WO2001054733A1 - Acides nucleiques, proteines et anticorps - Google Patents
Acides nucleiques, proteines et anticorps Download PDFInfo
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- WO2001054733A1 WO2001054733A1 PCT/US2001/001312 US0101312W WO0154733A1 WO 2001054733 A1 WO2001054733 A1 WO 2001054733A1 US 0101312 W US0101312 W US 0101312W WO 0154733 A1 WO0154733 A1 WO 0154733A1
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- polypeptide
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Classifications
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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
- C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
- C12N9/14—Hydrolases (3)
- C12N9/48—Hydrolases (3) acting on peptide bonds (3.4)
- C12N9/50—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
- C12N9/64—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue
- C12N9/6421—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue from mammals
- C12N9/6424—Serine endopeptidases (3.4.21)
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
- C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
- C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
- C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
- C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
-
- 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
- C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
-
- 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
- C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
- C12N9/14—Hydrolases (3)
- C12N9/48—Hydrolases (3) acting on peptide bonds (3.4)
- C12N9/50—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
- C12N9/64—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue
- C12N9/6421—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue from mammals
- C12N9/6489—Metalloendopeptidases (3.4.24)
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
-
- A—HUMAN NECESSITIES
- A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
- A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
- A01K2217/00—Genetically modified animals
- A01K2217/05—Animals comprising random inserted nucleic acids (transgenic)
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K38/00—Medicinal preparations containing peptides
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2319/00—Fusion polypeptide
- C07K2319/30—Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2500/00—Screening for compounds of potential therapeutic value
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
- Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
- Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
- Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change
Definitions
- the present invention relates to novel proteins. More specifically, isolated nucleic acid molecules are provided encoding novel polypeptides. Novel polypeptides and antibodies that bind to these polypeptides are provided. Also provided are vectors, host cells, and recombinant and synthetic methods for producing human polynucleotides and/or polypeptides, and antibodies.
- the mvention further relates to diagnostic and therapeutic methods useful for diagnosing, treating, preventing and/or prognosing disorders related to these novel polypeptides.
- the invention further relates to screening methods for identifying agonists and antagonists of polynucleotides and polypeptides of the invention.
- the present invention further relates to methods and/or compositions for inhibiting or enhancing the production and function of the polypeptides of the present invention.
- polypeptides of the invention comprise, or alternatively consist of, an amino acid sequence encoded by a polynucleotide in SEQ ID NO:X as delineated in columns 8 and 9, or fragments or variants thereof.
- Table 3 provides polynucleotide sequences that may be disclaimed according to certain embodiments of the invention.
- the polynucleotide can contain the nucleotide sequence of the full length cDNA sequence, including the 5' and 3' untranslated sequences, the coding region, as well as fragments, epitopes, domains, and variants of the nucleic acid sequence.
- a "polypeptide” refers to a molecule having an amino acid sequence encoded by a polynucleotide of the invention as broadly defined (obviously excluding poly-Phenylalanine or poly-Lysine peptide sequences which result from translation of a polyA tail of a sequence corresponding to a cDNA).
- ATCC American Type Culture Collection
- Library names contain four characters, for example, "HTWE.”
- the name of a cDNA clone (Clone ID) isolated from that library begins with the same four characters, for example "HTWEP07".
- Table 1 A correlates the Clone ID names with SEQ ID NO:X.
- SEQ ID NO:X the Clone ID names with SEQ ID NO:X.
- Tables 1, 6 and 7 the Clone ID names with SEQ ID NO:X.
- the ATCC is located at 10801 University Boulevard, Manassas, Virginia 20110-2209, USA.
- the ATCC deposits were made pmsuant to the terms of the Budapest Treaty on the international recognition of the deposit of microorganisms for the purposes of patent procedure.
- a "polynucleotide” of the present invention also includes those polynucleotides capable of hybridizing, under stringent hybridization conditions, to sequences contained in SEQ ID NO:X, or the complement thereof (e.g., the complement of any one, two, three, four, or more of the polynucleotide fragments described herein), the polynucleotide sequence delineated in columns 8 and 9 of Table 2 or the complement thereof, and/or cDNA sequences contained in Clone ID NO:Z (e.g., the complement of any one, two, three, four, or more of the polynucleotide fragments, or the cDNA clone within the pool of cDNA clones deposited with the ATCC, described herein), and/or the polynucleotide sequence delineated in column 6 of Table IB or the complement thereof.
- “Stringent hybridization conditions” refers to an overnight incubation at 42 degree C in a solution comprising 50% formamide, 5x SSC (750 mM NaCl, 75 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5x Denhardt's solution, 10% dextran sulfate, and 20 ⁇ g/ml denatured, sheared salmon sperm DNA, followed by washing the filters in O.lx SSC at about 65 degree C.
- the polynucleotide of the present invention can be composed of any polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA.
- polynucleotides can be composed of single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions.
- polynucleotide can be composed of triple-stranded regions comprising RNA or DNA or both RNA and DNA.
- a polynucleotide may also contain one or more modified bases or DNA or RNA backbones modified for stability or for other reasons.
- modified bases include, for example, tritylated bases and unusual bases such as inosine.
- polynucleotide embraces chemically, enzymatically, or metabolically modified forms.
- Modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer- RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination.
- SEQ ID NO:X refers to a polynucleotide sequence described, for example, in
- SEQ ID NO:Y refers to a polypeptide sequence described in column 6 of Table 1 A.
- SEQ ID NO:X is identified by an integer specified in column 4 of Table 1 A.
- the polypeptide sequence SEQ ID NO:Y is a translated open reading frame (ORF) encoded by polynucleotide SEQ ID NO:X.
- Clone ID NO:Z refers to a cDNA clone described in column 2 of Table 1A.
- a polypeptide having biological activity refers to a polypeptide exhibiting activity similar to, but not necessarily identical to, an activity of a polypeptide of the present invention, including mature forms, as measured in a particular biological assay, with or without dose dependency.
- the first column in Table 1A provides the gene number in the application corresponding to the clone identifier.
- the second column in Table 1A provides a unique "Clone ID NO:Z" for a cDNA clone related to each contig sequence disclosed in Table 1A.
- This clone ID references the cDNA clone which contains at least the 5' most sequence of the assembled contig and at least a portion of SEQ ID NO:X was determined by directly sequencing the referenced clone.
- the reference clone may have more sequence than described in the sequence listing or the clone may have less. In the vast majority of cases, however, the clone is believed to encode a full-length polypeptide. In the case where a clone is not full-length, a full-length cDNA can be obtained by methods described elsewhere herein.
- the third column in Table 1A provides a unique "Contig ID” identification for each contig sequence.
- the fourth column provides the "SEQ ID NO:” identifier for each of the contig polynucleotide sequences disclosed in Table 1 A.
- the fifth column, "ORF (From- To)" provides the location (i.e., nucleotide position numbers) within the polynucleotide sequence "SEQ ID NO:X” that delineate the preferred open reading frame (ORF) shown in the sequence listing and referenced in Table 1A, column 6, as SEQ ID NO:Y.
- the preferred ORF is the reverse complement of the referenced polynucleotide sequence.
- the sixth column in Table 1A provides the corresponding SEQ ID NO:Y for the polypeptide sequence encoded by the preferred ORF delineated in column 5.
- the invention provides an amino acid sequence comprising, or alternatively consisting of, a polypeptide encoded by the portion of SEQ ID NO:X delineated by "ORF (From-To)". Also provided are polynucleotides encoding such amino acid sequences and the complementary strand thereto.
- polypeptides of the invention comprise, or alternatively consist of, at least one, two, three, four, five or more of the predicted epitopes as described in Table 1A.
- Column 8 in Table 1 A provides an expression profile and library code: count for each of the contig sequences (SEQ ID NO:X) disclosed in Table 1A, which can routinely be combined with the information provided in Table 4 and used to determine the tissues, cells, and/or cell line libraries which predominantly express the polynucleotides of the mvention.
- the first number in column 8 represents the tissue/cell source identifier code corresponding to the code and description provided in Table 4.
- the second number in column 8 represents the number of times a sequence corresponding to the reference polynucleotide sequence was identified in the tissue/cell source.
- tissue/cell source identifier' codes in which the first two letters are "AR” designate information generated using DNA array technology. Utilizing this technology, cDNAs were amplified by PCR and then transferred, in duplicate, onto the array. Gene expression was assayed through hybridization of first strand cDNA probes to the DNA array. cDNA probes were generated from total RNA extracted from a variety of different tissues and cell lines. Probe synthesis was performed in the presence of 33 P dCTP, using oligo(dT) to prime reverse transcription.
- HCE3W04 379 615501 AC022366 1466 1-565 1503-1718 1838-1933 2011-2097 2265-2335 2588-2693 2905-2975 3090-3726 3809-3889 4080-4591 4847-5070 5355-5819
- Table IB summarizes additional polynucleotides encompassed by the mvention
- the fourth column provides a BAC identifier "BAC ID NO: A” for the BAC clone referenced in the corresponding row of the table.
- the fifth column provides the nucleotide sequence identifier, "SEQ ID NO:B" for a fragment of the BAC clone identified in column four of the corresponding row of the table.
- the sixth column provides the location (i.e., nucleotide position numbers) within the polynucleotide sequence of SEQ ID NO:B which delineate certain polynucleotides of the invention that are also exemplary members of polynucleotide sequences that encode polypeptides of the invention (e.g., polypeptides containing amino acid sequences encoded by the polynucleotide sequences delineated in column six, and fragments and variants thereof).
- Table 2 further characterizes certain encoded polypeptides of the invention, by providing the results of comparisons to protein and protein family databases.
- the first column provides a unique clone identifier, "Clone ID NO:”, corresponding to a cDNA clone disclosed in Table 1A.
- the second column provides the unique contig identifier, "Contig ID:” which allows correlation with the information in Table 1 A.
- the third column provides the sequence identifier, "SEQ ID NO:”, for the contig polynucleotide sequences.
- the fourth column provides the analysis method by which the homology/identity disclosed in the Table was determined.
- the fifth column provides a description of the PFAM/NR hit identified by each analysis.
- Column six provides the accession number of the PFAM/NR hit disclosed in the fifth column.
- Column seven, score/percent identity, provides a quality score or the percent identity, of the hit disclosed in column five. Comparisons were made between polypeptides encoded by polynucleotides of the mvention and a non-redundant protein database (herein referred to as "NR"), or a database of protein families (herein referred to as "PFAM”), as described below.
- NR non-redundant protein database
- PFAM database of protein families
- the NR database which comprises the NBRF PIR database, the NCBI GenPept database, and the SIB SwissProt and TrEMBL databases, was made non-redundant using the computer program nrdb2 (Warren Gish, Washington University in Saint Louis).
- nrdb2 Warren Gish, Washington University in Saint Louis.
- Each of the polynucleotides shown in Table 1 A, column 3 (e.g., SEQ ID NO:X or the 'Query' sequence) was used to search against the NR database.
- the computer program BLASTX was used to compare a 6-frame translation of the Query sequence to the NR database (for information about the BLASTX algorithm please see Altshul et al., J. Mol. Biol. 215:403-410 (1990); and Gish and States, Nat. Genet.
- the percent identity is determined by dividing the number of exact matches between the two aligned sequences in the HSP, dividing by the number of Query amino acids in the HSP and multiplying by 100.
- the polynucleotides of SEQ ID NO:X which encode the polypeptide sequence that generates an HSP are delineated by columns 8 and 9 of Table 2.
- HMM Hidden Markov Model
- a HMM derived from PFAM version 2.1 was said to be a significant match to a polypeptide of the invention if the score returned by HMMER 1.8 was greater than 0.8 times the HMMER 1.8 score obtained with the most distantly related known member of that protem family.
- the description of the PFAM family which shares a significant match with a polypeptide of the invention is listed in column 5 of Table 2, and the database accession number of the PFAM hit is provided in column 6.
- Column 7 provides the score returned by HMMER version 1.8 for the alignment.
- Columns 8 and 9 delineate the polynucleotides of SEQ ID NO:X which encode the polypeptide sequence which show a significant match to a PFAM protein family.
- the invention provides a protem comprising, or alternatively consisting of, a polypeptide encoded by the polynucleotides of SEQ ID NO:X delineated in columns 8 and 9 of Table 2. Also provided are polynucleotides encoding such proteins, and the complementary strand thereto.
- nucleotide sequence SEQ ID NO:X and the translated SEQ ID NO:Y are sufficiently accurate and otherwise suitable for a variety of uses well known in the art and described further below.
- the nucleotide sequences of SEQ ID NO:X are useful for designing nucleic acid hybridization probes that will detect nucleic acid sequences contained in SEQ ID NO:X or the cDNA contained in Clone ID NO:Z. These probes will also hybridize to nucleic acid molecules in biological samples, thereby enabling immediate applications in chromosome mapping, linkage analysis, tissue identification and/or typing, and a variety of forensic and diagnostic methods of the invention.
- polypeptides identified from SEQ ID NO:Y may be used to generate antibodies which bind specifically to these polypeptides, or fragments thereof, and/or to the polypeptides encoded by the cDNA clones identified in, for example, Table 1 A.
- DNA sequences generated by sequencing reactions can contain sequencing errors.
- the errors exist as misidentified nucleotides, or as insertions or deletions of nucleotides in the generated DNA sequence.
- the erroneously inserted or deleted nucleotides cause frame shifts in the reading frames of the predicted amino acid sequence.
- the predicted amino acid sequence diverges from the actual amino acid sequence, even though the generated DNA sequence may be greater than 99.9% identical to the actual DNA sequence (for example, one base insertion or deletion in an open reading frame of over 1000 bases).
- the present invention provides not only the generated nucleotide sequence identified as SEQ ID NO:X, and a predicted translated amino acid sequence identified as SEQ ID NO:Y, but also a sample of plasmid DNA containing cDNA Clone ID NO:Z (deposited with the ATCC on October 5, 2000, and receiving ATCC designation numbers PTA 2574 and PTA 2575; deposited with the ATCC on January 5, 2001, and having depositor reference numbers TS-1, TS-2, AC-1, and AC-2; and/or as set forth, for example, in Table 1A, 6 and 7).
- nucleotide sequence of each deposited clone can readily be determined by sequencing the deposited clone in accordance with known methods. Further, techniques known in the art can be used to verify the nucleotide sequences of SEQ ID NO:X. [67] The predicted amino acid sequence can then be verified from such deposits.
- amino acid sequence of the protein encoded by a particular clone can also be directly determined by peptide sequencing or by expressing the protein in a suitable host cell containing the deposited human cDNA, collecting the protein, and determining its sequence.
- Partial cDNA clones can be made full-length by utilizing the rapid amplification of cDNA ends (RACE) procedure described in Frohman, M.A., et al., Proc. Nat'l. Acad. Sci. USA, 85:8998-9002 (1988).
- RACE rapid amplification of cDNA ends
- RNA Poly A+ or total RNA is reverse transcribed with Superscript II (Gibco/BRL) and an antisense or complementary primer specific to the cDNA sequence.
- the primer is removed from the reaction with a Microcon Concentrator (Amicon).
- the first-strand cDNA is then tailed with dATP and terminal deoxynucleotide transferase (Gibco/BRL).
- the second strand is synthesized from the dA-tail in PCR buffer, Taq DNA polymerase (Perkin-Elmer Cetus), an oligo-dT primer containing three adjacent restriction sites (Xhol, Sail and Clal) at the. 5' end and a primer containing just these restriction sites.
- This double-stranded cDNA is PCR amplified for 40 cycles with the same primers as well as a nested cDNA-specific antisense primer.
- the PCR products are size-separated on an ethidium bromide-agarose gel and the region of gel containing cDNA products the predicted size of missing protein-coding DNA is removed.
- cDNA is purified from the agarose with the Magic PCR Prep kit (Promega), restriction digested with Xhol or Sail, and ligated to a plasmid such as pBluescript SKII (Stratagene) at Xhol and EcoRN sites.
- This D ⁇ A is transformed into bacteria and the plasmid clones sequenced to identify the correct protein-coding inserts. Correct 5' ends are confirmed by comparing this sequence with the putatively identified homologue and overlap with the partial cD ⁇ A clone. Similar methods known in the art and/or commercial kits are used to amplify and recover 3' ends.
- kits are commercially available for purchase. Similar reagents and methods to those above are supplied in kit form from Gibco/BRL for both 5' and 3' RACE for recovery of full length genes. A second kit is available from Clontech which is a modification of a related technique, SLIC (single-stranded ligation to single-stranded cD ⁇ A), developed by Dumas et al., Nucleic Acids Res., 19:5227-32 (1991). The major differences in procedure are that the RNA is alkaline hydrolyzed after reverse transcription and RNA ligase is used to join a restriction site-containing anchor primer to the first-strand cDNA. This obviates the necessity for the dA-tailing reaction which results in a polyT stretch that is difficult to sequence past.
- SLIC single-stranded ligation to single-stranded cD ⁇ A
- RNA Ligase Protocol For Generating The 5' or 3' End Sequences To Obtain Full Length Genes
- RNA oligonucleotide is ligated to the 5' ends of a population of RNA presumably containing full-length gene RNA transcript and a primer set containing a primer specific to the ligated RNA oligonucleotide and a primer specific to a known sequence of the gene of interest, is used to PCR amplify the 5' portion of the desired full length gene which may then be sequenced and used to generate the full length gene.
- This method starts with total RNA isolated from the desired source, poly A RNA may be used but is not a prerequisite for this procedure.
- RNA preparation may then be treated with phosphatase if necessary to eliminate 5' phosphate groups on degraded or damaged RNA which may interfere with the later RNA ligase step.
- the phosphatase if used is then inactivated and the RNA is treated with tobacco acid pyrophosphatase in order to remove the cap structure present at the 5' ends of messenger RNAs.
- This reaction leaves a 5' phosphate group at the 5' end of the cap cleaved RNA which can then be ligated to an RNA oligonucleotide using T4 RNA ligase.
- This modified RNA preparation can then be used as a template for first strand cDNA synthesis using a gene specific oligonucleotide.
- the first strand synthesis reaction can then be used as a template for PCR amplification of the desired 5' end using a primer specific to the ligated RNA oligonucleotide and a primer specific to the known sequence of the gene of interest.
- the resultant product is then sequenced and analyzed to confirm that the 5' end sequence belongs to the relevant gene.
- the present invention also relates to vectors or plasmids which include such DNA sequences, as well as the use of the DNA sequences.
- the material deposited with the ATCC (deposited with the ATCC on October 5, 2000, and receiving ATCC designation numbers PTA 2574 and PTA 2575; deposited with the ATCC on January 5, 2001, and receiving ATCC designation numbers TS-1, TS-2, AC-1, and AC-2; and/or as set forth, for example, in Table 1A, Table 6, or Table 7) is a mixture of cDNA clones derived from a variety of human tissue and cloned in either a plasmid vector or a phage vector, as described, for example, in Table 7. These deposits are referred to as "the deposits" herein.
- the tissues from which some of the clones were derived are listed in Table 7, and the vector in which the corresponding cDNA is contained is also indicated in Table 7.
- the deposited material includes cD A clones corresponding to SEQ ID NO:X described, for example, in Table 1 A (Clone ID NO:Z).
- a clone which is isolatable from the ATCC Deposits by use of a sequence listed as SEQ ID NO:X may include the entire coding region of a human gene or in other cases such clone may include a substantial portion of the coding region of a human gene.
- sequence listing may in some instances list only a portion of the DNA sequence in a clone included in the ATCC Deposits, it is well within the ability of one skilled in the art to sequence the DNA included in a clone contained in the ATCC Deposits by use of a sequence (or portion thereof) described in, for example Tables lAor 2 by procedures hereinafter further described, and others apparent to those skilled in the art.
- Table 7 Also provided in Table 7 is the name of the vector which contains the cDNA clone. Each vector is routinely used in the art. The following additional information is provided for convenience.
- Phagemid pBS contains an ampicillin resistance gene and pBK contains a neomycin resistance gene.
- Phagemid pBS may be excised from the Lambda Zap and Uni-Zap XR vectors, and phagemid pBK may be excised from the Zap Express vector. Both phagemids may be transformed into E. coli strain XL-1 Blue, also available from Stratagene.
- Nector pCR ® 2.1 which is available from Invitrogen, 1600 Faraday Avenue, Carlsbad, CA 92008, contains an ampicillin resistance gene and may be transformed into E. coli strain DH10B, available from Life Technologies. See, for instance, Clark, J. M., Nuc. Acids Res. 16:9611-9686 (1988) and Mead, D. et al, Bio/Technology 9: (1991).
- the present invention also relates to the genes corresponding to S ⁇ Q ID ⁇ O:X,
- S ⁇ Q ID NO:Y and/or the deposited clone (Clone ID NO:Z).
- the corresponding gene can be isolated in accordance with known methods using the sequence information disclosed herein. Such methods include preparing probes or primers from the disclosed sequence and identifying or amplifying the corresponding gene from appropriate sources of genomic material.
- allelic variants, orthologs, and/or species homologs are also provided in the present invention. Procedures known in the art can be used to obtain full-length genes, allelic variants, splice variants, full-length coding portions, orthologs, and/or species homologs of genes corresponding to S ⁇ Q ID NO:X or the complement thereof, polypeptides encoded by genes corresponding to S ⁇ Q ID NO:X or the complement thereof, and/or the cDNA contained in Clone ID NO:Z, using information from the sequences disclosed herein or the clones deposited with the ATCC.
- allelic variants and/or species homologs may be isolated and identified by making suitable probes or primers from the sequences provided herein and screening a suitable nucleic acid source for allelic variants and/or the desired homologue.
- polypeptides of the invention can be prepared in any suitable manner.
- Such polypeptides include isolated naturally occurring polypeptides, recombinantly produced polypeptides, synthetically produced polypeptides, or polypeptides produced by a combination of these methods. Means for preparing such polypeptides are well understood in the art.
- the polypeptides may be in the form of the secreted protein, including the mature form, or may be a part of a larger protein, such as a fusion protein (see below). It is often advantageous to include an additional amino acid sequence which contains secretory or leader sequences, pro-sequences, sequences which aid in purification, such as multiple histidine residues, or an additional sequence for stability during recombinant production.
- the polypeptides of the present invention are preferably provided in an isolated form, and preferably are substantially purified.
- a recombinantly produced version of a polypeptide, including the secreted polypeptide can be substantially purified using techniques described herein or otherwise known in the art, such as, for example, by the one- step method described in Smith and Johnson, Gene 67:31-40 (1988).
- Polypeptides of the invention also can be purified from natural, synthetic or recombinant sources using techniques described herein or otherwise known in the art, such as, for example, antibodies of the invention raised against the polypeptides of the present mvention in methods which are well known in the art.
- the present invention provides a polynucleotide comprising, or alternatively consisting of, the nucleic acid sequence of SEQ ID NO:X, and/or the cDNA sequence contained in Clone ID NO:Z.
- the present mvention also provides a polypeptide comprising, or alternatively, consisting of, the polypeptide sequence of SEQ ID NO:Y, a polypeptide encoded by SEQ ID NO:X or a complement thereof, a polypeptide encoded by the cDNA contained in Clone ID NO:Z, and/or the polypeptide sequence encoded by a nucleotide sequence in SEQ ID NO:B as defined in column 6 of Table IB.
- Polynucleotides encoding a polypeptide comprising, or alternatively consisting of the polypeptide sequence of SEQ ID NO:Y, a polypeptide encoded by SEQ ID NO:X, a polypeptide encoded by the cDNA contained in Clone ID NO:Z, and/or a polypeptide sequence encoded by a nucleotide sequence in SEQ ID NO:B as defined in column 6 of Table IB are also encompassed by the invention.
- the present invention further encompasses a polynucleotide comprising, or alternatively consisting of, the complement of the nucleic acid sequence of SEQ ID NO:X, a nucleic acid sequence encoding a polypeptide encoded by the complement of the nucleic acid sequence of SEQ ID NO:X, and/or the cDNA contained in Clone ID NO:Z.
- representative examples of polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the sequences delineated in Table IB column 6, or any combination thereof.
- polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the complementary strand(s) of the sequences delineated in Table IB column 6, or any combination thereof.
- the above-described polynucleotides of the mvention comprise, or alternatively consist of, sequences delineated in Table IB, column 6, and have a nucleic acid sequence which is different from that of the BAC fragment having the sequence disclosed in SEQ ID NO:B (see Table IB, column 5).
- the above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in Table IB, column 6, and have a nucleic acid sequence which is different from that published for the BAC clone identified as BAC ID NO:A (see Table IB, column 4). In additional embodiments, the above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in Table IB, column 6, and have a nucleic acid sequence which is different from that contained in the BAC clone identified as BAC ID NO:A (see Table IB, column 4).
- polypeptides encoded by these polynucleotides, other polynucleotides that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above- described polynucleotides and polypeptides are also encompassed by the mvention.
- representative examples of polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the sequences delineated in column 6 of Table IB which correspond to the same Clone ID NO:Z (see Table IB, column 1), or any combination thereof.
- polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the complementary strand(s) of the sequences delineated in column 6 of Table IB which correspond to the same Clone ID NO:Z (see Table IB, column 1), or any combination thereof.
- the above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in column 6 of Table IB which correspond to the same Clone ID NO:Z (see Table IB, column 1) and have a nucleic acid sequence which is different from that of the BAC fragment having the sequence disclosed in SEQ ID NO:B (see Table IB, column 5).
- polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in column 6 of Table IB which correspond to the same Clone ID NO:Z (see Table IB, column 1) and have a nucleic acid sequence which is different from that published for the BAC clone identified as BAC ID NO: A (see Table IB, column 4).
- the above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in column 6 of Table IB which correspond to the same Clone ID NO:Z (see Table IB, column 1) and have a nucleic acid sequence which is different from that contained in the BAC clone identified as BAC ID NO:A (see Table IB, column 4).
- Polypeptides encoded by these polynucleotides, other polynucleotides that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above- described polynucleotides and polypeptides are also encompassed by the invention.
- polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the sequences delineated in column 6 of Table IB which correspond to the same contig sequence identifer SEQ ID NO:X (see Table IB, column 2), or any combination thereof.
- polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the complementary strand(s) of the sequences delineated in column 6 of Table IB which correspond to the same contig sequence identifer SEQ ID NO:X (see Table IB, column 2), or any combination thereof.
- polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in column 6 of Table IB which correspond to the same contig sequence identifer SEQ ID NO:X (see Table IB, column 2) and have a nucleic acid sequence which is different from that published for the BAC clone identified as BAC ID NO:A (see Table IB, column 4).
- the above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in column 6 of Table IB which correspond to the same contig sequence identifer SEQ ID NO:X (see Table IB, column 2) and have a nucleic acid sequence which is different from that contained in the BAC clone identified as BAC ID NO:A (See Table IB, column 4).
- Polypeptides encoded by these polynucleotides, other polynucleotides that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the mvention. Additionally, fragments and variants of the above-described polynucleotides and polypeptides are also encompassed by the invention.
- the polynucleotides of the mvention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the complementary strand(s) of the sequences delineated in the same row of Table IB column 6, wherein sequentially delineated sequences in the table (i.e. corresponding to those exons located closest to each other) are directly contiguous in a 5' to 3' orientation.
- above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in the same row of Table IB, column 6, and have a nucleic acid sequence which is different from that of the BAC fragment having the sequence disclosed in SEQ ID NO:B (see Table IB, column 5).
- the above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in the same row of Table IB, column 6, and have a nucleic acid sequence which is different from that published for the BAC clone identified as BAC ID NO:A (see Table IB, column 4).
- polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in the same row of Table IB, column 6, and have a nucleic acid sequence which is different from that contained in the BAC clone identified as BAC ID NO:A (see Table IB, column 4).
- Polypeptides encoded by these polynucleotides, other polynucleotides that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the mvention.
- polynucleotides of the mvention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the sequences delineated in column 6 of Table IB, and the polynucleotide sequence of SEQ ID NO:X (e.g., as defined in Table IB, column 2) or fragments or variants thereof.
- Polypeptides encoded by these polynucleotides, other polynucleotides that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention.
- polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the sequences delineated in column 6 of Table IB which correspond to the same Clone ID NO:Z (see Table IB, column 1), and the polynucleotide sequence of SEQ ID NO:X (e.g., as defined in Table 1A or IB) or fragments or variants thereof.
- the delineated sequence(s) and polynucleotide sequence of SEQ ID NO:X correspond to the same Clone ID NO:Z.
- Polypeptides encoded by these polynucleotides, other polynucleotides that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention.
- polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the sequences delineated in the same row of column 6 of Table IB, and the polynucleotide sequence of SEQ ID NO:X (e.g., as defined in Table 1A or IB) or fragments or variants thereof.
- the delineated sequence(s) and polynucleotide sequence of SEQ ID NO:X correspond to the same row of column 6 of Table IB.
- polynucleotides of the invention comprise, or alternatively consist of a polynucleotide sequence in which the 3' 10 polynucleotides of one of the sequences delineated in column 6 of Table IB and the 5' 10 polynucleotides of the sequence of SEQ ID NO:X are directly contiguous.
- Nucleic acids which hybridize to the complement of these 20 contiguous polynucleotides under stringent hybridization conditions or alternatively, under lower stringency conditions are also encompassed by the mvention.
- Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the mvention. Additionally, fragments and variants of the above-described polynucleotides, nucleic acids, and polypeptides are also encompassed by the invention.
- polynucleotides of the invention comprise, or alternatively consist of, a polynucleotide sequence in which the 3' 10 polynucleotides of one of the sequences delineated in column 6 of Table IB and the 5' 10 polynucleotides of a fragment or variant of the sequence of SEQ ID NO:X are directly contiguous Nucleic acids which hybridize to the complement of these 20 contiguous polynucleotides under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the invention.
- Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids encoding these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above-described polynucleotides, nucleic acids, and polypeptides are also encompassed by the invention.
- polynucleotides of the invention -comprise, or alternatively consist of, a polynucleotide sequence in which the 3' 10 polynucleotides of the sequence of SEQ ID NO:X and the 5' 10 polynucleotides of the sequence of one of the sequences delineated in column 6 of Table IB are directly contiguous. Nucleic acids which hybridize to the complement of these 20 contiguous polynucleotides under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the invention.
- Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids encoding these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above-described polynucleotides, nucleic acids, and polypeptides are also encompassed by the mvention.
- polynucleotides of the invention comprise, or alternatively consist of, a polynucleotide sequence in which the 3' 10 polynucleotides of a fragment or variant of the sequence of SEQ ID NO:X and the 5' 10 polynucleotides of the sequence of one of the sequences delineated in column 6 of Table IB are directly contiguous.
- Nucleic acids which hybridize to the complement of these 20 contiguous polynucleotides under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the invention.
- Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids encoding these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above-described polynucleotides, nucleic acids, and polypeptides, are also encompassed by the invention.
- polynucleotides of the mvention comprise, or alternatively consist of, a polynucleotide sequence in which the 3' 10 polynucleotides of one of the sequences delineated in column 6 of Table IB and the 5' 10 polynucleotides of another sequence in column 6 are directly contiguous.
- Nucleic acids which hybridize to the complement of these 20 contiguous polynucleotides under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the invention.
- Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids encoding these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above- described polynucleotides, nucleic acids, and polypeptides are also encompassed by the invention.
- polynucleotides of the invention comprise, or alternatively consist of, a polynucleotide sequence in which the 3' 10 polynucleotides of one of the sequences delineated in column 6 of Table IB and the 5' 10 polynucleotides of another sequence in column 6 corresponding to the same Clone ID NO:Z (see Table IB, column 1) are directly contiguous. Nucleic acids which hybridize to the complement of these 20 lower stringency conditions, are also encompassed by the invention.
- Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids encoding these polypeptides, and antibodies that bind these polypeptides are also encompassed by the mvention. Additionally, fragments and variants of the above-described polynucleotides, nucleic acids, and polypeptides are also encompassed by the invention.
- polynucleotides of the invention comprise, or alternatively consist of, a polynucleotide sequence in which the 3' 10 polynucleotides of one sequence in column 6 corresponding to the same contig sequence identifer SEQ ID NO:X (see Table IB, column 2) are directly contiguous. Nucleic acids which hybridize to the complement of these 20 contiguous polynucleotides under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the invention.
- Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids encoding these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above- described polynucleotides, nucleic acids, and polypeptides are also encompassed by the invention.
- polynucleotides of the invention comprise, or alternatively consist of a polynucleotide sequence in which the 3' 10 polynucleotides of one of the sequences delineated in column 6 of Table IB and the 5' 10 polynucleotides of another sequence in column 6 corresponding to the same row are directly contiguous.
- the 3' 10 polynucleotides of one of the sequences delineated in column 6 of Table IB is directly contiguous with the 5' 10 polynucleotides of the next sequential exon delineated in Table IB, column 6.
- Nucleic acids which hybridize to the complement of these 20 contiguous polynucleotides under stringent hybridization conditions or alternatively, under lower stringency conditions are also encompassed by the mvention.
- Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids encoding these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above-described polynucleotides, nucleic acids, and polypeptides are also encompassed by the invention.
- each contig sequence (SEQ ID NO:X) listed in the fourth column of Table 1A preferably excluded are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 and the final nucleotide minus 15 of SEQ ID NO:X, b is an integer of 15 to the final nucleotide of SEQ ID NO:X, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:X, and where b is greater than or equal to a + 14.
- polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a and b are integers as defined in columns 4 and 5, respectively, of Table 3.
- the polynucleotides of the invention do not consist of at least one, two, three, four, five, ten, or more of the specific polynucleotide sequences referenced by the Genbank Accession No. as disclosed in column 6 of Table 3 (including for example, published sequence in connection with a particular BAC clone).
- preferably excluded from the invention are the specific polynucleotide sequence(s) contained in the clones corresponding to at least one, two, three, four, five, ten, or more of the available material having the accession numbers identified in the sixth column of this Table (including for example, the actual sequence contained in an identified BAC clone). In no way is this listing meant to encompass all of the sequences which may be excluded by the general formula, it is just a representative example. All references available through these accessions are hereby incorporated by reference in their entirety.
- H2CBH45 90 963811 1 - 470 15 - 484 AA307462, AA036880, AL133047, D89677, AC068243, and AC068243.
- HDPSR15 197 969666 1 - 1218 15 - 1232 AW195239, AW149418, AW005579, AI378013, AA147800, AI436586, AI392913, AW337924, AI377235, AI264931, AI203549, AW104319, AI094031, AA461376, H59980, AW166255, AA508841, AI360737, AA463275, AA417605, AI682196, H59937, AI208175, N30324, AA460078, AW001677, AA514325, N50317, AA741518, AI091790, T11446, AA360254, AI208678, AA214523, D20738, R61563, T12550, T11445, AA428834, AI276889, AB026289, and AR044150.
- HDQDX20 198 919027 1 - 1280 15 - 1294 AI905612, N75655, N94726, AA297704, H53438, AW339945, AW405560, AA719945, AI682436, AA971968, AW085268, H67340, HNTMH70 218 757184 1 - 674 15 - ( H19102, AI699883, AI383263, AC005726, and AC004807.
- HNTNB14 219 909942 1 - 644 15 - 658 AA082976, R60839, AA349498, F12661, T74243, L22557, AC068701, and AC068701.
- HODFF88 220 974911 1 - 1843 15 - 1857 D80164, D59502, D80193, D80195, D59275, C15076, D80227, D58283, D80022, D80166,, D81030, D59859, D51799, D59619, D80210, D80391, D80240, D59787, D51423, D80253, D80043, D80269, D50979, D80212, D80038, D80196, D80024, D80219, D80188, C14331, D59467, D57483, D59927, D80378, D80366, C14389, D59889, D50995, D80045, D59610, AA305409, C14429, D80241, D51060, T03269, C14014, AW178893, C75259, AA305578, D81026, D59695, D51022, AW179328, D
- HTOAK34 238 966800 1 - 1271 15 - 1285 AW408167, AA491322, AA505126, AI340133, AA831203, N27153, AA053564, AA809481, AF181985, and AF179867.
- HUTSF11 241 966029 1 - 416 15 - 430 AI384010, AI288640, Z20435, and A74523.
- HWAFG04 244 952878 1 - 1646 15 - 1660 AI302185, AI652375, AI936871, AW206793,
- polypeptide and Polypeptide Variants [98] The present invention is directed to variants of the polynucleotide sequence disclosed in SEQ ID NO:X or the complementary strand thereto, nucleotide sequences encoding the polypeptide of SEQ ID NO:Y, the nucleotide sequence of SEQ ID NO:X encoding the polypeptide sequence as defined in column 7 of Table 1A, nucleotide sequences encoding the polypeptide as defined in column 7 of Table 1 A, the nucleotide sequence as defined in columns 8 and 9 of Table 2, nucleotide sequences encoding the polypeptide encoded by the nucleotide sequence as defined in columns 8 and 9 of Table 2, the nucleotide sequence as defined in column 6 of Table IB, nucleotide sequences encoding the polypeptide encoded by the nucleotide sequence as defined in column 6 of Table IB, the cDNA sequence contained in Clone ID NO:Z, and/or nucleotide sequences
- the present invention also encompasses variants of the polypeptide sequence disclosed in SEQ ID NO:Y, the polypeptide sequence as defined in column 7 of Table 1A, a polypeptide sequence encoded by the polynucleotide sequence in SEQ ID NO:X, a polypeptide sequence encoded by the nucleotide sequence as defined in columns 8 and 9 of Table 2, a polypeptide sequence encoded by the nucleotide sequence as defined in column 6 of Table IB, a polypeptide sequence encoded by the complement of the polynucleotide sequence in SEQ ID NO:X, and/or a polypeptide sequence encoded by the cDNA sequence contained in Clone ID NO:Z.
- Variant refers to a polynucleotide or polypeptide differing from the polynucleotide or polypeptide of the present invention, but retaining essential properties thereof. Generally, variants are overall closely similar, and, in many regions, identical to the polynucleotide or polypeptide of the present mvention.
- one aspect of the invention provides an isolated nucleic acid molecule comprising, or alternatively consisting of, a polynucleotide having a nucleotide sequence selected from the group consisting of: (a) a nucleotide sequence described in SEQ ID NO:X or contained in the cDNA sequence of Clone ID NO:Z; (b) a nucleotide sequence in SEQ ID NO:X or the cDNA in Clone ID NO:Z which encodes the complete amino acid sequence of SEQ ID NO:Y or the complete amino acid sequence encoded by the cDNA in Clone ID NO:Z; (c) a nucleotide sequence in SEQ ID NO:X or the cDNA in Clone ID NO:Z which encodes a mature polypeptide; (d) a nucleotide sequence in SEQ ID NO:X or the cDNA sequence of Clone ID NO:Z, which encodes a biologically active fragment of a polypeptide; (e) a nucleotide sequence
- the present mvention is also directed to nucleic acid molecules which comprise, or alternatively consist of, a nucleotide sequence which is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%> or 100%), identical to, for example, any of the nucleotide sequences in (a), (b), (c), (d), (e), (f), (g), (h), (i), or (j) above, the nucleotide coding sequence in SEQ ID NO:X or the complementary strand thereto, the nucleotide coding sequence of the cDNA contained in Clone ID NO:Z or the complementary strand thereto, a nucleotide sequence encoding the polypeptide of SEQ ID NO:Y, a nucleotide sequence encoding a polypeptide sequence encoded by the nucleotide sequence in SEQ ID NO:X, a polypeptide sequence encoded by the complement of the polynucleotide sequence in SEQ ID NO:X,
- polynucleotides which hybridize to the complement of these nucleic acid molecules under stringent hybridization conditions or alternatively, under lower stringency conditions are also encompassed by the invention, as are polypeptides encoded by these polynucleotides and nucleic acids.
- the invention encompasses nucleic acid molecules which comprise, or alternatively, consist of a polynucleotide which hybridizes under stringent hybridization conditions, or alternatively, under lower stringency conditions, to a polynucleotide in (a), (b), (c), (d), (e), (f), (g), (h), or (i), above, as are polypeptides encoded by these polynucleotides.
- polynucleotides which hybridize to the complement of these nucleic acid molecules under stringent hybridization conditions, or alternatively, under lower stringency conditions are also encompassed by the invention, as are polypeptides encoded by these polynucleotides.
- the invention provides a purified protein comprising, or alternatively consisting of, a polypeptide having an amino acid sequence selected from the group consisting of: (a) the complete amino acid sequence of SEQ ID NO:Y or the complete amino acid sequence encoded by the cDNA in Clone ID NO:Z; (b) the amino acid sequence of a mature form of a polypeptide having the amino acid sequence of SEQ ID NO:Y or the amino acid sequence encoded by the cDNA in Clone ID NO:Z; (c) the amino acid sequence of a biologically active fragment of a polypeptide having the complete amino acid sequence of SEQ ID NO:Y or the complete amino acid sequence encoded by the cDNA in Clone ID NO:Z; and (d) the amino acid sequence of an antigenic fragment of a polypeptide having the complete amino acid sequence of SEQ ID NO:Y or the complete amino acid sequence encoded by the cDNA in Clone ID NO:Z.
- the present invention is also directed to proteins which comprise, or alternatively consist of, an amino acid sequence which is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100%), identical to, for example, any of the amino acid sequences in (a), (b), (c), or (d), above, the amino acid sequence shown in SEQ ID NO:Y, the amino acid sequence encoded by the cDNA contained in Clone ID NO:Z, the amino acid sequence of the polypeptide encoded by the nucleotide sequence in SEQ ID NO:X as defined in columns 8 and 9 of Table 2, the amino acid sequence of the polypeptide encoded by the nucleotide sequence in SEQ ID NO:B as defined in column 6 of Table IB, the amino acid sequence as defined in column 7 of Table 1A, an amino acid sequence encoded by the nucleotide sequence in SEQ ID NO:X, and an amino acid sequence encoded by the complement of the polynucleotide sequence in SEQ ID NO:X.
- polypeptides are also provided (e.g., those fragments described herein).
- Further proteins encoded by polynucleotides which hybridize to the complement of the nucleic acid molecules encoding these amino acid sequences under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the invention, as are the polynucleotides encoding these proteins.
- nucleic acid having a nucleotide sequence at least, for example, 95%> “identical" to a reference nucleotide sequence of the present invention it is intended that the nucleotide sequence of the nucleic acid is identical to the reference sequence except that the nucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence encoding the polypeptide.
- nucleic acid having a nucleotide sequence at least 95% identical to a reference nucleotide sequence up to 5% of the nucleotides in the reference sequence may be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence.
- the query sequence may be an entire sequence referred to in Table 1 A or 2 as the ORF (open reading frame), or any fragment specified as described herein.
- nucleic acid molecule or polypeptide is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a nucleotide sequence of the present invention can be determined conventionally using known computer programs.
- a preferred method for determining the best overall match between a query sequence (a sequence of the present invention) and a subject sequence, also referred to as a global sequence alignment, can be determined using the FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App. Biosci. 6:237-245 (1990)). In a sequence alignment the query and subject sequences are both DNA sequences.
- RNA sequence can be compared by converting U's to T's.
- the result of said global sequence alignment is expressed as percent identity.
- the percent identity is corrected by calculating the number of bases of the query sequence that are 5' and 3' of the subject sequence, which are not matched/aligned, as a percent of the total bases of the query sequence. Whether a nucleotide is matched/aligned is determined by results of the FASTDB sequence alignment.
- This percentage is then subtracted from the percent identity, calculated by the above FASTDB program using the specified parameters, to arrive at a final percent identity score.
- This corrected score is what is used for the purposes of the present mvention. Only bases outside the 5' and 3' bases of the subject sequence, as displayed by the FASTDB alignment, which are not matched/aligned with the query sequence, are calculated for the purposes of manually adjusting the percent identity score.
- a 90 base subject sequence is aligned to a 100 base query sequence to determine percent identity.
- the deletions occur at the 5' end of the subject sequence and therefore, the FASTDB alignment does not show a matched/alignment of the first 10 bases at 5' end.
- the 10 unpaired bases represent 10% of the sequence (number of bases at the 5' and 3' ends not matched/total number of bases in the query sequence) so 10% is subtracted from the percent identity score calculated by the FASTDB program. If the remaining 90 bases were perfectly matched the final percent identity would be 90%.
- a 90 base subject sequence is compared with a 100 base query sequence.
- deletions are internal deletions so that there are no bases on the 5' or 3' of the subject sequence which are not matched/aligned with the query.
- percent identity calculated by FASTDB is not manually corrected.
- bases 5' and 3' of the subject sequence which are not matched/aligned with the query sequence are manually corrected for. No other manual corrections are to be made for the purposes of the present invention.
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Abstract
Priority Applications (3)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
EP01912649A EP1261380A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
AU2001241404A AU2001241404A1 (en) | 2000-01-31 | 2001-01-17 | Nucleic acids, proteins and antibodies |
US09/908,711 US20020045230A1 (en) | 2000-08-14 | 2001-07-20 | Nucleic acids, proteins, and antibodies |
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PCT/US2001/001343 WO2001055323A2 (fr) | 2000-01-31 | 2001-01-17 | Acides ncleiques, proteines et anticorps |
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PCT/US2001/001338 WO2001055367A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et antigenes |
PCT/US2001/001335 WO2001055319A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
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PCT/US2001/001315 WO2001055311A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001317 WO2001055201A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
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PCT/US2001/001336 WO2001055204A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001313 WO2001055200A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001332 WO2001055318A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
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PCT/US2001/001342 WO2001059064A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001311 WO2001055309A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001358 WO2001055163A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines, et anticorps |
PCT/US2001/001330 WO2001055447A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucléiques, proteines et anticorps |
PCT/US2001/001354 WO2001057182A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
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PCT/US2001/001321 WO2001055312A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001308 WO2001055364A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucléiques, protéines et anticorps |
PCT/US2001/001341 WO2001055322A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
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PCT/US2001/001351 WO2001055355A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001340 WO2001055321A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001309 WO2001055308A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001333 WO2001055448A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001348 WO2001055368A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001343 WO2001055323A2 (fr) | 2000-01-31 | 2001-01-17 | Acides ncleiques, proteines et anticorps |
PCT/US2001/001355 WO2001055207A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
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PCT/US2001/001327 WO2001055203A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
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PCT/US2001/001314 WO2001055310A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001326 WO2001055315A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines, et anticorps |
PCT/US2001/001316 WO2001054473A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001325 WO2001055202A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001359 WO2001055328A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001301 WO2001055303A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001302 WO2001055304A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001240 WO2001055302A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001353 WO2001055206A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001352 WO2001055327A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001356 WO2001055173A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001349 WO2001054474A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001338 WO2001055367A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et antigenes |
PCT/US2001/001335 WO2001055319A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001344 WO2001055324A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001315 WO2001055311A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001317 WO2001055201A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001306 WO2001055307A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001336 WO2001055204A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001313 WO2001055200A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001332 WO2001055318A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001357 WO2001055208A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001342 WO2001059064A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001311 WO2001055309A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001358 WO2001055163A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines, et anticorps |
PCT/US2001/001330 WO2001055447A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucléiques, proteines et anticorps |
PCT/US2001/001354 WO2001057182A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001310 WO2001055387A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001321 WO2001055312A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001308 WO2001055364A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucléiques, protéines et anticorps |
PCT/US2001/001341 WO2001055322A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001239 WO2001055301A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001328 WO2001055316A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001350 WO2001055350A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001324 WO2001055314A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001337 WO2001055205A1 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001345 WO2001055325A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
PCT/US2001/001339 WO2001055320A2 (fr) | 2000-01-31 | 2001-01-17 | Acides nucleiques, proteines et anticorps |
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CA (37) | CA2395666A1 (fr) |
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- 2001-01-17 AU AU2001241406A patent/AU2001241406A1/en not_active Abandoned
- 2001-01-17 WO PCT/US2001/001339 patent/WO2001055320A2/fr not_active Application Discontinuation
- 2001-02-05 AU AU4313701A patent/AU4313701A/xx active Pending
- 2001-02-08 AU AU4141101A patent/AU4141101A/xx active Pending
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