736859 At_Drought Soit Dry 20001553 +
    12736859 At_Drought_Soil_Dry 20001554 +
    12736859 At_Drought_Soil_Dry 20001556 +
    12736859 At_Drought_Soil_Dry 20001559 +
    12736859 At_Interploidy_Crosses 20001654 +
    12736859 At_Far-red-enriched-adult 20001768 +
    12736859 At_Far-red-enriched-adult 20001769 +
    12736859 At_Far-red-enriched-adult 20001770 +
    12736859 At_Far-red-enriched-adult 20001773 +
    12736859 At_Far-red-enriched-adult 20001774 +
    12736859 At_Drought_Reproduction 20001904 +
    12736859 At_Drought_Reproduction 20001906 +
    12736859 At_Drought_Reproduction 20001908 +
    12736859 At_Drought_Reproduction 20001910 +
    12736859 At_8deg_Cold 20002105 +
    12736859 At_8deg_Cold 20002108 −
    12736859 At_Drought-Air-Dry 20002254 +
    12736859 At_Drought-Air-Dry 20002256 +
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12736859 At_100uM_ABA 20000166 Timepoint (hr) 1
    12736859 At_100uM_ABA 20000166 Age (day) 14
    12736859 At_100uM_ABA 20000166 Treatment 100uM ABA vs. No Treatment
    12736859 At_100uM_ABA 20000166 Organism A. thaliana
    12736859 At_100uM_ABA 20000166 Tissue Aerial
    12736859 At_100uM_ABA 20000166 Plant Line WS
    12736859 At_100uM_ABA 20000169 Timepoint (hr) 6
    12736859 At_100uM_ABA 20000169 Age (day) 14
    12736859 At_100uM_ABA 20000169 Treatment 100uM ABA vs. No Treatment
    12736859 At_100uM_ABA 20000169 Organism A. thaliana
    12736859 At_100uM_ABA 20000169 Tissue Aerial
    12736859 At_100uM_ABA 20000169 Plant Line WS
    12736859 At_Germinating_Seeds 20000179 Age (hr) 6 vs. 0
    12736859 At_Germinating_Seeds 20000179 Organism A. thaliana
    12736859 At_Germinating_Seeds 20000179 Tissue Germinating Seeds
    12736859 At_Germinating_Seeds 20000179 Plant Line WS
    12736859 At_Germinating_Seeds 20000180 Age (hr) 24 vs. 0
    12736859 At_Germinating_Seeds 20000180 Organism A. thaliana
    12736859 At_Germinating_Seeds 20000180 Tissue Germinating Seeds
    12736859 At_Germinating_Seeds 20000180 Plant Line WS
    12736859 At_2mM_SA 20000182 Timepoint (hr) 6
    12736859 At_2mM_SA 20000182 Age (day) 14
    12736859 At_2mM_SA 20000182 Treatment 2mM SA vs. No Treatment
    12736859 At_2mM_SA 20000182 Organism A. thaliana
    12736859 At_2mM_SA 20000182 Tissue Aerial
    12736859 At_2mM_SA 20000182 Plant Line WS
    12736859 At_Root-Tips-vs-Tops 20000227 Age (day) 7, 10, 14
    12736859 At_Root-Tips-vs-Tops 20000227 Organism A. thaliana
    12736859 At_Root-Tips-vs-Tops 20000227 Tissue Root Tips vs. Root Tops
    12736859 At_Root-Tips-vs-Tops 20000227 Plant Line WS
    12736859 At_Siliques 20000234 Age (day) 21
    12736859 At_Siliques 20000234 Tissue <5mm Siliques vs. Whole
    Plant
    12736859 At_Siliques 20000234 Organism A. thaliana
    12736859 At_Siliques 20000234 Plant Line WS
    12736859 At_Siliques 20000236 Age (day) 21
    12736859 At_Siliques 20000236 Tissue >10mm Siliques vs. Whole
    Plant
    12736859 At_Siliques 20000236 Organism A. thaliana
    12736859 At_Siliques 20000236 Plant Line WS
    12736859 At_Open_Flower 20000264 Age (day) 21
    12736859 At_Open_Flower 20000264 Organism A. thaliana
    12736859 At_Open_Flower 20000264 Tissue Open Flower vs. Whole Plant
    12736859 At_Open_Flower 20000264 Plant Line WS
    12736859 At_Open_Flower 20000265 Age (day) 21
    12736859 At_Open_Flower 20000265 Organism A. thaliana
    12736859 At_Open_Flower 20000265 Tissue Closed Flower vs. Whole Plant
    12736859 At_Open_Flower 20000265 Plant Line WS
    12736859 At_Drought 20000267 Timepoint (hr) 6
    12736859 At_Drought 20000267 Age (day) 7
    12736859 At_Drought 20000267 Organism A. thaliana
    12736859 At_Drought 20000267 Treatment Drought vs. No Drought
    12736859 At_Drought 20000267 Tissue Whole Plant
    12736859 At_Drought 20000267 Plant Line WS
    12736859 At_100mM_NaCl 20000268 Timepoint (hr) 6
    12736859 At_100mM_NaCl 20000268 Age (day) 14
    12736859 At_100mM_NaCl 20000268 Treatment 100mM NaCl vs. No Treatment
    12736859 At_100mM_NaCl 20000268 Organism A. thaliana
    12736859 At_100mM_NaCl 20000268 Tissue Whole Plant
    12736859 At_100mM_NaCl 20000268 Plant Line WS
    12736859 At_Open_Flower 20000286 Age (day) 21
    12736859 At_Open_Flower 20000286 Organism A. thaliana
    12736859 At_Open_Flower 20000286 Tissue Half Open vs. Whole Plant
    12736859 At_Open_Flower 20000286 Plant Line WS
    12736859 At_Drought 20000436 Age (day) 7
    12736859 At_Drought 20000436 Timepoint (hr) 12
    12736859 At_Drought 20000436 Organism A. thaliana
    12736859 At_Drought 20000436 Treatment Drought vs. No Drought
    12736859 At_Drought 20000436 Tissue Whole Plant
    12736859 At_Drought 20000436 Plant Line WS
    12736859 At_Drought 20000437 Age (day) 8
    12736859 At_Drought 20000437 Timepoint (hr) 24
    12736859 At_Drought 20000437 Organism A. thaliana
    12736859 At_Drought 20000437 Treatment Drought vs. No Drought
    12736859 At_Drought 20000437 Tissue Whole Plant
    12736859 At_Drought 20000437 Plant Line WS
    12736859 At_CS6879_Shoots-Roots 20000451 Age (day) 14
    12736859 At_CS6879_Shoots-Roots 20000451 Organism A. thaliana
    12736859 At_CS6879_Shoots-Roots 20000451 Plant Line CS6879 vs. WS
    12736859 At_CS6879_Shoots-Roots 20000451 Tissue Roots
    12736859 At_100uM_ABA 20000453 Age (day) 15
    12736859 At_100uM_ABA 20000453 Timepoint (hr) 24
    12736859 At_100uM_ABA 20000453 Treatment 100uM ABA vs. No Treatment
    12736859 At_100uM_ABA 20000453 Organism A. thaliana
    12736859 At_100uM_ABA 20000453 Tissue Aerial
    12736859 At_100uM_ABA 20000453 Plant Line WS
    12736859 At_100uM_ABA 20000455 Age (day) 16
    12736859 At_100uM_ABA 20000455 Timepoint (hr) 48
    12736859 At_100uM_ABA 20000455 Treatment 100uM ABA vs. No Treatment
    12736859 At_100uM_ABA 20000455 Organism A. thaliana
    12736859 At_100uM_ABA 20000455 Tissue Aerial
    12736859 At_100uM_ABA 20000455 Plant Line WS
    12736859 At_42deg_Heat 20000458 Timepoint (hr) 8
    12736859 At_42deg_Heat 20000458 Age (day) 14
    12736859 At_42deg_Heat 20000458 Temperature (deg C.) 42 vs. 22
    12736859 At_42deg_Heat 20000458 Organism A. thaliana
    12736859 At_42deg_Heat 20000458 Tissue Aerial
    12736859 At_42deg_Heat 20000458 Plant Line WS
    12736859 At_10percent_PEG 20000460 Age (day) 12
    12736859 At_10percent_PEG 20000460 Timepoint (day) 12
    12736859 At_10percent_PEG 20000460 Treatment 10percent PEG vs. No
    Treatment
    12736859 At_10percent_PEG 20000460 Organism A. thaliana
    12736859 At_10percent_PEG 20000460 Tissue Whole Plant
    12736859 At_10percent_PEG 20000460 Plant Line WS
    12736859 At_100uM_ABA Mutants 20000574 Organism A. thaliana
    12736859 At_100uM_ABA_Mutants 20000574 Plant Line CS23 vs. Ler wt
    12736859 At_100uM_ABA_Mutants 20000574 Timepoint (hr) N/A
    12736859 At_100uM_ABA_Mutants 20000574 Treatment None
    12736859 At_100uM_ABA_Mutants 20000574 Tissue Whole Plant
    12736859 At_CS8548_Mutant 20000606 Age (day) 14
    12736859 At_CS8548_Mutant 20000606 Plant Line CS8548 vs. wt
    12736859 At_CS8548_Mutant 20000606 Tissue Whole Plant
    12736859 At_Herbicide_Mutants 20000639 Timepoint (hr) 4
    12736859 At_Herbicide_Mutants 20000639 Plant Line 05377RR/BR27173
    12736859 At_Herbicide_Mutants 20000639 Treatment Roundup vs. No Treatment
    12736859 At_Herbicide_Mutants 20000639 Tissue Seedlings
    12736859 At_15mM_NH4NO3_L-to-H 20000709 Timepoint (hr) 4
    12736859 At_15mM_NH4NO3_L-to-H 20000709 Age (hr) 14
    12736859 At_15mM_NH4NO3_L-to-H 20000709 Treatment 15mM NH4NO3 vs. 30mM
    Mannitol
    12736859 At_15mM_NH4NO3_L-to-H 20000709 Organism A. thaliana
    12736859 At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial
    12736859 At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS
    12736859 At_Petals 20000794 Age (day) 23-25 days
    12736859 At_Petals 20000794 Organism A. thaliana
    12736859 At_Petals 20000794 Tissue Petals vs. Whole plant
    12736859 At_Petals 20000794 Plant Line WS
    12736859 At_Line_Comparisons 20001151 Plant Line ME01339-01 vs. WS
    12736859 At_Line_Comparisons 20001184 Plant Line ME01848-01 vs. WS
    12736859 At_Far-red-induction 20001247 Timepoint (hr) 1
    12736859 At_Far-red-induction 20001247 Age (day) 7
    12736859 At_Far-red-induction 20001247 Organism A. thaliana
    12736859 At_Far-red-induction 20001247 Plant Line Columbia
    12736859 At_Far-red-induction 20001247 Light Far-red vs. White
    12736859 At_Far-red-induction 20001247 Tissue Whole Plant
    12736859 At_Far-red-induction 20001248 Timepoint (hr) 4
    12736859 At_Far-red-induction 20001248 Age (day) 7
    12736859 At_Far-red-induction 20001248 Organism A. thaliana
    12736859 At_Far-red-induction 20001248 Plant Line Columbia
    12736859 At_Far-red-induction 20001248 Light Far-red vs. White
    12736859 At_Far-red-induction 20001248 Tissue Whole Plant
    12736859 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS
    12736859 At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS
    12736859 At_Line_Comparisons 20001310 Plant Line WBin4-WX1 7-A vs. WS
    12736859 At_Line_Comparisons 20001347 Plant Line ME01604-01 vs. WS
    12736859 At_Far-red-induction 20001450 Age (day) 7
    12736859 At_Far-red-induction 20001450 Timepoint (hr) 8
    12736859 At_Far-red-induction 20001450 Organism A. thaliana
    12736859 At_Far-red-induction 20001450 Plant Line Columbia
    12736859 At_Far-red-induction 20001450 Light Far-red vs. White
    12736859 At_Far-red-induction 20001450 Tissue Whole Plant
    12736859 At_Far-red-induction 20001451 Age (day) 8
    12736859 At_Far-red-induction 20001451 Timepoint (hr) 24
    12736859 At_Far-red-induction 20001451 Organism A. thaliana
    12736859 At_Far-red-induction 20001451 Plant Line Columbia
    12736859 At_Far-red-induction 20001451 Light Far-red vs. White
    12736859 At_Far-red-induction 20001451 Tissue Whole Plant
    12736859 At_Far-red-enriched 20001504 Timepoint (day) 6
    12736859 At_Far-red-enriched 20001504 Age (day) 10
    12736859 At_Far-red-enriched 20001504 Organism A. thaliana
    12736859 At_Far-red-enriched 20001504 Plant Line Columbia
    12736859 At_Far-red-enriched 20001504 Light Far-red enriched vs. White
    12736859 At_Far-red-enriched 20001504 Tissue Whole Plant
    12736859 At_Drought_Soil_Dry 20001553 Timepoint (day) 5
    12736859 At_Drought_Soil_Dry 20001553 Age (day) 19
    12736859 At_Drought_Soil_Dry 20001553 Organism A. thaliana
    12736859 At_Drought_Soil_Dry 20001553 Treatment Drought vs. No Drought
    12736859 At_Drought_Soil_Dry 20001553 Post Timepoint (hr) None
    12736859 At_Drought_Soil_Dry 20001553 Post-Treatment None
    12736859 At_Drought_Soil_Dry 20001553 Plant Line WS
    12736859 At_Drought_Soil_Dry 20001554 Timepoint (day) 7
    12736859 At_Drought_Soil_Dry 20001554 Age (day) 21
    12736859 At_Drought_Soil_Dry 20001554 Organism A. thaliana
    12736859 At_Drought_Soil_Dry 20001554 Treatment Drought vs. No Drought
    12736859 At_Drought_Soil_Dry 20001554 Post Timepoint (hr) None
    12736859 At_Drought_Soil_Dry 20001554 Post-Treatment None
    12736859 At_Drought_Soil_Dry 20001554 Plant Line WS
    12736859 At_Drought_Soil_Dry 20001556 Timepoint (day) 12
    12736859 At_Drought_Soil_Dry 20001556 Age (day) 26
    12736859 At_Drought_Soil_Dry 20001556 Organism A. thaliana
    12736859 At_Drought_Soil_Dry 20001556 Treatment Drought vs. No Drought
    12736859 At_Drought_Soil_Dry 20001556 Post Timepoint (hr) None
    12736859 At_Drought_Soil_Dry 20001556 Post-Treatment None
    12736859 At_Drought_Soil_Dry 20001556 Plant Line WS
    12736859 At_Drought_Soil_Dry 20001559 Timepoint (day) 14
    12736859 At_Drought_Soil_Dry 20001559 Age (day) 28
    12736859 At_Drought_Soil_Dry 20001559 Post Timepoint (hr) 29
    12736859 At_Drought_Soil_Dry 20001559 Organism A. thaliana
    12736859 At_Drought_Soil_Dry 20001559 Treatment Drought vs. No Drought
    12736859 At_Drought_Soil_Dry 20001559 Post-Treatment Re-Water vs. No Drought
    12736859 At_Drought_Soil_Dry 20001559 Plant Line WS
    12736859 At_Interploidy_Crosses 20001654 Age (day) 5
    12736859 At_Interploidy_Crosses 20001654 Cross 6X × 2X vs. 2X × 2X
    12736859 At_Interploidy_Crosses 20001654 Organism A. thaliana
    12736859 At_Interploidy_Crosses 20001654 Plant Line Columbia
    12736859 At_Interploidy_Crosses 20001654 Tissue Siliques
    12736859 At_Far-red-enriched-adult 20001768 Timepoint (hr) 1
    12736859 At_Far-red-enriched-adult 20001768 Age (day) 28
    12736859 At_Far-red-enriched-adult 20001768 Organism A. thaliana
    12736859 At_Far-red-enriched-adult 20001768 Tissue Aerial
    12736859 At_Far-red-enriched-adult 20001768 Plant Line Columbia
    12736859 At_Far-red-enriched-adult 20001768 Light Far-red enriched vs. White
    12736859 At_Far-red-enriched-adult 20001769 Timepoint (hr) 4
    12736859 At_Far-red-enriched-adult 20001769 Age (day) 28
    12736859 At_Far-red-enriched-adult 20001769 Organism A. thaliana
    12736859 At_Far-red-enriched-adult 20001769 Tissue Aerial
    12736859 At_Far-red-enriched-adult 20001769 Plant Line Columbia
    12736859 At_Far-red-enriched-adult 20001769 Light Far-red enriched vs. White
    12736859 At_Far-red-enriched-adult 20001770 Timepoint (hr) 8
    12736859 At_Far-red-enriched-adult 20001770 Age (day) 28
    12736859 At_Far-red-enriched-adult 20001770 Organism A. thaliana
    12736859 At_Far-red-enriched-adult 20001770 Tissue Aerial
    12736859 At_Far-red-enriched-adult 20001770 Plant Line Columbia
    12736859 At_Far-red-enriched-adult 20001770 Light Far-red enriched vs. White
    12736859 At_Far-red-enriched-adult 20001773 Age (day) 30
    12736859 At_Far-red-enriched-adult 20001773 Timepoint (hr) 48
    12736859 At_Far-red-enriched-adult 20001773 Organism A. thaliana
    12736859 At_Far-red-enriched-adult 20001773 Tissue Aerial
    12736859 At_Far-red-enriched-adult 20001773 Plant Line Columbia
    12736859 At_Far-red-enriched-adult 20001773 Light Far-red enriched vs. White
    12736859 At_Far-red-enriched-adult 20001774 Age (day) 31
    12736859 At_Far-red-enriched-adult 20001774 Timepoint (hr) 72
    12736859 At_Far-red-enriched-adult 20001774 Organism A. thaliana
    12736859 At_Far-red-enriched-adult 20001774 Tissue Aerial
    12736859 At_Far-red-enriched-adult 20001774 Plant Line Columbia
    12736859 At_Far-red-enriched-adult 20001774 Light Far-red enriched vs. White
    12736859 At_Drought_Reproduction 20001904 Timepoint (day) 7
    12736859 At_Drought_Reproduction 20001904 Age (day) 37
    12736859 At_Drought_Reproduction 20001904 Organism A. thaliana
    12736859 At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought
    12736859 At_Drought_Reproduction 20001904 Tissue Rosettes
    12736859 At_Drought_Reproduction 20001904 Plant Line WS
    12736859 At_Drought_Reproduction 20001906 Timepoint (day) 5
    12736859 At_Drought_Reproduction 20001906 Age (day) 35
    12736859 At_Drought_Reproduction 20001906 Organism A. thaliana
    12736859 At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought
    12736859 At_Drought_Reproduction 20001906 Tissue Siliques
    12736859 At_Drought_Reproduction 20001906 Plant Line WS
    12736859 At_Drought_Reproduction 20001908 Timepoint (day) 10
    12736859 At_Drought_Reproduction 20001908 Age (day) 40
    12736859 At_Drought_Reproduction 20001908 Organism A. thaliana
    12736859 At_Drought_Reproduction 20001908 Treatment Drought vs. No Drought
    12736859 At_Drought_Reproduction 20001908 Tissue Siliques
    12736859 At_Drought_Reproduction 20001908 Plant Line WS
    12736859 At_Drought_Reproduction 20001910 Timepoint (day) 7
    12736859 At_Drought_Reproduction 20001910 Age (day) 37
    12736859 At_Drought_Reproduction 20001910 Organism A. thaliana
    12736859 At_Drought_Reproduction 20001910 Treatment Drought vs. No Drought
    12736859 At_Drought_Reproduction 20001910 Tissue Flowers
    12736859 At_Drought_Reproduction 20001910 Plant Line WS
    12736859 At_8deg_Cold 20002105 Age (day) 7
    12736859 At_8deg_Cold 20002105 Timepoint (hr) 8
    12736859 At_8deg_Cold 20002105 Temperature (deg C.) 8 vs. 22
    12736859 At_8deg_Cold 20002105 Organism A. thaliana
    12736859 At_8deg_Cold 20002105 Tissue Whole Plant
    12736859 At_8deg_Cold 20002105 Plant Line WS
    12736859 At_8deg_Cold 20002108 Age (day) 14
    12736859 At_8deg_Cold 20002108 Timepoint (hr) 168
    12736859 At_8deg_Cold 20002108 Temperature (deg C.) 8 vs. 22
    12736859 At_8deg_Cold 20002108 Organism A. thaliana
    12736859 At_8deg_Cold 20002108 Tissue Whole Plant
    12736859 At_8deg_Cold 20002108 Plant Line WS
    12736859 At_Drought-Air-Dry 20002254 Timepoint (hr) 4
    12736859 At_Drought-Air-Dry 20002254 Age (day) 35
    12736859 At_Drought-Air-Dry 20002254 Organism A. thaliana
    12736859 At_Drought-Air-Dry 20002254 Treatment Drought vs. No Drought
    12736859 At_Drought-Air-Dry 20002254 Tissue Roots
    12736859 At_Drought-Air-Dry 20002254 Plant Line WS
    12736859 At_Drought-Air-Dry 20002256 Timepoint (hr) 4
    12736859 At_Drought-Air-Dry 20002256 Age (day) 35
    12736859 At_Drought-Air-Dry 20002256 Organism A. thaliana
    12736859 At_Drought-Air-Dry 20002256 Treatment Drought vs. No Drought
    12736859 At_Drought-Air-Dry 20002256 Tissue Shoots
    12736859 At_Drought-Air-Dry 20002256 Plant Line WS
    Promoter YP0380
    Modulates the gene: Responsive to Dehydration 20
    The GenBank description of the gene: : NM_128898 Arabidopsis thaliana RD20 protein (At2g33380)
    mRNA, complete cds gi|30685670|ref|NM_128898.2|[30685670]
    The promoter sequence:
    5′tttcaatgtatacaatcatcatgtgataaaaaaaaaaatgtaaccaatcaacacactgagatacggcca
    aaaaatggtaatacataaatgtttgtaggttttgtaatttaaatactttagttaagttatgattttattat
    ttttgcttatcacttatacgaaatcatcaatctattggtatctcttaatcccgctttttaatttccaccgc
    acacgcaaatcagcaaatggttccagccacgtgcatgtgaccacatattgtggtcacagtactcgtccttt
    ttttttcttttgtaatcaataaatttcaatcctaaaacttcacacattgagcacgtcggcaacgttagctc
    ctaaatcataacgagcaaaaaagttcaaattagggtatatgatcaattgatcatcactacatgtctacata
    attaatatgtattcaaccggtcggtttgttgatactcatagttaagtatatatgtgctaattagaattagg
    atgaatcagttcttgcaaacaactacggtttcatataatatgggagtgttatgtacaaaatgaaagaggat
    ggatcattctgagatgttatgggctcccagtcaatcatgttttgctcgcatatgctatcttttgagtctct
    tcctaaactcatagaataagcacgttggttttttccaccgtcctcctcgtgaacaaaagtacaattacatt
    ttagcaaattgaaaataaccacgtggatggaccatattatatgtgatcatattgcttgtcgtcttcgtttt
    cttttaaatgtttacaccactacttcctgacacgtgtccctattcacatcatccttgttatatcgttttac
    tTATAaaggatcacgaacaccaaaacatcaatgtgtacgtcttttgcataagaagaaacagagagcattat
    caattattaacaattacacaagacagcga 3′-aATG
    The promoter was cloned from the organism: Arabidopsis thaliana, Columbia ecotype
    Alternative nucleotides:
    Predicted Position (bp) Mismatch Predicted/Experimental
     5 PCR error or ecotype variant SNP g/- correct is -/-
    17 PCR error or ecotype variant SNP c/- correct is -/-
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower H pedicel H receptacle H sepal H petal H filament H anther H carpel
    H stigma Hepidermis Hstomata H silique H style
    Silique H stigma H style H carpet H septum H placentae H epidermis
    Stem L epidermis L cortex H stomata
    Leaf H mesophyll H stomata
    Hypocotyl H epidermis H stomata
    Cotyledon H mesophyll H epidermis
    Rosette Leaf H mesophyll H epidermis
    Primary Root H epidermis
    Observed expression pattern
    T1 mature: High expression throughout floral organs. High expression in stem guard cells and cortex cells
    surrounding stomal chamber (see Table 1 FIG. P). Not expressed in shoot apical meristem, early flower
    primordia, pollen and ovules.
    T2 seedling: Expressed in all tissues near seedling apex increasing toward root. High root epidermis
    expression.
    Optional Promoter Fragments: 5′ UTR region at base pairs 905-1000.
    Misc. promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12462179
    cDNA nucleotide sequence:
    AATGTGTACGTCTTTTGCATAAGAAGAAACAGAGAGCATTATGAATTATTAACAATTACACAA
    GACAGCGAGATTGTAAAAGAGTAAGAGAGAGAGAATGGCAGGAGAGGCAGAGGCTTTGGCC
    ACGACGGCACCGTTAGCTCCGGTCACCAGTCAGCGAAAAGTACGGAACGATTTGGAGGAAAC
    ATTACCAAAACCATACATGGCAAGAGCATTAGCAGCTGCAGATACAGAGCATCCGAATGGAA
    CAGAAGGTCACGATAGCAAAGGAATGAGTGTTATGCAACAACATGTTGCTTTCTTCGACCAAA
    ACGACGATGGAATCGTCTATCCTTGGGAGACTTATAAGGGATTTCGTGACCTTGGTTTCAACC
    CAATTTCCTCTATCTTTTGGAGCTTACTCATAAACTTAGCGTTCAGCTACGTTACACTTGCGAG
    TTGGGTGCCATCACCATTATTGCCGGTTTATATCGACAACATACACAAAGCCAAGCATGGGAG
    TGATTCGAGCACCTATGACACCGAAGGAAGGTATGTCCCAGTTAACCTCGAGAACATATTTAG
    CAAATACGCGCTAACGGTTAAAGATAAGTTATCATTTAAAGAGGTTTGGAATGTAACCGAGGG
    AAATGGAATGGCAATCGATCCTTTTGGATGGCTTTCAAACAAAGTTGAATGGATACTACTCTA
    TATTCTTGCTAAGGACGAAGATGGTTTCCTATCTAAAGAAGCTGTGAGAGGTTGCTTTGATGG
    AAGTTTATTTGAACAAATTGCCAAAGAGAGGGCCAATTCTCGCAAACAAGACTAAGAATGTGT
    GTGTTTGGTTAGGGAATAAAGCTTTTTGAAGAAAAGCATTGTGTAATTTAGCTTGTTTCGTCTT
    GTTATTCAGTTTGGGGATTTGTATAATTAATGTGTTTGTAAACTATGTTTCAAAGTTATATAAA
    TAAGAGAAGATGTTACAAAAAAAAAAAAAAGACTAATAAGAAGAATTTGGT
    Coding sequence:
    MAGEAEALATTAPLAPVTSQRKVRNDLEETLPKPYMARALAAPDTEHPNGTEGHDSKGMSVMQ
    QHVAFFDQNDDGIVYPWETYKGFRDLGFNPISSIFWTLLINLAFSYVTLPSWVPSPLLPVYIDNIHK
    AKHGSDSSTYDTEGRYVPVNLENIFSKYALTVKDKLSFKEVWNVTEGNRMAIDPFGWLSNKVEWI
    LLYILAKDEDGFLSKEAVRGCFDGSLFEQIAKERANSRKQD*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12462179 At_100uM_ABA 20000166 +
    12462179 At_100uM_ABA 20000169 +
    12462179 At_2mM_SA 20000182 +
    12462179 At_Shoots 20000184 −
    12462179 At_Roots 20000185 −
    12462179 At_0.001percent_MeJA 20000211 +
    12462179 At_Open_Flower 20000264 +
    12462179 At_Open_Flower 20000265 +
    12462179 At_100mM_NaCl 20000268 +
    12462179 At_100mM_NaCl 20000308 +
    12462179 At_Pollen 20000326 −
    12462179 At_Drought 20000436 +
    12462179 At_Drought 20000437 +
    12462179 At_Shoots 20000438 −
    12462179 At_Roots 20000439 −
    12462179 At_100uM_NAA 20000445 +
    12462179 At_100uM_ABA 20000453 +
    12462179 At_100uM_ABA 20000455 +
    12462179 At_42deg_Heat 20000458 +
    12462179 At_Wounding 20000506 +
    12462179 At_100uM_ABA_Mutants 20000575 +
    12462179 At_100uM_ABA_Mutants 20000576 +
    12462179 At_Herbicide_Mutants 20000640 −
    12462179 At_Herbicide_Mutants 20000642 −
    12462179 At_15mM_NH4NO3_L-to-H 20000709 −
    12462179 At_Petals 20000794 +
    12462179 At_Line_Comparisons 20001151 +
    12462179 At_Line_Comparisons 20001184 +
    12462179 At_Far-red-induction 20001248 −
    12462179 At_Line_Comparisons 20001307 +
    12462179 At_Line_Comparisons 20001310 −
    12462179 At_Interploidy_Crosses 20001316 −
    12462179 At_Line_Comparisons 20001319 +
    12462179 At_Line_Comparisons 20001347 +
    12462179 At_Far-red-induction 20001451 +
    12462179 At_Far-red-enriched 20001504 +
    12462179 At_Drought_Soil_Dry 20001553 +
    12462179 At_Drought_Soil_Dry 20001554 +
    12462179 At_Drought_Soil_Dry 20001555 +
    12462179 At_Drought_Soil_Dry 20001556 +
    12462179 At_Drought_Soil_Dry 20001559 +
    12462179 At_Interploidy_Crosses 20001654 +
    12462179 At_50mM_NH4NO3_L-to-H 20001757 −
    12462179 At_Far-red-enriched-adult 20001768 +
    12462179 At_Far-red-enriched-adult 20001770 +
    12462179 At_Far-red-enriched-adult 20001771 +
    12462179 At_Far-red-enriched-adult 20001774 +
    12462179 At_Drought_Reproduction 20001904 +
    12462179 At_Drought_Reproduction 20001905 +
    12462179 At_Drought_Reproduction 20001906 +
    12462179 At_Drought_Reproduction 20001908 +
    12462179 At_Drought_Reproduction 20001910 +
    12462179 At_Drought_Reproduction 20001911 +
    12462179 At_8deg_Cold 20002107 −
    12462179 At_8deg_Cold 20002108 −
    12462179 At_8deg_Cold 20002109 −
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12462179 At-100uM_ABA 20000166 Timepoint (hr) 1
    12462179 At_100uM_ABA 20000166 Age (day) 14
    12462179 At_100uM_ABA 20000166 Treatment 100uM ABA vs. No Treatment
    12462179 At_100uM_ABA 20000166 Organism A. thaliana
    12462179 At_100uM_ABA 20000166 Tissue Aerial
    12462179 At_100uM_ABA 20000166 Plant Line WS
    12462179 At_100uM_ABA 20000169 Timepoint (hr) 6
    12462179 At_100uM_ABA 20000169 Age (day) 14
    12462179 At_100uM_ABA 20000169 Treatment 100uM ABA vs. No Treatment
    12462179 At_100uM_ABA 20000169 Organism A. thaliana
    12462179 At_100uM_ABA 20000169 Tissue Aerial
    12462179 At_100uM_ABA 20000169 Plant Line WS
    12462179 At_2mM_SA 20000182 Timepoint (hr) 6
    12462179 At_2mM_SA 20000182 Age (day) 14
    12462179 At_2mM_SA 20000182 Treatment 2mM SA vs. No Treatment
    12462179 At_2mM_SA 20000182 Organism A. thaliana
    12462179 At_2mM_SA 20000182 Tissue Aerial
    12462179 At_2mM_SA 20000182 Plant Line WS
    12462179 At_Shoots 20000184 Age (day) 7 vs. 21
    12462179 At_Shoots 20000184 Organism A. thaliana
    12462179 At_Shoots 20000184 Tissue Shoots vs. Whole Plant
    12462179 At_Shoots 20000184 Plant Line WS
    12462179 At_Roots 20000185 Age (day) 7 vs. 21
    12462179 At_Roots 20000185 Organism A. thaliana
    12462179 At_Roots 20000186 Tissue Roots vs. Whole Plant
    12462179 At_Roots 20000185 Plant Line WS
    12462179 At_0.001percent_MeJA 20000211 Timepoint (hr) 1
    12462179 At_0.001percent_MeJA 20000211 Age (day) 14
    12462179 At_0.001percent_MeJA 20000211 Treatment 0.001percent MeJA vs. No
    Treatment
    12462179 At_0.001percent_MeJA 20000211 Organism A. thaliana
    12462179 At_0.001percent_MeJA 20000211 Tissue Aerial
    12462179 At_0.001percent_MeJA 20000211 Plant Line WS
    12462179 At_Open_Flower 20000264 Age (day) 21
    12462179 At_Open_Flower 20000264 Organism A. thaliana
    12462179 At_Open_Flower 20000264 Tissue Open Flower vs. Whole Plant
    12462179 At_Open_Flower 20000264 Plant Line WS
    12462179 At_Open_Flower 20000265 Age (day) 21
    12462179 At_Open_Flower 20000265 Organism A. thaliana
    12462179 At_Open_Flower 20000265 Tissue Closed Flower vs. Whole Plant
    12462179 At_Open_Flower 20000265 Plant Line WS
    12462179 At_100mM_NaCl 20000268 Timepoint (hr) 6
    12462179 At_100mM_NaCl 20000268 Age (day) 14
    12462179 At_100mM_NaCl 20000268 Treatment 100mM NaCl vs. No Treatment
    12462179 At_100mM_NaCl 20000268 Organism A. thaliana
    12462179 At_100mM_NaCl 20000268 Tissue Whole Plant
    12462179 At_100mM_NaCl 20000268 Plant Line WS
    12462179 At_100mM_NaCl 20000308 Age (day) 17
    12462179 At_100mM_NaCl 20000308 Timepoint (hr) 72
    12462179 At_100mM_NaCl 20000308 Treatment 100mM NaCl vs. No Treatment
    12462179 At_100mM_NaCl 20000308 Organism A. thaliana
    12462179 At_100mM_NaCl 20000308 Tissue Whole Plant
    12462179 At_100mM_NaCl 20000308 Plant Line WS
    12462179 At_Pollen 20000326 Age (day) 0 vs. 21
    12462179 At_Pollen 20000326 Organism A. thaliana
    12462179 At_Pollen 20000326 Tissue Pollen vs. Whole Plant
    12462179 At_Pollen 20000326 Plant Line WS
    12462179 At_Drought 20000436 Age (day) 7
    12462179 At_Drought 20000436 Timepoint (hr) 12
    12462179 At_Drought 20000436 Organism A. thaliana
    12462179 At_Drought 20000436 Treatment Drought vs. No Drought
    12462179 At_Drought 20000436 Tissue Whole Plant
    12462179 At_Drought 20000436 Plant Line WS
    12462179 At_Drought 20000437 Age (day) 8
    12462179 At_Drought 20000437 Timepoint (hr) 24
    12462179 At_Drought 20000437 Organism A. thaliana
    12462179 At_Drought 20000437 Treatment Drought vs. No Drought
    12462179 At_Drought 20000437 Tissue Whole Plant
    12462179 At_Drought 20000437 Plant Line WS
    12462179 At_Shoots 20000438 Age (day) 14 vs. 21
    12462179 At_Shoots 20000438 Organism A. thaliana
    12462179 At_Shoots 20000438 Tissue Shoots vs. Whole Plant
    12462179 At_Shoots 20000438 Plant Line WS
    12462179 At_Roots 20000439 Age (day) 14 vs. 21
    12462179 At_Roots 20000439 Organism A. thaliana
    12462179 At_Roots 20000439 Tissue Roots vs. Whole Plant
    12462179 At_Roots 20000439 Plant Line WS
    12462179 At_100uM_NAA 20000445 Timepoint (hr) 6
    12462179 At_100mM_NAA 20000445 Age (day) 14
    12462179 At_100uM_NAA 20000445 Treatment 100uM NAA vs. No Treatment
    12462179 At_100uM_NAA 20000445 Organism A. thaliana
    12462179 At_100uM_NAA 20000445 Tissue Aerial
    12462179 At_100uM_NAA 20000445 Plant Line WS
    12462179 At_100uM_ABA 20000453 Age (day) 15
    12462179 At_100uM_ABA 20000453 Timepoint (hr) 24
    12462179 At_100uM_ABA 20000453 Treatment 100uM ABA vs. No Treatment
    12462179 At_100uM ABA 20000453 Organism A. thaliana
    12462179 At_100uM_ABA 20000453 Tissue Aerial
    12462179 At_100uM_ABA 20000453 Plant Line WS
    12462179 At_100uM_ABA 20000455 Age (day) 16
    12462179 At_100uM_ABA 20000455 Timepoint (hr) 48
    12462179 At_100uM_ABA 20000455 Treatment 100uM ABA vs. No Treatment
    12462179 At_100uM_ABA 20000455 Organism A. thaliana
    12462179 At_100uM_ABA 20000455 Tissue Aerial
    12462179 At_100uM_ABA 20000455 Plant Line WS
    12462179 At_42deg_Heat 20000458 Timepoint (hr) 8
    12462179 At_42deg_Heat 20000458 Age (day) 14
    12462179 At_42deg_Heat 20000458 Temperature (deg C.) 42 vs. 22
    12462179 At_42deg_Heat 20000458 Organism A. thaliana
    12462179 At_42deg_Heat 20000458 Tissue Aerial
    12462179 At_42deg_Heat 20000458 Plant Line WS
    12462179 At_Wounding 20000506 Timepoint (hr) 6
    12462179 At_Wounding 20000506 Age (day) 14
    12462179 At_Wounding 20000506 Organism A. thaliana
    12462179 At_Wounding 20000506 Tissue Aerial
    12462179 At_Wounding 20000506 Treatment Wounding vs. No Wounding
    12462179 At_Wounding 20000506 Plant Line WS
    12462179 At_100uM_ABA_Mutants 20000575 Timepoint (hr) 6
    12462179 At_100uM_ABA_Mutants 20000575 Treatment 1uM ABA vs. No Treatment
    12462179 At_100uM_ABA_Mutants 20000575 Organism A. thaliana
    12462179 At_100uM_ABA_Mutants 20000575 Plant Line CS22
    12462179 At_100uM_ABA_Mutants 20000575 Tissue Whole Plant
    12462179 At_100uM_ABA_Mutants 20000576 Timepoint (hr) 6
    12462179 At_100uM_ABA_Mutants 20000576 Treatment 1uM ABA vs. No Treatment
    12462179 At_100mM_ABA_Mutants 20000576 Organism A. thaliana
    12462179 At_100uM_ABA_Mutants 20000576 Plant Line CS23
    12462179 At_100uM_ABA_Mutants 20000576 Tissue Whole Plant
    12462179 At_Herbicide_Mutants 20000640 Timepoint (hr) 12
    12462179 At_Herbicide_Mutants 20000640 Plant Line 05377RR/BR27173
    12462179 At_Herbicide_Mutants 20000640 Treatment Roundup vs. No Treatment
    12462179 At_Herbicide_Mutants 20000640 Tissue Seedlings
    12462179 At_Herbicide_Mutants 20000642 Timepoint (hr) 12
    12462179 At_Herbicide_Mutants 20000642 Plant Line 3950BR/PCJE10000
    12462179 At_Herbicide_Mutants 20000642 Treatment Finale vs. No Treatment
    12462179 At_Herbicide_Mutants 20000642 Tissue Seedlings
    12462179 At_15mM_NH4NO3_L-to-H 20000709 Timepoint (hr) 4
    12462179 At_15mM_NH4NO3_L-to-H 20000709 Age (hr) 14
    12462179 At_15mM_NH4NO3_L-to-H 20000709 Treatment 15mM NH4NO3 vs. 30mM
    Mannitol
    12462179 At_15mM_NH4NO3_L-to-H 20000709 Organism A. thaliana
    12462179 At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial
    12462179 At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS
    12462179 At_Petals 20000794 Age (day) 23-25 days
    12462179 At_Petals 20000794 Organism A. thaliana
    12462179 At_Petals 20000794 Tissue Petals vs. Whole plant
    12462179 At_Petals 20000794 Plant Line WS
    12462179 At_Line_Comparisons 20001151 Plant Line ME01339-01 vs. WS
    12462179 At_Line_Comparisons 20001184 Plant Line ME01848-01 vs. WS
    12462179 At_Far-red-induction 20001248 Timepoint (hr) 4
    12462179 At_Far-red-induction 20001246 Age (day) 7
    12462179 At_Far-red-induction 20001248 Organism A. thaliana
    12462179 At_Far-red-induction 20001248 Plant Line Columbia
    12462179 At_Far-red-induction 20001248 Light Far-red vs. White
    12462179 At_Far-red-induction 20001248 Tissue Whole Plant
    12462179 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS
    12462179 At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS
    12462179 At_Interploidy_Crosses 20001316 Age (day) 5
    12462179 At_Interploidy_Crosses 20001316 Organism A. thaliana
    12462179 At_Interploidy_Crosses 20001316 Plant Line Columbia
    12462179 At_Interploidy_Crosses 20001316 Cross hemi × 2X vs. 2X × 2X
    12462179 At_Interploidy_Crosses 20001316 Tissue Siliques
    12462179 At_Line_Comparisons 20001319 Plant Line WBin4-WX24-A vs. WS
    12462179 At_Line_Comparisons 20001347 Plant Line ME01604-01 vs. WS
    12462179 At_Far-red-induction 20001451 Age (day) 8
    12462179 At_Far-red-induction 20001451 Timepoint (hr) 24
    12462179 At_Far-red-induction 20001451 Organism A. thaliana
    12462179 At_Far-red-induction 20001451 Plant Line Columbia
    12462179 At_Far-red-induction 20001451 Light Far-red vs. White
    12462179 At_Far-red-induction 20001451 Tissue Whole Plant
    12462179 At_Far-red-enriched 20001504 Timepoint (day) 6
    12462179 At_Far-red-enriched 20001504 Age (day) 10
    12462179 At_Far-red-enriched 20001504 Organism A. thaliana
    12462179 At_Far-red-enriched 20001504 Plant Line Columbia
    12462179 At_Far-red-enriched 20001504 Light Far-red enriched vs. White
    12462179 At_Far-red-enriched 20001504 Tissue Whole Plant
    12462179 At_Drought_Soil_Dry 20001553 Timepoint (day) 5
    12462179 At_Drought_Soil_Dry 20001553 Age (day) 19
    12462179 At_Drought_Soil_Dry 20001553 Organism A. thaliana
    12462179 At_Drought_Soil_Dry 20001553 Treatment Drought vs. No Drought
    12462179 At_Drought_Soil_Dry 20001553 Post Timepoint (hr) None
    12462179 At_Drought_Soil_Dry 20001553 Post-Treatment None
    12462179 At_Drought_Soil_Dry 20001553 Plant Line WS
    12462179 At_Drought_Soil_Dry 20001554 Timepoint (day) 7
    12462179 At_Drought_Soil_Dry 20001554 Age (day) 21
    12462179 At_Drought_Soil_Dry 20001554 Organism A. thaliana
    12462179 At_Drought_Soil_Dry 20001554 Treatment Drought vs. No Drought
    12462179 At_Drought_Soil_Dry 20001554 Post Timepoint (hr) None
    12462179 At_Drought_Soil_Dry 20001554 Post-Treatment None
    12462179 At_Drought_Soil_Dry 20001554 Plant Line WS
    12462179 At_Drought_Soil_Dry 20001555 Timepoint (day) 10
    12462179 At_Drought_Soil_Dry 20001555 Age (day) 24
    12462179 At_Drought_Soil_Dry 20001555 Organism A. thaliana
    12462179 At_Drought_Soil_Dry 20001555 Treatment Drought vs. No Drought
    12462179 At_Drought_Soil_Dry 20001555 Post Timepoint (hr) None
    12462179 At_Drought_Soil_Dry 20001555 Post-Treatment None
    12462179 At_Drought_Soil_Dry 20001555 Plant Line WS
    12462179 At_Drought_Soil_Dry 20001556 Timepoint (day) 12
    12462179 At_Drought_Soil_Dry 20001556 Age (day) 26
    12462179 At_Drought_Soil_Dry 20001556 Organism A. thaliana
    12462179 At_Drought_Soil_Dry 20001556 Treatment Drought vs. No Drought
    12462179 At_Drought_Soil_Dry 20001556 Post Timepoint (hr) None
    12462179 At_Drought_Soil_Dry 20001556 Post-Treatment None
    12462179 At_Drought_Soil_Dry 20001556 Plant Line WS
    12462179 At_Drought_Soil_Dry 20001559 Timepoint (day) 14
    12462179 At_Drought_Soil_Dry 20001559 Age (day) 28
    12462179 At_Drought_Soil_Dry 20001559 Post Timepoint (hr) 29
    12462179 At_Drought_Soil_Dry 20001559 Organism A. thaliana
    12462179 At_Drought_Soil_Dry 20001559 Treatment Drought vs. No Drought
    12462179 At_Drought_Soil_Dry 20001559 Post-Treatment Re-Water vs. No Drought
    12462179 At_Drought_Soil_Dry 20001559 Plant Line WS
    12462179 At_Interploidy_Crosses 20001654 Age (day) 5
    12462179 At_Interploidy_Crosses 20001654 Cross 6X × 2X vs. 2X × 2X
    12462179 At_Interploidy_Crosses 20001654 Organism A. thaliana
    12462179 At_Interploidy_Crosses 20001654 Plant Line Columbia
    12462179 At_Interploidy_Crosses 20001654 Tissue Siliques
    12462179 At_50mM_NH4NO3_L-to-H 20001757 Timepoint (hr) 6
    12462179 At_50mM_NH4NO3_L-to-H 20001757 Treatment 50mM NH4NO3 vs 100mM
    Mannitol
    12462179 At_50mM_NH4NO3_L-to-H 20001757 Tissue Leaf
    12462179 At_Far-red-enriched-adult 20001768 Timepoint (hr) 1
    12462179 At_Far-red-enriched-adult 20001768 Age (day) 28
    12462179 At_Far-red-enriched-adult 20001768 Organism A. thaliana
    12462179 At_Far-red-enriched-adult 20001768 Tissue Aerial
    12462179 At_Far-red-enriched-adult 20001768 Plant Line Columbia
    12462179 At_Far-red-enriched-adult 20001768 Light Far-red enriched vs. White
    12462179 At_Far-red-enriched-adult 20001770 Timepoint (hr) 8
    12462179 At_Far-red-enriched-adult 20001770 Age (day) 28
    12462179 At_Far-red-enriched-adult 20001770 Organism A. thaliana
    12462179 At_Far-red-enriched-adult 20001770 Tissue Aerial
    12462179 At_Far-red-enriched-adult 20001770 Plant Line Columbia
    12462179 At_Far-red-enriched-adult 20001770 Light Far-red enriched vs. White
    12462179 At_Far-red-enriched-adult 20001771 Timepoint (hr) 16
    12462179 At_Far-red-enriched-adult 20001771 Age (day) 28
    12462179 At_Far-red-enriched-adult 20001771 Organism A. thaliana
    12462179 At_Far-red-enriched-adult 20001771 Tissue Aerial
    12462179 At_Far-red-enriched-adult 20001771 Plant Line Columbia
    12462179 At_Far-red-enriched-adult 20001771 Light Far-red enriched vs. White
    12462179 At_Far-red-enriched-adult 20001774 Age (day) 31
    12462179 At_Far-red-enriched-adult 20001774 Timepoint (hr) 72
    12462179 At_Far-red-enriched-adult 20001774 Organism A. thaliana
    12462179 At_Far-red-enriched-adult 20001774 Tissue Aerial
    12462179 At_Far-red-enriched-adult 20001774 Plant Line Columbia
    12462179 At_Far-red-enriched-adult 20001774 Light Far-red enriched vs. White
    12462179 At_Drought_Reproduction 20001904 Timepoint (day) 7
    12462179 At_Drought_Reproduction 20001904 Age (day) 37
    12462179 At_Drought_Reproduction 20001904 Organism A. thaliana
    12462179 At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought
    12462179 At_Drought_Reproduction 20001904 Tissue Rosettes
    12462179 At_Drought_Reproduction 20001904 Plant Line WS
    12462179 At_Drought_Reproduction 20001905 Timepoint (day) 10
    12462179 At_Drought_Reproduction 20001905 Age (day) 40
    12462179 At_Drought_Reproduction 20001905 Organism A. thaliana
    12462179 At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought
    12462179 At_Drought_Reproduction 20001905 Tissue Rosettes
    12462179 At_Drought_Reproduction 20001905 Plant Line WS
    12462179 At_Drought_Reproduction 20001906 Timepoint (day) 5
    12462179 At_Drought_Reproduction 20001906 Age (day) 35
    12462179 At_Drought_Reproduction 20001906 Organism A. thaliana
    12462179 At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought
    12462179 At_Drought_Reproduction 20001906 Tissue Siliques
    12462179 At_Drought_Reproduction 20001906 Plant Line WS
    12462179 At_Drought_Reproduction 20001908 Timepoint (day) 10
    12462179 At_Drought_Reproduction 20001908 Age (day) 40
    12462179 At_Drought_Reproduction 20001908 Organism A. thaliana
    12462179 At_Drought_Reproduction 20001908 Treatment Drought vs. No Drought
    12462179 At_Drought_Reproduction 20001908 Tissue Siliques
    12462179 At_Drought_Reproduction 20001908 Plant Line WS
    12462179 At_Drought_Reproduction 20001910 Timepoint (day) 7
    12462179 At_Drought_Reproduction 20001910 Age (day) 37
    12462179 At_Drought_Reproduction 20001910 Organism A. thaliana
    12462179 At_Drought_Reproduction 20001910 Treatment Drought vs. No Drought
    12462179 At_Drought_Reproduction 20001910 Tissue Flowers
    12462179 At_Drought_Reproduction 20001910 Plant Line WS
    12462179 At_Drought_Reproduction 20001911 Timepoint (day) 10
    12462179 At_Drought_Reproduction 20001911 Age (day) 40
    12462179 At_Drought_Reproduction 20001911 Organism A. thaliana
    12462179 At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought
    12462179 At_Drought_Reproduction 20001911 Tissue Flowers
    12462179 At_Drought_Reproduction 20001911 Plant Line WS
    12462179 At_8deg_Cold 20002107 Age (day) 11
    12462179 At_8deg_Cold 20002107 Timepoint (hr) 96
    12462179 At_8deg_Cold 20002107 Temperature (deg C.) 8 vs. 22
    12462179 At_8deg_Cold 20002107 Organism A. thaliana
    12462179 At_8deg_Cold 20002107 Tissue Whole Plant
    12462179 At_8deg_Cold 20002107 Plant Line WS
    12462179 At_8deg_Cold 20002108 Age (day) 14
    12462179 At_8deg_Cold 20002108 Timepoint (hr) 168
    12462179 At_8deg_Cold 20002108 Temperature (deg C.) 8 vs. 22
    12462179 At_8deg_Cold 20002108 Organism A. thaliana
    12462179 At_8deg_Cold 20002108 Tissue Whole Plant
    12462179 At_8deg_Cold 20002108 Plant Line WS
    12462179 At_8deg_Cold 20002109 Age (day) 16
    12462179 At_8deg_Cold 20002109 Timepoint (hr) 216
    12462179 At_8deg_Cold 20002109 Temperature (deg C.) 8 vs. 22
    12462179 At_8deg_Cold 20002109 Organism A. thaliana
    12462179 At_8deg_Cold 20002109 Tissue Whole Plant
    12462179 At_8deg_Cold 20002109 Plant Line WS
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    13613778 At_Root_Tips 108434 Tissue Root Tips
    13613778 At_20uM_KNO3_H-to-L 108455 Timepoint (hr) 1
    13613778 At_20uM_KNO3_H-to-L 108455 Treatment 20uM KNO3 vs. 50mM KNO3
    13613778 At_5-1-F2-137 108460 Plant Line 5-1-F2-137(mutant)
    13613778 At_5-1-F2-137 108460 Probe Method Amplified
    13613778 At_5-1-F2-137 108460 Tissue Inflorescences
    13613778 At_Germinating_Seeds 108464 Age (day) 4 vs. 0
    13613778 At_Germinating_Seeds 108464 Tissue Germinating Seeds
    13613778 At_Shoot_Apices 108480 Treatment 1uM BR vs. No Treatment
    13613778 At_Shoot_Apices 108480 Plant Line Ws-2
    13613778 At_Shoot_Apices 108481 Treatment 1uM BRZ vs. No Treatment
    13613778 At_Shoot_Apices 108481 Plant Line Ws-2
    13613778 At_15mM_NH4NO3_L-to- 108487 Timepoint (hr) 0.5
    H_Rosette
    13613778 At_15mM_NH4NO3_L-to- 108487 Treatment 15mM NH4NO3 vs. 30mM Mannitol
    H_Rosette
    13613778 At_15mM NH4NO3_L-to- 108487 Tissue Rosette
    H_Rosette
    13613778 At_15mM_NH4NO3_L-to- 108488 Timepoint (hr) 2
    H_Rosette
    13613778 At_15mM_NH4NO3_L-to- 108488 Treatment 15mM NH4NO3 vs. 30mM Mannitol
    H_Rosette
    13613778 At_15mM_NH4NO3_L-to- 108488 Tissue Rosette
    H_Rosette
    13613778 At_ap2_floral_buds 108501 Plant Line ap2 (Ler.)
    13613778 At_ap2_floral_buds 108501 Tissue Closed Flower
    13613778 At_42deg_Heat 108577 Timepoint (hr) 6
    13613778 At_42deg_Heat 108577 Temperature 42 vs.22
    (deg C.)
    13613778 At_42deg_Heat 108577 Tissue Aerial
    13613778 At_4deg_Cold 108578 Timepoint (hr) 1
    13613778 At_4deg_Cold 108578 Temperature 4 vs. 22
    (deg C.)
    13613778 At_4deg_Cold 108578 Tissue Aerial
    13613778 At_4deg_Cold 108579 Timepoint (hr) 6
    13613778 At_4deg_Cold 108579 Temperature 4 vs. 22
    (deg C.)
    13613778 At_4deg_Cold 108579 Tissue Aerial
    13613778 At_5mM_NaNP 108584 Timepoint (hr) 1
    13613778 At_5mM_NaNP 108584 Treatment 5mM sodium nitroprusside vs. No
    Treatment
    13613778 At_5mM_NaNP 108584 Tissue Aerial
    13613778 At_5mM_NaNP 108585 Timepoint (hr) 6
    13613778 At_5mM_NaNP 108585 Treatment 5mM sodium nitroprusside vs. No
    Treatment
    13613778 At_5mM_NaNP 108585 Tissue Aerial
    13613778 At_2mM_SA 108586 Timepoint (hr) 1
    13613778 At_2mM_SA 108586 Treatment 2mM SA vs. No Treatment
    13613778 At_2mM_SA 108586 Tissue Aerial
    13613778 At_2mM_SA 108587 Timepoint (hr) 6
    13613778 At_2mM_SA 108587 Treatment 2mM SA vs. No Treatment
    13613778 At_2mM_SA 108587 Tissue Aerial
    13613778 At_15mM_NH4NO3_L-to-H 108588 Timepoint (hr) 2
    13613778 At_15mM_NH4NO3_L-to-H 108588 Treatment 15mM NH4NO3 vs. 30mM Mannitol
    13613778 At_15mM_NH4NO3_L-to-H 108588 Tissue Aerial
    13613778 At_Ler-Pi_Ovule 108595 Plant Line Ler_pi
    13613778 At_Ler-Pi_Ovule 108595 Tissue Ovules
    13613778 At_100uM_ABA 108606 Timepoint (hr) 2
    13613778 At_100uM_ABA 108606 Treatment 100uM ABA vs. No Treatment
    13613778 At_100uM_ABA 108606 Tissue Aerial
    13613778 At_2mM_SA 108667 Timepoint (hr) 1
    13613778 At_2mM_SA 108667 Treatment 2mM SA vs. No Treatment
    13613778 At_2mM_SA 108667 Plant Line WS
    13613778 At_100uM_ABA_Mutants 20000069 Timepoint (hr) 6
    13613778 At_100uM_ABA_Mutants 20000069 Treatment 100uM ABA vs. No Treatment
    13613778 At_100uM_ABA_Mutants 20000069 Tissue Aerial
    13613778 At_100uM_ABA_Mutants 20000069 Plant Line CS23
    13613778 At_100uM_ABA_Mutants 20000071 Timepoint (hr) 6
    13613778 At_100uM_ABA_Mutants 20000071 Treatment 100uM ABA vs. No Treatment
    13613778 At_100uM_ABA_Mutants 20000071 Tissue Aerial
    13613778 At_100uM_ABA_Mutants 20000071 Plant Line CS8104
    13613778 At_100uM_ABA_Mutants 20000086 Timepoint (hr) 6
    13613778 At_100uM_ABA_Mutants 20000086 Treatment 100uM ABA vs. No Treatment
    13613778 At_100uM_ABA_Mutants 20000086 Tissue Aerial
    13613778 At_100uM_ABA_Mutants 20000086 Plant Line CS22
    13613778 At_100uM_ABA_Mutants 20000087 Timepoint (hr) 6
    13613778 At_100uM_ABA_Mutants 20000087 Treatment 100uM ABA vs. No Treatment
    13613778 At_100uM_ABA_Mutants 20000087 Tissue Aerial
    13613778 At_100uM_ABA_Mutants 20000087 Plant Line WS
    13613778 At_2mM_SA_CS3726- 20000091 Timepoint (hr) 0
    Columbia
    13613778 At_2mM_SA_CS3726- 20000091 Tissue Aerial
    Columbia
    13613778 At_2mM_SA_CS3726- 20000091 Plant Line CS3726 vs. Columbia
    Columbia
    13613778 At_2mM_SA_CS3726- 20000091 Treatment None
    Columbia
    13613778 At_100uM_ABA_Mutants 20000117 Timepoint (hr) 6
    13613778 At_100uM_ABA_Mutants 20000117 Treatment 100uM ABA vs. No Treatment
    13613778 At_100uM_ABA_Mutants 20000117 Tissue Aerial
    13613778 At_100uM_ABA_Mutants 20000117 Plant Line Columbia
    13613778 At_42deg_Heat 20000144 Timepoint (hr) 1
    13613778 At_42deg_Heat 20000144 Temperature 42 vs.22
    deg C.)
    13613778 At_42deg_Heat 20000144 Tissue Aerial
    13613778 At_42deg_Heat 20000171 Timepoint (hr) 1
    13613778 At_42deg_Heat 20000171 Age (day) 14
    13613778 At_42deg_Heat 20000171 Temperature 42 vs. 22
    (deg C.)
    13613778 At_42deg_Heat 20000171 Organism A. thaliana
    13613778 At_42deg_Heat 20000171 Tissue Aerial
    13613778 At_42deg_Heat 20000171 Plant Line WS
    13613778 At_42deg_Heat 20000173 Timepoint (hr) 6
    13613778 At_42deg_Heat 20000173 Age (day) 14
    13613778 At_42deg_Heat 20000173 Temperature 42 vs.22
    (deg C.)
    13613778 At_42deg_Heat 20000173 Organism A. thaliana
    13613778 At_42deg_Heat 20000173 Tissue Aerial
    13613778 At_42deg_Heat 20000173 Plant Line WS
    13613778 At_2mM_SA 20000181 Timepoint (hr) 1
    13613778 At_2mM_SA 20000181 Age (day) 14
    13613778 At_2mM_SA 20000181 Treatment 2mM SA vs. No Treatment
    13613778 At_2mM_SA 20000181 Organism A. thaliana
    13613778 At_2mM_SA 20000181 Tissue Aerial
    13613778 At_2mM_SA 20000181 Plant Line WS
    13613778 At_Shoots 20000184 Age (day) 7 vs.21
    13613778 At_Shoots 20000184 Organism A. thaliana
    13613778 At_Shoots 20000184 Tissue Shoots vs. Whole Plant
    13613778 At_Shoots 20000184 Plant Line WS
    13613778 At_Roots 20000185 Age (day) 7 vs. 21
    13613778 At_Roots 20000185 Organism A. thaliana
    13613778 At_Roots 20000185 Tissue Roots vs. Whole Plant
    13613778 At_Roots 20000185 Plant Line WS
    13613778 At_4deg_Cold 20000213 Timepoint (hr) 2
    13613778 At_Siliques 20000234 Age (day) 21
    13613778 At_Siliques 20000234 Tissue <5mm Siliques vs. Whole Plant
    13613778 At_Siliques 20000234 Organism A. thaliana
    13613778 At_Siliques 20000234 Plant Line WS
    13613778 At_Siliques 20000236 Age (day) 21
    13613778 At_Siliques 20000236 Tissue >10mm Siliques vs. Whole Plant
    13613778 At_Siliques 20000236 Organism A. thaliana
    13613778 At_Siliques 20000236 Plant Line WS
    13613778 At_Open_Flower 20000264 Age (day) 21
    13613778 At_Open_Flower 20000264 Organism A. thaliana
    13613778 At_Open_Flower 20000264 Tissue Open Flower vs. Whole Plant
    13613778 At_Open_Flower 20000264 Plant Line WS
    13613778 At_100mM_NaCl 20000268 Timepoint (hr) 6
    13613778 At_100mM_NaCl 20000268 Age (day) 14
    13613778 At_100mM_NaCl 20000268 Treatment 100mM NaCl vs. No Treatment
    13613778 At_100mM_NaCl 20000268 Organism A. thaliana
    13613778 At_100mM_NaCl 20000268 Tissue Whole Plant
    13613778 At_100mM_NaCl 20000268 Plant Line WS
    13613778 At_Open_Flower 20000286 Age (day) 21
    13613778 At_Open_Flower 20000286 Organism A. thaliana
    13613778 At_Open_Flower 20000286 Tissue Half Open vs. Whole Plant
    13613778 At_Open_Flower 20000286 Plant Line WS
    13613778 At_Pollen 20000326 Age (day) 0 vs. 21
    13613778 At_Pollen 20000326 Organism A. thaliana
    13613778 At_Pollen 20000326 Tissue Pollen vs. Whole Plant
    13613778 At_Pollen 20000326 Plant Line WS
    13613778 At_Shoots 20000438 Age (day) 14 vs. 21
    13613778 At_Shoots 20000438 Organism A. thaliana
    13613778 At_Shoots 20000438 Tissue Shoots vs. Whole Plant
    13613778 At_Shoots 20000438 Plant Line WS
    13613778 At_Roots 20000439 Age (day) 14 vs. 21
    13613778 At_Roots 20000439 Organism A. thaliana
    13613778 At_Roots 20000439 Tissue Roots vs. Whole Plant
    13613778 At_Roots 20000439 Plant Line WS
    13613778 At_1uM_BR-BRZ 20000441 Treatment 1 uM BR vs. No Treatment
    13613778 At_1uM_BR-BRZ 20000441 Tissue Shoot Apices
    13613778 At_1uM_BR-BRZ 20000443 Treatment 1uM BRZ vs. No Treatment
    13613778 At_1uM_BR-BRZ 20000443 Tissue Shoot Apices
    13613778 At_42deg_Heat 20000458 Timepoint (hr) 8
    13613778 At_42deg_Heat 20000458 Age (day) 14
    13613778 At_42deg_Heat 20000458 Temperature 42 vs. 22
    (deg C.)
    13613778 At_42deg_Heat 20000458 Organism A. thaliana
    13613778 At_42deg_Heat 20000458 Tissue Aerial
    13613778 At_42deg_Heat 20000458 Plant Line WS
    13613778 At_10percent_PEG 20000460 Age (day) 12
    13613778 At_10percent_PEG 20000460 Timepoint (day) 12
    13613778 At_10percent_PEG 20000460 Treatment 10percent PEG vs. No Treatment
    13613778 At_10percent_PEG 20000460 Organism A. thaliana
    13613778 At_10percent_PEG 20000460 Tissue Whole Plant
    13613778 At_10percent_PEG 20000460 Plant Line WS
    13613778 At_Guard_Cells 20000495 Harvest Date Aug. 2, 2002
    13613778 At_Guard_Cells 20000495 Organism A. thaliana
    13613778 At_Guard_Cells 20000495 Tissue Guard Cells vs. Leaves
    13613778 At_10percent_PEG 20000527 Age (day) 20
    13613778 At_10percent_PEG 20000527 Timepoint (day) 20
    13613778 At_10percent_PEG 20000527 Treatment 10percent PEG vs. No Treatment
    13613778 At_10percent_PEG 20000527 Organism A. thaliana
    13613778 At_10percent_PEG 20000527 Tissue Whole Plant
    13613778 At_10percent_PEG 20000527 Plant Line WS
    13613778 At_100uM_ABA_Mutants 20000573 Organism A. thaliana
    13613778 At_100uM_ABA_Mutants 20000573 Plant Line C522 vs. Lerwt
    13613778 At_100uM_ABA_Mutants 20000573 Timepoint (hr) N/A
    13613778 At_100uM_ABA_Mutants 20000573 Treatment None
    13613778 At_100uM_ABA_Mutants 20000573 Tissue Whole Plant
    13613778 At_100uM_ABA_Mutants 20000574 Organism A. thaliana
    13613778 At_100uM_ABA_Mutants 20000574 Plant Line C523 vs. Lerwt
    13613778 At_100uM_ABA_Mutants 20000574 Timepoint (hr) N/A
    13613778 At_100uM_ABA_Mutants 20000574 Treatment None
    13613778 At_100uM_ABA_Mutants 20000574 Tissue Whole Plant
    13613778 At_Herbicide_Mutants 20000640 Timepoint (hr) 12
    13613778 At_Herbicide_Mutants 20000640 Plant Line 05377RR/BR27173
    13613778 At_Herbicide_Mutants 20000640 Treatment Roundup vs. No Treatment
    13613778 At_Herbicide_Mutants 20000640 Tissue Seedlings
    13613778 At_15mM_NH4NO3_L-to-H 20000709 Timepoint (hr) 4
    13613778 At_15mM_NH4NO3_L-to-H 20000709 Age (day) 14
    13613778 At_15mM_NH4NO3_L-to-H 20000709 Treatment 15mM NH4NO3 vs. 30mM Mannitol
    13613778 At_15mM_NH4NO3_L-to-H 20000709 Organism A. thaliana
    13613778 At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial
    13613778 At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS
    13613778 At_Petals 20000794 Age (day) 23-25 days
    13613778 At_Petals 20000794 Organism A. thaliana
    13613778 At_Petals 20000794 Tissue Petals vs. Whole plant
    13613778 At_Petals 20000794 Plant Line WS
    13613778 At_Line_Comparisons 20001151 Plant Line ME01339-01 vs. WS
    13613778 At_Line_Comparisons 20001184 Plant Line ME01848-01 vs. WS
    13613778 At_Line_Comparisons 20001192 Plant Line WBin4-WX13R-A vs. WS
    13613778 At_Line_Comparisons 20001195 Plant Line WBin4-WX14-B vs. WS
    13613778 At_Far-red-induction 20001247 Timepoint (hr) 1
    13613778 At_Far-red-induction 20001247 Age (day) 7
    13613778 At_Far-red-induction 20001247 Organism A. thaliana
    13613778 At_Far-red-induction 20001247 Plant Line Columbia
    13613778 At_Far-red-induction 20001247 Light Far-red vs. White
    13613778 At_Far-red-induction 20001247 Tissue Whole Plant
    13613778 At_Far-red-induction 20001248 Timepoint (hr) 4
    13613778 At_Far-red-induction 20001248 Age (day) 7
    13613778 At_Far-red-induction 20001248 Organism A. thaliana
    13613778 At_Far-red-induction 20001248 Plant Line Columbia
    13613778 At_Far-red-induction 20001248 Light Far-red vs. White
    13613778 At_Far-red-induction 20001248 Tissue Whole Plant
    13613778 At_Line_Comparisons 20001300 Plant Line ME01338-05 vs. WS
    13613778 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS
    13613778 At_Line_Comparisons 20001308 Plant Line WBin4-WX49-C vs. WS
    13613778 At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS
    13613778 At_Line_Comparisons 20001310 Plant Line WBin4-WX1 7-A vs. WS
    13613778 At_Line_Comparisons 20001318 Plant Line WBin4-WX14R-A vs. WS
    13613778 At_Line_Comparisons 20001319 Plant Line WBin4-WX24-A vs. WS
    13613778 At_Line_Comparisons 20001347 Plant Line ME01604-01 vs.WS
    13613778 At_Line_Comparisons 20001448 Plant Line ME01323-01 vs. WS
    13613778 At_50mM NH4NO3_L-to-H 20001458 Timepoint (hr) 2
    13613778 At_50mM_NH4NO3_L-to-H 20001458 Treatment 50mM NH4NO3 vs. 100mM Manitol
    13613778 At_50mM_NH4NO3_L-to-H 20001458 Organism A. thaliana
    13613778 At_50mM_NH4NO3_L-to-H 20001458 Tissue Siliques
    13613778 At_50mM_NH4NO3_L-to-H 20001458 Age (day) Undefined
    13613778 At_50mM_NH4NO3_L-to-H 20001458 Plant Line WS
    13613778 At_Drought_Soil_Dry 20001554 Timepoint (day) 7
    13613778 At_Drought_Soil_Dry 20001554 Age (day) 21
    13613778 At_Drought_Soil_Dry 20001554 Organism A. thaliana
    13613778 At_Drought_Soil_Dry 20001554 Treatment Drought vs. No Drought
    13613778 At_Drought_Soil_Dry 20001554 Post Timepoint None
    (hr)
    13613778 At_Drought_Soil_Dry 20001554 Post-Treatment None
    13613778 At_Drought_Soil_Dry 20001554 Plant Line WS
    13613778 At_Drought_Soil_Dry 20001555 Timepoint (day) 10
    13613778 At_Drought_Soil_Dry 20001555 Age (day) 24
    13613778 At_Drought_Soil_Dry 20001555 Organism A. thaliana
    13613778 At_Drought_Soil_Dry 20001555 Treatment Drought vs. No Drought
    13613778 At_Drought_Soil_Dry 20001555 Post Timepoint None
    (hr)
    13613778 At_Drought_Soil_Dry 20001555 Post-Treatment None
    13613778 At_Drought_Soil_Dry 20001555 Plant Line WS
    13613778 At_Drought_Soil_Dry 20001556 Timepoint (day) 12
    13613778 At_Drought_Soil_Dry 20001556 Age (day) 26
    13613778 At_Drought_Soil_Dry 20001556 Organism A. thaliana
    13613778 At_Drought_Soil_Dry 20001556 Treatment Drought vs. No Drought
    13613778 At_Drought_Soil_Dry 20001556 Post Timepoint None
    (hr)
    13613778 At_Drought_Soil_Dry 20001556 Post-Treatment None
    13613778 At_Drought_Soil_Dry 20001556 Plant Line WS
    13613778 At_Drought_Soil_Dry 20001557 Post Timepoint 3
    (hr)
    13613778 At_Drought_Soil_Dry 20001557 Timepoint (day) 13
    13613778 At_Drought_Soil_Dry 20001557 Age (day) 27
    13613778 At_Drought_Soil_Dry 20001557 Organism A. thaliana
    13613778 At_Drought_Soil_Dry 20001557 Treatment Drought vs. No Drought
    13613778 At_Drought_Soil_Dry 20001557 Post-Treatment Re-Water vs. No Drought
    13613778 At_Drought_Soil_Dry 20001557 Plant Line WS
    13613778 At_Interploidy_Crosses 20001703 Age (day) 5
    13613778 At_Interploidy_Crosses 20001703 Cross 2X × 4X vs. 2X × 2X
    13613778 At_Interploidy_Crosses 20001703 Organism A. thaliana
    13613778 At_Interploidy_Crosses 20001703 Plant Line Columbia
    13613778 At_Interploidy_Crosses 20001703 Tissue Siliques
    13613778 At_50mM_NH4NO3_L-to-H 20001757 Timepoint (hr) 6
    13613778 At_50mM_NH4NO3_L-to-H 20001757 Treatment 50mM NH4NO3 vs 100mM Mannitol
    13613778 At_50mM_NH4NO3_L-to-H 20001757 Tissue Leaf
    13613778 At_Far-red-enriched-adult 20001773 Age (day) 30
    13613778 At_Far-red-enriched-adult 20001773 Timepoint (hr) 48
    13613778 At_Far-red-enriched-adult 20001773 Organism A. thaliana
    13613778 At_Far-red-enriched-adult 20001773 Tissue Aerial
    13613778 At_Far-red-enriched-adult 20001773 Plant Line Columbia
    13613778 At_Far-red-enriched-adult 20001773 Light Far-red enriched vs. White
    13613778 At_Far-red-enriched-adult 20001774 Age (day) 31
    13613778 At_Far-red-enriched-adult 20001774 Timepoint (hr) 72
    13613778 At_Far-red-enriched-adult 20001774 Organism A. thaliana
    13613778 At_Far-red-enriched-adult 20001774 Tissue Aerial
    13613778 At_Far-red-enriched-adult 20001774 Plant Line Columbia
    13613778 At_Far-red-enriched-adult 20001774 Light Far-red enriched vs. White
    13613778 At_Drought_Reproduction 20001904 Timepoint (day) 7
    13613778 At_Drought_Reproduction 20001904 Age (day) 37
    13613778 At_Drought_Reproduction 20001904 Organism A. thaliana
    13613778 At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought
    13613778 At_Drought_Reproduction 20001904 Tissue Rosettes
    13613778 At_Drought_Reproduction 20001904 Plant Line WS
    13613778 At_Drought_Reproduction 20001907 Timepoint (day) 7
    13613778 At_Drought_Reproduction 20001907 Age (day) 37
    13613778 At_Drought_Reproduction 20001907 Organism A. thaliana
    13613778 At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought
    13613778 At_Drought_Reproduction 20001907 Tissue Siliques
    13613778 At_Drought_Reproduction 20001907 Plant Line WS
    13613778 At_Line_Comparisons 20002012 Plant Line SALK_073455 vs. Columbia
    13613778 At_8deg_Cold 20002108 Age (day) 14
    13613778 At_8deg_Cold 20002108 Timepoint hr 168
    13613778 At_8deg_Cold 20002108 Temperature 8 vs.22
    (deg C.)
    13613778 At_8deg_Cold 20002108 Organism A. thaliana
    13613778 At_8deg_Cold 20002108 Tissue Whole Plant
    13613778 At_8deg_Cold 20002108 Plant Line WS
    13613778 At_8deg_Cold 20002109 Age (day) 16
    13613778 At_8deg_Cold 20002109 Timepoint (hr) 216
    13613778 At_8deg_Cold 20002109 Temperature 8 vs. 22
    (deg C.)
    13613778 At_8deg_Cold 20002109 Organism A. thaliana
    13613778 At_8deg_Cold 20002109 Tissue Whole Plant
    13613778 At_8deg_Cold 20002109 Plant Line WS
    Promoter YP00374
    Modulates the gene: Putative cytochrome P450
    The GenBank description of the gene: NM_112814 Arabidopsis thaliana cytochrome P450, putative
    (At3g19270) mRNA, complete cds gi|18402178|ref|NM 112814.1|[18402178]
    The promoter sequence:
    5′agaagaaactagaaacgttaaacgcatcaaatcaagaaattaaattgaaggtaatttttaacgccgcct
    ttcaaatattcttcctaggagaggctacaagacgcgtatttctttcgaattctccaaaccattaccatttt
    gatatataataccgacatgccgttgataaagtttgtatgcaaatcgttcattgggtatgagcaaatgccat
    ccattggttcttgtaattaaatggtccaaaaatagtttgttcccactactagttactaatttgtatcactc
    tgcaaaataatcatgatataaacgtatgtgctatttctaattaaaactcaaaagtaatcaatgtacaatgc
    agagatgaccataaaagaacattaaaacactacttccactaaatctatggggtgccttggcaaggcaattg
    aataaggagaatgcatcaagatgatatagaaaatgctattcagtttataacattaatgttttggcggaaaa
    ttttctatatattagacctttctgtaaaaaaaaaaaaatgatgtagaaaatgctattatgtttcaaaaatt
    tcgcactagtataatacggaacattgtagtttacactgctcattaccatgaaaaccaaggcagtatatacc
    aacattaataaactaaatcgcgatttctagcacccccattaattaattttactattatacattctctttgc
    ttctcgaaataataaacttctctatatcattctacataataaataagaaagaaatcgacaagatctaaatt
    tagatctattcagctttttcgcctgagaagccaaaattgtgaatagaagaaagcagtcgtcatcttcccac
    gtttggacgaaataaaacataacaataataaaataataaatcaaatatataaatccctaatttgtctttat
    tactccacaattttctatgtgtatataTA 3′-
    tgtatgtttttgttccctattatatcttctagcttctttcttcctcttcttccttaaaaattcatcctcca
    aaacattctatcatcaacgaaacatttcatattaaattaaataataatcgATG
    The promoter was cloned from the organism: Arabidopsis thaliana
    Alternative nucleotides:
    Query = Predicted
    Subject = Experimental
    Predicted Position (bp) Mismatch Predicted/Experimental
    1-1000 None Identities = 1000/1000 (100%)
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in:
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in +TL,1/64
    expression in any or all of the following:
    Flower M vascular
    Silique M placenta, M vascular
    Elypocotyl H vascular
    Cotyledon H vascular, H petiole
    Primary Root H vascular
    Observed expression pattern of the promoter-marker vector was in:
    T1 mature: GFP expressed in outer integument of developing ovule primordium. Higher integument
    expression at chalazal pole observed through maturity.
    T2 seedling: Medium to low expression in root vascular bundles weakening toward hypocotyl.
    Weak expression in epidermal cells at root transition zone..
    Misc. promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: : 12370888
    cDNA nucleotide sequence:
    GTATGTTTTTGTTCCCTATTATATCTTCTAGCTTCTTTCTTCCTCTTCTTCCTTAAAAATTCATCC
    TCCAAAACATTCTATCATCAACGAAACATTTCATATTAAATTAAATAATAATCGATGGCTGAA
    ATTTGGTTCTTGGTTGTAGCAATCCTCATCTTATGCTTGCTTTTGGTAAGAGTGATTGTTTCAA
    AGAAGAAAAAGAACAGTAGAGGTAAGCTTCCTCCTGGTTCCATGGGATGGGCTTACTTAGGAG
    AGACTCTACAACTCTATTCACAAAACCCCAATGTTTTCTTCACCTCCAAGCAAAAGAGATATG
    GAGAGATATTCAAAACCCGAATCCTCGGCTATCCATGCGTGATGTTGGGTAGCCCTGAGGCTG
    CGAGGTTTGTAGTTGTGACTCATGCCCATATGTTGAAACCAACTTATCCGAGAAGCAAAGAGA
    AGCTGATAGGACCCTCTGCACTCTTTTTCCACCAAGGAGATTATCATTCCCATATAAGGAAACT
    TGTTCAATCCTCTTTCTACCCTGAAACCATCCGTAAACTCATCCCTGATATCGAGCACATTGCC
    CTTTCTTCCTTACAATCTTGGGCGAATATGCCGATTGTCTCCACCTACCAGGAGATGAAGAAGT
    TCGCCTTTGATGTGGGTATTCTAGCCATATTTGGACATTTGGAGAGTTCTTACAAAGAGATCTT
    GAAACATAAGTACAATATTGTGGACAAAGGCTACAACTCTTTCCCCATGAGTCTCCCCGGAAC
    ATCTTATCACAAAGCTCTCATGGCGAGAAAGCAGCTAAAGACGATAGTAAGCGAGATTATATG
    CGAAAGAAGAGAGAAAAGGGCCTTGCAAACGGACTTTCTTGGTCATGTACTCAACTTCAAGAA
    CGAAAAAGGTCGTGTGCTAACCCAAGAACAGATTGCAGACAACATCATCGGAGTCCTTTTCGC
    CGCACAGGACACGACAGCTAGTTGCTTAACTTGGATTCTTAAGTACTTACATGATGATCAGAA
    ACTTCTAGAAGCTGTTAAGGCTGAGCAAAAGGCTATATATGAAGAAAACAGTAGAGAGAAGA
    AACCTTTAACATGGAGACAAACGAGGAATATGCCACTGACACATAAGGTTATAGTTGAAAGCT
    TGAGGATGGCAAGCATCATATCCTTCACATTCAGAGAAGCAGTGGTTGATGTTGAATATAAGG
    GATATTTGATACCTAAGGGATGGAAAGTGATGCCACTGTTTCGGAATATTCATCACAATCCGA
    AATATTTTTCAAACCCTGAGGTTTTCGACCCATCTAGATTCGAGGTAAATCCGAAGCCGAATA
    CATTCATGCCTTTTGGAAGTGGAGTTCATGCTTGTCCCGGGAACGAACTCGCCAAGTTACAAA
    TTCTTATATTTCTCCACCATTTAGTTTCCAATTTCCGATGGGAAGTGAAGGGAGGAGAGAAAG
    GAATACAGTACAGTCCATTTGCAATACCTCAAAACGGTCTTCCCGCTACATTTCGTCGACATTC
    TCTTTAGTTCCTTAAACCTTTGTAGTAATCTTTGTTGTAGTTAGCCAAATCTAATCCAAATTCG
    ATATAAAAAATCCCCTTTCTATTTTTTTTTAAAATCATTGTTGTAGTCTTGAGGGGGTTTAACA
    TGTAACAACTATGATGAAGTAAAATGTCGATTCCGGT
    Coding sequence:
    MAEIWFLVVPILILCLLLVRVIVSKKKKNSRGKLPPGSMGWPYLGETLQLYSQNPNVFFTSKQKRY
    GEIFKTRILGYPCVMLASPEAARFVLVTHAHMFKPTYPRSKEKLIGPSALFFHQGDYHSHIRKLVQS
    SFYPETIRKLIPDIEHIALSSLQSWANMPIVSTYQEMKKFAFDVGILAIFGHLESSYKEILKHNYNIVD
    KGYNSFPMSLPGTSYHKALMARKQLKTIVSEIICERREKRALQTDFLGHLLNFKNEKGRVLTQEQI
    ADNIIGVLFAAQDTTASCLTWILKYLHDDQKLLEAVKAEQKAIYEENSREKKPLTWRQTRNMPLT
    HKVIVESLRMASIISFTFREAVVDVEYKGYLIPKGWKVMPLFRNIHHNPKYFSNPEVFDPSRFEVNP
    KPNTFMPFGSGVHACPGNELAKLQILIFLHHLVSNFRWEVKGGEKGIQYSPFPIPQNGLPATFRRHS
    L*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12370888 At_100uM_ABA 20000166 +
    12370888 At_100uM_ABA 20000169 +
    12370888 At_42deg_Heat 20000171 +
    12370888 At_42deg_Heat 20000173 +
    12370888 At_2mM_SA 20000182 +
    12370888 At_Open_Flower 20000264 +
    12370888 At_Shoots 20000438 +
    12370888 At_100uM_ABA 20000453 +
    12370888 At_42deg_Heat 20000457 −
    12370888 At_42deg_Heat 20000458 +
    12370888 At_Guard_Cells 20000495 +
    12370888 At_10percent_PEG 20000527 +
    12370888 At_Petals 20000794 +
    12370888 At_Far-red-induction 20001248 −
    12370888 At_Far-red-enriched 20001504 +
    12370888 At_Far-red-enriched-adult 20001771 +
    12370888 At_Drought_Reproduction 20001906 +
    12370888 At_Drought_Reproduction 20001907 +
    12370888 At_Drought_Reproduction 20001910 +
    12370888 At_8deg_Cold 20002107 −
    12370888 At_8deg_Cold 20002108 −
    12370888 At_8deg_Cold 20002109 −
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12370888 At_100uM_ABA 20000166 Timepoint (hr) 1
    12370888 At_100uM_ABA 20000166 Age (day) 14
    12370888 At_100uM_ABA 20000166 Treatment 100uM ABA vs. No Treatment
    12370888 At_100uM_ABA 20000166 Organism A. thaliana
    12370888 At_100uM_ABA 20000166 Tissue Aerial
    12370888 At_100uM_ABA 20000166 Plant Line WS
    12370888 At_100uM_ABA 20000169 Timepoint (hr) 6
    12370888 At_100uM ABA 20000169 Age (day) 14
    12370888 At_100uM_ABA 20000169 Treatment 100uM ABA vs. No Treatment
    12370888 At_100uM_ABA 20000169 Organism A. thaliana
    12370888 At_100uM_ABA 20000169 Tissue Aerial
    12370888 At_100uM_ABA 20000169 Plant Line WS
    12370888 At_42deg_Heat 20000171 Timepoint (hr) 1
    12370888 At_42deg_Heat 20000171 Age (day) 14
    12370888 At_42deg_Heat 20000171 Temperature (deg C.) 42 vs. 22
    12370888 At_42deg_Heat 20000171 Organism A. thaliana
    12370888 At_42deg_Heat 20000171 Tissue Aerial
    12370888 At_42deg_Heat 20000171 Plant Line WS
    12370888 At_42deg_Heat 20000173 Timepoint (hr) 6
    12370888 At_42deg_Heat 20000173 Age (day) 14
    12370888 At_42deg_Heat 20000173 Temperature (deg C.) 42 vs. 22
    12370888 At_42deg_Heat 20000173 Organism A. thaliana
    12370888 At_42deg_Heat 20000173 Tissue Aerial
    12370888 At_42deg_Heat 20000173 Plant Line WS
    12370888 At_2mM_SA 20000182 Timepoint (hr) 6
    12370888 At_2mM_SA 20000182 Age (day) 14
    12370888 At_2mM_SA 20000182 Treatment 2mM SA vs. No Treatment
    12370888 At_2mM_SA 20000182 Organism A. thaliana
    12370888 At_2mM_SA 20000182 Tissue Aerial
    12370888 At_2mM_SA 20000182 Plant Line WS
    12370888 At_Open_Flower 20000264 Age (day) 21
    12370888 At_Open_Flower 20000264 Organism A. thaliana
    12370888 At_Open_Flower 20000264 Tissue Open Flower vs. Whole Plant
    12370888 At_Open_Flower 20000264 Plant Line WS
    12370888 At_Shoots 20000438 Age (day) 14 vs. 21
    12370888 At_Shoots 20000438 Organism A. thaliana
    12370888 At_Shoots 20000438 Tissue Shoots vs. Whole Plant
    12370888 At_Shoots 20000438 Plant Line WS
    12370888 At_100uM_ABA 20000453 Age (day) 15
    12370888 At_100uM_ABA 20000453 Timepoint (hr) 24
    12370888 At_100uM_ABA 20000453 Treatment 100uM ABA vs. No Treatment
    12370888 At_100uM_ABA 20000453 Organism A. thaliana
    12370888 At_100uM_ABA 20000453 Tissue Aerial
    12370888 At_100uM_ABA 20000453 Plant Line WS
    12370888 At_42deg_Heat 20000457 Timepoint (hr) 0.166
    12370888 At_42deg_Heat 20000457 Age (day) 14
    12370888 At_42deg_Heat 20000457 Temperature (deg C.) 42 vs. 22
    12370888 At_42deg_Heat 20000457 Organism A. thaliana
    12370888 At_42deg_Heat 20000457 Tissue Aerial
    12370888 At_42deg_Heat 20000457 Plant Line WS
    12370888 At_42deg_Heat 20000458 Timepoint (hr) 8
    12370888 At_42deg_Heat 20000458 Age (day) 14
    12370888 At_42deg_Heat 20000458 Temperature (deg C.) 42 vs. 22
    12370888 At_42deg_Heat 20000458 Organism A. thaliana
    12370888 At_42deg_Heat 20000458 Tissue Aerial
    12370888 At_42deg_Heat 20000458 Plant Line WS
    12370888 At_Guard_Cells 20000495 Harvest Date Aug. 2, 2002
    12370888 At_Guard_Cells 20000495 Organism A. thaliana
    12370888 At_Guard_Cells 20000495 Tissue Guard Cells vs. Leaves
    12370888 At_10percent_PEG 20000527 Age (day) 20
    12370888 At_10percent_PEG 20000527 Timepoint (day) 20
    12370888 At_10percent_PEG 20000527 Treatment 10percent PEG vs. No
    Treatment
    12370888 At_10percent_PEG 20000527 Organism A. thaliana
    12370888 At_10percent_PEG 20000527 Tissue Whole Plant
    12370888 At_10percent_PEG 20000527 Plant Line WS
    12370888 At_Petals 20000794 Age (day) 23-25 days
    12370888 At_Petals 20000794 Organism A. thaliana
    12370888 At_Petals 20000794 Tissue Petals vs. Whole plant
    12370888 At_Petals 20000794 Plant Line WS
    12370888 At_Far-red-induction 20001248 Timepoint (hr) 4
    12370888 At_Far-red-induction 20001248 Age (day) 7
    12370888 At_Far-red-induction 20001248 Organism A. thaliana
    12370888 At_Far-red-induction 20001248 Plant Line Columbia
    12370888 At_Far-red-induction 20001248 Light Far-red vs. White
    12370888 At_Far-red-induction 20001248 Tissue Whole Plant
    12370888 At_Far-red-enriched 20001504 Timepoint (day) 6
    12370888 At_Far-red-enriched 20001504 Age (day) 10
    12370888 At_Far-red-enriched 20001504 Organism A. thaliana
    12370888 At_Far-red-enriched 20001504 Plant Line Columbia
    12370888 At_Far-red-enriched 20001504 Light Far-red enriched vs. White
    12370888 At_Far-red-enriched 20001504 Tissue Whole Plant
    12370888 At_Far-red-enriched-adult 20001771 Timepoint (hr) 16
    12370888 At_Far-red-enriched-adult 20001771 Age (day) 28
    12370888 At_Far-red-enriched-adult 20001771 Organism A. thaliana
    12370888 At_Far-red-enriched-adult 20001771 Tissue Aerial
    12370888 At_Far-red-enriched-adult 20001771 Plant Line Columbia
    12370888 At_Far-red-enriched-adult 20001771 Light Far-red enriched vs. White
    12370888 At_Drought_Reproduction 20001906 Timepoint (day) 5
    12370888 At_Drought_Reproduction 20001906 Age (day) 35
    12370888 At_Drought_Reproduction 20001906 Organism A. thaliana
    12370888 At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought
    12370888 At_Drought_Reproduction 20001906 Tissue Siliques
    12370888 At_Drought_Reproduction 20001906 Plant Line WS
    12370888 At_Drought_Reproduction 20001907 Timepoint (day) 7
    12370888 At_Drought_Reproduction 20001907 Age (day) 37
    12370888 At_Drought_Reproduction 20001907 Organism A. thaliana
    12370888 At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought
    12370888 At_Drought_Reproduction 20001907 Tissue Siliques
    12370888 At_Drought_Reproduction 20001907 Plant Line WS
    12370888 At_Drought_Reproduction 20001910 Timepoint (day) 7
    12370888 At_Drought_Reproduction 20001910 Age (day) 37
    12370888 At_Drought_Reproduction 20001910 Organism A. thaliana
    12370888 At_Drought_Reproduction 20001910 Treatment Drought vs. No Drought
    12370888 At_Drought_Reproduction 20001910 Tissue Flowers
    12370888 At_Drought_Reproduction 20001910 Plant Line WS
    12370888 At_8deg_Cold 20002107 Age (day) 11
    12370888 At_8deg_Cold 20002107 Timepoint (hr) 96
    12370888 At_8deg_Cold 20002107 Temperature (deg C.) 8 vs. 22
    12370888 At_8deg_Cold 20002107 Organism A. thaliana
    12370888 At_8deg_Cold 20002107 Tissue Whole Plant
    12370888 At_8deg_Cold 20002107 Plant Line WS
    12370888 At_8deg_Cold 20002108 Age (day) 14
    12370888 At_8deg_Cold 20002108 Timepoint (hr) 168
    12370888 At_8deg_Cold 20002108 Temperature (deg C.) 8 vs. 22
    12370888 At_8deg_Cold 20002108 Organism A. thaliana
    12370888 At_8deg_Cold 20002108 Tissue Whole Plant
    12370888 At_8deg_Cold 20002108 Plant Line WS
    12370888 At_8deg_Cold 20002109 Age (day) 16
    12370888 At_8deg_Cold 20002109 Timepoint (hr) 216
    12370888 At_8deg_Cold 20002109 Temperature (deg C.) 8 vs. 22
    12370888 At_8deg_Cold 20002109 Organism A. thaliana
    12370888 At_8deg_Cold 20002109 Tissue Whole Plant
    12370888 At_8deg_Cold 20002109 Plant Line WS
    Promoter YP0371
    Modulates the gene: Unknown protein. Contains putative conserved domains: [ATPase family associated
    with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that
    assist in the assembly, operation, or disassembly of protein complexes].
    The GenBank description of the gene: NM_179511 Arabidopsis thaliana AAA-type ATPase family
    protein (At1g64110) mRNA, complete cds gi|30696967|ref|NM_179511.1|[30696967].
    The promoter sequence:
    5′gattctgcgaagacaggagaagccatacctttcaatctaagccgtcaacttgttcccttacgtgggatc
    ctattatacaatccaacggttctaaatgagccacgccttccagatctaacacagtcatgctttctacagtc
    tgcaccccttttttttttagtgttttatctacattttttcctttgtgtttaattttgtgccaacatctata
    acttacccctataaaaatattcaattatcacagaatacccacaatcgaaaacaaaatttaccggaataatt
    taattaaagctggactataatgacaattccgaaactatcaaggaataaattaaagaaactaaaaaactaaa
    gggcattagagtaaagaagcggcaacatcagaattaaaaaactgccgaaaaaccaacctagtagccgttta
    tatgacaacacgtacgcaaagtctcggtaatgactcatcagttttcatgtgcaaacatattacccccatga
    aataaaaaagcagagaagcgatcaaaaaaatcttcattaaaagaaccctaaatctctcatatccgccgccg
    tctttgcctcattttcaacaccggtgatgacgtgtaaatagatctggttttcacggttctcactactctct
    gtgatttttcagactattgaatcgttaggaccaaaacaagtacaaagaaactgcagaagaaaagatttgag
    agagatatcttacgaaacaaggtatatatttctcttgttaaatctttgaaaatactttcaaagtttcggtt
    ggattctcgaataagttaggttaaatagtcaatatagaattatagataaatcgataccttttgtttgttat
    cattcaatttttattgttgttacgattagtaacaacgttttagatcttgatctaTATAttaataatactaa
    tactttgtttttttttgttttttttttaa 3′-aATG
    The promoter was cloned from the organism: Arabidopsis thaliana, Columbia ecotype
    Alternative nucleotides:
    Predicted Position (bp) Mismatch Predicted/Experimental
    155 PCR error or ecotype variant SNP t/c
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower M pedicel M stomata
    Primary Root L epidermis
    Observed expression pattern of the promoter-marker vector was in:
    T1 mature: Weak guard cell expression in pedicles.
    T2 seedling: Weak root epidermal expression.
    Misc. promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No
    An overlap in an exon with the endogenous coding sequence to the promoter occurs at base pairs
    537-754
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12657397
    cDNA nucleotide sequence:
    AGCGATCAAAAAAATCTTCATTAAAAGAACCCTAAATCTCTCATATCCGCCGCCGTCTTTGCCT
    CATTTTCAACACCGGTGATGACGTGTAAATAGATCTGGTTTTCACGGTTCTCACTACTCTCTGT
    GATTTTTCAGACTATTGAATCGTTAGGACCAAAACAAGTACAAAGAAACTGCAGAAGAAAAG
    ATTTGAGAGAGATATCTTACGAAACAAGCAAACAGATGTTGTTGTCGGCGCTTGGCGTCGGAG
    TTGGAGTAGGTGTGGGTTTAGGCTTGGCTTCTGGTCAAGCCGTCGGAAAATGGGCCGGCGGGA
    ACTCGTCGTCAAATAACGCCGTCACGGCGGATAAGATGGAGAAGGAGATACTCCGTCAAGTT
    GTTGACGGCAGAGAGAGTAAAATTACTTTCGATGAGTTTCCTTATTATCTCAGTGAACAAACA
    CGAGTGCTTCTAACAAGTGCAGCTTATGTCCATTTGAAGCACTTCGATGCTTCAAAATATACG
    AGAAACTTGTCTCCAGCTAGCCGAGCCATTCTCTTGTCCGGCGCTGCCGAGCTTTACGAACAA
    ATGCTAGCCAAAGCCCTAGCTCATTTCTTCGATGCCAAGTTACTTCTTCTAGACGTCAACGATT
    TTGCACTCAAGATACAGAGCAAATACGGCAGTGGAAATACAGAATCATGGTCATTCAAGAGAT
    CTCCCTCAGAATCTGCTTTAGAGCAACTATCAGGACTGTTTAGTTCCTTCTCCATCCTTCCTCA
    GAGAGAAGAGTCAAAAGCTGGTGGTACCTTGAGGAGGCAAAGCAGTGGTGTGGATATCAAAT
    CAAGCTCAATGGAAGGCTCTAGTAATCCTCCAAAGCTTCGTCGAAACTCTTCAGCAGCAGGTA
    ATATTAGCAACCTTGCATCTTCCTCAAATCAAGTTTCAGCGCCTTTGAAACGAAGTAGCAGTTG
    GTCATTCGATGAAAAGCTTCTCGTCCAATCTTTATATAAGGTCTTGGCCTATGTCTCCAAGGCG
    AATCCGATTGTGTTATATCTTCGAGACGTCGAGAACTTTCTGTTCCGCTCACAGAGAACTTACA
    ACTTGTTCCAGAAGCTTCTCCAGAAACTCAGTGGACCGGTCCTCATTCTCGGTTCAAGAATTGT
    GGACTTGTCAAGCGAAGACGCTCAAGAAATTGATGAGAAGCTCTCTGCTGTTTTCCCTTATAA
    TATCGACATAAGACCTCCTGAGGATGAGACTCATCTAGTGAGCTGGAAATCGCAGCTTGAACG
    CGACATGAACATGATCCAAACTCAGGACAATAGGAAGCATATCATGGAAGTTTTGTCGGAGAA
    TGATCTTATATGGGATGACCTTGAATCCATCTCTTTTGAGGACACGAAGGTTTTAAGCAATTAC
    ATTGAAGAGATCGTTGTCTCTGCTCTTTCCTATCATCTGATGAACAACAAAGATCCTGAGTACA
    GAAACGGAAAACTGGTGATATCTTCTATAAGTTTGTCGCATGGATTCAGTCTCTTCAGAGAAG
    GCAAAGCTGGCGGTCGTGAGAAGCTGAAGCAAAAAACTAAGGAGGAATCATCCAAGGAAGTA
    AAAGCTGAATCAATCAAGCCGGAGACAAAAACAGAGAGTGTCACCACGGTAAGCAGCAAGGA
    AGAACCAGAGAAAGAAGCTAAAGCTGAGAAAGTTACCCCAAAAGCTCCGGAAGTTGCACCGG
    ATAACGAGTTTGAGAAACGGATAAGACCGGAAGTAATCCCAGCAGAAGAAATTAACGTCACA
    TTCAAAGACATTGGTGCACTTGAGGAGATAAAAGAGTCACTACAAGAACTTGTAATGCTTCCT
    CTCCGTAGGCCAGACCTCTTCACAGGAGGTCTCTTGAAGCCCTGCAGAGGAATCTTACTCTTC
    GGTCCACCGGGTACAGGTAAAACAATGCTAGCTAAAGCCATTGCCAAAGAGGCAGGAGCGAG
    TTTCATAAACGTTTCGATGTCAACAATAAGTTCGAAATGGTTTGGAGAAGACGAGAAGAATGT
    TAGGGCTTTGTTTACTCTAGCTTCGAAGGTGTCACCAACCATAATATTTGTGGATGAAGTTGAT
    AGTATGTTGGGACAGAGAACAAGAGTTGGAGAACATGAAGCTATGAGAAAGATCAAGAATGA
    GTTTATGAGTCATTGGGATGGGTTAATGACTAAACCTGGTGAACGTATCTTAGTCCTTGCTGCT
    ACTAATCGGCCTTTCGATCTTGATGAAGCCATTATCAGACGATTCGAACGAAGGATCATGGTG
    GGACTACCGGCTGTAGAGAACAGAGAAAAGATTCTAAGAACATTGTTGGCGAAGGAGAAAGT
    AGATGAAAACTTGGATTACAAGGAACTAGCAATGATGACAGAAGGATACACAGGAAGTGATC
    TTAAGAATCTGTGCACAACCGCTGCGTATAGGCCGGTGAGAGAACTTATACAGCAAGAGAGG
    ATCAAAGACACAGAGAAGAAGAAGCAGAGAGAGCCTACAAAAGCAGGTGAAGAAGATGAAG
    GAAAAGAAGAGAGAGTTATAACACTTCGTCCGTTGAACAGACAAGACThFAAAGAAGCCAAG
    AATCAGGTGGCGGCGAGTTTTGCGGCTGAGGGAGCGGGAATGGGAGAGTTGAAGCAGTGGAA
    TGAATTGTATGGAGAAGGAGGATCGAGGAAGAAAGAACAACTCACTTACTTCTTGTAATGATG
    ATGATGAATCATGATGCTGGTAATGGATTATGAAATTTGGTAATGTAATAGTATGGTGAATTT
    TTGTTTCCATGGTTAATAAGAGAATAAGAATATGATGATATTGCTAAAAGTTTGACCCGT
    Coding sequence:
    MLLSALGVGVGVGVGLGLASGQAVGKWAGGNSSSNNAVTADKMEKEILRQVVDGRESKITFDEF
    PYYLSEQTRVLLTSAAYVHLKHFDASKYTRNLSPASRAILLSGPAELYQQMLAKALAHFFDAKLLL
    LDVNDFALKIQSKYGSGNTESSSFKRSPSESALEQLSGLFSSFSILPQREESKAGGTLRRQSSGVDIKS
    SSMEGSSNPPKLRRNSSAAANISNLASSSNQVSAPLKRSSSWSFDEKLLVQSLYKVLAYVSKANPIV
    LYLRDVENFLFRSQRTYNLFQKLLQKLSGPVLILGSRIVDLSSEDAQEIDEKLSAVFPYNIDIRPPEDE
    THLVSWKSQLERDMNMIQTQDNRNHIMEVLSENDLICDDLESISFEDTKVLSNYIEEIVVSALSYHL
    MNNKDPEYRNGKLVISSISLSHGFSLFREGKAGGREKLKQKTKEESSKEVKAESIKPETKTESVTTV
    SSKEEPEKEAKAEKVTPKAPEVAPDNEFEKRIRPEVIPAEEINVTFKDIGALDEIKESLQELVMLPLR
    RPDLFTGGLLKPCRGILLFGPPGTGKTMLAKAIAKEAGASFINVSMSTITSKWFGEDEKNVRALFTL
    ASKVSPTIIFVDEVDSMLGQRTRVGEHEAMRKIKNEFMSHWDGLMTKPGERILVLAATNRPFDLD
    EAIIRRFERRIMVGLPAVENREKILRTLLAKEKVDENLDYKELAMMTEGYTGSDLKNLCTTAAYRP
    VRELIQQERIKDTEKKKQREPTKAGEEDEGKEERVITLRPLNRQDFKEAKNQVAASFAAEGAGMG
    ELKQWNELYGEGGSRKKEQLTYFL*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12657397 At_100uM_ABA 20000169 +
    12657397 At_Germinating_Seeds 20000180 −
    12657397 At_Roots 20000185 +
    12657397 At_Siliques 20000234 −
    12657397 At_Siliques 20000235 −
    12657397 At_Siliques 20000236 −
    12657397 At_Drought 20000267 +
    12657397 At_100mM_NaCl 20000268 +
    12657397 At_100mM_NaCl 20000308 +
    12657397 At_Pollen 20000326 +
    12657397 At_Drought 20000436 +
    12657397 At_Drought 20000437 +
    12657397 At_Roots 20000439 +
    12657397 At_10percent_PEG 20000460 +
    12657397 At_10percent_PEG 20000527 +
    12657397 At_100uM_ABA_Mutants 20000575 +
    12657397 At_100uM_ABA_Mutants 20000576 +
    12657397 At_Herbicide_Mutants 20000639 +
    12657397 At_Herbicide_Mutants 20000642 +
    12657397 At_Line_Comparisons 20001300 −
    12657397 At_Line_Comparisons 20001307 +
    12657397 At_Line_Comparisons 20001309 −
    12657397 At_Line_Comparisons 20001310 −
    12657397 At_Line_Comparisons 20001319 +
    12657397 At_Far-red-induction 20001451 +
    12657397 At_Far-red-enriched 20001504 +
    12657397 At_Drought_Soil_Dry 20001554 +
    12657397 At_Drought_Soil_Dry 20001555 +
    12657397 At_Drought_Soil_Dry 20001556 +
    12657397 At_Drought_Soil_Dry 20001557 +
    12657397 At_Drought_Soil_Dry 20001559 +
    12657397 At_Drought Soil_Dry 20001560 +
    12657397 At_Drought_Reproduction 20001904 +
    12657397 At_Drought_Reproduction 20001906 +
    12657397 At_Drought_Reproduction 20001907 +
    12657397 At_Drought_Reproduction 20001909 +
    12657397 At_Line_Comparisons 20002009 +
    12657397 At_Drought-Air-Dry 20002256 +
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12657397 At_100uM_ABA 20000169 Timepoint (hr) 6
    12657397 At_100uM_ABA 20000169 Age (day) 14
    12657397 At_100uM_ABA 20000169 Treatment 100uM ABA vs. No Treatment
    12657397 At_100uM_ABA 20000169 Organism A. thaliana
    12657397 At_100uM_ABA 20000169 Tissue Aerial
    12657397 At_100uM_ABA 20000169 Plant Line WS
    12657397 At_Germinating_Seeds 20000180 Age (hr) 24 vs. 0
    12657397 At_Germinating_Seeds 20000180 Organism A. thaliana
    12657397 At_Germinating_Seeds 20000180 Tissue Germinating Seeds
    12657397 At_Germinating_Seeds 20000180 Plant Line WS
    12657397 At_Roots 20000185 Age (day) 7 vs. 21
    12657397 At_Roots 20000185 Organism A. thaliana
    12657397 At_Roots 20000185 Tissue Roots vs. Whole Plant
    12657397 At_Roots 20000185 Plant Line WS
    12657397 At_Siliques 20000234 Age (day) 21
    12657397 At_Siliques 20000234 Tissue <5mm Siliques vs. Whole Plant
    12657397 At_Siliques 20000234 Organism A. thaliana
    12657397 At_Siliques 20000234 Plant Line WS
    12657397 At_Siliques 20000235 Age (day) 21
    12657397 At_Siliques 20000235 Tissue 5-10mm Siliques vs. Whole
    Plant
    12657397 At_Siliques 20000235 Organism A. thaliana
    12657397 At_Siliques 20000235 Plant Line WS
    12657397 At_Siliques 20000236 Age (day) 21
    12657397 At_Siliques 20000236 Tissue >10mm Siliques vs. Whole
    Plant
    12657397 At_Siliques 20000236 Organism A. thaliana
    12657397 At_Siliques 20000236 Plant Line WS
    12657397 At_Drought 20000267 Timepoint (hr) 6
    12657397 At_Drought 20000267 Age (day) 7
    12657397 At_Drought 20000267 Organism A. thaliana
    12657397 At_Drought 20000267 Treatment Drought vs. No Drought
    12657397 At_Drought 20000267 Tissue Whole Plant
    12657397 At_Drought 20000267 Plant Line WS
    12657397 At_100mM_NaCl 20000268 Timepoint (hr) 6
    12657397 At_100mM_NaCl 20000268 Age (day) 14
    12657397 At_100mM_NaCl 20000268 Treatment 100mM NaCl vs. No Treatment
    12657397 At_100mM_NaCl 20000268 Organism A. thaliana
    12657397 At_100mM_NaCl 20000268 Tissue Whole Plant
    12657397 At_100mM_NaCi 20000268 Plant Line WS
    12657397 At_100mM_NaCl 20000308 Age (day) 17
    12657397 At_100mM_NaCl 20000308 Timepoint (hr) 72
    12657397 At_100mM_NaCl 20000308 Treatment 100mM NaCl vs. No Treatment
    12657397 At_100mM_NaCl 20000308 Organism A. thaliana
    12657397 At_100mM_NaCl 20000308 Tissue Whole Plant
    12657397 At_100mM_NaCl 20000308 Plant Line WS
    12657397 At_Pollen 20000326 Age (day) 0 vs. 21
    12657397 At_Pollen 20000326 Organism A. thaliana
    12657397 At_Pollen 20000326 Tissue Pollen vs. Whole Plant
    12657397 At_Pollen 20000326 Plant Line WS
    12657397 At_Drought 20000436 Age (day) 7
    12657397 At_Drought 20000436 Timepoint (hr) 12
    12657397 At_Drought 20000436 Organism A. thaliana
    12657397 At_Drought 20000436 Treatment Drought vs. No Drought
    12657397 At_Drought 20000436 Tissue Whole Plant
    12657397 At_Drought 20000436 Plant Line WS
    12657397 At_Drought 20000437 Age (day) 8
    12657397 At_Drought 20000437 Timepoint (hr) 24
    12657397 At_Drought 20000437 Organism A. thaliana
    12657397 At_Drought 20000437 Treatment Drought vs. No Drought
    12657397 At_Drought 20000437 Tissue Whole Plant
    12657397 At_Drought 20000437 Plant Line WS
    12657397 At_Roots 20000439 Age (day) 14 vs. 21
    12657397 At_Roots 20000439 Organism A. thaliana
    12657397 At_Roots 20000439 Tissue Roots vs. Whole Plant
    12657397 At_Roots 20000439 Plant Line WS
    12657397 At_10percent_PEG 20000460 Age (day) 12
    12657397 At_10percent_PEG 20000460 Timepoint (day) 12
    12657397 At_10percent_PEG 20000460 Treatment 10percent PEG vs. No
    Treatment
    12657397 At_10percent_PEG 20000460 Organism A. thaliana
    12657397 At_10percent_PEG 20000460 Tissue Whole Plant
    12657397 At_10percent_PEG 20000460 Plant Line WS
    12657397 At_10percent_PEG 20000527 Age (day) 20
    12657397 At_10percent_PEG 20000527 Timepoint (day) 20
    12657397 At_10percent_PEG 20000527 Treatment 10percent PEG vs. No
    Treatment
    12657397 At_10percent_PEG 20000527 Organism A. thaliana
    12657397 At_10percent_PEG 20000527 Tissue Whole Plant
    12657397 At_10percent_PEG 20000527 Plant Line WS
    12657397 At_100uM_ABA_Mutants 20000575 Timepoint (hr) 6
    12657397 At_100uM_ABA_Mutants 20000575 Treatment 1uM ABA vs. No Treatment
    12657397 At_100uM_ABA_Mutants 20000575 Organism A. thaliana
    12657397 At_100uM_ABA_Mutants 20000575 Plant Line CS22
    12657397 At_100uM_ABA_Mutants 20000575 Tissue Whole Plant
    12657397 At_100mM_ABA_Mutants 20000576 Timepoint (hr) 6
    12657397 At_100mM_ABA_Mutants 20000576 Treatment 1uM ABA vs. No Treatment
    12657397 At_100mM_ABA_Mutants 20000576 Organism A. thaliana
    12657397 At_100mM_ABA_Mutants 20000576 Plant Line CS23
    12657397 At_100uM_ABA_Mutants 20000576 Tissue Whole Plant
    12657397 At_Herbicide_Mutants 20000639 Timepoint (hr) 4
    12657397 At_Herbicide_Mutants 20000639 Plant Line 05377RR/BR27173
    12657397 At_Herbicide_Mutants 20000639 Treatment Roundup vs. No Treatment
    12657397 At_Herbicide_Mutants 20000639 Tissue Seedlings
    12657397 At_Herbicide_Mutants 20000642 Timepoint (hr) 12
    12657397 At_Herbicide_Mutants 20000642 Plant Line 3950BR/PCJE1 0000
    12657397 At_Herbicide_Mutants 20000642 Treatment Finale vs. No Treatment
    12657397 At_Herbicide_Mutants 20000642 Tissue Seedlings
    12657397 At_Line_Comparisons 20001300 Plant Line ME01338-05 vs. WS
    12657397 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS
    12657397 At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS
    12657397 At_Line_Comparisons 20001310 Plant Line WBin4-WX1 7-A vs. WS
    12657397 At_Line_Comparisons 20001319 Plant Line WBin4-WX24-A vs. WS
    12657397 At_Far-red-induction 20001451 Age (day) 8
    12657397 At_Far-red-induction 20001451 Timepoint (hr) 24
    12657397 At_Far-red-induction 20001451 Organism A. thaliana
    12657397 At_Far-red-induction 20001451 Plant Line Columbia
    12657397 At_Far-red-induction 20001451 Light Far-red vs. White
    12657397 At_Far-red-induction 20001451 Tissue Whole Plant
    12657397 At_Far-red-enriched 20001504 Timepoint (day) 6
    12657397 At_Far-red-enriched 20001504 Age (day) 10
    12657397 At_Far-red-enriched 20001504 Organism A. thaliana
    12657397 At_Far-red-enriched 20001504 Plant Line Columbia
    12657397 At_Far-red-enriched 20001504 Light Far-red enriched vs. White
    12657397 At_Far-red-enriched 20001504 Tissue Whole Plant
    12657397 At_Drought_Soil_Dry 20001554 Timepoint (day) 7
    12657397 At_Drought_Soil_Dry 20001554 Age (day) 21
    12657397 At_Drought_Soil_Dry 20001554 Organism A. thaliana
    12657397 At_Drought_Soil_Dry 20001554 Treatment Drought vs. No Drought
    12657397 At_Drought_Soil_Dry 20001554 Post Timepoint (hr) None
    12657397 At_Drought_Soil_Dry 20001554 Post-Treatment None
    12657397 At_Drought_Soil_Dry 20001554 Plant Line WS
    12657397 At_Drought_Soil_Dry 20001555 Timepoint (day) 10
    12657397 At_Drought_Soil_Dry 20001555 Age (day) 24
    12657397 At_Drought_Soil_Dry 20001555 Organism A. thaliana
    12657397 At_Drought_Soil_Dry 20001555 Treatment Drought vs. No Drought
    12657397 At_Drought_Soil_Dry 20001555 Post Timepoint (hr) None
    12657397 At_Drought_Soil_Dry 20001555 Post-Treatment None
    12657397 At_Drought_Soil_Dry 20001555 Plant Line WS
    12657397 At_Drought_Soil_Dry 20001556 Timepoint (day) 12
    12657397 At_Drought_Soil_Dry 20001556 Age (day) 26
    12657397 At_Drought_Soil_Dry 20001556 Organism A. thaliana
    12657397 At_Drought_Soil_Dry 20001556 Treatment Drought vs. No Drought
    12657397 At_Drought_Soil_Dry 20001556 Post Timepoint (hr) None
    12657397 At_Drought_Soil_Dry 20001556 Post-Treatment None
    12657397 At_Drought_Soil_Dry 20001556 Plant Line WS
    12657397 At_Drought_Soil_Dry 20001557 Post Timepoint (hr) 3
    12657397 At_Drought_Soil_Dry 20001557 Timepoint (day) 13
    12657397 At_Drought_Soil_Dry 20001557 Age (day) 27
    12657397 At_Drought_Soil_Dry 20001557 Organism A. thaliana
    12657397 At_Drought_Soil_Dry 20001557 Treatment Drought vs. No Drought
    12657397 At_Drought_Soil_Dry 20001557 Post-Treatment Re-Water vs. No Drought
    12657397 At_Drought_Soil_Dry 20001557 Plant Line WS
    12657397 At_Drought_Soil_Dry 20001559 Timepoint (day) 14
    12657397 At_Drought_Soil_Dry 20001559 Age (day) 26
    12657397 At_Drought_Soil_Dry 20001559 Post Timepoint (hr) 29
    12657397 At_Drought_Soil_Dry 20001559 Organism A. thaliana
    12657397 At_Drought_Soil_Dry 20001559 Treatment Drought vs. No Drought
    12657397 At_Drought_Soil_Dry 20001559 Post-Treatment Re-Water vs. No Drought
    12657397 At_Drought_Soil_Dry 20001559 Plant Line WS
    12657397 At_Drought_Soil_Dry 20001560 Timepoint (day) 14
    12657397 At_Drought_Soil_Dry 20001560 Age (day) 28
    12657397 At_Drought_Soil_Dry 20001560 Organism A. thaliana
    12657397 At_Drought_Soil_Dry 20001560 Treatment Drought vs. No Drought
    12657397 At_Drought_Soil_Dry 20001560 Post Timepoint (hr) None
    12657397 At_Drought_Soil_Dry 20001560 Post-Treatment None
    12657397 At_Drought_Soil_Dry 20001560 Plant Line WS
    12657397 At_Drought_Reproduction 20001904 Timepoint (day) 7
    12657397 At_Drought_Reproduction 20001904 Age (day) 37
    12657397 At_Drought_Reproduction 20001904 Organism A. thaliana
    12657397 At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought
    12657397 At_Drought_Reproduction 20001904 Tissue Rosettes
    12657397 At_Drought_Reproduction 20001904 Plant Line WS
    12657397 At_Drought_Reproduction 20001906 Timepoint (day) 5
    12657397 At_Drought_Reproduction 20001906 Age (day) 35
    12657397 At_Drought_Reproduction 20001906 Organism A. thaliana
    12657397 At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought
    12657397 At_Drought_Reproduction 20001906 Tissue Siliques
    12657397 At_Drought_Reproduction 20001906 Plant Line WS
    12657397 At_Drought_Reproduction 20001907 Timepoint (day) 7
    12657397 At_Drought_Reproduction 20001907 Age (day) 37
    12657397 At_Drought_Reproduction 20001907 Organism A. thaliana
    12657397 At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought
    12657397 At_Drought_Reproduction 20001907 Tissue Siliques
    12657397 At_Drought_Reproduction 20001907 Plant Line WS
    12657397 At_Drought_Reproduction 20001909 Timepoint (day) 5
    12657397 At_Drought_Reproduction 20001909 Age (day) 35
    12657397 At_Drought_Reproduction 20001909 Organism A. thaliana
    12657397 At_Drought_Reproduction 20001909 Treatment Drought vs. No Drought
    12657397 At_Drought_Reproduction 20001909 Tissue Flowers
    12657397 At_Drought_Reproduction 20001909 Plant Line WS
    12657397 At_Line_Comparisons 20002009 Plant Line ME01642 vs. WS
    12657397 At_Drought-Air-Dry 20002256 Timepoint (hr) 4
    12657397 At_Drought-Air-Dry 20002256 Age (day) 35
    12657397 At_Drought-Air-Dry 20002256 Organism A. thaliana
    12657397 At_Drought-Air-Dry 20002256 Treatment Drought vs. No Drought
    12657397 At_Drought-Air-Dry 20002256 Tissue Shoots
    12657397 At_Drought-Air-Dry 20002256 Plant Line WS
    Promoter YP0356
    Modulates the gene: Dehydration-induced protein RD22
    The GenBank description of the geneNM_122472 Arabidopsis thaliana dehydration-induced protein
    RD22 (At5g25610) mRNA, complete cds gi|30689960|ref|NM_122472.2|[30689960]
    The promoter sequence:
    5′tacttgcaaccactttgtaggaccattaactgcaaaataagaattctctaagcttcacaaggggttcgt
    ttggtgctataaaaacattgttttaagaactggtttactggttctataaatctataaatccaaatatgaag
    tatggcaataataataacatgttagcacaaaaaatactcattaaattcctacccaaaaaaaatctttatat
    gaaactaaaacttatatacacaataatagtgatacaaagtaggtcttgatattcaactattcgggattttc
    tggtttcgagtaattcgtataaaaggtttaagatctattatgttcactgaaatcttaactttgttttgttt
    ccagttttaactagtagaaattgaaagttttaaaaattgttacttacaataaaatttgaatcaatatcctt
    aatcaaaggatcttaagactagcacaattaaaacatataacgtagaatatctgaaataactcgaaaatatc
    tgaactaagttagtagttttaaaatataatcccggtttggaccgggcagtatgtacttcaatacttgtggg
    ttttgacgattttggatcggattgggcgggccagccagattgatctattacaaatttcacctgtcaacgct
    aactccgaacttaatcaaagattttgagctaaggaaaactaatcagtgatcacccaaagaaaacattcgtg
    aataattgtttgctttccatggcagcaaaacaaataggacccaaataggaatgtcaaaaaaaagaaagaca
    cgaaacgaagtagtataacgtaacacacaaaaataaactagagatattaaaaacacatgtccacacatgga
    tacaagagcatttaaggagcagaaggcacgtagtggttagaaggtatgtgatataattaatcggcccaaat
    agattggtaagtagtagccgtcTATAtca 3′-
    cagctcctttctactaaaacccttttactataaattctacgtacacgtaccacttcttctcctcaaattca
    tcaaacccatttctattccaactcccaaaaATG
    The promoter was cloned from the organism: Arabidopsis thaliana, WS ecotype
    Alternative nucleotides:
    Predicted (Columbia)
    Experimental (Wassilewskija)
    Predicted Position (bp) Mismatch Columbia/Wassilewskija
    405 SNP g/t
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower H pedicel H petal H epidermis
    Silique H stigma L style L carpel L septum Lepidermis
    Ovule H outer integument
    Stem H epidermis H stomata
    Hypocotyl H epidermis
    Cotyledon H epidermis
    Rosette Leaf H epidermis H trichome
    Observed expression pattern of the promoter-marker vector was in:
    T1 mature: GFP expression specific to epidermal call types. High GFP expression in epidermis of stem
    decreasing toward pedicles and inflorescence apex. In the flower, high expression observed in epidermal
    cells of petals and stigma, and lower expression in carpels. High expression in outer integuments of
    matureing ovules. High expression throughout epidermal cells of mature lower stem.
    T2 seedling: GEP expression specific to epidermal cell types. High expression in epidermis of hypocotyl,
    cotyledon, and trichomes of rosette leaves. Not detected in root.
    Misc. promoter information:  Bidirectionality: Pass  Exons: Pass  Repeats: None:
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12394809
    cDNA nucleotide sequence:
    agCTCCTTTCTACTAAAACCCTTTTACTATAAATTCTAGGTACACGTACCACTTCTTCTCCTCAA
    ATTCATCAAACCCATTTCTATTCCAACTCCCAAAAATGGCGATTCGTGTTCCTCTGATCTGTCT
    TCTTGGTTCATTCATGGTAGTGGCGATTGCGGCTGATTTAACACCGGAGCGTTATTGGAGCAC
    TGGTTTACCAAACACTCCCATTCCCAACTCTCTCCATAATCTTTTGACTTTCGATTTTACCGACG
    AGAAAAGTACCAACGTCCAAGTAGGTAAAGGCGGAGTAAACGTTAACACCCATAAAGGTAAA
    ACCGGTAGCGGAACCGCCGTGAACGTTGGAAAGGGAGGTGTACGCGTGGACACAGGCAAGGG
    CAAGCCCGGAGGAGGGACACACGTGAGCGTTGGCAGGGGAAAAGGTCACGGAGGTGGCGTCG
    CAGTCGACACGGGTAAACCCGGTAAAAGAACCGACGTAGGAGTCGGTAAAGGCGGTGTGACG
    GTGCACACGCGCCACAAGGGAAGACCGATTTACGTTGGTGTGAAACCAGGAGCAAACCCTTTC
    GTGTATAACTATGCAGCGAAGGAGACTCAGCTCCACGACGATCCTAACGCGGCTCTCTTCTTC
    TTGGAGAAGGACTTGGTTCGCGGGAAAGAAATGAATGTCCGGTTTAACGCTGAGGATGGTTA
    CGGAGGCAAAACTGCGTTCTTGCCACGTGGAGAGGCTGAAACGGTGCCTTTTGGATCGGAGA
    AGTTTTCGGAGACGTTGAAACGTTTCTCGGTGGAAGCTGGTTCGGAAGAAGCGGAGATGATG
    AAGAAGACCATTGAGGAGTGTGAAGCCAGAAAAGTTAGTGGAGAGGAGAAGTATTGTGCGAC
    GTCTTTGGAGTCGATGGTCGACTTTAGTGTTTCGAAACTTGGTAAATATCACGTCAGGGCTGTT
    TCGACTGAGGTGGCTAAGAAGAACGCACCGATGCAGAAGTACAAAATCGCGGCGGCTGGGGT
    AAAGAAGTTGTCTGACGATAAATCTGTGGTGTGTCACAAACAGAAGTACCCATTCGCGGTGTT
    CTACTGCCACAAGGCGATGATGACGACCGTCTACGCGGTTCCGCTCGAGGGAGAGAACGGGA
    TGCGAGCTAAAGCAGTTGCGGTATGCCACAAGAACACCTCAGCTTGGAACCCAAACCACTTGG
    CCTTCAAAGTGTTAAAGGTGAAGCCAGGGACCGTTCCGGTCTGCCACTTCCTCCCGGAGACTC
    ATGTTGTGTGGTTCAGCTACTAGATAGATCTGTTTTCTATCTTATTGTGGGTTATGTATAATTA
    CGTTTCAGATAATCTATCTTTTGGGATGTTTTGGTTATGAATATACATACATATACATATAGTA
    ATGCGTGGTTTCCATATAAGAGTGAAGGCATCTATATGTTTTTTTTTTTATTAACCTACGTAGC
    TGTCTTTTGTGGTCTGTATCTTGTGGTTTTGCAAAAACCTATAATAAAATTAGAGCTGAAATGT
    TACCATTTC
    Coding sequence:
    <MAIRLPLICLLGSFMVVAIA>
    ADLTPERYWSTALPNTPIPNSLHNLLTFDFTDEKSTNVQVGKGGVNVNTHKGKTGSGTAVNVGK
    GGVRVDTGKGKPGGGTHVSVGSGKGHGGGVAVHTGKPGKRTDVGVGKGGVTVHTRHKGRPIY
    VGVKPGANPFVYNYAAKETQLHDDPNAALFFLEKDLVRGKEMNVRFNAEDGYGGKTAFLPRGE
    AETVPFGSEKFSETLKRFSVEAGSEEAEMMKKTIEECEARKVSGEEKYCATSLESMVDFSVSKLGK
    YHVRAVSTEVAKKNAPMQKYKIAAAGVKKLSDDKSVVCHKQKYPFAVFYCHKAMMTTVYAVP
    LEGENGMRAKAVAVCHKNTSAWNPNHLAFKVLKVKPGTVPVCHFLPETHVVWFSY*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12394809 At_100uM_ABA_Mutants 20000071 +
    12394809 At_100uM_ABA 20000169 +
    12394809 At_Roots 20000185 −
    12394809 At_Drought 20000267 +
    12394809 At_100mM_NaCl 20000268 +
    12394809 At_Pollen 20000326 −
    12394809 At_Drought 20000436 +
    12394809 At_Drought 20000437 +
    12394809 At_Roots 20000439 −
    12394809 At_100uM_ABA 20000453 +
    12394809 At_100uM_ABA_Mutants 20000573 −
    12394809 At_100uM_ABA_Mutants 20000574 −
    12394809 At_Far-red-induction 20001247 +
    12394809 At_Far-red-induction 20001248 −
    12394809 At_Line_Comparisons 20001310 −
    12394809 At_Interploidy_Crosses 20001316 −
    12394809 At_Far-red-induction 20001450 −
    12394809 At_Far-red-induction 20001451 −
    12394809 At_Drought_Soil_Dry 20001554 +
    12394809 At_Drought_Soil_Dry 20001555 +
    12394809 At_Drought_Soil_Dry 20001556 +
    12394809 At_Drought_Soil_Dry 20001559 +
    12394809 At_Interploidy_Crosses 20001853 +
    12394809 At_Drought_Reproduction 20001904 +
    12394809 At_Drought_Reproduction 20001911 +
    12394809 At_8deg_Cold 20002107 +
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12394809 At_100uM_ABA_Mutants 20000071 Timepoint (hr) 6
    12394809 At_100uM_ABA_Mutants 20000071 Treatment 100uM ABA vs. No Treatment
    12394809 At_100uM_ABA_Mutants 20000071 Tissue Aerial
    12394809 At_100uM_ABA_Mutants 20000071 Plant Line CS8104
    12394809 At_100uM_ABA 20000169 Timepoint (hr) 6
    12394809 At_100uM_ABA 20000169 Age (day) 14
    12394809 At_100uM_ABA 20000169 Treatment 100uM ABA vs. No Treatment
    12394809 At_100uM_ABA 20000169 Organism A. thaliana
    12394809 At_100uM_ABA 20000169 Tissue Aerial
    12394809 At_100uM_ABA 20000169 Plant Line WS
    12394809 At_Roots 20000185 Age (day) 7 vs. 21
    12394809 At_Roots 20000185 Organism A. thaliana
    12394809 At_Roots 20000185 Tissue Roots vs. Whole Plant
    12394809 At_Roots 20000185 Plant Line WS
    12394809 At_Drought 20000267 Timepoint (hr) 6
    12394809 At_Drought 20000267 Age (day) 7
    12394809 At_Drought 20000267 Organism A. thaliana
    12394809 At_Drought 20000267 Treatment Drought vs. No Drought
    12394809 At_Drought 20000267 Tissue Whole Plant
    12394809 At_Drought 20000267 Plant Line WS
    12394809 At_100mM_NaCl 20000268 Timepoint (hr) 6
    12394809 At_100mM_NaCl 20000268 Age (day) 14
    12394809 At_100mM_NaCl 20000268 Treatment 100mM NaCl vs. No
    Treatment
    12394809 At_100mM_NaCl 20000268 Organism A. thaliana
    12394809 At_100mM_NaCl 20000268 Tissue Whole Plant
    12394809 At_100mM_NaCl 20000268 Plant Line WS
    12394809 At_Pollen 20000326 Age (day) 0 vs. 21
    12394809 At_Pollen 20000326 Organism A. thaliana
    12394809 At_Pollen 20000326 Tissue Pollen vs. Whole Plant
    12394809 At_Pollen 20000326 Plant Line WS
    12394809 At_Drought 20000436 Age (day) 7
    12394809 At_Drought 20000436 Timepoint (hr) 12
    12394809 At_Drought 20000436 Organism A. thaliana
    12394809 At_Drought 20000436 Treatment Drought vs. No Drought
    12394809 At_Drought 20000436 Tissue Whole Plant
    12394809 At_Drought 20000436 Plant Line WS
    12394809 At_Drought 20000437 Age (day) 8
    12394809 At_Drought 20000437 Timepoint (hr) 24
    12394809 At_Drought 20000437 Organism A. thaliana
    12394809 At_Drought 20000437 Treatment Drought vs. No Drought
    12394809 At_Drought 20000437 Tissue Whole Plant
    12394809 At_Drought 20000437 Plant Line WS
    12394809 At_Roots 20000439 Age (day) 14 vs. 21
    12394809 At_Roots 20000439 Organism A. thaliana
    12394809 At_Roots 20000439 Tissue Roots vs. Whole Plant
    12394809 At_Roots 20000439 Plant Line WS
    12394809 At_100uM_ABA 20000453 Age (day) 15
    12394809 At_100uM_ABA 20000453 Timepoint (hr) 24
    12394809 At_100uM_ABA 20000453 Treatment 100uM ABA vs. No Treatment
    12394809 At_100uM_ABA 20000453 Organism A. thaliana
    12394809 At_100uM_ABA 20000453 Tissue Aerial
    12394809 At_100uM ABA 20000453 Plant Line WS
    12394809 At_100uM_ABA_Mutants 20000573 Organism A. thaliana
    12394809 At_100uM_ABA_Mutants 20000573 Plant Line CS22 vs. Ler wt
    12394809 At_100uM_ABA_Mutants 20000573 Timepoint (hr) N/A
    12394809 At_100uM_ABA_Mutants 20000573 Treatment None
    12394809 At_100uM_ABA_Mutants 20000573 Tissue Whole Plant
    12394809 At_100uM_ABA_Mutants 20000574 Organism A. thaliana
    12394809 At_100uM_ABA_Mutants 20000574 Plant Line CS23 vs. Ler wt
    12394809 At_100uM_ABA_Mutants 20000574 Timepoint (hr) N/A
    12394809 At_100uM_ABA_Mutants 20000574 Treatment None
    12394809 At_100uM_ABA_Mutants 20000574 Tissue Whole Plant
    12394809 At_Far-red-induction 20001247 Timepoint (hr) 1
    12394809 At_Far-red-induction 20001247 Age (day) 7
    12394809 At_Far-red-induction 20001247 Organism A. thaliana
    12394809 At_Far-red-induction 20001247 Plant Line Columbia
    12394809 At_Far-red-induction 20001247 Light Far-red vs. White
    12394809 At_Far-red-induction 20001247 Tissue Whole Plant
    12394809 At_Far-red-induction 20001248 Timepoint (hr) 4
    12394809 At_Far-red-induction 20001248 Age (day) 7
    12394809 At_Far-red-induction 20001248 Organism A. thaliana
    12394809 At_Far-red-induction 20001248 Plant Line Columbia
    12394809 At_Far-red-induction 20001248 Light Far-red vs. White
    12394809 At_Far-red-induction 20001248 Tissue Whole Plant
    12394809 At_Line_Comparisons 20001310 Plant Line WBin4-WX1 7-A vs. WS
    12394809 At_Interploidy_Crosses 20001316 Age (day) 5
    12394809 At_Interploidy_Crosses 20001316 Organism A. thaliana
    12394809 At_Interploidy_Crosses 20001316 Plant Line Columbia
    12394809 At_Interploidy_Crosses 20001316 Cross hemi × 2X vs. 2X × 2X
    12394809 At_Interploidy_Crosses 20001316 Tissue Siliques
    12394809 At_Far-red-induction 20001450 Age (day) 7
    12394809 At_Far-red-induction 20001450 Timepoint (hr) 8
    12394809 At_Far-red-induction 20001450 Organism A. thaliana
    12394809 At_Far-red-induction 20001450 Plant Line Columbia
    12394809 At_Far-red-induction 20001450 Light Far-red vs. White
    12394809 At_Far-red-induction 20001450 Tissue Whole Plant
    12394809 At_Far-red-induction 20001451 Age (day) 8
    12394809 At_Far-red-induction 20001451 Timepoint (hr) 24
    12394809 At_Far-red-induction 20001451 Organism A. thaliana
    12394809 At_Far-red-induction 20001451 Plant Line Columbia
    12394809 At_Far-red-induction 20001451 Light Far-red vs. White
    12394809 At_Far-red-induction 20001451 Tissue Whole Plant
    12394809 At_Drought_Soil_Dry 20001554 Timepoint (day) 7
    12394809 At_Drought_Soil_Dry 20001554 Age (day) 21
    12394809 At_Drought_Soil_Dry 20001554 Organism A. thaliana
    12394809 At_Drought_Soil_Dry 20001554 Treatment Drought vs. No Drought
    12394809 At_Drought_Soil_Dry 20001554 Post Timepoint (hr) None
    12394809 At_Drought_Soil_Dry 20001554 Post-Treatment None
    12394809 At_Drought_Soil_Dry 20001554 Plant Line WS
    12394809 At_Drought_Soil_Dry 20001555 Timepoint (day) 10
    12394809 At_Drought_Soil_Dry 20001555 Age (day) 24
    12394809 At_Drought_Soil_Dry 20001555 Organism A. thaliana
    12394809 At_Drought_Soil_Dry 20001555 Treatment Drought vs. No Drought
    12394809 At_Drought_Soil_Dry 20001555 Post Timepoint (hr) None
    12394809 At_Drought_Soil_Dry 20001555 Post-Treatment None
    12394809 At_Drought_Soil_Dry 20001555 Plant Line WS
    12394809 At_Drought_Soil_Dry 20001556 Timepoint (day) 12
    12394809 At_Drought_Soil_Dry 20001556 Age (day) 26
    12394809 At_Drought_Soil_Dry 20001556 Organism A. thaliana
    12394809 At_Drought_Soil_Dry 20001556 Treatment Drought vs. No Drought
    12394809 At_Drought_Soil_Dry 20001556 Post Timepoint (hr) None
    12394809 At_Drought_Soil_Dry 20001556 Post-Treatment None
    12394809 At_Drought_Soil_Dry 20001556 Plant Line WS
    12394809 At_Drought_Soil_Dry 20001559 Timepoint (day) 14
    12394809 At_Drought_Soil_Dry 20001559 Age (day) 28
    12394809 At_Drought_Soil_Dry 20001559 Post Timepoint (hr) 29
    12394809 At_Drought_Soil_Dry 20001559 Organism A. thaliana
    12394809 At_Drought_Soil_Dry 20001559 Treatment Drought vs. No Drought
    12394809 At_Drought_Soil_Dry 20001559 Post-Treatment Re-Water vs. No Drought
    12394809 At_Drought_Soil_Dry 20001559 Plant Line WS
    12394809 At_Interploidy_Crosses 20001853 Age (day) 5
    12394809 At_Interploidy_Crosses 20001853 Organism A. thaliana
    12394809 At_Interploidy_Crosses 20001853 Plant Line Columbia
    12394809 At_Interploidy_Crosses 20001853 Cross Fis1 vs. 2X × 2X
    12394809 At_Interploidy_Crosses 20001853 Tissue Siliques
    12394809 At_Drought_Reproduction 20001904 Timepoint (day) 7
    12394809 At_Drought_Reproduction 20001904 Age (day) 37
    12394809 At_Drought_Reproduction 20001904 Organism A. thaliana
    12394809 At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought
    12394809 At_Drought_Reproduction 20001904 Tissue Rosettes
    12394809 At_Drought_Reproduction 20001904 Plant Line WS
    12394809 At_Drought_Reproduction 20001911 Timepoint (day) 10
    12394809 At_Drought_Reproduction 20001911 Age (day) 40
    12394809 At_Drought_Reproduction 20001911 Organism A. thaliana
    12394809 At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought
    12394809 At_Drought_Reproduction 20001911 Tissue Flowers
    12394809 At_Drought_Reproduction 20001911 Plant Line WS
    12394809 At_8deg_Cold 20002107 Age (day) 11
    12394809 At_8deg_Cold 20002107 Timepoint (hr) 96
    12394809 At_8deg_Cold 20002107 Temperature (deg C.) 8 vs. 22
    12394809 At_8deg_Cold 20002107 Organism A. thaliana
    12394809 At_8deg_Cold 20002107 Tissue Whole Plant
    12394809 At_8deg_Cold 20002107 Plant Line WS
    Promoter YP0337
    Modulates the gene: Unknown protein.
    The GenBank description of the gene: NM_101546 Arabidopsis thaliana expressed protein (At1g16850)
    mRNA, complete cds gi|18394408|ref|NM_101546.1|[18394408]
    The promoter sequence:
    5′acttattagtttaggtttccatcacctatttaattcgtaattcttatacatgcatgcatataatagagataca
    tatatacaaatttatgatcatttttgcacaacatgtgatctcattcattagtatgcattatgcgaaaacct
    cgacgcgcaaaagacacgtaatagctaataatgttactcatttataatgattgaagcaagacgaaaacaac
    aacatatatatcaaattgtaaactagatatttcttaaaagtgaaaaaaaacaaagaaatataaaggacaat
    tttgagtcagtctcttaatattaaaacatatatacataaataagcacaaacgtggttacctgtcttcatgc
    aatgtggactttagtttatctaatcaaaatcaaaataaaaggtgtaatagttctcgtcatttttcaaattt
    taaaaatcagaaccaagtgatttttgtttgagtattgatccattgtttaaacaatttaacacagtatatac
    gtctcttgagatgttgacatgatgataaaatacgagatcgtctcttggttttcgaattttgaactttaata
    gtttttttttttagggaaactttaatagttgtttatcataagattagtcacctaatggttacgttgcagta
    ccgaaccaattttttacccttttttctaaatgtggtcgtggcataatttccaaaagagatccaaaacccgg
    tttgctcaactgataagccggtcggttctggtttgaaaaacaagaaataatctgaaagtgtgaaacagcaa
    cgtgtctcggtgtttcatgagccacctgccacctcattcacgtcggtcattttgtcgtttcacggttcacg
    ctctagacacgtgctctgtccccaccatgactttcgctgccgactcgcttcgctttgcaaactcaaacatg
    tgtgTATAtgtaagtttcatcctaataag 3′-caaagaaaacatcaaaATG
    The promoter was cloned from the organism: Arabidopsis thaliana, WS ecotype
    Alternative nucleotides:
    Predicted (Columbia)
    Experimental (Wassilewskija)
    Sequence (bp) Mismatch Columbia/Vassilewskija
    597 SNP t/c
    996 SNP t/a
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Primary Root L epidermis L trichoblast L atrichoblast L root hair
    Observed expression pattern of the promoter-marker vector was in:
    T1 mature: No expression.
    T2 seedling: Low expression in root epidermal cells at transition zone decreasing to expression in single
    cells at mid root
    Misc. promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12326510
    cDNA nucleotide sequence:
    ACCACATTAATTTAAAACAAAGAAAACATCAAAATGGCTGAAAAAGTAAAGTCTGGTCAAGTT
    TTTAACCTATTATGCATATTCTCGATCTTTTTCTTCCTCTTTGTGTTATCAGTGAATGTTTCGGC
    TGATGTCGATTCTGAGAGAGCGGTGCCATCTGAAGATAAAACGACGACTGTTTGGCTAACTAA
    AATCAAACGGTCCGGTAAAAATTATTGGGCTAAAGTTAGAGAGACTTTGGATCGTGGACAGTC
    GCACTTCTTTCCTCCGAACACATATTTTACGGGAAAGAATGATGCGCCGATGGGAGCCGGTGA
    AAATATGAAAGAGGCGGCGACGAGGAGCTTTGAGCATAGCAAAGCGACGGTGGAGGAAGCTG
    CTAGATCAGCGGGAGAAGTGGTGAGTGATACGGCGGAAGCTGTGAAAGAAAAGGTGAAGAGG
    AGCGTTTCCGGTGGAGTGACGCAGCCGTCGGAGGGATCTGAGGAGCTATAAATACGCAGTTGT
    TCTAAGCTTATGGGTTTTAATTATTTAAATAATTAGTGTGTGTTTGAGATCAAAATGACACAGT
    TTTGGGGGAGTATATCTCCACATCATATGTTGTTTGCATCACATGGTTTCTCTGTATACAACGA
    CCAGATCCACATCACTCATTCTCGTCCTTCTTTTTGTCATGAATACAGAATAATATTTTAGATT
    CTAC
    Coding sequence:
    MAEKVKSGQVFNLLCIFSIFFFLFVLSVNVSADVDSERAVPSEDKTTTVWLTKIKRSGKNYWAKVR
    ETLDRGQSHFFPPNTYFTGKNDAPMGAGENMKEAATRSFEHSKATVEEAARSAAEVVSDTAEAV
    KEKVKRSVSGGVTQPSEGSEEL*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12326510 At_Germinating_Seeds 108461 −
    12326510 At_Germinating_Seeds 108462 −
    12326510 At_Germinating_Seeds 108464 −
    12326510 At_Drought_Flowers 108473 +
    12326510 At_ap2_floral_buds 108501 −
    12326510 At_100uM_ABA 108560 +
    12326510 At_100uM_ABA 108561 +
    12326510 At_Drought 108572 +
    12326510 At_Drought 108573 −
    12326510 At_Wounding 108574 +
    12326510 At_4deg_Cold 108579 +
    12326510 At_15mM_NH4NO3_L-to-H 108588 −
    12326510 At_15mM_NH4NO3_L-to-H 108589 −
    12326510 At_15mM_NH4NO3_L-to-H 108590 −
    12326510 At_15mM_NH4NO3_L-to-H 108591 −
    12326510 At_Ler-rhl_Root 108594 +
    12326510 At_Ler-pi_Ovule 108595 +
    12326510 At_100uM_ABA 108605 +
    12326510 At_100uM_ABA 108606 +
    12326510 At_100uM_ABA 108607 +
    12326510 At_100uM_ABA 108608 +
    12326510 At_100uM_ABA 108609 +
    12326510 At_100uM_ABA_Mutants 108624 −
    12326510 At_100uM_ABA_Mutants 20000069 +
    12326510 At_100uM_ABA_Mutants 20000070 +
    12326510 At_100uM_ABA_Mutants 20000071 +
    12326510 At_100uM_ABA_Mutants 20000072 +
    12326510 At_100uM_ABA_Mutants 20000086 +
    12326510 At_100uM_ABA_Mutants 20000087 +
    12326510 At_100uM_ABA_Mutants 20000088 +
    12326510 At_2mM_SA_CS3726-Columbia 20000089 +
    12326510 At_2mM_SA_CS3726-Columbia 20000090 +
    12326510 At_100uM_ABA_Mutants 20000117 +
    12326510 At_100uM_ABA 20000166 +
    12326510 At_100uM_ABA 20000169 +
    12326510 At_Germinating_Seeds 20000179 −
    12326510 At_Germinating_Seeds 20000180 −
    12326510 At_Shoots 20000184 −
    12326510 At_Root-Tips-vs-Tops 20000227 +
    12326510 At_Drought 20000267 +
    12326510 At_100mM_NaCl 20000268 +
    12326510 At_100mM_NaCl 20000308 +
    12326510 At_Drought 20000436 +
    12326510 At_Drought 20000437 +
    12326510 At_1uM_BR-BRZ 20000441 −
    12326510 At_1uM_BR-BRZ 20000443 −
    12326510 At_100uM_ABA 20000453 +
    12326510 At_Guard_Cells 20000495 −
    12326510 At_100uM_ABA_Mutants 20000573 −
    12326510 At_100uM_ABA_Mutants 20000574 −
    12326510 At_100uM_ABA_Mutants 20000575 +
    12326510 At_100uM_ABA_Mutants 20000576 +
    12326510 At_15mM_NH4NO3_L-to-H 20000709 −
    12326510 At_Far-red-induction 20001248 +
    12326510 At_Line_Comparisons 20001309 −
    12326510 At_Line_Comparisons 20001310 −
    12326510 At_Far-red-induction 20001450 +
    12326510 At_Far-red-induction 20001451 +
    12326510 At_Drought_Soil_Dry 20001553 +
    12326510 At_Drought_Soil_Dry 20001554 +
    12326510 At_Drought_Soil_Dry 20001555 +
    12326510 At_Drought_Soil_Dry 20001556 +
    12326510 At_Drought_Soil_Dry 20001557 +
    12326510 At_Drought_Soil_Dry 20001559 +
    12326510 At_Far-red-enriched-adult 20001770 +
    12326510 At_Interploidy-Crosses 20001853 +
    12326510 At_Drought_Reproduction 20001904 +
    12326510 At_Drought_Reproduction 20001905 +
    12326510 At_Drought_Reproduction 20001906 +
    12326510 At_Drought_Reproduction 20001907 +
    12326510 At_Drought_Reproduction 20001908 +
    12326510 At_Drought_Reproduction 20001911 +
    12326510 At_Line_Comparisons 20002009 +
    12326510 At_8deg_Cold 20002105 +
    12326510 At_8deg_Cold 20002107 +
    12326510 At_8deg_Cold 20002108 +
    12326510 At_8deg_Cold 20002109 +
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12326510 At_Germinating_Seeds 108461 Age (day) 1 vs. 0
    12326510 At_Germinating-Seeds 108461 Tissue Germinating
    Seeds
    12326510 At_Germinating_Seeds 108462 Age (day) 2 vs. 0
    12326510 At_Germinating_Seeds 108462 Tissue Germinating
    Seeds
    12326510 At_Germinating_Seeds 108464 Age (day) 4 vs. 0
    12326510 At_Germinating_Seeds 108464 Tissue Germinating
    Seeds
    12326510 At_Drought_Flowers 108473 Timepoint (hr) 7 d
    12326510 At_Drought_Flowers 108473 Treatment Drought vs. No
    Drought
    12326510 At_Drought_Flowers 108473 Tissue Flower
    12326510 At_ap2_floral_buds 108501 Plant Line ap2 (Ler.)
    12326510 At_ap2_floral_buds 108501 Tissue Closed Flower
    12326510 At_100uM_ABA 108560 Timepoint (hr) 1
    12326510 At_100uM_ABA 108560 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA 108560 Tissue Aerial
    12326510 At_100uM_ABA 108561 Timepoint (hr) 6
    12326510 At_100uM_ABA 108561 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA 108561 Tissue Aerial
    12326510 At_Drought 108572 Timepoint (hr) 1
    12326510 At_Drought 108572 Tissue Aerial
    12326510 At_Drought 108572 Treatment Drought vs. No
    Drought
    12326510 At_Drought 108573 Timepoint (hr) 6
    12326510 At_Drought 108573 Tissue Aerial
    12326510 At_Drought 108573 Treatment Drought vs. No
    Drought
    12326510 At_Wounding 108574 Timepoint (hr) 1
    12326510 At_Wounding 108574 Tissue Aerial
    12326510 At_Wounding 108574 Treatment Wounding vs.
    No Wounding
    12326510 At_4deg_Cold 108579 Timepoint (hr) 6
    12326510 At_4deg_Cold 108579 Temperature 4 vs. 22
    (deg C.)
    12326510 At_4deg_Cold 108579 Tissue Aerial
    12326510 At_15mM_NH4NO3_L-to-H 108588 Timepoint (hr) 2
    12326510 At_15mM_NH4NO3_L-to-H 108588 Treatment 15mM
    NH4NO3 vs.
    30mM
    Mannitol
    12326510 At_15mM_NH4NO3_L-to-H 108588 Tissue Aerial
    12326510 At_15mM_NH4NO3_L-to-H 108589 Timepoint (hr) 6
    12326510 At_15mM_NH4NO3_L-to-H 108589 Treatment 15mM
    NH4NO3 vs.
    30mM
    Mannitol
    12326510 At_15mM_NH4NO3_L-to-H 108589 Tissue Aerial
    12326510 At 15mM NH4NO3 L-to-H 108590 Timepoint (hr) 9
    12326510 At_15mM_NH4NO3_L-to-H 108590 Treatment 15mM
    NH4NO3 vs.
    30mM
    Mannitol
    12326510 At_15mM_NH4NO3_L-to-H 108590 Tissue Aerial
    12326510 At_15mM_NH4NO3_L-to-H 108591 Timepoint (hr) 12
    12326510 At_15mM_NH4NO3_L-to-H 108591 Treatment 15mM
    NH4NO3 vs.
    30mM
    Mannitol
    12326510 At_15mM_NH4NO3_L-to-H 108591 Tissue Aerial
    12326510 At_Ler-rhl_Root 108594 Plant Line Ler_rhl
    12326510 At_Ler-rhl_Root 108594 Tissue Roots
    12326510 At_Ler-pi_Ovule 108595 Plant Line Ler_pi
    12326510 At_Ler-pi_Ovule 108595 Tissue Ovules
    12326510 At_100uM_ABA 108605 Timepoint (hr) 6
    12326510 At_100uM_ABA 108605 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA 108605 Tissue Aerial
    12326510 At_100uM_ABA 108606 Timepoint (hr) 2
    12326510 At_100uM_ABA 108606 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA 108606 Tissue Aerial
    12326510 At_100uM_ABA 108607 Timepoint (hr) 4
    12326510 At_100uM_ABA 108607 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA 108607 Tissue Aerial
    12326510 At_100uM_ABA 108608 Timepoint (hr) 1
    12326510 At_100uM_ABA 108608 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA 108608 Tissue Aerial
    12326510 At_100uM_ABA 108609 Timepoint (hr) 24
    12326510 At_100uM_ABA 108609 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA 108609 Tissue Aerial
    12326510 At_100uM_ABA_Mutants 108624 Timepoint (hr) 6
    12326510 At_100uM_ABA_Mutants 108624 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA_Mutants 108624 Tissue Aerial
    12326510 At_100uM_ABA_Mutants 108624 Plant Line CS8105
    12326510 At_100uM_ABA_Mutants 20000069 Timepoint (hr) 6
    12326510 At_100uM_ABA_Mutants 20000069 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA_Mutants 20000069 Tissue Aerial
    12326510 At_100uM_ABA_Mutants 20000069 Plant Line CS23
    12326510 At_100uM_ABA_Mutants 20000070 Timepoint (hr) 6
    12326510 At_100uM_ABA_Mutants 20000070 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA_Mutants 20000070 Tissue Aerial
    12326510 At_100uM_ABA_Mutants 20000070 Plant Line CS24
    12326510 At_100uM_ABA_Mutants 20000071 Timepoint (hr) 6
    12326510 At_100uM_ABA_Mutants 20000071 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA_Mutants 20000071 Tissue Aerial
    12326510 At_100uM_ABA_Mutants 20000071 Plant Line CS8104
    12326510 At_100uM_ABA_Mutants 20000072 Timepoint (hr) 6
    12326510 At_100uM_ABA_Mutants 20000072 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA_Mutants 20000072 Tissue Aerial
    12326510 At_100uM_ABA_Mutants 20000072 Plant Line CS8105
    12326510 At_100uM_ABA_Mutants 20000086 Timepoint (hr) 6
    12326510 At_100uM_ABA_Mutants 20000086 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA_Mutants 20000086 Tissue Aerial
    12326510 At_100uM_ABA_Mutants 20000086 Plant Line CS22
    12326510 At_100uM_ABA_Mutants 20000087 Timepoint (hr) 6
    12326510 At_100uM_ABA_Mutants 20000087 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA_Mutants 20000087 Tissue Aerial
    12326510 At_100uM_ABA_Mutants 20000087 Plant Line WS
    12326510 At_100uM_ABA_Mutants 20000088 Timepoint (hr) 6
    12326510 At_100uM_ABA_Mutants 20000088 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA_Mutants 20000088 Tissue Aerial
    12326510 At_100uM_ABA_Mutants 20000088 Plant Line Landsberg
    12326510 At_2mM_SA_CS3726- 20000089 Timepoint (hr) 6
    Columbia
    12326510 At_2mM_SA_CS3726- 20000089 Treatment 2mM SA vs.
    Columbia No Treatment
    12326510 At_2mM_SA_CS3726- 20000089 Tissue Aerial
    Columbia
    12326510 At_2mM_SA_CS3726- 20000089 Plant Line CS3726
    Columbia
    12326510 At_2mM_SA_CS3726- 20000090 Timepoint (hr) 6
    Columbia
    12326510 At_2mM_SA_CS3726- 20000090 Treatment 2mM SA vs.
    Columbia No Treatment
    12326510 At_2mM_SA_CS3726- 20000090 Tissue Aerial
    Columbia
    12326510 At_2mM_SA_CS3726- 20000090 Plant Line Columbia
    Columbia
    12326510 At_100uM_ABA_Mutants 20000117 Timepoint(hr) 6
    12326510 At_100uM_ABA_Mutants 20000117 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA_Mutants 20000117 Tissue Aerial
    12326510 At_100uM_ABA_Mutants 20000117 Plant Line Columbia
    12326510 At_100uM_ABA 20000166 Timepoint (hr) 1
    12326510 At_100uM_ABA 20000166 Age (day) 14
    12326510 At_100uM_ABA 20000166 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA 20000166 Organism A. thaliana
    12326510 At_100uM_ABA 20000166 Tissue Aerial
    12326510 At_100uM_ABA 20000166 Plant Line WS
    12326510 At_100uM_ABA 20000169 Timepoint (hr) 6
    12326510 At_100uM_ABA 20000169 Age (day) 14
    12326510 At_100uM_ABA 20000169 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA 20000169 Organism A. thaliana
    12326510 At_100uM_ABA 20000169 Tissue Aerial
    12326510 At_100uM_ABA 20000169 Plant Line WS
    12326510 At_Germinating_Seeds 20000179 Age (hr) 6 vs. 0
    12326510 At_Germinating_Seeds 20000179 Organism A. thaliana
    12326510 At_Germinating_Seeds 20000179 Tissue Germinating
    Seeds
    12326510 At_Germinating_Seeds 20000179 Plant Line WS
    12326510 At_Germinating_Seeds 20000180 Age (hr) 24 vs. 0
    12326510 At Germinating_Seeds 20000180 Organism A. thaliana
    12326510 At_Germinating_Seeds 20000180 Tissue Germinating
    Seeds
    12326510 At_Germinating_Seeds 20000180 Plant Line WS
    12326510 At_Shoots 20000184 Age (day) 7 vs.21
    12326510 At_Shoots 20000184 Organism A. thaliana
    12326510 At_Shoots 20000184 Tissue Shoots vs.
    Whole Plant
    12326510 At_Shoots 20000184 Plant Line WS
    12326510 At_Root-Tips-vs-Tops 20000227 Age (day) 7, 10, 14
    12326510 At_Root-Tips-vs-Tops 20000227 Organism A. thaliana
    12326510 At_Root-Tips-vs-Tops 20000227 Tissue Root Tips vs.
    Root Tops
    12326510 At_Root-Tips-vs-Tops 20000227 Plant Line WS
    12326510 At_Drought 20000267 Timepoint (hr) 6
    12326510 At_Drought 20000267 Age (day) 7
    12326510 At_Drought 20000267 Organism A. thaliana
    12326510 At_Drought 20000267 Treatment Drought vs. No
    Drought
    12326510 At_Drought 20000267 Tissue Whole Plant
    12326510 At_Drought 20000267 Plant Line WS
    12326510 At_100mM_NaCl 20000268 Timepoint (hr) 6
    12326510 At_100mM_NaCl 20000268 Age (day) 14
    12326510 At_100mM_NaCl 20000268 Treatment 100mM NaCl
    vs. No
    Treatment
    12326510 At_100mM_NaCl 20000268 Organism A. thaliana
    12326510 At_100mM_NaCl 20000268 Tissue Whole Plant
    12326510 At_100mM_NaCl 20000268 Plant Line WS
    12326510 At_100mM_NaCl 20000308 Age (day) 17
    12326510 At_100mM_NaCl 20000308 Timepoint (hr) 72
    12326510 At_100mM_NaCl 20000308 Treatment 100mM NaCl
    vs. No
    Treatment
    12326510 At_100mM_NaCl 20000308 Organism A. thaliana
    12326510 At_100mM_NaCl 20000308 Tissue Whole Plant
    12326510 At_100mM_NaCl 20000308 Plant Line WS
    12326510 At_Drought 20000436 Age (day) 7
    12326510 At_Drought 20000436 Timepoint (hr) 12
    12326510 At_Drought 20000436 Organism A. thaliana
    12326510 At_Drought 20000436 Treatment Drought vs. No
    Drought
    12326510 At_Drought 20000436 Tissue Whole Plant
    12326510 At_Drought 20000436 Plant Line WS
    12326510 At_Drought 20000437 Age (day) 8
    12326510 At_Drought 20000437 Timepoint (hr) 24
    12326510 At_Drought 20000437 Organism A. thaliana
    12326510 At_Drought 20000437 Treatment Drought vs. No
    Drought
    12326510 At_Drought 20000437 Tissue Whole Plant
    12326510 At_Drought 20000437 Plant Line WS
    12326510 At_1uM_BR-BRZ 20000441 Treatment 1uM BR vs. No
    Treatment
    12326510 At_1uM_BR-BRZ 20000441 Tissue Shoot Apices
    12326510 At_1uM_BR-BRZ 20000443 Treatment 1uM BRZ vs.
    No Treatment
    12326510 At_1uM_BR-BRZ 20000443 Tissue Shoot Apices
    12326510 At_100uM_ABA 20000453 Age (day) 15
    12326510 At_100uM_ABA 20000453 Timepoint (hr) 24
    12326510 At_100uM_ABA 20000453 Treatment 100uM ABA
    vs. No
    Treatment
    12326510 At_100uM_ABA 20000453 Organism A. thaliana
    12326510 At_100uM_ABA 20000453 Tissue Aerial
    12326510 At_100uM_ABA 20000453 Plant Line WS
    12326510 At_Guard_Cells 20000495 Harvest Date Aug. 2, 2002
    12326510 At_Guard_Cells 20000495 Organism A. thaliana
    12326510 At_Guard_Cells 20000495 Tissue Guard Cells
    vs. Leaves
    12326510 At_100uM_ABA_Mutants 20000573 Organism A. thaliana
    12326510 At_100uM_ABA_Mutants 20000573 Plant Line CS22 vs. Ler
    wt
    12326510 At_100uM_ABA_Mutants 20000573 Timepoint (hr) N/A
    12326510 At_100uM_ABA_Mutants 20000573 Treatment None
    12326510 At_100uM_ABA_Mutants 20000573 Tissue Whole Plant
    12326510 At_100uM_ABA_Mutants 20000574 Organism A. thaliana
    12326510 At_100uM_ABA_Mutants 20000574 Plant Line CS23 vs. Ler
    wt
    12326510 At_100uM_ABA_Mutants 20000574 Timepoint (hr) N/A
    12326510 At_100uM_ABA_Mutants 20000574 Treatment None
    12326510 At_100uM_ABA_Mutants 20000574 Tissue Whole Plant
    12326510 At_100uM_ABA_Mutants 20000575 Timepoint (hr) 6
    12326510 At_100uM_ABA_Mutants 20000575 Treatment 1uM ABA vs.
    No Treatment
    12326510 At_100uM_ABA Mutants 20000575 Organism A. thaliana
    12326510 At_100uM_ABA_Mutants 20000575 Plant Line CS22
    12326510 At_100uM_ABA_Mutants 20000575 Tissue Whole Plant
    12326510 At_100uM_ABA_Mutants 20000576 Timepoint (hr) 6
    12326510 At_100uM_ABA_Mutants 20000576 Treatment 1uM ABA vs.
    No Treatment
    12326510 At_100uM_ABA_Mutants 20000576 Organism A. thaliana
    12326510 At_100uM_ABA_Mutants 20000576 Plant Line CS23
    12326510 At_100uM_ABA_Mutants 20000576 Tissue Whole Plant
    12326510 At_15mM_NH4NO3_L-to-H 20000709 Timepoint (hr) 4
    12326510 At_15mM_NH4NO3_L-to-H 20000709 Age (hr) 14
    12326510 At_15mM_NH4NO3_L-to-H 20000709 Treatment 15mM
    NH4NO3 vs.
    30mM
    Mannitol
    12326510 At_15mM_NH4NO3_L-to-H 20000709 Organism A. thaliana
    12326510 At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial
    12326510 At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS
    12326510 At_Far-red-induction 20001248 Timepoint (hr) 4
    12326510 At_Far-red-induction 20001248 Age (day) 7
    12326510 At_Far-red-induction 20001248 Organism A. thaliana
    12326510 At_Far-red-induction 20001248 Plant Line Columbia
    12326510 At_Far-red-induction 20001248 Light Far-red vs.
    White
    12326510 At_Far-red-induction 20001248 Tissue Whole Plant
    12326510 At_Line_Comparisons 20001309 Plant Line WBin4-
    WX49R-A vs.
    WS
    12326510 At_Line_Comparisons 20001310 Plant Line WBin4-WX17-
    A vs. WS
    12326510 At_Far-red-induction 20001450 Age (day) 7
    12326510 At_Far-red-induction 20001450 Timepoint (hr) 8
    12326510 At_Far-red-induction 20001450 Organism A. thaliana
    12326510 At_Far-red-induction 20001450 Plant Line Columbia
    12326510 At_Far-red-induction 20001450 Light Far-red vs.
    White
    12326510 At_Far-red-induction 20001450 Tissue Whole Plant
    12326510 At_Far-red-induction 20001451 Age (day) 8
    12326510 At_Far-red-induction 20001451 Timepoint (hr) 24
    12326510 At_Far-red-induction 20001451 Organism A. thaliana
    12326510 At_Far-red-induction 20001451 Plant Line Columbia
    12326510 At_Far-red-induction 20001451 Light Far-red vs.
    White
    12326510 At_Far-red-induction 20001451 Tissue Whole Plant
    12326510 At_Drought_Soil_Dry 20001553 Timepoint (day) 5
    12326510 At_Drought_Soil_Dry 20001553 Age (day) 19
    12326510 At_Drought_Soil_Dry 20001553 Organism A. thaliana
    12326510 At_Drought_Soil_Dry 20001553 Treatment Drought vs. No
    Drought
    12326510 At_Drought_Soil_Dry 20001553 Post Timepoint None
    12326510 At_Drought_Soil_Dry 20001553 Post-Treatment None
    12326510 At_Drought_Soil_Dry 20001553 Plant Line WS
    12326510 At_Drought_Soil_Dry 20001554 Timepoint (day) 7
    12326510 At_Drought_Soil_Dry 20001554 Age (day) 21
    12326510 At_Drought_Soil_Dry 20001554 Organism A. thaliana
    12326510 At_Drought_Soil_Dry 20001554 Treatment Drought vs. No
    Drought
    12326510 At_Drought_Soil_Dry 20001554 Post Timepoint None
    12326510 At_Drought_Soil_Dry 20001554 Post-Treatment None
    12326510 At_Drought_Soil_Dry 20001554 Plant Line WS
    12326510 At_Drought_Soil_Dry 20001555 Timepoint (day) 10
    12326510 At_Drought_Soil_Dry 20001555 Age (day) 24
    12326510 At_Drought_Soil_Dry 20001555 Organism A. thaliana
    12326510 At_Drought_Soil_Dry 20001555 Treatment Drought vs. No
    Drought
    12326510 At_Drought_Soil_Dry 20001555 Post Timepoint None
    12326510 At_Drought Soil Dry 20001555 Post-Treatment None
    12326510 At_Drought_Soil_Dry 20001555 Plant Line WS
    12326510 At_Drought_Soil_Dry 20001556 Timepoint (day) 12
    12326510 At_Drought_Soil_Dry 20001556 Age (day) 26
    12326510 At_Drought_Soil_Dry 20001556 Organism A. thaliana
    12326510 At_Drought_Soil_Dry 20001556 Treatment Drought vs. No
    Drought
    12326510 At_Drought_Soil_Dry 20001556 Post Timepoint None
    12326510 At_Drought_Soil_Dry 20001556 Post-Treatment None
    12326510 At_Drought_Soil_Dry 20001556 Plant Line WS
    12326510 At_Drought_Soil_Dry 20001557 Post Timepoint 3
    12326510 At_Drought_Soil_Dry 20001557 Timepoint (day) 13
    12326510 At_Drought_Soil_Dry 20001557 Age (day) 27
    12326510 At_Drought_Soil_Dry 20001557 Organism A. thaliana
    12326510 At_Drought_Soil_Dry 20001557 Treatment Drought vs. No
    Drought
    12326510 At_Drought_Soil_Dry 20001557 Post-Treatment Re-Water vs.
    No Drought
    12326510 At_Drought_Soil_Dry 20001557 Plant Line WS
    12326510 At_Drought_Soil_Dry 20001559 Timepoint (day) 14
    12326510 At_Drought_Soil_Dry 20001559 Age (day) 28
    12326510 At_Drought_Soil_Dry 20001559 Post Timepoint 29
    12326510 At_Drought_Soil_Dry 20001559 Organism A. thaliana
    12326510 At_Drought_Soil_Dry 20001559 Treatment Drought vs. No
    Drought
    12326510 At_Drought_Soil_Dry 20001559 Post-Treatment Re-Water vs.
    No Drought
    12326510 At_Drought_Soil_Dry 20001559 Plant Line WS
    12326510 At_Far-red-enriched-adult 20001770 Timepoint (hr) 8
    12326510 At_Far-red-enriched-adult 20001770 Age (day) 28
    12326510 At_Far-red-enriched-adult 20001770 Organism A. thaliana
    12326510 At_Far-red-enriched-adult 20001770 Tissue Aerial
    12326510 At_Far-red-enriched-adult 20001770 Plant Line Columbia
    12326510 At_Far-red-enriched-adult 20001770 Light Far-red
    enriched vs.
    White
    12326510 At_Interploidy_Crosses 20001853 Age (day) 5
    12326510 At_Interploidy_Crosses 20001853 Organism A. thaliana
    12326510 At_Interploidy_Crosses 20001853 Plant Line Columbia
    12326510 At_Interploidy_Crosses 20001853 Cross Fis1 vs. 2X ×
    2X
    12326510 At_Interploidy_Crosses 20001853 Tissue Siliques
    12326510 At_Drought_Reproduction 20001904 Timepoint (day) 7
    12326510 At_Drought_Reproduction 20001904 Age (day) 37
    12326510 At_Drought_Reproduction 20001904 Organism A. thaliana
    12326510 At_Drought_Reproduction 20001904 Treatment Drought vs. No
    Drought
    12326510 At_Drought_Reproduction 20001904 Tissue Rosettes
    12326510 At_Drought_Reproduction 20001904 Plant Line WS
    12326510 At_Drought_Reproduction 20001905 Timepoint (day) 10
    12326510 At_Drought_Reproduction 20001905 Age (day) 40
    12326510 At_Drought_Reproduction 20001905 Organism A. thaliana
    12326510 At_Drought_Reproduction 20001905 Treatment Drought vs. No
    Drought
    12326510 At_Drought_Reproduction 20001905 Tissue Rosettes
    12326510 At_Drought_Reproduction 20001905 Plant Line WS
    12326510 At_Drought_Reproduction 20001906 Timepoint (day) 5
    12326510 At_Drought_Reproduction 20001906 Age (day) 35
    12326510 At_Drought_Reproduction 20001906 Organism A. thaliana
    12326510 At_Drought_Reproduction 20001906 Treatment Drought vs. No
    Drought
    12326510 At_Drought_Reproduction 20001906 Tissue Siliques
    12326510 At_Drought_Reproduction 20001906 Plant Line WS
    12326510 At_Drought_Reproduction 20001907 Timepoint (day) 7
    12326510 At_Drought_Reproduction 20001907 Age (day) 37
    12326510 At_Drought_Reproduction 20001907 Organism A. thaliana
    12326510 At_Drought_Reproduction 20001907 Treatment Drought vs. No
    Drought
    12326510 At_Drought_Reproduction 20001907 Plant Line WS
    12326510 At_Drought_Reproduction 20001908 Timepoint (day) 10
    12326510 At_Drought_Reproduction 20001908 Age (day) 40
    12326510 At_Drought_Reproduction 20001908 Organism A. thaliana
    12326510 At_Drought_Reproduction 20001908 Treatment Drought vs. No
    Drought
    12326510 At_Drought_Reproduction 20001908 Tissue Siliques
    12326510 At_Drought_Reproduction 20001908 Plant Line WS
    12326510 At_Drought_Reproduction 20001911 Timepoint (day) 10
    12326510 At_Drought_Reproduction 20001911 Age (day) 40
    12326510 At_Drought_Reproduction 20001911 Organism A. thaliana
    12326510 At_Drought_Reproduction 20001911 Treatment Drought vs. No
    Drought
    12326510 At_Drought_Reproduction 20001911 Tissue Flowers
    12326510 At_Drought_Reproduction 20001911 Plant Line WS
    12326510 At_Line_Comparisons 20002009 Plant Line ME01642 vs.
    Ws
    12326510 At_8deg_Cold 20002105 Age (day) 7
    12326510 At_8deg_Cold 20002105 Timepoint (hr) 8
    12326510 At_8deg_Cold 20002105 Temperature 8 vs. 22
    (deg C.)
    12326510 At_8deg_Cold 20002105 Organism A. thaliana
    12326510 At_8deg_Cold 20002105 Tissue Whole Plant
    12326510 At_8deg_Cold 20002105 Plant Line WS
    12326510 At_8deg_Cold 20002107 Age (day) 11
    12326510 At_8deg_Cold 20002107 Timepoint (hr) 96
    12326510 At_8deg_Cold 20002107 Temperature 8 vs. 22
    (deg C.)
    12326510 At_8deg_Cold 20002107 Organism A. thaliana
    12326510 At_8deg_Cold 20002107 Tissue Whole Plant
    12326510 At_8deg_Cold 20002107 Plant Line WS
    12326510 At_8deg_Cold 20002108 Age (day) 14
    12326510 At_8deg_Cold 20002108 Timepoint (hr) 168
    12326510 At_8deg_Cold 20002108 Temperature 8 vs. 22
    (deg C.)
    12326510 At_8deg_Cold 20002108 Organism A. thaliana
    12326510 At_8deg_Cold 20002108 Tissue Whole Plant
    12326510 At_8deg_Cold 20002108 Plant Line WS
    12326510 At_8deg_Cold 20002109 Age (day) 16
    12326510 At_8deg_Cold 20002109 Timepoint(hr) 216
    12326510 At_8deg_Cold 20002109 Temperature 8 vs. 22
    (deg C.)
    12326510 At_8deg_Cold 20002109 Organism A. thaliana
    12326510 At_8deg_Cold 20002109 Tissue Whole Plant
    12326510 At_8deg_Cold 20002109 Plant Line WS
    Promoter YP0289
    Modulates the gene: phi-1-related protein
    The GenBank description of the gene: NM_125822 Arabidopsis thaliana phi-1-related protein
    (At5g64260) mRNA, complete cds gi|30697983|ref|NM_125822.2|[30697983]
    The promoter sequence:
    5′caaacaattactgctcaatgtatttgcgtatagagcatgtccaataccatgcctcatgatgtgagattg
    cgaggcggagtcagagaacgagttaaagtgacgacgttttttttgttttttttgggcatagtgtaaagtga
    tattaaaatttcatggttggcaggtgactgaaaataaaaatgtgtataggatgtgtttatatgctgacgga
    aaaatagttactcaactaatacagatctttataaagagtatataagtctatggttaatcatgaatggcaat
    atataagagtagatgagatttatgtttatattgaaacaagggaaagatatgtgtaattgaaacaatggcaa
    aatataagtcaaatcaaactggtttctgataatatatgtgttgaatcaatgtatatcttggtattcaaaac
    caaaacaactacaccaatttctttaaaaaaccagttgatctaataactacattttaatactagtagctatt
    agctgaatttcataatcaatttcttgcattaaaatttaaagtgggttttgcatttaaacttactcggtttg
    tattaatagactttcaaagattaaaagaaaactactgcattcagagaataaagctatcttactaaacacta
    cttttaaagtttcttttttcacttattaatcttcttttacaaatggatctgtctctctgcatggcaaaata
    tcttacactaattttattttctttgtttgataacaaatttatcggctaagcatcacttaaatttaatacac
    gttatgaagacttaaaccacgtcacacTATAagaaccttacaggctgtcaaacacccttccctacccactc
    acatctctccacgtggcaatctttgatattgacaccttagccactacagctgtcacactcctctctcggtt
    tcaaaacaacatctctggtataaata 3′-
    aatcaaaacctctcctatatctcttcaatctgatataactacccttctcaATG
    The promoter was cloned from the organism: Arabidopsis thaliana, WS ecotype
    Alternative nucleotides:
    Predicted (Columbia)
    Experimental (Wassilewskija)
    Predicted Position (bp) Mismatch Columbia/Wassilewskija
    138 SNP t/-
    529 SNP a/t
    561 SNP a/g
    666 Read Error c/c
    702 SNP t/a
    820 SNP t/a
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower L anther
    Ovule Post-fertilization: L endothelium
    Cotyledon H epidermis H petiole
    Rosette Leaf H trichome
    Primary Root H epidermis H root hairs
    Observed expression pattern of the promoter-marker vector was in:
    Expression very weak and may not have been detected by standard screen. Only tissue with visible GFP
    expression is analyzed by confocal microscopy. This may account for the expressing/screened ratio.
    T1 mature: Low GFP expression in endothelium cells of mature ovules and tapetum cell layer of anthers.
    Not expressed in pollen.
    T2 seedling: High GFP expression specific to epidermal tissues of cotyledons,
    root and trichomes of rosette leaves.
    Misc. promoter informaiton:   Bidirectionality:   Exons:   Repeats:
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12326995
    cDNA nucleotide sequence:
    aaatcaaaacctctcctatatctcttcaatctgatataactacccttctcaatggcttctaattaccgttt
    tgccatcttcctcactctctttttcgccaccgctggtttctccgccgccgcgttggtcgaggagcagccgc
    ttgttatgaaataccacaacggagttctgttgaaaggtaacatcacagtcaatctcgtatggtacgggaaa
    ttcacaccgatccaacggtccgtaatcgtcgatttcatccactcgctaaactccaaagacgttgcatcttc
    cgccgcagttccttccgttgcttcgtggtggaagacgacggagaaatacaaaggtggctcttcaacactcg
    tcgtcgggaaacagcttctactcgagaactatcctctcggaaaatctctcaaaaatccttacctccgtgct
    ttatccaccaaacttaacggcggtctccgttccataaccgtcgttctaacggcgaaagatgttaccgtcga
    aagattctgtatgagccggtgcgggactcacggatcctccggttcgaatccccgtcgcgcagctaacggcg
    cggcttacgtatgggtcgggaactccgagacgcagtgccctggatattgcgcgtggccgtttcaccagccg
    atttacggaccacaaacgccgccgttagtagcgcctaacggtgacgttggagttgacggaatgattataaa
    ccttgccacacttctagctaacaccgtgacgaatccgtttaataacggatattaccaaggcccaccaactg
    caccgcttgaagctgtgtctgcttgtcctggtatattcgggtcaggttcttatccgggttacgcgggtcgg
    gtacttgttgacaaaacaaccgggtctagttacaacgctcgtggactcgccggtaggaaatatctattgcc
    ggcgatgtgggatccgcagagttcgacgtgcaagactctggtttgatccaagggatgtgagtaagacacgt
    ggcatagtagtgagagcgatgacgagatctagacggcatgtgtagtcaaaatcaagttgcacgcgagcgtg
    tgtataaaaaaatctttcgggtttgggtctcgggtttggattgtggatagggctctctctttgctttttgt
    cgttttgtaatgacgtgtaaaaactgtactcggaaatgtgaagaatgcatataaaataataaaaaatcatt
    ttgtttctact
    Coding sequence:
    MASNYRFAIFLTLFFATAGFSAAALVEEQPLVMKYHNGVLLKGN1TVNLVWYGKFTPIQRSVIVDF
    IHSLNSKDVASSAAVPSVASWWKTTEKYKGGSSTLVVGKQLLLENYPLGKSLKNPYLRALSTKLN
    GGLRSITVVLTAKDVTVERFCMSRCGTHGSSGSNPRRAANGAAYVWVGNSETQCPGYCAWPFHQ
    PIYGPQTPPLVAPNGDVGVDGMIINLATLLANTVTNPFNNGYYQGPPTAPLEAVSACPGIFGSGSYP
    GYAGRVLVDKTTGSSYNARGLAGRKYLLPAMWDPQSSTCKTLV*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12326995 At_Root_Tips 108434 −
    12326995 At_Germinating_Seeds 108462 +
    12326995 At_Germinating_Seeds 108463 −
    12326995 At_42deg_Heat 108576 +
    12326995 At_100uM_ABA_Mutants 20000072 +
    12326995 At_42deg_Heat 20000111 +
    12326995 At_42deg_Heat 20000144 +
    12326995 At_100uM_ABA 20000166 +
    12326995 At_100uM_ABA 20000169 +
    12326995 At_2mM_SA 20000181 +
    12326995 At_Siliques 20000234 −
    12326995 At_Siliques 20000235 −
    12326995 At_Siliques 20000236 −
    12326995 At_Open_Flower 20000265 −
    12326995 At Open_Flower 20000286 −
    12326995 At_Pollen 20000326 −
    12326995 At_100uM_ABA 20000453 +
    12326995 At_Far-red-induction 20001247 +
    12326995 At_Far-red-induction 20001248 +
    12326995 At_Far-red-induction 20001450 +
    12326995 At_Far-red-induction 20001451 +
    12326995 At_DroughtSoiLDry 20001556 −
    12326995 At_Drought_Soil_Dry 20001557 −
    12326995 At_Drought_Soil_Dry 20001558 −
    12326995 At_Interploidy Crosses 20001654 +
    12326995 At_Drought_Reproduction 20001904 −
    12326995 At_8deg_Cold 20002103 −
    12326995 At_8deg_Cold 20002105 −
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12326995 At_Root_Tips 108434 Tissue Root Tips
    12326995 At Germinating_Seeds 108462 Age (day) 2 vs. 0
    12326995 At_Germinating_Seeds 108462 Tissue Germinating Seeds
    12326995 At_Germinating_Seeds 108463 Age (day) 3 vs. 0
    12326995 At_Germinating_Seeds 108463 Tissue Germinating Seeds
    12326995 At_42deg_Heat 108576 Timepoint (hr) 1
    12326995 At_42deg_Heat 108576 Temperature (deg C.) 42 vs. 22
    12326995 At_42deg_Heat 108576 Tissue Aerial
    12326995 At_100uM_ABA_Mutants 20000072 Timepoint (hr) 6
    12326995 At_100uM_ABA_Mutants 20000072 Treatment 100uM ABA vs. No Treatment
    12326995 At_100uM_ABA_Mutants 20000072 Tissue Aerial
    12326995 At_100uM_ABA_Mutants 20000072 Plant Line CS8105
    12326995 At_42deg_Heat 20000111 Timepoint (hr) 6
    12326995 At_42deg_Heat 20000111 Temperature (deg C.) 42 vs. 22
    12326995 At_42deg_Heat 20000111 Tissue Aerial
    12326995 At_42deg_Heat 20000144 Timepoint (hr) 1
    12326995 At_42deg_Heat 20000144 Temperature (deg C.) 42 vs. 22
    12326995 At_42deg_Heat 20000144 Tissue Aerial
    12326995 At_100uM_ABA 20000166 Timepoint (hr) 1
    12326995 At_100uM_ABA 20000166 Age (day) 14
    12326995 At_100uM_ABA 20000166 Treatment 100uM ABA vs. No Treatment
    12326995 At_100uM_ABA 20000166 Organism A. thaliana
    12326995 At_100uM_ABA 20000166 Tissue Aerial
    12326995 At_100uM_ABA 20000166 Plant Line WS
    12326995 At_100uM_ABA 20000169 Timepoint (hr) 6
    12326995 At_100uM_ABA 20000169 Age (day) 14
    12326995 At_100uM_ABA 20000169 Treatment 100uM ABA vs. No Treatment
    12326995 At_100uM_ABA 20000169 Organism A. thaliana
    12326995 At_100uM_ABA 20000169 Tissue Aerial
    12326995 At_100uM_ABA 20000169 Plant Line WS
    12326995 At_2mM_SA 20000181 Timepoint (hr) 1
    12326995 At_2mM_SA 20000181 Age (day) 14
    12326995 At_2mM_SA 20000181 Treatment 2mM SA vs. No Treatment
    12326995 At_2mM_SA 20000181 Organism A. thaliana
    12326995 At_2mM_SA 20000181 Tissue Aerial
    12326995 At_2mM_SA 20000181 Plant Line WS
    12326995 At_Siliques 20000234 Age (day) 21
    12326995 At_Siliques 20000234 Tissue <5mm Siliques vs. Whole Plant
    12326995 At_Siliques 20000234 Organism A. thaliana
    12326995 At_Siliques 20000234 Plant Line WS
    12326995 At_Siliques 20000235 Age (day) 21
    12326995 At_Siliques 20000235 Tissue 5-10mm Siliques vs. Whole
    Plant
    12326995 At_Siliques 20000235 Organism A. thaliana
    12326995 AlSiliques 20000235 Plant Line WS
    12326995 At_Siliques 20000236 Age (day) 21
    12326995 At_Siliques 20000236 Tissue >10mm Siliques vs. Whole Plant
    12326995 At_Siliques 20000236 Organism A. thaliana
    12326995 At_Siliques 20000236 Plant Line WS
    12326995 At_Open_Flower 20000265 Age (day) 21
    12326995 At_Open_Flower 20000265 Organism A. thaliana
    12326995 At_Open_Flower 20000265 Tissue Closed Flower vs. Whole Plant
    12326995 At_Open_Flower 20000265 Plant Line WS
    12326995 At_Open_Flower 20000286 Age (day) 21
    12326995 At_Open_Flower 20000286 Organism A. thaliana
    12326995 At_Open_Flower 20000286 Tissue Half Open vs. Whole Plant
    12326995 At_Open_Flower 20000286 Plant Line WS
    12326995 At_Pollen 20000326 Age (day) 0 vs. 21
    12326995 At_Pollen 20000326 Organism A. thaliana
    12326995 At_Pollen 20000326 Tissue Pollen vs. Whole Plant
    12326995 At_Pollen 20000326 Plant Line WS
    12326995 At_100uM_ABA 20000453 Age (day) 15
    12326995 At_100uM_ABA 20000453 Timepoint (hr) 24
    12326995 At_100uM_ABA 20000453 Treatment 100uM ABA vs. No Treatment
    12326995 At_100uM_ABA 20000453 Organism A. thaliana
    12326995 At_100uM_ABA 20000453 Tissue Aerial
    12326995 At_100uM_ABA 20000453 Plant Line WS
    12326995 At_Far-red-induction 20001247 Timepoint (hr) 1
    12326995 At_Far-red-induction 20001247 Age (day) 7
    12326995 At_Far-red-induction 20001247 Organism A. thaliana
    12326995 At_Far-red-induction 20001247 Plant Line Columbia
    12326995 At_Far-red-induction 20001247 Light Far-red vs. White
    12326995 At_Far-red-induction 20001247 Tissue Whole Plant
    12326995 At_Far-red-induction 20001248 Timepoint (hr) 4
    12326995 At_Far-red-induction 20001248 Age (day) 7
    12326995 At_Far-red-induction 20001248 Organism A. thaliana
    12326995 At_Far-red-induction 20001248 Plant Line Columbia
    12326995 At_Far-red-induction 20001248 Light Far-red vs. White
    12326995 At_Far-red-induction 20001248 Tissue Whole Plant
    12326995 At_Far-red-induction 20001450 Age (day) 7
    12326995 At_Far-red-induction 20001450 Timepoint (hr) 8
    12326995 At_Far-red-induction 20001450 Organism A. thaliana
    12326995 At_Far-red-induction 20001450 Plant Line Columbia
    12326995 At_Far-red-induction 20001450 Light Far-red vs. White
    12326995 At_Far-red-induction 20001450 Tissue Whole Plant
    12326995 At_Far-red-induction 20001451 Age (day) 8
    12326995 At_Far-red-induction 20001451 Timepoint (hr) 24
    12326995 At_Far-red-induction 20001451 Organism A. thaliana
    12326995 At_Far-red-induction 20001451 Plant Line Columbia
    12326995 At_Far-red-induction 20001451 Light Far-red vs. White
    12326995 At_Far-red-induction 20001451 Tissue Whole Plant
    12326995 At_Drought_Soil_Dry 20001556 Timepoint (day) 12
    12326995 At_Drought_Soil_Dry 20001556 Age (day) 26
    12326995 At_Drought_Soil_Dry 20001556 Organism A. thaliana
    12326995 At_Drought_Soil_Dry 20001556 Treatment Drought vs. No Drought
    12326995 At_Drought_Soil_Dry 20001556 Post Timepoint (hr) None
    12326995 At_Drought_Soil_Dry 20001556 Post-Treatment None
    12326995 At_Drought_Soil_Dry 20001556 Plant Line WS
    12326995 At_Drought_Soil_Dry 20001557 Post Timepoint (hr) 3
    12326995 At_Drought_Soil_Dry 20001557 Timepoint (day) 13
    12326995 At_Drought_Soil_Dry 20001557 Age (day) 27
    12326995 At_Drought_Soil_Dry 20001557 Organism A. thaliana
    12326995 At_Drought_Soil_Dry 20001557 Treatment Drought vs. No Drought
    12326995 At_Drought_Soil_Dry 20001557 Post-Treatment Re-Water vs. No Drought
    12326995 At_Drought_Soil_Dry 20001557 Plant Line WS
    12326995 At_Drought_Soil_Dry 20001558 Post Timepoint (hr) 6
    12326995 At_Drought_Soil_Dry 20001558 Timepoint (day) 13
    12326995 At_Drought_Soil_Dry 20001558 Age (day) 27
    12326995 At_Drought_Soil_Dry 20001558 Organism A. thaliana
    12326995 At_Drought_Soil_Dry 20001558 Treatment Drought vs. No Drought
    12326995 At_Drought_Soil_Dry 20001558 Post-Treatment Re-Water vs. No Drought
    12326995 At_Drought_Soil_Dry 20001558 Plant Line WS
    12326995 At_Interploidy_Crosses 20001654 Age (day) 5
    12326995 At_Interploidy_Crosses 20001654 Cross 6X × 2X vs. 2X × 2X
    12326995 At_Interploidy_Crosses 20001654 Organism A. thaliana
    12326995 At_Interploidy_Crosses 20001654 Plant Line Columbia
    12326995 At_Interploidy_Crosses 20001654 Tissue Siliques
    12326995 At_Drought_Reproduction 20001904 Timepoint (day) 7
    12326995 At_Drought_Reproduction 20001904 Age (day) 37
    12326995 At_Drought_Reproduction 20001904 Organism A. thaliana
    12326995 At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought
    12326995 At_Drought_Reproduction 20001904 Tissue Rosettes
    12326995 At_Drought_Reproduction 20001904 Plant Line WS
    12326995 At_8deg_Cold 20002103 Timepoint (hr) 2
    12326995 At_8deg_Cold 20002103 Age (day) 7
    12326995 At_8deg_Cold 20002103 Temperature (deg C.) 8 vs. 22
    12326995 At_8deg_Cold 20002103 Organism A. thaliana
    12326995 At_8deg_Cold 20002103 Tissue Whole Plant
    12326995 At_8deg_Cold 20002103 Plant Line WS
    12326995 At_8deg_Cold 20002105 Age (day) 7
    12326995 At_8deg_Cold 20002105 Timepoint (hr) 8
    12326995 At_8deg_Cold 20002105 Temperature (deg C.) 8 vs. 22
    12326995 At_8deg_Cold 20002105 Organism A. thaliana
    12326995 At_8deg_Cold 20002105 Tissue Whole Plant
    12326995 At_8deg_Cold 20002105 Plant Line WS
    Promoter YP0286
    Modulates the gene: Hypothetical protein
    The GenBank description of the gene: NM_102758 Arabidopsis thaliana hypothetical protein
    (Atlg30190) mRNA, complete cds gi|18397396|ref|NM_102758.1|[18397396]
    The promoter sequence:
    5′atcatcgaaaggtatgtgatgcatattcccattgaaccagatttccatatattttatttgtaaagtgat
    aatgaatcacaagatgattcaatattaaaaatgggtaactcactttgacgtgtagtacgtggaagaatagt
    tagctatcacgcatatatatatctatgattaagtgtgtatgacataagaaactaaaatatttacctaaagt
    ccagttactcatactgattttatgcatatatgtattatttatttatttttaataaagaagcgattggtgtt
    ttcatagaaatcatgatagattgataggtatttcagttccacaaatctagatctgtgtgctatacatgcat
    gtattaattttttccccttaaatcatttcagttgataatattgctctttgttccaactttagaaaaggtat
    gaaccaacctgacgattaacaagtaaacattaattaatctttatatatatgagataaaaccgaggatatat
    atgattgtgttgctgtctattgatgatgtgtcgatattatgcttgttgtaccaatgctcgagccgagcgtg
    atcgatgccttgacaaactatatatgtttcccgaattaattaagttttgtatcttaattagaataacattt
    ttatacaatgtaatttctcaagcagacaagatatgtatcctatattaattactatatatgaattgccgggc
    acctaccaggatgtttcaaatacgagagcccattagtttccacgtaaatcacaatgacgcgacaaaatcta
    gaatcgtgtcaaaactctatcaatacaataatatatatttcaagggcaatttcgacttctcctcaactcaa
    tgattcaacgccatgaatctctaTATAaaggctacaacaccacaaaggatcatcagtcatcacaaccacat
    taactcttcaccactatctctcaatctct 3′-ATG
    The promoter was cloned from the organism: Arabidopsis thaliana, WS ecotype
    Alternative nucleotides:
    Predicted (Columbia)
    Experimental (Wassilewskija)
    Predicted Position (bp) Mismatch Columbia/Wassilewskija
    194 SNP t/a
    1257 SNP t/c
    491-494 SSLP tata/----
    527 No g in Ws -/-
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower L pedicel L epidermis
    Stem L epidermis
    Hypocotyl H epidermis
    Cotyledon H mesophyll H vascular H epidermis H petiole
    Rosette Leaf H epidermis H petiole
    Primary Root H epidermis
    Lateral root H lateral root cap
    Observed expression pattern of the promoter-marker vector was in:
    T1 mature: GFP expressed in vasculature of silique and pedicles of flowers.
    T2 seedling: High GFP expression throughout vasculature of root, hypocotyl, and petioles.
    Misc, promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12669548
    cDNA nucleotide sequence:
    ATGACAGAAATGCCCTCGTACATGATCGAGAACCCAAAGTTCGAGCCAAAGAAACGACGTTAT
    TACTCTTCTTCGATGCTTACCATCTTCTTACCGATCTTCACATACATTATGATCTTTCACGTTTT
    CGAAGTATCACTATCTTCGGTCTTTAAAGACACAAAGGTCTTGTTCTTCATCTCCAATACTCTC
    ATCCTCATAATAGGCGCCGATTATGGTTCCTTCTCTGATAAAGAGAGTCAAGACTTTTACGGTG
    AATACACTGTCGCAGCGGCAACGATGCGAAACCGAGCTGATAACTACTCTCCGATTCCCGTCT
    TGACATACCGAGAAAACACTAAAGATGGAGAAATCAAGAACCCTAAAGATGTCGAATTCAGG
    AACCCTGAAGAAGAAGACGAACGGATGGTGAAAGATATCATTTGCGTTTCTCCTCCCGAGAAA
    ATAGTACGAGTGGTGAGTGAGAAGAAACAGAGAGATGATGTAGCTATGGAAGAATACAAACC
    AGTTACAGAACAAACTCTTGCTAGCGAAGAAGCTTGCAACACAAGAAACGATGTGAACCCTAA
    TAAACCGTACGGGCGAAGTAAATCAGATAAGCCACGGAGAAAGAGGCTCAGCGTAGATACAG
    AGACGAGCAAACGTAAAAGTTATGGTCGAAAGAAATCAGATTGCTGGAGATGGATGGTTATTC
    CGGAGAAGTGGGAATATGTTAAAGAAGAATCTGAAGAGTTTTCAAAGTTGTCCAACGAGGAG
    TTGAACAAACGAGTCGAAGAATTCATCCAACGGTTCAATAGACAGATGAGATCACAATCACCG
    CGAGTTTCGTGTACTTGA
    Coding sequence:
    MTEMPSYMIENPKFEPKKRRYYSSSMLTIFLPIFTYIMIFHVFEVSLSSVFKDTKVLFFI
    SNTLILITAADYGSFSDKESQDFYGEYTVAAATMRNRADNYSPIPVLTYRENTKDGEIKN
    PKDVEFRNPEEEDEPMVKDIICVSPPEKIVRVVSEKKQRDDVAMEEYKPVTEQTLASEEA
    CNTRNHVNPNKPYGRSKSDKPRRKRLSVDTETTKRKSYGRKKSDCSRWMVIPEKWEYVKE
    ESEEFSKLSNEELNKRVEEFIQRFNRQIRSQSPRVSST*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12669548 At_100uM_ABA 20000169 +
    12669548 At_42deg_Heat 20000171 +
    12669548 At_42deg_Heat 20000173 +
    12669548 At_2mM_SA 20000182 +
    12669548 At_0.001percent_MeJA 20000211 −
    12669548 At_Open_Flower 20000264 −
    12669548 At_Open_Flower 20000265 −
    12669548 At_Drought 20000267 +
    12669548 At_100mM_NaCl 20000268 +
    12669548 At_Open_Flower 20000286 −
    12669548 At_Drought 20000436 +
    12669548 At_Drought 20000437 +
    12669548 At_100uM_NAA 20000444 +
    12669548 At_100uM_NAA 20000445 +
    12669548 At_100uM_ABA 20000453 +
    12669548 At_42deg_Heat 20000457 −
    12669548 At_10percent_PEG 20000527 +
    12669548 At_Line_Comparisons 20001192 −
    12669548 At_Line_Comparisons 20001307 +
    12669548 At_Line_Comparisons 20001309 −
    12669548 At_Line_Comparisons 20001310 −
    12669548 At_Drought_Soil_Dry 20001554 +
    12669548 At_Drought_Soil_Dry 20001555 +
    12669548 At_Drought_Soil_Dry 20001556 +
    12669548 At_Drought_Soil_Dry 20001559 +
    12669548 At_50mM_NH4NO3_L-to-H 20001757 −
    12669548 At_Drought_Reproduction 20001904 +
    12669548 At_Drought_Reproduction 20001905 +
    12669548 At_Drought_Reproduction 20001910 +
    12669548 At_Drought_Reproduction 20001911 +
    12669548 At_Line_Comparisons 20002009 +
    12669548 At_Line_Comparisons 20002010 +
    12669548 At_Drought-Air-Dry 20002253 −
    12669548 At_Drought-Air-Dry 20002256 +
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12669548 At_100uM_ABA 20000169 Timepoint (hr) 6
    12669548 At_100uM_ABA 20000169 Age (day) 14
    12669548 At_100uM_ABA 20000169 Treatment 100uM ABA vs. No Treatment
    12669548 At_100uM_ABA 20000169 Organism A. thaliana
    12669548 At_100uM_ABA 20000169 Tissue Aerial
    12669548 At_100uM_ABA 20000169 Plant Line WS
    12669548 At_42deg_Heat 20000171 Timepoint (hr) 1
    12669548 At_42deg_Heat 20000171 Age (day) 14
    12669548 At_42deg_Heat 20000171 Temperature (deg C.) 42 vs. 22
    12669548 At_42deg_Heat 20000171 Organism A. thaliana
    12669548 At_42deg_Heat 20000171 Tissue Aerial
    12669548 At_42deg_Heat 20000171 Plant Line WS
    12669548 At_42deg_Heat 20000173 Timepoint (hr) 6
    12669548 At_42deg_Heat 20000173 Age (day) 14
    12669548 At_42deg_Heat 20000173 Temperature (deg C.) 42 vs. 22
    12669548 At_42deg_Heat 20000173 Organism A. thaliana
    12669548 At_42deg_Heat 20000173 Tissue Aerial
    12669548 At_42deg_Heat 20000173 Plant Line WS
    12669548 At_2mM_SA 20000182 Timepoint (hr) 6
    12669548 At_2mM_SA 20000182 Age (day) 14
    12669548 At_2mM_SA 20000182 Treatment 2mM SA vs. No Treatment
    12669548 At_2mM_SA 20000182 Organism A. thaliana
    12669548 At_2mM_SA 20000182 Tissue Aerial
    12669548 At_2mM_SA 20000182 Plant Line WS
    12669548 At_0.001percent_MeJA 20000211 Timepoint (hr) 1
    12669548 At_0.001percent_MeJA 20000211 Age (day) 14
    12669548 At_0.001percent_MeJA 20000211 Treatment 0.001percent MeJA vs. No
    Treatment
    12669548 At_0.001percent_MeJA 20000211 Organism A. thaliana
    12669548 At_0.001percent_MeJA 20000211 Tissue Aerial
    12669548 At_0.001percent_MeJA 20000211 Plant Line WS
    12669548 At_Open_Flower 20000264 Age (day) 21
    12669548 At_Open_Flower 20000264 Organism A. thaliana
    12669548 At_Open_Flower 20000264 Tissue Open Flower vs. Whole Plant
    12669548 At_Open_Flower 20000264 Plant Line WS
    12669548 At_Open_Flower 20000265 Age (day) 21
    12669548 At_Open_Flower 20000265 Organism A. thaliana
    12669548 At_Open_Flower 20000265 Tissue Closed Flower vs. Whole Plant
    12669548 At_Open_Flower 20000265 Plant Line WS
    12669548 At_Drought 20000267 Timepoint (hr) 6
    12669548 At_Drought 20000267 Age (day) 7
    12669548 At_Drought 20000267 Organism A. thaliana
    12669548 At_Drought 20000267 Treatment Drought vs. No Drought
    12669548 At_Drought 20000267 Tissue Whole Plant
    12669548 At_Drought 20000267 Plant Line WS
    12669548 At_100mM_NaCl 20000268 Timepoint (hr) 6
    12669548 At_100mM_NaCl 20000268 Age (day) 14
    12669548 At_100mM_NaCl 20000268 Treatment 100mM NaCl vs. No Treatment
    12669548 At_100mM_NaCl 20000268 Organism A. thaliana
    12669548 At_100mM_NaCl 20000268 Tissue Whole Plant
    12669548 At_100mM_NaCl 20000268 Plant Line WS
    12669548 At_Open_Flower 20000286 Age (day) 21
    12669548 At_Open_Flower 20000286 Organism A. thaliana
    12669548 At_Open_Flower 20000286 Tissue Half Open vs. Whole Plant
    12669548 At_Open_Flower 20000286 Plant Line WS
    12669548 At_Drought 20000436 Age (day) 7
    12669548 At_Drought 20000436 Timepoint (hr) 12
    12669548 At_Drought 20000436 Organism A. thaliana
    12669548 At_Drought 20000436 Treatment Drought vs. No Drought
    12669548 At_Drought 20000436 Tissue Whole Plant
    12669548 At_Drought 20000436 Plant Line WS
    12669548 At_Drought 20000437 Age (day) 8
    12669548 At_Drought 20000437 Timepoint hr 24
    12669548 At_Drought 20000437 Organism A. thaliana
    12669548 At_Drought 20000437 Treatment Drought vs. No Drought
    12669548 At_Drought 20000437 Tissue Whole Plant
    12669548 At_Drought 20000437 Plant Line WS
    12669548 At_100uM_NAA 20000444 Timepoint (hr) 1
    12669548 At_100uM_NAA 20000444 Age (day) 14
    12669548 At_100uM_NAA 20000444 Treatment 100uM NAA vs. No Treatment
    12669548 At_100uM_NAA 20000444 Organism A. thaliana
    12669548 At_100uM_NAA 20000444 Tissue Aerial
    12669548 At_100uM_NAA 20000444 Plant Line WS
    12669548 At_100uM_NAA 20000445 Timepoint (hr) 6
    12669548 At_100uM_NAA 20000445 Age (day) 14
    12669548 At_100uM_NAA 20000445 Treatment 100uM NAA vs. No Treatment
    12669548 At_100uM_NAA 20000445 Organism A. thaliana
    12669548 At_100uM_NAA 20000445 Tissue Aerial
    12669548 At_100uM_NAA 20000445 Plant Line WS
    12669548 At_100uM_ABA 20000453 Age (day) 15
    12669548 At_100uM_ABA 20000453 Timepoint (hr) 24
    12669548 At_100uM_ABA 20000453 Treatment 100uM ABA vs. No Treatment
    12669548 At_100uM_ABA 20000453 Organism A. thaliana
    12669548 At_100uM_ABA 20000453 Tissue Aerial
    12669548 At_100uM_ABA 20000453 Plant Line WS
    12669548 At_42deg_Heat 20000457 Timepoint (hr) 0.166
    12669548 At_42deg_Heat 20000457 Age (day) 14
    12669548 At_42deg_Heat 20000457 Temperature (deg C.) 42 vs. 22
    12669548 At_42deg_Heat 20000457 Organism A. thaliana
    12669548 At_42deg_Heat 20000457 Tissue Aerial
    12669548 At_42deg_Heat 20000457 Plant Line WS
    12669548 At_10percent_PEG 20000527 Age (day) 20
    12669548 At_10percent_PEG 20000527 Timepoint (day) 20
    12669548 At_10percent_PEG 20000527 Treatment 10percent PEG vs. No
    Treatment
    12669548 At_10percent_PEG 20000527 Organism A. thaliana
    12669548 At_10percent_PEG 20000527 Tissue Whole Plant
    12669548 At_10percent_PEG 20000527 Plant Line WS
    12669548 At_Line_Comparisons 20001192 Plant Line WBin4-WX13R-A vs. WS
    12669548 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS
    12669548 At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS
    12669548 At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS
    12669548 At_Drought_Soil_Dry 20001554 Timepoint (day) 7
    12669548 At_Drought_Soil_Dry 20001554 Age (day) 21
    12669548 At_Drought_Soil_Dry 20001554 Organism A. thaliana
    12669548 At_Drought_Soil_Dry 20001554 Treatment Drought vs. No Drought
    12669548 At_Drought_Soil_Dry 20001554 Post Timepoint (hr) None
    12669548 At_Drought_Soil_Dry 20001554 Post-Treatment None
    12669548 At_Drought_Soil_Dry 20001554 Plant Line WS
    12669548 At_Drought_Soil_Dry 20001555 Timepoint (day) 10
    12669548 At_Drought_Soil_Dry 20001555 Age (day) 24
    12669548 At_Drought_Soil_Dry 20001555 Organism A. thaliana
    12669548 At_Drought_Soil_Dry 20001555 Treatment Drought vs. No Drought
    12669548 At_Drought_Soil_Dry 20001555 Post Timepoint (hr) None
    12669548 At_Drought_Soil_Dry 20001555 Post-Treatment None
    12669548 At_Drought_Soil_Dry 20001555 Plant Line WS
    12669548 At_Drought_Soil_Dry 20001556 Timepoint (day) 12
    12669548 At_Drought_Soil_Dry 20001556 Age (day) 26
    12669548 At_Drought_Soil_Dry 20001556 Organism A. thaliana
    12669548 At_Drought_Soil_Dry 20001556 Treatment Drought vs. No Drought
    12669548 At_Drought_Soil_Dry 20001556 Post Timepoint (hr) None
    12669548 At_Drought_Soil_Dry 20001556 Post-Treatment None
    12669548 At_Drought_Soil_Dry 20001556 Plant Line WS
    12669548 At_Drought_Soil_Dry 20001559 Timepoint (day) 14
    12669548 At_Drought_Soil_Dry 20001559 Age (day) 28
    12669548 At_Drought_Soil_Dry 20001559 Post Timepoint (hr) 29
    12669548 At_Drought_Soil_Dry 20001559 Organism A. thaliana
    12669548 At_Drought_Soil_Dry 20001559 Treatment Drought vs. No Drought
    12669548 At_Drought_Soil_Dry 20001559 Post-Treatment Re-Water vs. No Drought
    12669548 At_Drought_Soil_Dry 20001559 Plant Line WS
    12669548 At_50mM_NH4NO3_L-to-H 20001757 Timepoint (hr) 6
    12669548 At_50mM NH4NO3_L-to-H 20001757 Treatment 50mM NH4NO3 vs 100mM
    Mannitol
    12669548 At_50mM_NH4NO3_L-to-H 20001757 Tissue Leaf
    12669548 At_Drought_Reproduction 20001904 Timepoint (day) 7
    12669548 At_Drought_Reproduction 20001904 Age (day) 37
    12669548 At_Drought_Reproduction 20001904 Organism A. thaliana
    12669548 At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought
    12669548 At_Drought_Reproduction 20001904 Tissue Rosettes
    12669548 At_Drought_Reproduction 20001904 Plant Line WS
    12669548 At_Drought_Reproduction 20001905 Timepoint (day) 10
    12669548 At_Drought_Reproduction 20001905 Age (day) 40
    12669548 At_Drought_Reproduction 20001905 Organism A. thaliana
    12669548 At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought
    12669548 At_Drought_Reproduction 20001905 Tissue Rosettes
    12669548 At_Drought_Reproduction 20001905 Plant Line WS
    12669548 At_Drought_Reproduction 20001910 Timepoint (day) 7
    12669548 At_Drought_Reproduction 20001910 Age (day) 37
    12669548 At_Drought_Reproduction 20001910 Organism A. thaliana
    12669548 At_Drought_Reproduction 20001910 Treatment Drought vs. No Drought
    12669548 At_Drought_Reproduction 20001910 Tissue Flowers
    12669548 At_Drought_Reproduction 20001910 Plant Line WS
    12669548 At_Drought_Reproduction 20001911 Timepoint (day) 10
    12669548 At_Drought_Reproduction 20001911 Age (day) 40
    12669548 At_Drought_Reproduction 20001911 Organism A. thaliana
    12669548 At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought
    12669548 At_Drought_Reproduction 20001911 Tissue Flowers
    12669548 At_Drought_Reproduction 20001911 Plant Line WS
    12669548 At_Line_Comparisons 20002009 Plant Line ME01642 vs. WS
    12669548 At_Line_Comparisons 20002010 Plant Line ME02031 vs. WS
    12669548 At_Drought-Air-Dry 20002253 Timepoint (hr) 1
    12669548 At_Drought-Air-Dry 20002253 Age (day) 35
    12669548 At_Drought-Air-Dry 20002253 Organism A. thaliana
    12669548 At_Drought-Air-Dry 20002253 Treatment Drought vs. No Drought
    12669548 At_Drought-Air-Dry 20002253 Tissue Roots
    12669548 At_Drought-Air-Dry 20002253 Plant Line WS
    12669548 At_Drought-Air-Dry 20002256 Timepoint (hr) 4
    12669548 At_Drought-Air-Dry 20002256 Age (day) 35
    12669546 At_Drought-Air-Dry 20002256 Organism A. thaliana
    12669548 At_Drought-Air-Dry 20002256 Treatment Drought vs. No Drought
    12669548 At_Drought-Air-Dry 20002256 Tissue Shoots
    12669548 At_Drought-Air-Dry 20002256 Plant Line WS
    Promoter YPE1275
    Modulates the gene: Glycosyl hydrolase family.
    The GenBank description of the gene: NM_115876 Arabidopsis thaliana glycosyl hydrolase family 1
    (At3g60130) mRNA, complete cds gi|30695130|ref|NM_115876.2|[30695130]
    The promoter sequence:
    5′gcgtatgctttactttttaaaatgggcctatgctataattgaatgacaaggattaaacaactaataaaa
    gtgtagatgggttaagatgacttatttttttacttaccaatttataaatgggcttcgatgtactgaaatat
    atcgcgcctattaacgaggccattcaacgaatgttttaagggccctatttcgacattttaaagaaCaccta
    ggtcatcattccagaaatggatattataggatttagataatttcccacgtttggtttatttatctattttt
    tgacgttgaccaacataatcgtgcccaaccgtttcacgcaacgaatttatatacgaaatatatatattttt
    caaattaagataccacaatcaaaacagctgttgattaacaaagagattttttttttttggttttgagttac
    aataacgttagaggataaggtttcttgcaacgattaggaaatcgtataaaataaaatatgttataattaag
    tgttttattttataatgagtattaatataaataaaacctgcaaaaggatagggatattgaataataaagag
    aaacgaaagagcaattttacttctttataattgaaattatgtgaatgttatgtttacaatgaatgattcat
    cgttctatatattgaagtaaagaatgagtttattgtgcttgcataatgacgttaacttcacatatacactt
    attacataacatttatcacatgtgcgtctttttttttttttactttgtaaaatttcctcactttaaagact
    tttataacaattactagtaaaataaagttgcttggggctacaccctttctccctccaacaactctatttat
    agataacattatatcaaaatcaaaacatagtccctttcttctataaaggttttttcacaaccaaatttcca
    tTATAaatcaaaaaataaaaacttaatta 3′-aATG
    The promoter was cloned from the organism: Arabidopsis thaliana, WS ecotype
    Alternative nucleotides:
    Predicted (Columbia)
    Experimental (Wassilewskija)
    Sequence (bp) Mismatch Columbia/Wassilewskia
     95 SNP g/t
    1798 SNP a/t
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Primary Root H epidermis H trichoblast H atrichoblast L root cap H root hairs
    Observed expression pattern of the promoter-marker vector was in:
    T1 mature: No expression.
    T2 seedling: High expression in root epidermal at transition zone decreasing toward root tip.
    Misc. promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12668112
    cDNA nucleotide sequence:
    ATAAAAACTTAAYFAGTTTTTACAGAAGAAAAGAAAACAATGAGAGGTAAATTTCTAAGTTTA
    CTGTTGCTCATTACTTTGGCCTGCATTGGAGTTTCCGCCAAGAAGCATTCCACAAGGCCTAGAT
    TAAGAAGAAATGATTTCCCACAAGATTTCGTTTTTGGATCTGCTACTTCTGCTTATCAGTGTGA
    AGGAGCTGCACATGAAGATGGTAGAGGTCCAAGTATCTGGGACTCCTTCTCTGAAAAATTCCC
    AGAAAAGATAATGGATGGTAGTAATGGGTCCATTGCAGATGATTCTTACAATCTTTACAAGGA
    AGATGTGAATTTGCTGCATCAAATTGGCTTCGATGCTTACCGATTTTCGATGTCATGGTCACGG
    ATTTTGGCTCGTGGGACTCTAAAGGGAGGAATCAACCAGGCTGGAATTGAATATTATAACAAC
    TTGATTAATCAACTTATATCTAAAGGAGTGAAGCCATTTGTCACACTCTTTCACTGGGACTTAC
    CAGATGCACTCGAAAATGGTTACGGTGGCCTCCTTGGAGATGAATTTGTGAACGATTTCCGAG
    ACTATGCAGAACTTTGTTTCCAGAAGTTTGGAGATAGAGTGAAGCAGTGGACGACACTAAACG
    AGCCATATACAATGGTACATGAAGGTTATATAACAGGTCAAAAGGCACCTGGAAGATGTTCCA
    ATTTCTATAAACCTGATTGCTTAGGTGGCGATGCAGCCACGGAGCCTTACATCGTCGGCCATA
    ACCTCCTCCTTGCTCATGGAGTTGCGGTAAAAGTATATAGAGAAAAGTACCAGGCAACTCAGA
    AAGGTGAAATTGGTATTGCCTTAAACACAGCATGGCACTACGCTTATTCAGATTCATATGCTG
    ACCGGTTAGCTGCGACTCGAGCGACTGCCTTCACCTTCGACTACTTCATGGAGCCAATCGTGT
    ACGGTAGATATCCAATTGAAATGGTCAGCCACGTTAAAGACGGTCGTCTTCCTACCTTCACAC
    CAGAAGAGTCCGAAATGCTCAAAGGATCATATGATTTCATAGGCGTTAACTATTACTCATCTC
    TTTACGCAAAAGACGTGCCGTGTGCAACTGAAAACATCACCATGACCACCGATTCTTGCGTCA
    GCCTCGTAGGTGAACGAAATGGAGTGCCTATCGGTCCAGCGGCTGGATCGGATTGGCTTTTGA
    TATATCCCAAGGGTATTCGTGATCTCCTACTACATGCAAAATTCAGATACAATGATCCCGTCTT
    GTACATTACAGAGAATGGAGTGGATGAAGCAAATATTGGCAAAATATTTCTTAACGACGATTT
    GAGAATTGATTACTATGCTCATCACCTCAAGATGGTTAGCGATGCTATCTCGATCGGGGTGAA
    TGTGAAGGGATATTTCGCGTGGTCATTGATGGATAATTTCGAGTGGTCGGAAGGATACACGGT
    CCGGTTCGGGCTAGTGTTTGTGGACTTTGAAGATGGACGTAAGAGGTATCTGAAGAAATCAGC
    TAAGTGGTTTAGGAGATTGTTGAAGGGAGCGCATGGTGGGACGAATGAGCAGGTGGCTGTTA
    TTTAATAAACCACGAGTCATTGGTCAATTTAGTCTACTGTTTCTTTTGCTCTATGTACAGAAAG
    AAAATAAACTTTCCAAAATAAGAGGTGGCTTTGTTTGGACTTTGGATGTTACTATATATATTG
    GTAATTCTTGGCGTTTGTTAGTTTCCAAACCAAACATTAAT
    Coding sequence:
    MRGKFLSLLLLITLACIGVSAKKHSTRPRLRRNDFPQDFVFGSATSAYQCEGAAHEDGRGPSIWDSF
    SEKFPEKIMDGSNGSIADDSYNLYKEDVNLLHQIGFDAYRFSISWSRILPRGTLKGGINQAGIEYYN
    NLINQLISKGVKPFVTLFHWDLPDALENAYGGLLGDIBFVNDFRDYAELCFQKFGDRVKQWTTLNE
    PYTMVHEGYITGQKAPGRCSNFYKPDCLGGDAATEPYIVGHNLLLAHGVAVKVYREKYQATQKG
    EIGIALNTAWHYPYSDSYADRLAATRATAFTFDYFMEPIVYGRYPIEMVSHVKDGRLPTFTPEESE
    MLKGSYDFIGVNYYSSLYAKDVPCATENITMTTDSCVSLVGERNGVPIGPAAGSDWLLIYPKGIRD
    LLLHAKFRYNDPVLYITENGVDEANIGKIFLNDDLRIDYYAHHLKMVSDAISIGVNVKGYFAWSL
    MDNFEWSEGYTVRFGLVFVDFEDGRKRYLKKSAKWFRRLLKGAHGGTNEQVAVI*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12668112 At_4deg_Cold 20000214 −
    12668112 At_10percent_PEG 20000527 −
    12668112 At_Drought_Soil_Dry 20001554 −
    12668112 At_Drought_Soil_Dry 20001555 −
    12668112 At_Interploidy_Crosses 20001853 −
    12668112 At_8deg_Cold 20002105 −
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12668112 At_4deg_Cold 20000214 Timepoint (hr) 6
    12668112 At_10percent_PEG 20000527 Age (day) 20
    12668112 At_10percent_PEG 20000527 Timepoint (day) 20
    12668112 At_10percent_PEG 20000527 Treatment 10percent PEG vs. No
    Treatment
    12668112 At_10percent_PEG 20000527 Organism A. thaliana
    12668112 At_10percent_PEG 20000527 Tissue Whole Plant
    12668112 At_10percent_PEG 20000527 Plant Line WS
    12668112 At_Drought_Soil_Dry 20001554 Timepoint (day) 7
    12668112 At_Drought_Soil_Dry 20001554 Age (day) 21
    12668112 At_Drought_Soil_Dry 20001554 Organism A. thaliana
    12668112 At_Drought_Soil_Dry 20001554 Treatment Drought vs. No Drought
    12668112 At_Drought_Soil_Dry 20001554 Post Timepoint (hr) None
    12668112 At_Drought_Soil_Dry 20001554 Post-Treatment None
    12668112 At_Drought_Soil_Dry 20001554 Plant Line WS
    12668112 At_Drought_Soil_Dry 20001555 Timepoint (day) 10
    12668112 At_Drought_Soil_Dry 20001555 Age (day) 24
    12668112 At_Drought_Soil_Dry 20001555 Organism A. thaliana
    12668112 At_Drought_Soil_Dry 20001555 Treatment Drought vs. No Drou ht
    12668112 At_Drought_Soil_Dry 20001555 Post Timepoint (hr) None
    12668112 At_Drought_Soil_Dry 20001555 Post-Treatment None
    12668112 At_Drought_Soil_Dry 20001555 Plant Line
    12668112 At_Interploidy_Crosses 20001853 Age (day) 5
    12668112 At_Interploidy_Crosses 20001853 Organism A. thaliana
    12668112 At_Interploidy_Crosses 20001853 Plant Line Columbia
    12668112 At_Interploidy_Crosses 20001853 Cross Fis1 vs. 2X × 2X
    12668112 At_Interploidy_Crosses 20001853 Tissue Siliques
    12668112 At_8deg_Cold 20002105 Age (day) 7
    12668112 At_8deg_Cold 20002105 Timepoint (hr) 8
    12668112 At_8deg_Cold 20002105 Temperature (deg C.) 8 vs. 22
    12668112 At_8deg_Cold 20002105 Organism A. thaliana
    12668112 At_8deg_Cold 20002105 Tissue Whole Plant
    12668112 At_8deg_Cold 20002105 Plant Line WS
    Promoter YP0244
    Modulates the gene: Ca2 + -ATPase 7
    The GenBank description of the gene: NM_127860 Arabidopsis thaliana potential calcium-transporting
    ATPase 7, plasma membrane-type (Ca2 + -ATPase, isoform 7) (At2g22950) mRNA, complete cds
    gi|18400128|ref|NM_127860.1|[18400128]
    The promoter sequence:
    5′aaagtcttatttgtgaaattttacaaatgttggaaaaaagcattttatggtgctatatttgtcaatttc
    ccttgattatatatccttttgaaaagtaatgttttttttatgtgtgtgtattcatgaaccttggaaaaact
    acaaatcagatcatggtttgttttaggtgaaaaatttagaacacagttacgcaagaaagatatcggtaaat
    ttttgtttctttgaatcgaaattaatcaaaaagtattttccattatataacaacaactaatctctgttttt
    tttttttttttttaacaactaatctcttatcaaaatgacactacagaatcacgattgtaaatctttaaaag
    gcagtctgaaaaatattcatgaggatgagattttattcattcatggttgtaagtaatcattatgtaaagtt
    taggataaggacgttcaaaatcatataaaaaaactctacgaataaagtttatagtctatcatattgattca
    tatttcatagaaagttactggaaaacattacacaagtattctcgatttttacgagtttgtttagtagtcgc
    aaaattttattttacttttgagtatacgaacccataagctgattttctttccaagttccaataatgatatc
    atagtgtactcttcatgaatgtttcaagcatataattataacgttcataagtaatattctactgcatgttt
    gttatTATAaattaactaataatcgaacgtatgagttttgattgagattgttgtgctcacgaaatgaagga
    ctcggtcaattctaaagcttaaaataagaagctcagatcttaaaactcgctttcgtcttcgtcctccattt
    aagtttgcgattcttttgctcttctttctctctcacatttttgtcccaaaacaataaaaagaaacaataat
    agaaagtgttacagaaaaagaaagaaaac 3′-ATG
    The promoter was cloned from the organism: Arabidopsis thaliana, WS ecotype
    Alternative nucleotides:
    Predicted (Columbia)
    Experimental (Wassilewskija)
    Sequence Position (bp) Mismatch Columbia/Wassilewskija
     90 SNP a/g
    183 SNP t/c
    373 SNP t/c
    380 No g in Ws -/-
    393 No g in Ws -/-
    717 SNP t/c
    774 SNP a/g
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower    H pollen
    Observed expression pattern of the promoter-marker vector was in:
    T1 mature: Pollen specific expression in mature plants.
    T2 seedling: No GFP expression observed.
    The promoter can be of use in the following trait and sub-trait areas: (search for the trait and sub-
    trait table)
    Trait Area:       Paternal inheritance trait where 50%is desired
    Sub-trait Area:   Yield
    The promoter has utility in:
    Utility:     Modulation of pollen tube growth, incompatibility
    Misc. promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No
    The Ceres eDNA ID of the endo enous codin Se uence to the romoter: 12736016
    cDNA nucleotide sequence:
    atggagagttacctcaactcgaatttcgacgttaaggcgaagcattcgtcggaggaagtgctagaaaaatg
    gcggaatctttgcagtgtcgtcaagaacccgaaacgtcggtttcgattcactgccaatctctccaaacgtt
    acgaagctgctgccatgcgccgcaccaaccaggagaaattaaggattgcagttctcgtgtcaaaagccgca
    tttcaatttatctctggtgtttctccaagtgactacaaggtgcctgaggaagttaaagcagcaggctttga
    catttgtgcagacgagttaggatcaatagtggaaggtcatgatgtgaagaagctcaagttccatggtggtg
    ttgatggtctttcaggtaagctcaaggcatgtcccaatgctggtctctcaacaggtgaacctgagcagtta
    agcaaacgacaagagcttttcggaatcaataagtttgcagagagtgaattacgaagtttctgggtgtttgt
    ttgggaagcacttcaagatatgactcttatgattcttggtgtttgtgctttcgtctctttgattgttggga
    ttgcaactgaaggatggcctcaaggatcgcatgatggtcttggcattgttgctagtattcttttagttgtg
    tttgtgacagcaactagtgactatagacaatctttgcagttccgggatzttggataaagagaagaagaagat
    cacggttcaagttacgcgaaacgggtttagacaaaagatgtctatatatgatttgctccctggagatgttg
    ttcatcttgctatcggagatcaagtccctgcagatggtcttttcctctcgggattctctgttgttatcgat
    gaatcgagtttaactggagagagtgagcctgtgatggtgactgcacagaaccctttccttctctctggaac
    caaagttcaagatgggtcatgtaagatgttggttacaacagttgggatgagaactcaatggggaaagttaa
    tggcaacacttagtgaaggaggagatgacgaaactccgttgcaggtgaaacttaatggagttgcaaccatc
    attgggaaaattggtctttccttcgctattgttacctttgcggttttggtacaaggaatgtttatgaggaa
    gctttcattaggccctcattggtggtggtccggagatgatgcattagagcttttggagtattttgctattg
    ctgtcacaattgttgttgttgcggttcctgaaggtttaccattagctgtcacacttagtctcgcgtttgcg
    atgaagaagatgatgaacgataaagcgcttgttcgccatttagcagcttgtgagacaatgggatctgcaac
    taccatttgtagtgacaagactggtacattaacaacaaatcacatgactgttgtgaaatcttgcatttgta
    tgaatgttcaagatgtagctagcaaaagttctagtttacaatctgatatccctgaagctgccttgaaacta
    cttctccagttgatttttaataataccggtggagaagttgttgtgaacgaacgtggcaagactgagatatt
    ggggacaccaacagagactgctatattggagttaggactatctcttggaggtaagtttcaagaagagagac
    aatctaacaaagttattaaagttgagccttttaactcaacaaagaaaagaatgggagtagtcattgagctg
    cctgaaggaggacgcattcgcgctcacacgaaaggagcttcagagatagttttagcggcttgtgataaagt
    catcaactcaagtggtgaagttgttccgcttgatgatgaatccatcaagttcttgaatgttacaatcgatg
    agtttgcaaatgaagctcttcgtactctttgccttgcttatatggatatcgaaagcgggttttcggctgat
    gaaggtattccggaaaaagggtttacatgcatagggattgttggtatcaaagaccctgttcgtcctggagt
    tcgggagtccgtggaactttgtcgccgtgcgggtattatggtgagaatggttacaggagataacattaaca
    ccgcaaaggctattgctagagaatgtggaattctcactgatgatggtatagcaattgaaggtcctgtgttt
    agagagaagaaccaagaagagatgcttgaactcattcccaagattcaggtcatggctcgttcttccccaat
    ggacaagcatacactggtgaagcagttgaggactacttttgatgaagttgttgctgtgactggcgacggga
    caaacgatgcaccagcgctccacgaggctgacataggattagcaatgggcattgccgggactgaagtagcg
    aaagagattgcggatgtcatcattctcgacgataacttcagcacaatcgtcaccgtagcgaaatggggacg
    ttctgtttacattaacattcagaaatttgtgcagtttcaactaacagtcaatgttgttgcccttattgtta
    acttctcttcagcttgcttgactggaagtgctcctctaactgctgttcaactgctttgggttaacatgatc
    atggacacacttggagctcttgctctagctacagaacctccgaacaacgagctgatgaaacgtatgcctgt
    tggaagaagagggaatttcattaccaatgcgatgtggagaaacatcttaggacaagctgtgtatcaattta
    ttatcatatggattctacaggccaaagggaagtccatgtttggtcttgttggttctgactctactctcgta
    ttgaacacacttatcttcaactgctttgtattctgccaggttttcaatgaagtaagctcgcgggagatgga
    agagatcgatgttttcaaaggcatactcgacaactatgttttcgtggttgttattggtgcaacagttttct
    ttcagatcataatcattgagttcttgggcacatttgcaagcaccacacctcttacaatagttcaatggttc
    ttcagcattttcgttggcttcttgggtatgccgatcgctgctggcttgaagaaaatacccgtgtga
    Coding sequence:
    MESYLNSNFDVKAKHSSEEVLEKWRNLCSVVKNPKRRFRFTANLSKRYEAAAMRRTNQEKLRIA
    VLVSKAAFQFISGVSPSDYKVPEEVKAAGFDICADELGSIVEGHDVKKLKFHGGVDGLSGKLKACP
    NAGLSTGEPEQLSKRQELFGINKFAESELRSFWVFVWEALQDMTLMILGVCAFVSLIVGIATEGWP
    QGSHDGLGIVASILLVVFVTATSDYRQSLQFRDLDKEKKKITVQVTRNGFRQKMSIYDLLPGDVVH
    LAIGDQVPADGLFLSGFSVVIDESSLTGESEPVMVTAQNPFLLSGTKVQDGSCKMLVTTVGMRTQ
    WGKLMATLSEGGDDETPLQVKLNGVATIIGKIGLSFAIVTFAVLVQGMFMRKLSLGPHWWWSGD
    DALELLEYFAIAVTIVVVAVPEGLPLAVTLSLAFAMKKMMNDKALVRHLAACETMGSATTICSDK
    TGTLTTNHMTVVKSCICMNVQDVASKSSSLQSDIPEAALKLLLQLIFNNTGGEVVVNERGKTEILG
    TPTETAILELGLSLGGKFQEERQSNKVIKVEPFNSTKKRMGVVIELPEGGRIRAHTKGASEIVLAAC
    DKVINSSGEVVPLDDESIKFLNVTIDEFANEALRTLCLAYMDIESGFSADEGIPEKGFTCIGIVGIKDP
    VRPGVRESVELCRRAGIMVRMVTGDNINTAKAIARECGILTDDGIAIEGPVFREKNQEEMLELIPKI
    QVMARSSPMDKHTLVKQLRTTFDEVVAVTGDGTNDAPALHEADIGLAMGIAGTEVAKEIADVIIL
    DDNFSTIVTVAKWGRSVYINIQKFVQFQLTVNVVALIVNFSSACLTGSAPLTAVQLLWVNMIMDTL
    GALALATEPPNNELMKRMPVGRRGNFITNAMWRNILGQAVYQFIIIWILQAKGKSMFGLVGSDST
    LVLNTLIFNCFVFCQVFNEVSSREMEEIDVFKGILDNYVFVVVIGATVFFQIIIIEFLGTFASTTPLTIV
    QWFFSIFVGFLGMPIAAGLKKIPV*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    Promoter YP0226
    Modulates the gene: Indoleacetic acid-induced protein 12
    The GenBank description of the gene: NM_100334 Arabidopsis thaliana auxin-responsive protein
    1AA12 (Indoleacetic acid-induced protein 12) (At1g04550) mRNA, complete cds gi|30678909|
    ref|NM_100334.2
    The promoter sequence:
    5′tcaaaagtgtaatttccacaaaccaattgcgcctgcaaaagttttcaaaggatcatcaaacataatgat
    gaatatctcatcaccacgattttataataatgcatcttttcccaccattttttttccctcactttctttta
    taatcttgttcgacaacaatcatggtctaaggaaaaagttgaaaatatatattatcttagttattagaaaa
    gaaagataatcaaatggtcaatatgcaaatggcatatgaccataaacgagtttgctagtataaagaatgat
    ggccaacctgttaaagagagactaaaattaggtctaaaatctaggagcaatgtaaccaatacatagtatat
    gaaatataaaagttaatttagattttttgattagcccaaattaaagaaaaatggtatttaaaacagagact
    cttcatcctaaaggctaaagcaatacaatttttggttaagaaaagaaaaaaaccacaagcggaaaagaaaa
    caaaaaagaactatattatgatgcaacagcaacacaaagcaaaaccttgcacacacacatacaactgtaaa
    caagtttcttgggactctctattttctcttgctgcttgaaccaaacacaacaacgatatcccaacgagagc
    acaacaggtttgattatgtcggaagacaagttttgagagaaaacaaacaatatttTATAacaaaggagaag
    acttttggttagaaaaaattggtatggccattacaagacatatgggtcccaattctcatcactctctccac
    caccaaaatcctcctctctctctctctcttttactctgttttcatcatctctttctctcgtctctctcaaa
    ccctaaatacactctttctcttcttgttgtctccattctctctgtgtcatcaagcttcttttttgtgtggg
    ttatttgaaagacactttctctgctggtatcattggagt 3′-ATG
    The promoter was cloned from the organism: Arabidopsis thaliana, WS ecotype
    Alternative nucleotides:
    Sequence (bp) Mismatch Columbia/Wassilewskija
    1523 SNP g/-
    558 SNP a/c
    741 SNP a/g
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower M vascular
    Silique M placenta, M vascular
    Hypocotyl H vascular
    Cotyledon H vascular, H petiole
    Primary Root H vascular
    Observed expression pattern of the promoter-marker vector was in:
    T1 mature: GFP expressed in vasculature of silique and pedicles of flowers.
    T2 seedling: High GFP expression throughout vasculature of root, hypocotyl, and petioles.
    Misc. promoter information:   Bidirectionality: Pass   Exons:Pass   Repeats:No
    Optional Promoter Fragments: 5′UTR region at base pairs 832-1000
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12327003
    cDNA nucleotide sequence:
    ACTCTGTTTTCATCTCTTTCTCTCGTCTCTCTCAAACCCTAAATACACTCTTTCTCTTCTTG
    TTGTCTCCATTCTCTCTGTGTCATCAAGCTTCTTTTTTGTGTGGGTTATTTGAAAGACACTTTCT
    CTGGTGGTATCATTGGAGTCTAGGGTTTTGTTATTGACATGCGTGGTGTGTCAGAATTGGAGG
    TGGGGAAGAGTAATCTTCCGGCGGAGAGTGAGCTGGAATTGGGATTAGGGCTCAGCCTCGGT
    GGTGGCGCGTGGAAAGAGCGTGGGAGGATTCTTACTGCTAAGGATTTTCCTTCCGTTGGGTCT
    AAACGCTCTGCTGAATCTTCCTCTCACCAAGGAGCTTCTCCTCCTCGTTCAAGTCAAGTGGTAG
    GATGGGCACCAATTGGGTTACACAGGATGAACAGTTTGGTTAATAACGAAGCTATGAAGGCAG
    GAAGAGCGGAAGAAGGAGACGGGGAGAAGAAAGTTGTGAAGAATGATGAGCTCAAAGATGT
    GTCAATGAAGGTGAATCCGAAAGTTCAGGGCTTAGGGTTTGTTAAGGTGAATATGGATGGAGT
    TGGTATAGGCAGAAAAGTGGATATGAGAGCTCATTCGTCTTACGAAAACTTGGCTCAGACGCT
    TGAGGAAATGTTCTTTGGAATGACAGGTACTACTTGTCGAGAAAAGGTTAAACCTTTAAGGCT
    TTTAGATGGATCATCAGACTTTGTACTCACTTATGAAGATAAGGAAGGGGATTGGATGCTTGT
    TGGAGATGTTCCATGGAGAATGTTTATCAACTGGGTGAAAAGGCTTCGGATCATGGGAACCTC
    AGAAGCTAGTGGACTAGCTCCAAGACGTCAAGAGCAGAAGGATAGACAAAGAAACAACCCTG
    TTTAGCTTCCCTTCCAAAGCTGGCATTGTTTATGTATTGYFTGAGGTTTGCAATTTACTCGATA
    CTTTTTGAAGAAAGTATTTTGGAGAATATGGATAAAAGCATGCAGAAGCTTAGATATGATTTG
    AATCGGGTTTTCGGATATGGTTTTGCTTAGGTCATTCAATTCGTAGTTTTCCAGTTTGTTTCTTC
    TTTGGCTGTGTAGCAATTATCTATGTTCTGTGAGAGAAAGCTCTTGTTTATTTGTTCTCTCAGA
    TTGTAAATAGTTGAAGTTATCTAATTAATGTGATAAGAGTTATGTTTATGATTCC
    Coding sequence:
    MRGVSELEVGKSNLPAESELELGLGLSLGGGAWKERGRILTAKDFPSVGSKRSAESSSHQGASPPR
    SSQVVGWPPIGLHRMNSLVNNQAMKAARAEEGDGEKKVVKNDELKDVSMKVNPKVQGLGFVK
    VNMDGVGIGRKVDMRAHSSYENLAQTLEEMFFGMTGTTCREKVKPLRLLDGSSDFVLTYEDKEG
    DWMLVGDVPWRMFINSVKRLRIMGTSEASGLAPRRQEQKDRQRNNPV*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12327003 At_Diversity_Expt 108457 −
    12327003 At_100uM_ABA 108561 −
    12327003 At_100uM_ABA_Mutants 20000069 −
    12327003 At_100uM_ABA_Mutants 20000070 −
    12327003 At_100uM_ABA_Mutants 20000072 −
    12327003 At_100uM_ABA_Mutants 20000086 −
    12327003 At_100mM_ABA_Mutants 20000087 −
    12327003 At_100uM_ABA_Mutants 20000088 −
    12327003 At_2mM_SA_CS3726-Columbia 20000089 −
    12327003 At_100mM_ABA_Mutants 20000117 −
    12327003 At_Far-red-induction 20001248 −
    12327003 At_8deg_Cold 20002105 +
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12327003 At_Diversity_Expt 108457 Plant Line Canola vs. WS
    12327003 At_Diversity_Expt 108457 Tissue Hypocotyl
    12327003 At_100uM_ABA 108561 Timepoint (hr) 6
    12327003 At_100uM_ABA 108561 Treatment 100uM ABA vs. No
    Treatment
    12327003 At_100uM_ABA 108561 Tissue Aerial
    12327003 At_100uM_ABA_Mutants 20000069 Timepoint (hr) 6
    12327003 At_100uM_ABA_Mutants 20000069 Treatment 100uM ABA vs. No
    Treatment
    12327003 At_100uM_ABA_Mutants 20000069 Tissue Aerial
    12327003 At_100uM_ABA_Mutants 20000069 Plant Line CS23
    12327003 At_100uM_ABA_Mutants 20000070 Timepoint (hr) 6
    12327003 At_100uM_ABA_Mutants 20000070 Treatment 100uM ABA vs. No
    Treatment
    12327003 At_100uM_ABA_Mutants 20000070 Tissue Aerial
    12327003 At_100uM_ABA_Mutants 20000070 Plant Line CS24
    12327003 At_100uM_ABA_Mutants 20000072 Timepoint (hr) 6
    12327003 At_100uM_ABA_Mutants 20000072 Treatment 100uM ABA vs. No
    Treatment
    12327003 At_100uM_ABA_Mutants 20000072 Tissue Aerial
    12327003 At_100uM_ABA_Mutants 20000072 Plant Line CS8105
    12327003 At_100uM_ABA_Mutants 20000086 Timepoint (hr) 6
    12327003 At_100uM_ABA_Mutants 20000086 Treatment 100uM ABA vs. No
    Treatment
    12327003 At_100uM_ABA_Mutants 20000086 Tissue Aerial
    12327003 At_100uM_ABA_Mutants 20000086 Plant Line CS22
    12327003 At_100uM_ABA_Mutants 20000087 Timepoint (hr) 6
    12327003 At_100uM_ABA_Mutants 20000087 Treatment 100uM ABA vs. No
    Treatment
    12327003 At_100uM_ABA_Mutants 20000087 Tissue Aerial
    12327003 At_100uM_ABA_Mutants 20000087 Plant Line WS
    12327003 At_100uM_ABA_Mutants 20000088 Timepoint (hr) 6
    12327003 At_100uM_ABA_Mutants 20000088 Treatment 100uM ABA vs. No
    Treatment
    12327003 At_100uM_ABA_Mutants 20000086 Tissue Aerial
    12327003 At_100uM_ABA_Mutants 20000088 Plant Line Landsberg
    12327003 At_2mM_SA_CS3726- 20000089 Timepoint (hr) 6
    Columbia
    12327003 At_2mM_SA_CS3726- 20000089 Treatment 2mM SA vs. No Treatment
    Columbia
    12327003 At_2mM_SA_CS3726- 20000089 Tissue Aerial
    Columbia
    12327003 At_2mM_SA_CS3726- 20000089 Plant Line CS3726
    Columbia
    12327003 At_100mM_ABA_Mutants 20000117 Timepoint (hr) 6
    12327003 At_100uM_ABA_Mutants 20000117 Treatment 100uM ABA vs. No
    Treatment
    12327003 At_100mM_ABA_Mutants 20000117 Tissue Aerial
    12327003 At_100uM_ABA Mutants 20000117 Plant Line Columbia
    12327003 At_Far-red-induction 20001248 Timepoint (hr) 4
    12327003 At_Far-red-induction 20001248 Age (day) 7
    12327003 At_Far-red-induction 20001248 Organism A. thaliana
    12327003 At_Far-red-induction 20001248 Plant Line Columbia
    12327003 At_Far-red-induction 20001248 Light Far-red vs. White
    12327003 At_Far-red-induction 20001248 Tissue Whole Plant
    12327003 At_8deg_Cold 20002105 Age (day) 7
    12327003 At_8deg_Cold 20002105 Timepoint (hr) 8
    12327003 At_8deg_Cold 20002105 Temperature (deg C.) 8 vs. 22
    12327003 At_8deg_Cold 20002105 Organism A. thaliana
    12327003 At_8deg_Cold 20002105 Tissue Whole Plant
    12327003 At_8deg_Cold 20002105 Plant Line WS
    Promoter PTO511
    Modulates the gene: Major intrinsic protein (MIP)
    The GenBank description of the gene: : NM_106724 Arabidopsis thaliana major intrinsic protein (MIP)
    family (At1g80760) mRNA, complete cds gi|30699534|ref|NM_106724.2|[30699534].
    The promoter sequence:
    5′gacgggtcatcacagattcttcgtttttttatagatagaaaaggaataacgttaaaagtatacaaatta
    tatgcaagagtcattcgaaagaattaaataaagagatgaactcaaaagtgattttaaattttaatgataag
    aatatacatctcacagaaatcttttatttgacatgtaaaatcttgttttcacctatcttttgttagtaaac
    aagaatatttaatttgagcctcacttggaacgtgataataatatacatcttatcataattgcatattttgc
    ggatagtttttgcatggggagattaaaggcttaataaagccttgaatttccgaggggaggaatcatgtttt
    atacttgcaaactatacaaccatctgcatcgataattggtgttaatacatgcaaggattatacactaaaac
    aaatcatttatttccttacaaaaagagagtcgactgtgagtcacattctgtgacaaggaaaggtcaagaac
    catcgcttttatcatcattctctttgctaacaacttacaaccacacaaacgcaagagttccattctcatgg
    agaagaacatattatgcaaaataatgtatgtcgatcgatagagaaaaggatccacaattattgctccatct
    caaaagcttctttagtacacgatacatgtatcatgtaaatagaaatatgaaagatacaatacacgacccat
    tctcataaagatagcaacatttcatgttatgtaaagagtcttccttaggacacatgcattaaaactaagga
    ttaccaacccacttactcctcactccaaccaaatatcaatcatctattttgggtccttcactcataagtca
    actctcatgccttcctctataaataccgtaccctacgcatcccttagttctacatcacataaaaacaatca
    tagcaaaaacaTATAtcctcaaattaatt 3′-cATG
    The promoter was cloned from the organism: Arabidopsis thaliana, Columbia ecotype
    Alternative nucleotides:
    Predicted Position (bp) Mismatch Predicted/Experimental
    1-1000 None Identities = 1000/1000 (100%)
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower H filament H anther L vascular
    Cotyledon L vascular L petiole
    Primary Root L epidermis
    Observed exoression pattern of the promoter-marker vector was in:
    T1 mature: High expression at vascular connective tissue between locules of anther.
    T2 Seedling: Low expression in root epidermal cells and vasculature of petioles.
    Misc. promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No
    Optional Promoter Fragments: 5′ UTR region at base pairs 927-1000.
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12711931
    cDNA nucleotide sequence:
    ATGGATCATGAGGAAATTCCATCCACGCCCTCAACGGCGGCGACAACCCCGGGGACTCCAGGA
    GCGCCGCTCTTTGGAGGATTCGAAGGGAAGAGGAATGGACACAATGGTAGATACACACGAAA
    GTCACTTCTCAAAAGCTGCAAATGTTTCAGTGTTGACAATGAATGGGCTCTTGAAGATGGAAG
    ACTCCCTCCGGTCACTTGCTCTCTCCCTCCCCCTAACGTTTCCCTCTACCGCAAGTTGGGAGCA
    GAGTTTGTTGGGACATTGATCCTGATATTCGCCGGAACAGCGACGGCGATCGTGAACCAGAAG
    ACAGATGGAGCTGAGACGCTTATTGGTTGCGCCGCCTCGGCTGGTTTGGCGGTTATGATCGTT
    ATATTATCGACCGGTCACATCTCCGGGGCACATCTCAATCCGGCTGTAACCATTGCCTTTGCTG
    CTGTCAAACACTTCCCTTGGAAACACGTGCCGGTGTATATCGGAGCTCAGGTGATGGCCTCCG
    TGAGTGCGGCGTTTGCACTGAAAGCAGTGTTTGAACCAACGATGAGCGGTGGCGTGACGGTG
    CCGACGGTGGGTCTCAGCCAAGCTTTCGCCTTGGAATTCATTATCAGCTTCAACCTCATGTTCG
    TTGTCACAGCCGTAGCCACCGACACGAGAGCTGTGGGAGAGTTGGCGGGAATTGCCGTAGGA
    GCAACGGTCATGCTTAACATACTTATAGCTGGACCTGCAAGTTCTGCTTCGATGAACCCTGTAA
    GAACACTGGGTCCAGGCATTGCAGCAAACAATTACAGAGCTATTTGGGTTTACCTCACTGCCC
    CCATTCTTGGAGCGTTAATCGGAGCAGGTACATACACAATTGTCAAGTTGCCAGAGGAAGATG
    AAGCACCCAAAGAGAGGAGGAGCTTCAGAAGATGA
    Coding sequence:
    MDHEEIPSTPSTPATTPGTPGAPLFGGFEGKRNGHNGRYTPKSLLKSCKCFSVDNEWALEDGRLPP
    VTCSLPPPNVSLYRKLGAEFVGTLILIFAGTATAIVNQKTDGAETLIGCAASAGLAVMIVILSTGHIS
    GAHLNPAVTIAFAALKHFPWKHVPVYIGAQVMASVSAAFALKAVFEPTMSGGVTVPTVGLSQAF
    ALEFIISFNLMFVVTAVATDTRAVGELAGIAVGATVMLNILIAGPATSASMNPVRTLGPAIAANNYR
    AIWVYLTAPILGALIGAGTYT1VKLPEEDEAPKERRSFRR*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    12711931 At_Root_Tips 108434 −
    12711931 At_stm_Mutants 108435 +
    12711931 At_Diversity_Expt 108457 +
    12711931 At_Diversity_Expt 108458 +
    12711931 At_Germinating_Seeds 108464 +
    12711931 At_ap2_floral_buds 108501 +
    12711931 At_4deg_Cold 108579 +
    12711931 At_Ler-pi_Ovule 108595 +
    12711931 At_100uM_ABA_Mutants 20000069 −
    12711931 At_100uM_ABA_Mutants 20000070 −
    12711931 At_100uM_ABA_Mutants 20000071 −
    12711931 At_100uM_ABA_Mutants 20000086 −
    12711931 At_100uM_ABA_Mutants 20000087 −
    12711931 At_100uM_ABA_Mutants 20000088 −
    12711931 At_2mM_SA_C53726-Columbia 20000089 −
    12711931 At_2mM_SA_C53726-Columbia 20000090 −
    12711931 At_100uM_ABA_Mutants 20000117 −
    12711931 At_CS6632_Shoots-Roots 20000224 +
    12711931 At_Root-Tips-vs-Tops 20000227 +
    12711931 At_Siliques 20000234 +
    12711931 At_Siliques 20000236 +
    12711931 At_Caf_Knockout 20000244 −
    12711931 At_Open_Flower 20000264 +
    12711931 At_Open_Flower 20000286 +
    12711931 At_Drought 20000437 −
    12711931 At_Shoots 20000438 +
    12711931 At_C56879_Shoots-Roots 20000451 −
    12711931 At_42deg_Heat 20000458 −
    12711931 At_Guard_Cells 20000495 +
    12711931 At_100uM_ABA_Mutants 20000576 +
    12711931 At_Herbicide_Mutants 20000640 −
    12711931 At_Herbicide_Mutants 20000642 −
    12711931 At_Petals 20000794 +
    12711931 At_Line_Comparisons 20001151 +
    12711931 At_Line_Comparisons 20001184 +
    12711931 At_Far-red-induction 20001248 −
    12711931 At_Line_Comparisons 20001307 +
    12711931 At_Line_Comparisons 20001318 +
    12711931 At_Line_Comparisons 20001319 +
    12711931 At_Line_Comparisons 20001347 +
    12711931 At_50mM_NH4NO3_L-to-H 20001458 −
    12711931 At_Drought_Soil_Dry 20001556 −
    12711931 At_Drought_Soil_Dry 20001557 −
    12711931 At_Drought_Soil_Dry 20001558 −
    12711931 At_Drought_Reproduction 20001905 −
    12711931 At_Drought_Reproduction 20001906 −
    12711931 At_Drought_Reproduction 20001907 −
    12711931 At_8deg_Cold 20002105 +
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    12711931 At_Root_Tips 108434 Tissue Root Tips
    12711931 At_stm_Mutants 108435 Tissue Shoot Apical Meristem Region
    12711931 At_stm_Mutants 108435 Plant Line wt Landsburg vs stm
    12711931 At_Diversity_Expt 108457 Plant Line Canola vs. WS
    12711931 At_Diversity_Expt 108457 Tissue Hypocotyl
    12711931 At_Diversity_Expt 108458 Plant Line Holbolilie vs. WS
    12711931 At_Diversity_Expt 108458 Tissue Hypocotyl
    12711931 At_Germinating_Seeds 108464 Age (day) 4 vs. 0
    12711931 At_Germinating_Seeds 108464 Tissue Germinating_Seeds
    12711931 At_ap2_floral_buds 108501 Plant Line ap2 (Ler.)
    12711931 At_ap2_floral_buds 108501 Tissue Closed Flower
    12711931 At_4deg_Cold 108579 Timepoint (hr) 6
    12711931 At_4deg_Cold 108579 Temperature (deg 4 vs. 22
    C.)
    12711931 At_4deg_Cold 108579 Tissue Aerial
    12711931 At_Ler-pi_Ovule 108595 Plant Line Lerpi
    12711931 At_Ler-pi_Ovule 108595 Tissue Ovules
    12711931 At_100uM_ABA_Mutants 20000069 Timepoint (hr) 6
    12711931 At_100uM_ABA_Mutants 20000069 Treatment 100uM ABA vs. No Treatment
    12711931 At_100uM_ABA_Mutants 20000069 Tissue Aerial
    12711931 At_100uM_ABA_Mutants 20000069 Plant Line CS23
    12711931 At_100uM_ABA_Mutants 20000070 Timepoint (hr) 6
    12711931 At_100uM_ABA_Mutants 20000070 Treatment 100uM ABA vs. No Treatment
    12711931 At_100uM_ABA_Mutants 20000070 Tissue Aerial
    12711931 At_100uM_ABA_Mutants 20000070 Plant Line C524
    12711931 At_100uM_ABA_Mutants 20000071 Timepoint (hr) 6
    12711931 At_100uM_ABA_Mutants 20000071 Treatment 100uM ABA vs. No Treatment
    12711931 At_100uM_ABA_Mutants 20000071 Tissue Aerial
    12711931 At_100uM_ABA_Mutants 20000071 Plant Line C58104
    12711931 At_100uM_ABA_Mutants 20000086 Timepoint (hr) 6
    12711931 At_100uM_ABA_Mutants 20000086 Treatment 100uM ABA vs. No Treatment
    12711931 At_100uM_ABA_Mutants 20000086 Tissue Aerial
    12711931 At_100uM_ABA_Mutants 20000086 Plant Line C522
    12711931 At_100uM_ABA_Mutants 20000087 Timepoint (hr) 6
    12711931 At_100uM_ABA_Mutants 20000087 Treatment 100uM ABA vs. No Treatment
    12711931 At_100uM_ABA_Mutants 20000087 Tissue Aerial
    12711931 At_100uM_ABA_Mutants 20000087 Plant Line WS
    12711931 At_100uM_ABA_Mutants 20000088 Timepoint (hr) 6
    12711931 At_100uM_ABA_Mutants 20000088 Treatment 100uM ABA vs. No Treatment
    12711931 At_100uM_ABA_Mutants 20000088 Tissue Aerial
    12711931 At_100uM_ABA_Mutants 20000088 Plant Line Landsberg
    12711931 At_2mM SA CS3726- 20000089 Timepoint (hr) 6
    Columbia
    12711931 At_2mM_SA_053726- 20000089 Treatment 2mM SA vs. No Treatment
    Columbia
    12711931 At_2mM_SA_053726- 20000089 Tissue Aerial
    Columbia
    12711931 At_2mM_SA C53726- 20000089 Plant Line CS3726
    Columbia
    12711931 At_2mM_SA_C53726- 20000090 Timepoint (hr) 6
    Columbia
    12711931 At_2mM_SA CS3726- 20000090 Treatment 2mM SA vs. No Treatment
    Columbia
    12711931 At_2mM_SA CS3726- 20000090 Tissue Aerial
    Columbia
    12711931 At_2mM_SA_C53726- 20000090 Plant Line Columbia
    Columbia
    12711931 At_100uM_ABA_Mutants 20000117 Timepoint (hr) 6
    12711931 At_100uM_ABA_Mutants 20000117 Treatment 100uM ABA vs. No Treatment
    12711931 At_100uM_ABA_Mutants 20000117 Tissue Aerial
    12711931 At_100uM_ABA_Mutants 20000117 Plant Line Columbia
    12711931 At_CS6632_Shoots-Roots 20000224 Age (day) 14
    12711931 At_CS6632_Shoots-Roots 20000224 Organism A. thaliana
    12711931 At_CS6632_Shoots-Roots 20000224 Plant Line CS6632 vs. WS
    12711931 At_CS6632_Shoots-Roots 20000224 Tissue Shoots
    12711931 At_Root-Tips-vs-Tops 20000227 Age (day) 7, 10, 14
    12711931 At_Root-Tips-vs-Tops 20000227 Organism A. thaliana
    12711931 At_Root-Tips-vs-Tops 20000227 Tissue Root_Tips vs. Root Tops
    12711931 At_Root-Tips-vs-Tops 20000227 Plant Line WS
    12711931 At_Siliques 20000234 Age (day) 21
    12711931 At_Siliques 20000234 Tissue <5mm Siliques vs. Whole
    Plant
    12711931 At_Siliques 20000234 Organism A. thaliana
    12711931 At_Siliques 20000234 Plant Line WS
    12711931 At_Siliques 20000236 Age (day) 21
    12711931 At_Siliques 20000236 Tissue >10mm Siliques vs. Whole
    Plant
    12711931 At_Siliques 20000236 Organism A. thaliana
    12711931 At_Siliques 20000236 Plant Line WS
    12711931 At_Caf_Knockout 20000244 Plant Line caf Knockout vs. wt
    12711931 At_Caf_Knockout 20000244 Tissue Rosette
    12711931 At_Open_Flower 20000264 Age (day) 21
    12711931 At_Open_Flower 20000264 Organism A. thaliana
    12711931 At_Open_Flower 20000264 Tissue Open_Flower vs. Whole Plant
    12711931 At_Open_Flower 20000264 Plant Line WS
    12711931 At_Open_Flower 20000286 Age (day) 21
    12711931 At_Open_Flower 20000286 Organism A. thaliana
    12711931 At_Open_Flower 20000286 Tissue Half Open vs. Whole Plant
    12711931 At_Open_Flower 20000286 Plant Line WS
    12711931 At_Drought 20000437 Age (day) 8
    12711931 At_Drought 20000437 Timepoint (hr) 24
    12711931 At_Drought 20000437 Organism A. thaliana
    12711931 At_Drought 20000437 Treatment Drought vs. No Drought
    12711931 At_Drought 20000437 Tissue Whole Plant
    12711931 At_Drought 20000437 Plant Line WS
    12711931 At_Shoots 20000438 Age (day) 14 vs. 21
    12711931 At_Shoots 20000438 Organism A. thaliana
    12711931 At_Shoots 20000438 Tissue Shoots vs. Whole Plant
    12711931 At_Shoots 20000438 Plant Line WS
    12711931 At_C56879_Shoots-Roots 20000451 Age (day) 14
    12711931 At_C56879_Shoots-Roots 20000451 Organism A. thaliana
    12711931 At_C56879_Shoots-Roots 20000451 Plant Line C56879 vs. WS
    12711931 At_C56879_Shoots-Roots 20000451 Tissue Roots
    12711931 At_42deg_Heat 20000458 Timepoint (hr) 8
    12711931 At_42deg_Heat 20000458 Age (day) 14
    12711931 At_42deg_Heat 20000458 Temperature (deg 42 vs. 22
    C.)
    12711931 At_42deg_Heat 20000458 Organism A. thaliana
    12711931 At_42deg_Heat 20000458 Tissue Aerial
    12711931 At_42deg_Heat 20000458 Plant Line WS
    12711931 At_Guard_Cells 20000495 Harvest Date Aug. 2, 2002
    12711931 At_Guard_Cells 20000495 Organism A. thaliana
    12711931 At_Guard_Cells 20000495 Tissue Guard Cells vs. Leaves
    12711931 At_100uM_ABA_Mutants 20000576 Timepoint (hr) 6
    12711931 At_100uM_ABA_Mutants 20000576 Treatment 1uM ABA vs. No Treatment
    12711931 At_100uM_ABA_Mutants 20000576 Organism A. thaliana
    12711931 At_100uM_ABA_Mutants 20000576 Plant Line CS23
    12711931 At_100uM_ABA_Mutants 20000576 Tissue Whole Plant
    12711931 At_Herbicide_Mutants 20000640 Timepoint (hr) 12
    12711931 At_Herbicide_Mutants 20000640 Plant Line 05377RR/BR27173
    12711931 At_Herbicide_Mutants 20000640 Treatment Roundup vs. No Treatment
    12711931 At_Herbicide_Mutants 20000640 Tissue Seedlings
    12711931 At_Herbicide_Mutants 20000642 Timepoint (hr) 12
    12711931 At_Herbicide_Mutants 20000642 Plant Line 395OBR/PCJE10000
    12711931 At_Herbicide_Mutants 20000642 Treatment Finale vs. No Treatment
    12711931 At_Herbicide_Mutants 20000642 Tissue Seedlings
    12711931 At_Petals 20000794 Age (day) 23-25 days
    12711931 At_Petals 20000794 Organism A. thaliana
    12711931 At_Petals 20000794 Tissue Petals vs. Whole plant
    12711931 At_Petals 20000794 Plant Line WS
    12711931 At_Line_Comparisons 20001151 Plant Line ME01339-01 vs. WS
    12711931 At_Line_Comparisons 20001184 Plant Line ME01848-01 vs. WS
    12711931 At_Far-red-induction 20001248 Timepoint (hr) 4
    12711931 At_Far-red-induction 20001248 Age (day) 7
    12711931 At_Far-red-induction 20001248 Organism A. thaliana
    12711931 At_Far-red-induction 20001248 Plant Line Columbia
    12711931 At_Far-red-induction 20001248 Light Far-red vs. White
    12711931 At_Far-red-induction 20001248 Tissue Whole Plant
    12711931 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS
    12711931 At_Line_Comparisons 20001318 Plant Line WBin4-WX14R-A vs. WS
    12711931 At_Line_Comparisons 20001319 Plant Line WBin4-WX24-A vs. WS
    12711931 At_Line_Comparisons 20001347 Plant Line ME01604-01 vs. WS
    12711931 At_50mM_NH4NO3_L-to-H 20001458 Timepoint (hr) 2
    12711931 At_50mM_NH4NO3_L-to-H 20001458 Treatment 50mM NH4NO3 vs. 100mM
    Manitol
    12711931 At_50mM_NH4NO3_L-to-H 20001458 Organism A. thaliana
    12711931 At_50mM_NH4NO3_L-to-H 20001458 Tissue Siliques
    12711931 At_50mM_NH4NO3_L-to-H 20001458 Age (day) Undefined
    12711931 At_50mM_NH4NO3_L-to-H 20001458 Plant Line WS
    12711931 At_Drought_Soil_Dry 20001556 Timepoint (day) 12
    12711931 At_Drought_Soil_Dry 20001556 Age (day) 26
    12711931 At_Drought_Soil_Dry 20001556 Organism A. thaliana
    12711931 At_Drought_Soil_Dry 20001556 Treatment Drought vs. No Drought
    12711931 At_Drought_Soil_Dry 20001556 Post Timepoint (hr) None
    12711931 At_Drought_Soil_Dry 20001556 Post-Treatment None
    12711931 At_Drought_Soil_Dry 20001556 Plant Line WS
    12711931 At_Drought_Soil_Dry 20001557 Post Timepoint (hr) 3
    12711931 At_Drought_Soil_Dry 20001557 Timepoint (day) 13
    12711931 At_Drought_Soil_Dry 20001557 Age (day) 27
    12711931 At_Drought_Soil_Dry 20001557 Organism A. thaliana
    12711931 At_Drought_Soil_Dry 20001557 Treatment Drought vs. No Drought
    12711931 At_Drought_Soil_Dry 20001557 Post-Treatment Re-Water vs. No Drought
    12711931 At_Drought_Soil_Dry 20001557 Plant Line WS
    12711931 At_Drought_Soil_Dry 20001558 Post Timepoint (hr) 6
    12711931 At_Drought_Soil_Dry 20001558 Timepoint (day) 13
    12711931 At_Drought_Soil_Dry 20001558 Age (day) 27
    12711931 At_Drought_Soil_Dry 20001558 Organism A. thaliana
    12711931 At_Drought_Soil_Dry 20001558 Treatment Drought vs. No Drought
    12711931 At_Drought_Soil_Dry 20001558 Post-Treatment Re-Water vs. No Drought
    12711931 At_Drought_Soil_Dry 20001558 Plant Line WS
    12711931 At_Drought_Reproduction 20001905 Timepoint (day) 10
    12711931 At_Drought_Reproduction 20001905 Age (day) 40
    12711931 At_Drought_Reproduction 20001905 Organism A. thaliana
    12711931 At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought
    12711931 At_Drought_Reproduction 20001905 Tissue Rosettes
    12711931 At_Drought_Reproduction 20001905 Plant Line WS
    12711931 At_Drought_Reproduction 20001906 Timepoint (day) 5
    12711931 At_Drought_Reproduction 20001906 Age (day) 35
    12711931 At_Drought_Reproduction 20001906 Organism A. thaliana
    12711931 At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought
    12711931 At_Drought_Reproduction 20001906 Tissue Siliques
    12711931 At_Drought_Reproduction 20001906 Plant Line WS
    12711931 At_Drought_Reproduction 20001907 Timepoint (day) 7
    12711931 At_Drought_Reproduction 20001907 Age (day) 37
    12711931 At_Drought_Reproduction 20001907 Organism A. thaliana
    12711931 At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought
    12711931 At_Drought_Reproduction 20001907 Tissue Siliques
    12711931 At_Drought_Reproduction 20001907 Plant Line WS
    12711931 At_8deg_Cold 20002105 Age (day) 7
    12711931 At_8deg_Cold 20002105 Timepoint (hr) 8
    12711931 At_8deg_Cold 20002105 Temperature (deg 8 vs. 22
    C.)
    12711931 At_8deg_Cold 20002105 Organism A. thaliana
    12711931 At_8deg_Cold 20002105 Tissue Whole Plant
    12711931 At_8deg_Cold 20002105 Plant Line WS
    Promoter PT0506
    Modulates the gene: CYCD1
    The CenBank description of the gene: NM_105689 Arabidopsis thaliana cyclin delta-1 (CYCD1)
    (At1g70210) mRNA, complete cds gi|3O698007|ref|NM_105689.2|[30698007]. Go function: cyclin-
    dependent protein kinase regulator.
    The promoter sequence:
    5′cgctccagaccactgtttgctttcctctgattaaccaatctcaattaaactactaatttataattcaag
    ataattagataaccaatcttaaaatttggaatcttcttccctcacttgatattacaaaaaaaaaactgatt
    tatcatacggttaattcaagaaaacagcaaaaaaattgcactataatgcaaaacatcaattaattacattc
    gattaaaaaatcat cattgaatctaaaatggcctcaaatctattgagcatttgtcatgtgcctaaaatggt
    tcaggagttttacatctaatcacataaaaagcaaacaataaccaaaaaaattgcattttagcaaatcaaat
    acttatatatatacgtatgattaagcgtcatgactttaaaacctctgtaaaattttgatttatttttcgat
    gcttttattttttaaccaatagtaataaagtccaaatcttaaatacgaaaaaatgtttctttctaagcgac
    caacaaaatggtccaaatcacagaaaatgttccataatccaggcccattaagctaatcaccaagtaataca
    ttacacgtcaccaattaatacattacacgtacggccttctctcttcacgagtaatatgcaaacaaacgtac
    attagctgtaatgtactcactcatgcaacgtcttaacctgccacgtattacgtaattacaccactccttgt
    tcctaacctacgcatttcactttagcgcatgttagtcaaaaaacacaaacataaactacaaataaaaaaac
    tcaaaacaaaacccaatgaacgaacggaccagccccgtctcgattgatggaacagtgacaacagtcccgtt
    ttctcgggcataacggaaacggtaaccgtctctctgtttcatttgcaacaacaccattttTATAaataaaa
    acacatttaaataaaaaattattaaaacc 3′-
    tatatccaaacaaatgaatgtgttaaaccttcactcttctctccacacaaaattcaaaaacctcacatttc
    acttctctcttctcgcttcttctagatctcaccggtttatctagctccggtttgattcatctccggttatg
    gggagagaATG
    The promoter was cloned from the organism: Arabidopsis thaliana, Columbia ecotype
    Alternative nucleotides:
    Predicted Position (bp) Mismatch Predicted/Experimental
    1-1000 None Identities 1000/1000 (100%)
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower     L anther
    Observed expression pattern of the promoter-marker vector was in:
    T1 mature: Low expression in anther walls early in stamen development through pre-dehiscence stage. Not
    in pollen
    T2 seedling: No expression observed.
    Misc, promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 13497447
    cDNA nucleotide sequence:
    ATATATCCAAACAAATGAATGTGTTAAACCTTCACTCTTCTCTCCACACAAAATTCAAAAACCT
    CACATTTCACTTCTCTCTTCTCGCTTGTTCTAGATCTCACCGGTTTATCTAGCTCCGGTTTGATT
    CATCTCCGGTTATGGGGAGAGAATGAGGAGTTACCGTTTTAGTGATTATCTACACATGTCTGT
    TTCATTCTCTAACGATATGGATTTGTTTTGTGGAGAAGACTCCGGTGTGTTTTCCGGTGAGTCA
    ACGGTTGATTTCTCGTCTTCCGAGGTTGATTCATGGCCTGGTGATTCTATCGcTTGTTTTATCG
    AAGACGAGCGTCACTTCGTTCCTGGACATGATTATCTCTCTAGATTTCAAACTCGATCTCTCGA
    TGCTTCCGCTAGAGAAGATTCCGTCGCATGGATTCTCAAGGTACAAGCGTATTATAACTTTCA
    GCGTTTAACGGCGTACCTCGCCGTTAACTATATGGATCGGTTTCTTTACGCTCGTCGATTACCG
    GAAACGAGTGGTTGGCCAATGCAACTTTTAGCAGTGGCATGCTTGTCTTTAGCTGCAAAGATG
    GAGGAAATTCTCGTTCCTTCTCTTTTTGATTTTCAGGTTGCAGGAGTGAAGTATTTATTTGAAG
    CAAAAACTATAAAAAGAATGGAACTTCTTGTTCTAAGTGTGTTAGATTGGAGACTAAGATCGG
    TTACAGCGTTTGATTTCATTAGCTTCTTTGCTTACAAGATCGATCCTTCGGGTACCTTTCTCGG
    GTTCTTTATCTCCCATGCTACAGAGATTATACTCTCCAACATAAAAGAAGCGAGCTTTCTTGAG
    TACTGGCCATCGAGTATAGCTGCAGCCGCGATTCTCTGTGTAGCGAACGAGTTACCTTCTCTAT
    CCTCTGTTGTCAATCCCCACGAGAGCCCTGAGACTTGGTGTGACGGATTGAGCAAAGAGAAGA
    TAGTGAGATGCTATAGACTGATGAAAGCGATGGCCATCGAGAATAACCGGTTAAATACACCA
    AAAGTGATAGCAAAGCTTCGAGTGAGTGTAAGGGCATCATCGACGTTAACAAGGCGAAGTGA
    TGAATCCTCTTTCTCATCCTCTTCTCCTTGTAAAAGGAGAAAATTAAGTGGCTATTCATGGGTA
    GGTGATGAAACATCTACCTCTAATTAAAATTTGGGGAGTGAAAGTAGAGGACCAAGGAAACA
    AAACCTAGAAGAAAAAAAACCCTCTTCTGTTTAAGTAGAGTATATTTTTTAACAAGTACATAG
    TAATAAGGGAGTGATGAAGAAAAGTAAAAGTGTTTATTGGCTGAGTTAAAGTAATTAAGAGT
    TTTCCAACCAAGGGGAAGGAATAAGAGTTTTGGTTACAATTTCTTTTATGGAAAGGGTAAAAA
    TTGGGTTTTGGGGTTGGTTGGTTGGTTGGGAGAGACGAAGCTCATCATTAATGGCTTTGCAGA
    TTCCCAAGAAAGCAAAATGAGTAAGTGAGTGTAACACACACGTGTTAGAGAAAAGATATGAT
    CATGTGAGTGTGTGTGTGTGAGAGAGAGAGAGAAGAGTATTTGCATTAGAGTCCTCATCACAC
    AGGTACTGATGGATAAGAGAGGGGAGCGTTTGCAAAAGATTTGTGAGTGGAGATTTTTCTGAG
    CTCTTTGTCTTAATGGATCGCAGCAGTTCATGGGACGCTTCCTCAGCTTCATCATCAAACAAAA
    AAAAAATCAAGTTGCGAAGTATATATAATTTGTTTTTTTGTTTGGATTTTTAAGATTTTTGATT
    CCTTGTGTGTGACTTCACGTGACGGAGGCGTGTGTCTCACGTGTTTGTTTTCTCTTCAAATCTT
    TTATTTTGGCGGGAAATTTTGTGTTTTTGATTTCTACGTATTCGTGGACTCCAAATGAGTTTTG
    TCACGGTGCGTTTTAGTAGCGTTTGCATGCGTGTAAGGTGTCACGTATGTGTATATATATGATT
    TTTTTTTGGTTTCTTGAAAGGTTGAATTTTATAAATAAAACGTTTCTATTAT
    Coding sequence:
    MRSYRFSDYLHMSVSFSNDMDLFCGEDSGVFSGESTVDFSSSEVDSWPGDSIACFIEDERHFVPGH
    DYLSRFQTRSLDASAREDSVAWILKVQAYYNFQPLTAYLAVNYMDRFLYARRLPETSGWPMQLL
    AVACLSLAAKMEEILVPSLFDFQVAGVKYLFEAKTIKRMELLVLSVLDWRLRSVTPFDFISFFAYKI
    DPSGTFLGFFISHATEIILSNIKEASFLEYWPSSIAAAAILCVANELPSLSSVVNPHESPETWCDGLSK
    EKIVRCYRLMKAMAIENNRLNTPKVIAKLRVSVRASSTLTRPSDESSFSSSSPCKRRKLSGYSWVG
    DETSTSN*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    13497447 At_Diversity_Expt 108457 −
    13497447 At_Diversity_Expt 108458 −
    13497447 At_5-1-F2-137 108460 −
    13497447 At_Germinating_Seeds 108463 +
    13497447 At_Germinating_Seeds 108464 +
    13497447 At_100uM_ABA_Mutants 20000069 −
    13497447 At_42deg_Heat 20000173 −
    13497447 At_Open_Flower 20000286 +
    13497447 At_100uM_ABA_Mutants 20000573 −
    13497447 At_100uM_ABA_Mutants 20000574 −
    13497447 At_Drought_Reproduction 20001906 −
    13497447 At_Drought_Reproduction 20001911 −
    13497447 At_8deg_Cold 20002108 −
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    13497447 At_Diversity_Expt 108457 Plant Line Canola vs. WS
    13497447 At_Diversity_Expt 108457 Tissue Hypocotyl
    13497447 At_Diversity_Expt 108458 Plant Line Holbolliie vs. WS
    13497447 At_Diversity_Expt 108458 Tissue Hypocotyl
    13497447 At_5-1-F2-137 108460 Plant Line 5-1-F2-137(mutant)
    13497447 At_5-1-F2-137 108460 Probe Method Amplified
    13497447 At_5-1-F2-137 108460 Tissue Inflorescences
    13497447 At_Germinating_Seeds 108463 Age (day) 3 vs. 0
    13497447 At_Germinating_Seeds 108463 Tissue Germinating Seeds
    13497447 At_Germinating_Seeds 108464 Age (day) 4 vs. 0
    13497447 At_Germinating_Seeds 108464 Tissue Germinating Seeds
    13497447 At_100uM_ABA_Mutants 20000069 Timepoint (hr) 6
    13497447 At_100uM_ABA_Mutants 20000069 Treatment 100uM ABA vs. No Treatment
    13497447 At_100uM_ABA_Mutants 20000069 Tissue Aerial
    13497447 At_100uM_ABA_Mutants 20000069 Plant Line C523
    13497447 At_42deg_Heat 20000173 Timepoint (hr) 6
    13497447 At_42deg_Heat 20000173 Age (day) 14
    13497447 At_42deg_Heat 20000173 Temperature (deg C.) 42 vs. 22
    13497447 At_42deg_Heat 20000173 Organism A. thaliana
    13497447 At_42deg_Heat 20000173 Tissue Aerial
    13497447 At_42deg_Heat 20000173 Plant Line WS
    13497447 At_Open_Flower 20000286 Age (day) 21
    13497447 At_Open_Flower 20000286 Organism A. thaliana
    13497447 At_Open_Flower 20000286 Tissue Half Open vs. Whole Plant
    13497447 At_Open_Flower 20000286 Plant Line WS
    13497447 At_100uM_ABA_Mutants 20000573 Organism A. thaliana
    13497447 At_100uM_ABA_Mutants 20000573 Plant Line C522 vs. Ler wt
    13497447 At_100uM_ABA_Mutants 20000573 Timepoint (hr) N/A
    13497447 At_100uM_ABA_Mutants 20000573 Treatment None
    13497447 At_100uM_ABA_Mutants 20000573 Tissue Whole Plant
    13497447 At_100uM_ABA_Mutants 20000574 Organism A. thaliana
    13497447 At_100uM_ABA_Mutants 20000574 Plant Line C523 vs. Ler wt
    13497447 At_100uM_ABA_Mutants 20000574 Timepoint (hr) N/A
    13497447 At_100uM_ABA_Mutants 20000574 Treatment None
    13497447 At_100uM_ABA_Mutants 20000574 Tissue Whole Plant
    13497447 At_Drought_Reproduction 20001906 Timepoint (day) 5
    13497447 At_Drought_Reproduction 20001906 Age (day) 35
    13497447 At_Drought_Reproduction 20001906 Organism A. thaliana
    13497447 At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought
    13497447 At_Drought_Reproduction 20001906 Tissue Siliques
    13497447 At_Drought_Reproduction 20001906 Plant Line WS
    13497447 At_Drought_Reproduction 20001911 Timepoint (day) 10
    13497447 At_Drought_Reproduction 20001911 Age (day) 40
    13497447 At_Drought_Reproduction 20001911 Organism A. thaliana
    13497447 At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought
    13497447 At_Drought_Reproduction 20001911 Tissue Flowers
    13497447 At_Drought_Reproduction 20001911 Plant Line WS
    13497447 At_8deg_Cold 20002108 Age (day) 14
    13497447 At_8deg_Cold 20002108 Timepoint (hr) 168
    13497447 At_8deg_Cold 20002108 Temperature (deg C.) 8 vs. 22
    13497447 At_8deg_Cold 20002108 Organism A. thaliana
    13497447 At_8deg_Cold 20002108 Tissue Whole Plant
    13497447 At_8deg_Cold 20002108 Plant Line WS
    Promoter YP0377
    Modulates the gene: product = “glycine-rich protein”, note: unknown protein
    The GenBank description of the gene: : NM_100587 Arabidopsis thaliana glycine-rich protein
    (At1g07135) mRNA, complete cds gi|22329385|ref|NM_100587.2|[22329385]
    The promoter sequence:
    5′tttaaacataacaatgaattgcttggatttcaaactttattaaatttggattttaaattttaatttgat
    tgaattatacccccttaattggataaattcaaatatgtcaactttttttttttgtaagatttttttatgga
    aaaaaaaattgattattcactaaaaagatgacaggttacttataatttaatatatgtaaaccctaaaaaga
    agaaaatagtttctgttttcactttaggtcttattatctaaacttctttaagaaaatcgcaataaattggt
    ttgagttctaactttaaacacattaatatttgtgtgctatttaaaaaataatttacaaaaaaaaaaacaaa
    ttgacagaaaatatcaggttttgtaataagatatttcctgataaatatzttagggaatataacatatcaaaa
    gattcaaattctgaaaatcaagaatggtagacatgtgaaagttgtcatcaatatggtccacttttctttgc
    tctataacccaaaattgaccctgacagtcaacttgtacacgcggccaaacctttttataatcatgctattt
    atttccttcatttttattctatttgctatctaactgatttttcattaacatgataccagaaatgaatttag
    atggattaattcttttccatccacgacatctggaaacacttatctcctaattaaccttactttttttttag
    tttgtgtgctccttcataaaatctatattgtttaaaacaaaggtcaataaatataaatatggataagtata
    ataaatctttattggatatttctttttttaaaaaagaaataaatcttttttggatattttcgtggcagcat
    cataatgagagactacgtcgaaactgctggcaaccacttttgccgcgtttaatttctttctgaggcttata
    taaatagatcaaaggggaaagtgagaTAT 3′
    The promoter was cloned from the organism: Arabidopsis thaliana, Columbia ecotype
    Alternative nucleotides:
    Predicted Position (bp) Mismatch Predicted/Experimental
    145 Sequence or PCR error ctttttttttttg/
    ctttttttt-ttg Exp.1
    ctttttttt--tg Exp.2
    The promoter was cloned in the vector: pNewbin4-HAP1-GFP
    When cloned into the vector the promoter was operably linked to a marker, which was the type:
    GFP-ER
    Promoter-marker vector was tested in: Arabidopsis thaliana, WS ecotype
    Generation screened:  XT1 Mature XT2 Seedling  T2 Mature T3 Seedling
    The spatial expression of the promoter-marker vector was found observed in and would be useful in
    expression in any or all of the following:
    Flower M sepal M petal M epidermis
    Hypocotyl L epidermis L vascular H stomata
    Cotyledon M vascular L epidermis
    Primary Root M epidermis M vascular M root hairs
    Observed expression pattern of the promoter-marker vector was in:
    T1 mature: Expressed in epidermal cells of sepals and petals in developing flowers.
    T2 seedling: Medium to low expression in epidermal and vascular cells of hypocotyls and cotyledons.
    Epidermal and vascular expression at root transition zone decreasing toward root tip.
    Misc. promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No
    The Ceres cDNA ID of the endogenous coding sequence to the promoter: 13613778
    cDNA nucleotide sequence:
    AAAGAAAATGGGTTTGAGAAGAACATGGTTGGTTTTGTACATTCTCTTCATCTTTCATCTTCAG
    CACAATCTTCCTTCCGTGAGCTCACGACCTTCCTCAGTCGATACAAACCACGAGACTCTCCCTT
    TTAGTGTTFCAAAGCCAGACGTTGTTGTGTTTGAAGGAAAGGCTCGGGAATTAGCTGTGGTTA
    TCAAAAAAGGAGGAGGTGGAGGAGGTGGAGGACGCGGAGGCGGTGGAGCACGAAGCGGCGG
    TAGGAGCAGGGGAGGAGGAGGTGGCAGCAGTAGTAGCCGCAGCCGTGACTGGAAACGCGGC
    GGAGGGGTGGTTCCGATTCATACGGGTGGTGGTAATGGCAGTCTGGGTGGTGGATCGGCAGG
    ATCACATAGATCAAGCGGCAGCATGAATCTTCGAGGAACAATGTGTGCGGTCTGTTGGTTGGC
    TTTATCGGYFFTAGCCGGTTTAGTCTTGGTTCAGTAGGGTTCAGAGTAATTATTGGCCATTTAT
    TTAYFGGTTTTGTAACGYFTATGTTTGTGGTCCGGTCTGATATTTATTTGGGCAAACGGTACAT
    TAAGGTGTAGACTGTTAATATTATATGTAGAAAGAGATTCTTAGCAGGATTCTACTGGTAGTA
    TTAAGAGTGAGTTATCTTTAGTATGCCATTTGTAAATGGAAATTTAATGAAATAAGAAATTGT
    GAAATTTAAAC
    Coding sequence:
    KKMGLRRTWLVLYILFIFHLQHNLPSVSSRPSSVDTNHETLPFSVSKPDVVVFEGKARELAVV
    IKKGGGGGGGGRGGGGARSGGRSRGGCGGSSSSRSRDWKRGGGVVPIHTGGGNGSLGGGS
    AGSHRSSGSMNLRCTMCAVCWLALSVLAGLVLVQ*
    Microarray data shows that the coding sequence was expressed in the following experiments, which
    shows that the promoter would be useful to modulate expression in situations similar to the
    following:
    CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP
    13613778 At_Root_Tips 108434 −
    13613778 At_20uM_KNO3_H-to-L 108455 +
    13613778 At_5-1-F2-137 108460 +
    13613778 At_Germinating_Seeds 108464 +
    13613778 At_Shoot_Apices 108480 +
    13613778 At_Shoot_Apices 108481 +
    13613778 At_15mM_NH4NO3_L-to-H_Rosette 108487 −
    13613778 At_15mM_NH4NO3_L-to-H_Rosette 108488 −
    13613778 At_ap2_floral_buds 108501 −
    13613778 At_42deg_Heat 108577 −
    13613778 At_4deg_Cold 108578 +
    13613778 At_4deg_Cold 108579 +
    13613778 At_5mM_NaNP 108584 +
    13613778 At_5mM_NaNP 108585 +
    13613778 At_2mM_SA 108586 −
    13613778 At_2mM_SA 108587 −
    13613778 At_15mM_NH4NO3 L-to-H 108588 +
    13613778 At_Ler-pi_Ovule 108595 +
    13613778 At_100uM_ABA 108606 −
    13613778 At_2mM_SA 108667 +
    13613778 At_100uM_ABA_Mutants 20000069 +
    13613778 At_100uM_ABA_Mutants 20000071 +
    13613778 At_100uM_ABA_Mutants 20000086 +
    13613778 At_100uM_ABA_Mutants 20000087 +
    13613778 At_2mM_SA_CS3726-Columbia 20000091 +
    13613778 At_100uM_ABA_Mutants 20000117 +
    13613778 At_42deg_Heat 20000144 −
    13613778 At_42deg_Heat 20000171 −
    13613778 At_42deg_Heat 20000173 −
    13613778 At_2mM_SA 20000181 +
    13613778 At_Shoots 20000184 −
    13613778 At_Roots 20000185 −
    13613778 At_4deg_Cold 20000213 +
    13613778 At_Siliques 20000234 −
    13613778 At_Siliques 20000236 −
    13613778 At_Open_Flower 20000264 −
    13613778 At_100mM_NaCl 20000268 −
    13613778 At_Open_Flower 20000286 −
    13613778 At_Pollen 20000326 −
    13613778 At_Shoots 20000438 −
    13613778 At_Roots 20000439 −
    13613778 At_1uM_BR-BRZ 20000441 +
    13613778 At_1uM_BR-BRZ 20000443 +
    13613778 At_42deg_Heat 20000458 −
    13613778 At_10percent_PEG 20000460 +
    13613778 At_Guard_Cells 20000495 −
    13613778 At_10percent_PEG 20000527 +
    13613778 At_100uM_ABA Mutants 20000573 −
    13613778 At_100uM_ABA_Mutants 20000574 −
    13613778 At_Herbicide_Mutants 20000640 −
    13613778 At_15mM_NH4NO3_L-to-H 20000709 +
    13613778 At_Petals 20000794 −
    13613778 At_Line_Comparisons 20001151 −
    13613778 At_Line_Comparisons 20001184 −
    13613778 At_Line_Comparisons 20001192 −
    13613778 At_Line_Comparisons 20001195 −
    13613778 At_Far-red-induction 20001247 +
    13613778 At_Far-red-induction 20001248 +
    13613778 At_Line_Comparisons 20001300 −
    13613778 At_Line_Comparisons 20001307 −
    13613778 At_Line_Comparisons 20001308 +
    13613778 At_Line_Comparisons 20001309 +
    13613778 At_Line_Comparisons 20001310 +
    13613778 At_Line_Comparisons 20001318 −
    13613778 At_Line_Comparisons 20001319 −
    13613778 At_Line_Comparisons 20001347 −
    13613778 At_Line_Comparisons 20001448 −
    13613778 At_50mM_NH4NO3_L-to-H 20001458 +
    13613778 At_Drought_Soil_Dry 20001554 −
    13613778 At_Drought_Soil_Dry 20001555 −
    13613778 At_Drought_Soil_Dry 20001556 −
    13613778 At_Drought_Soil_Dry 20001557 +
    13613778 At_Interploidy_Crosses 20001703 −
    13613778 At_50mM_NH4NO3_L-to-H 20001757 −
    13613778 At_Far-red-enriched-adult 20001773 −
    13613778 At_Far-red-enriched-adult 20001774 −
    13613778 At_Drought_Reproduction 20001904 −
    13613778 At_Drought_Reproduction 20001907 −
    13613778 At_Line_Comparisons 20002012 +
    13613778 At_8deg_Cold 20002108 −
    13613778 At_8deg_Cold 20002109 −
    The parameters for the microarray experiments listed above by Expt_Rep_ID and Short_Name are
    as follow below:
    CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE
    13613778 At_Root_Tips 108434 Tissue Root Tips
    13613778 At_20uM_KNO3_H-to-L 108455 Timepoint (hr) 1
    13613778 At_20uM_KNO3_H-to-L 108455 Treatment 20uM KNO3 vs. 50mM KNO3
    13613778 At_5-1-F2-137 108460 Plant Line 5-1-F2-137 mutant
    13613778 At_5-1-F2-137 108460 Probe Method Amplified
    13613778 At_5-1-F2-137 108460 Tissue Inflorescences
    13613778 At_Germinating_Seeds 108464 Age (day) 4 vs. 0
    13613778 At_Germinating_Seeds 108464 Tissue Germinating_Seeds
    13613778 At_Shoot_Apices 108480 Treatment 1uM BR vs. No Treatment
    13613778 At_Shoot_Apices 108480 Plant Line Ws-2
    13613778 At_Shoot_Apices 108481 Treatment 1uM BRZ vs. No Treatment
    13613778 At_Shoot_Apices 108481 Plant Line Ws-2
    13613778 At_15mM_NH4NO3_L-to-H 108487 Timepoint (hr) 0.5
    Rosette
    13613778 At_15mM_NH4NO3_L-to-H 108487 Treatment 15mM NH4NO3 vs. 30mM Mannitol
    Rosette
    13613778 At_15mM_NH4NO3_L-to-H 108487 Tissue Rosette
    Rosette
    13613778 At_15mM_NH4NO3_L-to-H 108488 Timepoint (hr) 2
    Rosette
    13613778 At_15mM_NH4NO3_L-to-H 108488 Treatment 15mM NH4NO3 vs. 30mM Mannitol
    Rosette
    13613778 At_15mM_NH4NO3_L-to-H 108488 Tissue Rosette
    Rosette
    13613778 At_ap2_floral_buds 108501 Plant Line ap2 (Ler.)
    13613778 At_ap2_floral_buds 108501 Tissue Closed Flower
    13613778 At_42deg_Heat 108577 Timepoint (hr) 6
    13613778 At_42deg_Heat 108577 Temperature 42 vs. 22
    (deg C.)
    13613778 At_42deg_Heat 108577 Tissue Aerial
    13613778 At_4deg_Cold 108578 Timepoint (hr) 1
    13613778 At_4deg_Cold 108578 Temperature 4 vs. 22
    (deg C.)
    13613778 At_4deg_Cold 108578 Tissue Aerial
    13613778 At_4deg_Cold 108579 Timepoint (hr) 6
    13613778 At_4deg_Cold 108579 Temperature 4 vs.22
    (degC.)
    13613778 At_4deg_Cold 108579 Tissue Aerial
    13613778 At_5mM_NaNP 108584 Timepoint (hr) 1
    13613778 At_5mM_NaNP 108584 Treatment 5mM sodium nitroprusside vs. No
    Treatment
    13613778 At_5mM_NaNP 108584 Tissue Aerial
    13613778 At_5mM_NaNP 108585 Timepoint (hr) 6
    13613778 At_5mM_NaNP 108585 Treatment 5mM sodium nitroprusside vs. No
    Treatment
    13613778 At_5mM_NaNP 108585 Tissue Aerial
    13613778 At_2mM_SA 108586 Timepoint (hr) 1
    13613778 At_2mM_SA 108586 Treatment 2mM SA vs. No Treatment
    13613778 At_2mM_SA 108586 Tissue Aerial
    13613778 At_2mM_SA 108587 Timepoint (hr) 6
    13613778 At_2mM_SA 108587 Treatment 2mM SA vs. No Treatment
    13613778 At_2mM_SA 108587 Tissue Aerial
    13613778 At_15mM_NH4NO3_L-to-H 108588 Timepoint (hr) 2
    13613778 At_15mM_NH4NO3_L-to-H 108588 Treatment 15mM NH4NO3 vs. 30mM Mannitol
    13613778 At_15mM_NH4NQ3_L-to-H 108588 Tissue Aerial
    13613778 At_Ler-pi_Ovule 108595 Plant Line Ler-pi
    13613778 At_Ler-pi_Ovule 108595 Tissue Ovules
    13613778 At_100uM_ABA 108606 Timepoint (hr) 2
    13613778 At_100uM_ABA 108606 Treatment 100uM ABA vs. No Treatment
    13613778 At_100uM_ABA 108606 Tissue Aerial
    13613778 At_2mM_SA 108667 Timepoint (hr) 1
    13613778 At_2mM_SA 108667 Treatment 2mM SA vs. No Treatment
    13613778 At_2mM_SA 108667 Plant Line WS
    13613778 At_100uM_ABA_Mutants 20000069 Timepoint (hr) 6
    13613778 At_100uM_ABA_Mutants 20000069 Treatment 100uM ABA vs. No Treatment
    13613778 At_100uM_ABA Mutants 20000069 Tissue Aerial
    13613778 At_100uM_ABA_Mutants 20000069 Plant Line CS23
    13613778 At_100uM_ABA_Mutants 20000071 Timepoint (hr) 6
    13613778 At_100uM_ABA_Mutants 20000071 Treatment 100uM ABA vs. No Treatment
    13613778 At_100uM_ABA_Mutants 20000071 Tissue Aerial
    13613778 At_100uM_ABA_Mutants 20000071 Plant Line CS8104
    13613778 At_100uM_ABA_Mutants 20000086 Timepoint (hr) 6
    13613778 At_100uM_ABA_Mutants 20000086 Treatment 1 OQuM ABA vs. No Treatment
    13613778 At_100uM_ABA_Mutants 20000086 Tissue Aerial
    13613778 At_100uM_ABA_Mutants 20000086 Plant Line CS22
    13613778 At_100uM_ABA_Mutants 20000087 Timepoint (hr) 6
    13613778 At_100uM_ABA_Mutants 20000087 Treatment 100uM ABA vs. No Treatment
    13613775 At_100uM_ABA_Mutants 20000087 Tissue Aerial
    13613778 At_100uM_ABA_Mutants 20000087 Plant Line WS
    13613778 At_2mM_SA_CS3726- 20000091 Timepoint (hr) 0
    Columbia
    13613778 At_2mM_SA_CS3726- 20000091 Tissue Aerial
    Columbia
    13613778 At_2mM_SA_CS3726- 20000091 Plant Line CS3726 vs. Columbia
    Columbia
    13613778 At_2mM_SA_CS3726- 20000091 Treatment None
    Columbia
    13613778 At_100uM_ABA_Mutants 20000117 Timepoint (hr) 6
    13613778 At_100uM_ABA_Mutants 20000117 Treatment 100uM ABA vs. No Treatment
    13613778 At_100uM_ABA_Mutants 20000117 Tissue Aerial
    13613778 At_100uM_ABA_Mutants 20000117 Plant Line Columbia
    13613778 At_42deg_Heat 20000144 Timepoint (hr) 1
    13613778 At_42deg_Heat 20000144 Temperature 42 vs. 22
    (deg C.)
    13613778 At_42deg_Heat 20000144 Tissue Aerial
    13613778 At_42deg_Heat 20000171 Timepoint (hr) 1
    13613778 At_42deg_Heat 20000171 Age (day) 14
    13613778 At_42deg_Heat 20000171 Temperature 42 vs. 22
    (deg C.)
    13613778 At_42deg_Heat 20000171 Organism A. thaliana
    13613778 At_42deg_Heat 20000171 Tissue Aerial
    13613778 At_42deg_Heat 20000171 Plant Line WS
    13613778 At_42deg_Heat 20000173 Timepoint (hr) 6
    13613778 At_42deg_Heat 20000173 Age (day) 14
    13613778 At_42deg_Heat 20000173 Temperature 42 vs. 22
    (deg C.)
    13613778 At_42deg_Heat 20000173 Organism A. thaliana
    13613778 At_42deg_Heat 20000173 Tissue Aerial
    13613778 At_42deg_Heat 20000173 Plant Line WS
    13613778 At_2mM_SA 20000181 Timepoint (hr) 1
    13613778 At_2mM_SA 20000181 Age (day) 14
    13613778 At_2mM_SA 20000181 Treatment 2mM SA vs. No Treatment
    13613778 At_2mM_SA 20000181 Organism A. thaliana
    13613778 At_2mM_SA 20000181 Tissue Aerial
    13613778 At_2mM_SA 20000181 Plant Line WS
    13613778 At_Shoots 20000184 Age (day) 7 vs.21
    13613778 At_Shoots 20000184 Organism A. thaliana
    13613778 At_Shoots 20000184 Tissue Shoots vs. Whole Plant
    13613778 At_Shoots 20000184 Plant Line WS
    13613778 At_Roots 20000185 Age (day) 7 vs. 21
    13613778 At_Roots 20000185 Organism A. thaliana
    13613778 At_Roots 20000185 Tissue Roots vs. Whole Plant
    13613778 At_Roots 20000185 Plant Line WS
    13613778 At_4deg_Cold 20000213 Timepoint (hr) 2
    13613778 At_Siliques 20000234 Age (day) 21
    13613778 At_Siliques 20000234 Tissue <5mm Siliques vs. Whole Plant
    13613778 At_Siliques 20000234 Organism A. thaliana
    13613778 At_Siliques 20000234 Plant Line WS
    13613778 At_Siliques 20000236 Age (day) 21
    13613778 At_Siliques 20000236 Tissue >10mm Siliques vs. Whole Plant
    13613778 At_Siliques 20000236 Organism A. thaliana
    13613778 At_Siliques 20000236 Plant Line WS
    13613778 At_Open_Flower 20000264 Age (day) 21
    13613778 At_Open_Flower 20000264 Organism A. thaliana
    13613778 At_Open_Flower 20000264 Tissue Open_Flower vs. Whole Plant
    13613778 At_Open_Flower 20000264 Plant Line WS
    13613778 At_100mM_NaCl 20000268 Timepoint (hr) 6
    13613778 At_100mM_NaCl 20000268 Age (day) 14
    13613778 At_100mM_NaCl 20000268 Treatment 100mM NaCl vs. No Treatment
    13613778 At_100mM_NaCl 20000268 Organism A. thaliana
    13613778 At_100mM_NaCl 20000268 Tissue Whole Plant
    13613778 At_100mM_NaCl 20000268 Plant Line WS
    13613778 At_Open_Flower 20000286 Age (day) 21
    13613778 At_Open_Flower 20000286 Organism A. thaliana
    13613778 At_Open_Flower 20000286 Tissue Half Open vs. Whole Plant
    13613778 At_Open_Flower 20000286 Plant Line WS
    13613778 At_Pollen 20000326 Age (day) 0 vs. 21
    13613778 At_Pollen 20000326 Organism A. thaliana
    13613778 At_Pollen 20000326 Tissue Pollen vs. Whole Plant
    13613778 At_Pollen 20000326 Plant Line WS
    13613778 At_Shoots 20000438 Age (day) 14 vs. 21
    13613778 At_Shoots 20000438 Organism A. thaliana
    13613778 At_Shoots 20000438 Tissue Shoots vs. Whole Plant
    13613778 At_Shoots 20000438 Plant Line WS
    13613778 At_Roots 20000439 Age (day) 14 vs. 21
    13613778 At_Roots 20000439 Organism A. thaliana
    13613778 At_Roots 20000439 Tissue Roots vs. Whole Plant
    13613778 At_Roots 20000439 Plant Line WS
    13613778 At_1uM_BR-BRZ 20000441 Treatment 1uM BR vs. No Treatment
    13613778 At_1uM_BR-BRZ 20000441 Tissue Shoot Apices
    13613778 At_1uM_BR-BRZ 20000443 Treatment 1uM BRZ vs. No Treatment
    13613778 At_1uM_BR-BRZ 20000443 Tissue Shoot Apices
    13613778 At_42deg_Heat 20000458 Timepoint (hr) 8
    13613778 At_42deg_Heat 20000458 Age (day) 14
    13613778 At_42deg_Heat 20000458 Temperature 42 vs. 22
    (degC.)
    13613778 At_42deg_Heat 20000458 Organism A. thaliana
    13613778 At_42deg_Heat 20000458 Tissue Aerial
    13613778 At_42deg_Heat 20000458 Plant Line WS
    13613778 At_10percent_PEG 20000460 Age (day) 12
    13613778 At_10percent_PEG 20000460 Timepoint (day) 12
    13613778 At_10percent_PEG 20000460 Treatment 10percent PEG vs. No Treatment
    13613778 At_10percent_PEG 20000460 Organism A. thaliana
    13613778 At_10percent_PEG 20000460 Tissue Whole Plant
    13613778 At_10percent_PEG 20000460 Plant Line WS
    13613778 At_Guard_Cells 20000495 Harvest Date Aug. 2, 2002
    13613778 At_Guard_Cells 20000495 Organism A. thaliana
    13613778 At_Guard_Cells 20000495 Tissue Guard Cells vs. Leaves
    13613778 At_10percent_PEG 20000527 Age (day) 20
    13613778 At_10percent_PEG 20000527 Timepoint (day) 20
    13613778 At_10percent_PEG 20000527 Treatment 10percent PEG vs. No Treatment
    13613778 At_10percent_PEG 20000527 Organism A. thaliana
    13613778 At_10percent_PEG 20000527 Tissue Whole Plant
    13613778 At_10percent_PEG 20000527 Plant Line WS
    13613778 At_100uM_ABA_Mutants 20000573 Organism A. thaliana
    13613778 At_100uM_ABA_Mutants 20000573 Plant Line 0522 vs. Lerwt
    13613778 At_100uM_ABA_Mutants 20000573 Timepoint (hr) N/A
    13613778 At_100uM_ABA_Mutants 20000573 Treatment None
    13613778 At_100uM_ABA_Mutants 20000573 Tissue Whole Plant
    13613778 At_100uM_ABA_Mutants 20000574 Organism A. thatiana
    13613778 At_100uM_ABA_Mutants 20000574 Plant Line CS23 vs. Lerwt
    13613778 At_100uM_ABA_Mutants 20000574 Timepoint (hr) N/A
    13613778 At_100uM_ABA_Mutants 20000574 Treatment None
    13613778 At_100uM_ABA_Mutants 20000574 Tissue Whole Plant
    13613778 At_Herbicide_Mutants 20000640 Timepoint (hr) 12
    13613778 At_Herbicide_Mutants 20000640 Plant Line 05377RR/BR27173
    13613778 At_Herbicide_Mutants 20000640 Treatment Roundup vs. No Treatment
    13613778 At_Herbicide_Mutants 20000640 Tissue Seedlings
    13613778 At_15mM_NH4NO3_L-to-H 20000709 Timepoint (hr) 4
    13613778 At_15mM_NH4NO3_L-to-H 20000709 Age(hr) 14
    13613778 At_15mM_NH4NO3_L-to-H 20000709 Treatment 15mM NH4NO3 vs. 30mM Mannitol
    13613778 At_15mM_NH4NO3_L-to-H 20000709 Organism A. thaliana
    13613778 At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial
    13613778 At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS
    13613778 At_Petals 20000794 Age (day) 23-25 days
    13613778 At_Petals 20000794 Organism A. thaliana
    13613778 At_Petals 20000794 Tissue Petals vs. Whole plant
    13613778 At_Petals 20000794 Plant Line WS
    13613778 At_Line_Comparisons 20001151 Plant Line ME01339-01 vs. WS
    13613778 At_Line_Comparisons 20001184 Plant Line ME01848-01 vs. WS
    13613778 At_Line_Comparisons 20001192 Plant Line WBin4-WX13R-A vs. WS
    13613778 At_Line_Comparisons 20001195 Plant Line WBin4-WX14-B vs. WS
    13613778 At_Far-red-induction 20001247 Timepoint (hr) 1
    13613778 At_Far-red-induction 20001247 Age (day) 7
    13613778 At_Far-red-induction 20001247 Organism A. thaliana
    13613778 At_Far-red-induction 20001247 Plant Line Columbia
    13613778 At_Far-red-induction 20001247 Light Far-red vs. White
    13613778 At_Far-red-induction 20001247 Tissue Whole Plant
    13613778 At_Far-red-induction 20001248 Timepoint (hr) 4
    13613778 At_Far-red-induction 20001248 Age (day) 7
    13613778 At_Far-red-induction 20001248 Organism A. thaliana
    13613778 At_Far-red-induction 20001248 Plant Line Columbia
    13613778 At_Far-red-induction 20001248 Light Far-red vs. White
    13613778 At_Far-red-induction 20001248 Tissue Whole Plant
    13613778 At_Line_Comparisons 20001300 Plant Line ME01338-05 vs. WS
    13613778 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS
    13613778 At_Line_Comparisons 20001308 Plant Line WBin4-WX49-C vs. WS
    13613778 At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS
    13613778 At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS
    13613778 At_Line_Comparisons 20001318 Plant Line WBin4-WX14R-A vs. WS
    13613778 At_Line_Comparisons 20001319 Plant Line WBin4-WX24-A vs. WS
    13613778 At_Line_Comparisons 20001347 Plant Line ME01604-01 vs. WS
    13613778 At_Line_Comparisons 20001448 Plant Line ME01323-01 vs. WS
    13613778 At_50mM_NH4NO3_L-to-H 20001458 Timepoint (hr) 2
    13613778 At_50mM_NH4NO3_L-to-H 20001458 Treatment 50mM NH4NO3 vs. 100mM Manitol
    13613778 At_50mM_NH4NO3_L-to-H 20001458 Organism A. thaliana
    13613778 At 50mM_NH4NO3_L-to-H 20001458 Tissue Siliques
    13613778 At_50mM NH4NO3_L-to-H 20001458 Age (day) Undefined
    13613778 At_50mM_NH4NO3_L-to-H 20001458 Plant Line WS
    13613778 At_Drought_Soil_Dry 20001554 Timepoint (day) 7
    13613778 At_Drought_Soil_Dry 20001554 Age (day) 21
    13613778 At_Drought_Soil_Dry 20001554 Organism A. thaliana
    13613778 At_Drought_Soil_Dry 20001554 Treatment Drought vs. No Drought
    13613778 At_Drought_Soil_Dry 20001554 Post Timepoint None
    (hr)
    13613778 At_Drought_Soil_Dry 20001554 Post-Treatment None
    13613778 At_Drought_Soil_Dry 20001554 Plant Line WS
    13613778 At_Drought_Soil_Dry 20001555 Timepoint (day) 10
    13613778 At_Drought_Soil_Dry 20001555 Age (day) 24
    13613778 At_Drought_Soil_Dry 20001555 Organism A thaliana
    13613778 At_Drought_Soil_Dry 20001555 Treatment Drought vs. No Drought
    13613778 At_Drought_Soil_Dry 20001555 Post Timepoint None
    (hr)
    13613778 At_Drought_Soil_Dry 20001555 Post-Treatment None
    13613778 At_Drought_Soil_Dry 20001555 Plant Line WS
    13613778 At_Drought_Soil_Dry 20001556 Timepoint (day) 12
    13613778 At_Drought_Soil_Dry 20001556 Age (day) 26
    13613778 At_Drought_Soil_Dry 20001556 Organism A. thaliana
    13613778 At_Drought_Soil_Dry 20001556 Treatment Drought vs. No Drought
    13613778 At_Drought_Soil_Dry 20001556 Post Timepoint None
    (hr)
    13613778 At_Drought_Soil_Dry 20001556 Post-Treatment None
    13613778 At_Drought_Soil_Dry 20001556 Plant Line WS
    13613778 At_Drought_Soil_Dry 20001557 Post Timepoint 3
    (hr)
    13613778 At_Drought_Soil_Dry 20001557 Timepoint (day) 13
    13613778 At_Drought_Soil_Dry 20001557 Age (day) 27
    13613778 At_Drought_Soil_Dry 20001557 Organism A. thaliana
    13613778 At_Drought_Soil_Dry 20001557 Treatment Drought vs. No Drought
    13613778 At_Drought_Soil_Dry 20001557 Post-Treatment Re-Water vs. No Drought
    13613778 At_Drought_Soil_Dry 20001557 Plant Line WS
    13613778 At_Interploidy_Crosses 20001703 Age (day) 5
    13613778 At_Interploidy_Crosses 20001703 Cross 2X × 4X vs. 2X × 2X
    13613778 At_Interploidy_Crosses 20001703 Organism A. thaliana
    13613778 At_Interploidy_Crosses 20001703 Plant Line Columbia
    13613778 At_Interploidy_Crosses 20001703 Tissue Siliques
    13613778 At_50mM_NH4NO3-L-to-H 20001757 Timepoint (hr) 6
    13613778 At_50mM_NH4NO3_L-to-H 20001757 Treatment 50mM NH4NO3 vs 100mM Mannitol
    13613778 At_50mM_NH4NO3_L-to-H 20001757 Tissue Leaf
    13613778 At_Far-red-enriched-adult 20001773 Age (day) 30
    13613778 At_Far-red-enriched-adult 20001773 Timepoint (hr) 48
    13613778 At_Far-red-enriched-adult 20001773 Organism A. thaliana
    13613778 At_Far-red-enriched-adult 20001773 Tissue Aerial
    13613778 At_Far-red-enriched-adult 20001773 Plant Line Columbia
    13613778 At_Far-red-enriched-adult 20001773 Light Far-red enriched vs. White
    13613778 At_Far-red-enriched-adult 20001774 Age (day) 31
    13613778 At_Far-red-enriched-adult 20001774 Timepoint (hr) 72
    13613778 At_Far-red-enriched-adult 20001774 Organism A. thaliana
    13613778 At_Far-red-enriched-adult 20001774 Tissue Aerial
    13613778 At_Far-red-enriched-adult 20001774 Plant Line Columbia
    13613778 At_Far-red-enriched-adult 20001774 Light Far-red enriched vs. White
    13613778 At_Drought_Reproduction 20001904 Timepoint da 7
    13613778 At_Drought_Reproduction 20001904 Age (day) 37
    13613778 At_Drought_Reproduction 20001904 Organism A. thaliana
    13613778 At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought
    13613778 At_Drought_Reproduction 20001904 Tissue Rosettes
    13613778 At_Drought_Reproduction 20001904 Plant Line WS
    13613778 At_Drought_Reproduction 20001907 Timepoint (day) 7
    13613778 At_Drought_Reproduction 20001907 Age (day) 37
    13613778 At_Drought_Reproduction 20001907 Organism A. thaliana
    13613778 At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought
    13613778 At_Drought_Reproduction 20001907 Tissue Siliques
    13613778 At_Drought_Reproduction 20001907 Plant Line WS
    13613778 At_Line_Comparisons 20002012 Plant Line SALK 073455 vs. Columbia
    13613778 At_8deg_Cold 20002108 Age (day) 14
    13613778 At_8deg_Cold 20002108 Timepoint (hr) 168
    13613778 At_8deg_Cold 20002108 Temperature 8 vs. 22
    (deg C.)
    13613778 At_8deg_Cold 20002108 Organism A. thaliana
    13613778 At_8deg_Cold 20002108 Tissue Whole Plant
    13613778 At_8deg_Cold 20002108 Plant Line WS
    13613778 At_8deg_Cold 20002109 Age (day) 16
    13613778 At_8deg_Cold 20002109 Timepoint (hr) 216
    13613778 At_8deg_Cold 20002109 Temperature 8 vs. 22
    (deg C.)
    13613778 At_8deg_Cold 20002109 Organism A. thaliana
    13613778 At_8deg_Cold 20002109 Tissue Whole Plant
    13613778 At_8deg_Cold 20002109 Plant Line WS
  • TABLE 2
    Promoter Utilities Based on Differential Expression Experiments
    EXPT_REP_ID SHORT_NAME UTILITY
    20000166 At_100 uM_ABA Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    in modulating ABA, stress, and drought
    induced and/or regulated responses
    20000169 At_100 uM_ABA Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    in modulating ABA, stress, and drought
    induced and/or regulated responses
    20000171 At_42deg_Heat Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    in modulating stress, heat and cold induced
    and/or regulated responses
    20000173 At_42deg_Heat Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    in modulating stress, heat and cold induced
    and/or regulated responses
    20000179 At_Germinating_Seeds Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating growth, yield and plant
    development
    20000180 At_Germinating_Seeds Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating growth, yield and plant
    development
    20000182 At_2 mM_SA Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    in modulating stress and SA induced and/or
    regulated responses
    20000184 At_Shoots Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating growth, yield, and plant
    development for instance in roots and/or
    shoots
    20000185 At_Roots Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating growth, yield, and plant
    development for instance in roots and/or
    shoots
    20000227 At_Root-Tips-vs-Tops Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating growth, yield, and plant
    development for instance in roots and/or
    shoots
    20000234 At_Siliques Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating fertility, fruit and seed size,
    number and/or yield
    20000235 At_Siliques Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating fertility, fruit and seed size,
    number and/or yield
    20000264 At_Open_Flower Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating fertility, fruit and seed size,
    number and/or yield, including flowers
    development and number
    20000265 At_Open_Flower Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating fertility, fruit and seed size,
    number and/or yield, including flowers
    development and number
    20000267 At_Drought Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20000286 At_Open_Flower Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating fertility, fruit and seed size,
    number and/or yield, including flowers
    development and number
    20000436 At_Drought Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20000437 At_Drought Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20000438 At_Shoots Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating growth, yield, and plant
    development for instance in roots and/or
    shoots
    20000439 At_Roots Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating growth, yield, and plant
    development for instance in roots and/or
    shoots
    20000441 At_1 uM_BR-BRZ Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating growth, yield and BR induced
    and/regulated responses
    20000443 At_1 uM_BR-BRZ Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating growth, yield and BR induced
    and/regulated responses
    20000451 At_CS6879_Shoots-Roots Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating growth, yield, and plant
    development for instance in roots and/or
    shoots
    20000453 At_100 uM_ABA Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    in modulating ABA, stress, and drought
    induced and/or regulated responses
    20000457 At_42deg_Heat Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    in modulating stress, heat and cold induced
    and/or regulated responses
    20000458 At_42deg_Heat Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    in modulating stress, heat and cold induced
    and/or regulated responses
    20000460 At_10percent_PEG Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress, drought tolerance, and
    osmotic stress
    20000495 At_Guard_Cells Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating guard cells, drought and stress
    tolerance
    20000527 At_10percent_PEG Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress, drought tolerance, and
    osmotic stress
    20000573 At_100 uM_ABA_Mutants Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    in modulating ABA, stress, and drought
    induced and/or regulated responses
    20000574 At_100 uM_ABA_Mutants Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    in modulating ABA, stress, and drought
    induced and/or regulated responses
    20000709 At_15 mM_NH4NO3_L-to-H Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating growth, yield and nitrogen
    induced and/regulated responses
    20000794 At_Petals Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating fertility, fruit and seed size,
    number and/or yield, including flowers
    development and number
    20001151 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating alkaloid biosynthesis and
    alkaloid induced and/or regulated responses
    20001184 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating methyl jasmonate induced
    and/or regulated responses including
    biosynthesis. They are useful also to
    modulate stress responses.
    20001195 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating alkaloid biosynthesis and
    alkaloid induced and/or regulated responses
    20001247 At_Far-red-induction Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating shade avoidance
    20001248 At_Far-red-induction Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating shade avoidance
    20001307 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating alkaloid biosynthesis and
    alkaloid induced and/or regulated responses
    20001308 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating alkaloid biosynthesis and
    alkaloid induced and/or regulated responses
    20001309 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating alkaloid biosynthesis and
    alkaloid induced and/or regulated responses
    20001310 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating alkaloid biosynthesis and
    alkaloid induced and/or regulated responses
    20001318 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating alkaloid biosynthesis and
    alkaloid induced and/or regulated responses
    20001319 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating alkaloid biosynthesis and
    alkaloid induced and/or regulated responses
    20001347 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating methyl jasmonate induced
    and/or regulated responses including
    biosynthesis. They are useful also to
    modulate stress responses.
    20001450 At_Far-red-induction Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating shade avoidance
    20001451 At_Far-red-induction Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating shade avoidance
    20001458 At_50 mM_NH4NO3_L-to-H Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating growth, yield and nitrogen
    induced and/regulated responses
    20001504 At_Far-red-enriched Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating shade avoidance
    20001554 At_Drought_Soil_Dry Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20001555 At_Drought_Soil_Dry Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20001556 At_Drought_Soil_Dry Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20001557 At_Drought_Soil_Dry Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20001558 At_Drought_Soil_Dry Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20001559 At_Drought_Soil_Dry Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20001560 At_Drought_Soil_Dry Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20001653 At_Interploidy_Crosses Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating fertility, fruit and seed size,
    number and/or yield, including endosperm
    size and seed abortion
    20001654 At_Interploidy_Crosses Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating fertility, fruit and seed size,
    number and/or yield, including endosperm
    size and seed abortion
    20001704 At_Interploidy_Crosses Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating fertility, fruit and seed size,
    number and/or yield, including endosperm
    size and seed abortion
    20001757 At_50 mM_NH4NO3_L-to-H Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating growth, yield and nitrogen
    induced and/regulated responses
    20001768 At_Far-red-enriched-adult Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating shade avoidance
    20001770 At_Far-red-enriched-adult Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating shade avoidance
    20001771 At_Far-red-enriched-adult Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating shade avoidance
    20001773 At_Far-red-enriched-adult Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating shade avoidance
    20001853 At_Interploidy_Crosses Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating fertility, fruit and seed size,
    number and/or yield, including endosperm
    size and seed abortion
    20001904 At_Drought_Reproduction Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20001905 At_Drought_Reproduction Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20001906 At_Drought_Reproduction Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20001907 At_Drought_Reproduction Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20001908 At_Drought_Reproduction Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20001909 At_Drought_Reproduction Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20001910 At_Drought_Reproduction Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20001911 At_Drought_Reproduction Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating stress and drought tolerance
    20002007 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating sterol biosynthesis and sterol
    induced and/or regulated responses.
    20002008 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating sterol biosynthesis and sterol
    induced and/or regulated responses.
    20002009 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating sterol biosynthesis and sterol
    induced and/or regulated responses.
    20002010 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating sterol biosynthesis and sterol
    induced and/or regulated responses.
    20002012 At_Line_Comparisons Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    for modulating triterpene biosynthesis and
    triterpene induced and/or regulated
    responses.
    20002103 At_8deg_Cold Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    in modulating stress, heat and cold induced
    and/or regulated responses
    20002107 At_8deg_Cold Promoters and cDNAs corresponding to
    endogenous cDNAs which were differentially
    expressed in this experiment would be useful
    in modulating stress, heat and cold induced
    and/or regulated responses
  • TABLE 3
    Promoter
    Name Fl Si Lf St Em Ov Hy Co Rt
    YP0226 Y Y Y Y Y
    YP0244 Y
    YP0286 Y Y Y Y Y
    YP0289 Y Y Y Y
    YP0356 Y Y Y Y Y Y
    YP0374 Y Y Y
    YP0377 Y Y Y Y
    YP0380 Y Y Y Y Y Y Y
    VP0381 Y Y Y
    YP0382 Y Y
    YP0388 Y Y Y Y Y
    YP0396 Y Y Y Y Y
    PT0506 Y
    PT0511 Y Y Y
    YP0275 Y
    YP0337 Y
    YP0384 Y
    YP0385 Y Y Y
    YP0371 Y Y

    Legend for Table 3

    Fl Flower

    Si Silique

    Lf Leaf

    St Stem

    Em Embryo

    Ov Ovule

    Hy Hypocotyl

    Co Cotyledon

    Rt Rosette Leaf
  • The invention being thus described, it will be apparent to one of ordinary skill in the art that various modifications of the materials and methods for practicing the invention can be made. Such modifications are to be considered within the scope of the invention as defined by the following claims.
  • Each of the references from the patent and periodical literature cited herein is hereby expressly incorporated in its entirety by such citation.

Claims (17)

1. An isolated nucleic acid molecule capable of modulating transcription wherein the nucleic acid molecule shows at least 80% sequence identity to one of the promoter sequences in Table 1, or a complement thereof.
2. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid is capable of functioning as a promoter.
3. The isolated nucleic acid molecule of claim 2, wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of one of the promoter sequences in Table 1 having at least one of the corresponding optional promoter fragments identified in Table 1.
4. The isolated nucleic acid molecule of claim 2, wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of one of the promoter sequences in Table 1 having all of the corresponding optional promoter fragments identified in Table 1.
5. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid molecule is capable of modulating transcription during the developmental times, or in response to a stimuli, or in a cell, tissue, or organ as set forth in Table 1 in the section “The spatial expression of the promoter-marker-vector”.
6. A vector construct comprising:
a) a first nucleic acid capable of modulating transcription wherein the nucleic acid molecule shows at least 80% sequence identity tone of the promoter sequences in Table 1; and
b) a second nucleic acid having to be transcribed,
wherein said first and second nucleic acid molecules are heterologous to each other and are operably linked together.
7. The vector construct according to claim 6, wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of one of the promoter sequences in Table 1 having at least one of the corresponding optional promoter fragments identified in Table 1 deleted therefrom.
8. The vector construct according to claim 6, wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of one of the promoter sequences in Table 1 having all of the corresponding optional promoter fragments identified in Table 1 deleted therefrom.
9. A host cell comprising an isolated nucleic acid molecule according to claim 1, wherein said nucleic acid molecule is flanked by exogenous sequence.
10. The host cell according to claim 9, wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of one of the promoter sequences in Table 1 having at least one of the corresponding optional promoter fragments identified in Table 1 deleted therefrom.
11. The host cell according to claim 9, wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of one of the promoter sequences in Table 1 having all of the corresponding optional promoter fragments identified in Table 1 deleted therefrom.
12. A host cell comprising a vector construct of claim 6.
13. A method of modulating transcription by combining, in an environment suitable for transcription:
a) a first nucleic acid molecule capable of modulating transcription wherein the nucleic acid molecule shows at least 80% sequence identity to one of the promoter sequences in Table 1; and
b) a second molecule to be transcribed;
wherein the first and second nucleic acid molecules are heterologous to each other and operably linked together.
14. The method of claim 13, wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of one of the promoter sequences in Table 1 having at least one of the corresponding optional promoter fragments identified in Table 1 deleted therefrom.
15. The method of claim 13, wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of one of the promoter sequences in Table 1 having all of the corresponding optional promoter fragments identified in Table 1 deleted therefrom.
16. The method according to any one of claims 13-15, wherein said first nucleic acid molecule is capable of modulating transcription during the developmental times, or in response to a stimuli, or in a cell tissue, or organ as set forth in Table 1 in the section entitled “The spatial expression of the promoter-marker-vector” wherein said first nucleic acid molecule is inserted into a plant cell and said plant cell is regenerated into a plant.
17. A plant comprising a vector construct according to claim 6.
US11/598,118 2003-09-11 2006-11-10 Promoter, promoter control elements, and combinations, and uses thereof Abandoned US20070136839A1 (en)

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US54477104P 2004-02-13 2004-02-13
US10/950,321 US7173121B2 (en) 2003-10-14 2004-09-23 Promoter, promoter control elements, and combinations, and uses thereof
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US9101100B1 (en) 2014-04-30 2015-08-11 Ceres, Inc. Methods and materials for high throughput testing of transgene combinations
US9546376B2 (en) 2009-03-12 2017-01-17 Toyota Jidosha Kabushiki Kaisha Gene for increasing the production of plant biomass and/or seeds and method for use thereof
US9695435B2 (en) 2008-03-14 2017-07-04 Toyota Jidosha Kabushiki Kaisha Gene for increasing the production of plant biomass and/or seeds and method for use thereof
US9758790B2 (en) 2004-12-08 2017-09-12 Ceres, Inc. Modulating the level of components within plants
US10604766B2 (en) 2008-02-15 2020-03-31 Ceres, Inc. Drought and heat tolerance in plants

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US9758790B2 (en) 2004-12-08 2017-09-12 Ceres, Inc. Modulating the level of components within plants
US10604766B2 (en) 2008-02-15 2020-03-31 Ceres, Inc. Drought and heat tolerance in plants
US11530417B2 (en) 2008-02-15 2022-12-20 Ceres, Inc. Drought and heat tolerance in plants
US11578337B2 (en) 2008-02-15 2023-02-14 Ceres, Inc. Drought and heat tolerance in plants
US11946060B2 (en) 2008-02-15 2024-04-02 Ceres, Inc. Drought and heat tolerance in plants
US9695435B2 (en) 2008-03-14 2017-07-04 Toyota Jidosha Kabushiki Kaisha Gene for increasing the production of plant biomass and/or seeds and method for use thereof
US10287604B2 (en) 2008-03-14 2019-05-14 Toyota Jidosha Kabushiki Kaisha Gene for increasing the production of plant biomass and/or seeds and method for use thereof
US9546376B2 (en) 2009-03-12 2017-01-17 Toyota Jidosha Kabushiki Kaisha Gene for increasing the production of plant biomass and/or seeds and method for use thereof
US9101100B1 (en) 2014-04-30 2015-08-11 Ceres, Inc. Methods and materials for high throughput testing of transgene combinations

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