CA2447935A1 - Novel antibodies that bind to antigenic polypeptides, nucleic acids encoding the antigens, and methods of use - Google Patents

Abstract

Disclosed herein are nucleic acid sequences that encode polypeptides. Also disclosed are antibodies, which immunospecifically-bind to the polypeptide, as well as derivatives, variants, mutants, or fragments of the aforementioned polypeptide, polynucleotide, or antibody. The invention further discloses therapeutic, diagnostic and research methods for diagnosis, treatment, and prevention of disorders involving any one of these novel human nucleic acids , polypeptides, or antibodies, or fragments thereof.

Description

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NOVEL ANTIBODIES THAT BIND TO ANTIGENIC
POLYPEPTIDES, NUCLEIC ACIDS ENCODING THE ANTIGENS, AND METHODS OF USE
FIELD OF THE INVENTION
The present invention relates to novel antibodies that bind immunospecifically to antigenic polypeptides, wherein the polypeptides have characteristic properties related to biochemical or physiological responses in a cell, a tissue, an organ or an organism. The novel polypeptides are gene products of novel genes, or are specified biologically active fragments or derivatives thereof. Methods of use of the antibodies encompass procedures for diagnostic and prognostic assay of the polypeptides, as well as methods of treating diverse pathological conditions.

BACKGROUND OF THE INVENTION
Eukaryotic cells are characterized by biochemical and physiological processes which under normal conditions are exquisitely balanced to achieve the preservation and propagation of the cells. When such cells are components of multicellular organisms such as vertebrates, or more particularly organisms such as mammals, the regulation of the biochemical and physiological processes involves intricate signaling pathways.
Frequently, such signaling pathways involve extracellulax signaling proteins, cellular receptors that bind the signaling proteins, and signal transducing components located within the cells.
Signaling proteins may be classified as endocrine effectors, paracrine effectors or autocrine effectors. Endocrine effectors are signaling molecules secreted by a given organ into the circulatory system, which are then transported to a distant target organ or tissue.
The target cells include the receptors for the endocrine effector, and when the endocrine effector binds, a signaling cascade is induced. Paracrine effectors involve secreting cells and receptor cells in close proximity to each other, for example two different classes of cells in the same tissue or organ. One class of cells secretes the paracrine effector, which then reaches the second class of cells, for example by diffusion through the extracellular fluid. The second class of cells contains the receptors for the paracrine effector; binding of the effector results in induction of the signaling cascade that elicits the corresponding biochemical or physiological effect. Autocrine effectors are highly analogous to paracrine effectors, except that the same cell type that secretes the autocrine effector also contains the receptor. Thus the autocrine effector binds to receptors on the same cell, or on identical neighboring cells. The binding process then elicits the characteristic biochemical or physiological effect.
Signaling processes may elicit a variety of effects on cells and tissues including by way of nonlimiting example induction of cell or tissue proliferation, suppression of growth or proliferation, induction of differentiation or maturation of a cell or tissue, and suppression of differentiation or maturation of a cell or tissue.
Many pathological conditions involve dysregulation of expression of important effector proteins. In certain classes of pathologies the dysregulation is manifested as elevated or excessive synthesis and secretion of protein effectors. In a clinical setting a subject may be suspected of suffering from a condition brought on by elevated or excessive levels of a protein effector of interest.

Antibodies are multichain proteins that bind specifncally to a gmen antigen, and bind poorly, or not at all, to substances deemed not to be cognate antigens.
Antibodies are comprised of two short chains termed light chains and two long chains termed heavy chains. These chains are constituted of immunoglobulin domains, of which generally there are two classes: one variable domain per chain, one constant domain in light chains, and three or more constant domains in heavy chains. The antigen-specific portion of the immunoglobulin molecules resides in the variable domains; the variable domains of one light chain and one heavy chain associate with each other to generate the antigen-binding moiety. Antibodies that bind immunospecifically to a cognate or target antigen bind with high affinities. Accordingly, they are useful in assaying specifically for the presence of the antigen in a sample. In addition, they have the potential of inactivating the activity of the antigen.
Therefore there is a need to assay for the level of a protein effector of interest in a biological sample from such a subject, and to compare this level with that characteristic of a nonpathological condition. In particular, there is a need for such an assay based on the use of an antibody that binds immunospecifically to the antigen. There fm-ther is a need to inhibit the activity of the protein effector in cases where a pathological condition arises from elevated or excessive levels of the effector based on the use of an antibody that binds immunospecifically to the effector. Thus, there is a need for the antibody as a product of manufacture. There further is a need for a method of treatment of a pathological condition brought on by an elevated or excessive level of the protein effector of interest based on administering the antibody to the subject.
SUMMARY OF THE INVENTION
The invention is based in part upon the discovery of nucleic acid sequences encoding novel polypeptides. The novel nucleic acids and polypeptides are referred to herein as NOVX, or NOV l, NOV2, NOV3, etc., nucleic acids and polypeptides.
These nucleic acids and polypeptides, as well as derivatives, homologs, analogs and fragments thereof, will hereinafter be collectively designated as "NOVX" nucleic acid or polypeptide sequences.
In one aspect, the invention provides an isolated polypeptide comprising a mature form of a NOVX amino acid. The polypeptide can be, for example, a NOVX amino acid sequence or a variant of a NOVX amino acid sequence, wherein any amino acid specified in the chosen sequence is changed to a different amino acid, provided that no more than 15% of the amino acid residues in the sequence are so cha~igea. We-invention also includes fragments of any of NOVX polypeptides. In another aspect, the invention also includes an isolated nucleic acid that encodes a NOVX polypeptide, or a fragment, homolog, analog or derivative thereof.
Also included in the invention is a NOVX polypeptide that is a naturally occurring variant of a NOVX sequence. In one embodiment, the variant includes an amino acid sequence that is the translation of a nucleic acid sequence differing by a single nucleotide from a NOVX nucleic acid sequence. In another embodiment, the NOVX polypeptide is a variant polypeptide described therein, wherein any amino acid specified in the chosen sequence is changed to provide a conservative substitution.
In another aspect, invention provides a method for determining the presence or amount of the NOVX polypeptide in a sample by providing a sample; introducing the sample to an antibody that binds immunospecifically to the polypeptide; and determining the presence or amount of antibody bound to the NOVX polypeptide, thereby determining the presence or amount of the NOVX polypeptide in the sample.
In yet another aspect, the invention includes a method for deternuning the presence of or predisposition to a disease associated with altered levels of a NOVX
polypeptide in a mammalian subject by measuring the level of expression of the polypeptide in a sample from the first mammalian subject; and comparing the amount of the polypeptide in the sample of the first step to the amount of the polypeptide present in a control sample from a second mammalian subject known not to have, or not to be predisposed to, the disease. An alteration in the expression level ofthe polypeptide in the first subject as compared to the control sample indicates the presence of or predisposition to the disease.
In another aspect, the invention includes pharmaceutical compositions that include therapeutically- or prophylactically-effective amounts of a therapeutic and a pharmaceutically-acceptable carrier. The therapeutic can be, e.g., a NOVX
nucleic acid, a NOVX polypeptide, or an antibody specific for a NOVX polypeptide. In a further aspect, the invention includes, in one or more containers, a therapeutically- or prophylactically-effective amount of this pharmaceutical composition.
In still another aspect, the invention provides the use of a therapeutic in the manufacture of a medicament for treating a syndrome associated with a human disease that is associated with a NOVX polypeptide.
In a further aspect, the invention provides a method for modulating the activity of a NOVX polypeptide by contacting a cell sample expressing the NOVX polypeptide with antibody that binds the NOVX polypeptide in an amount suiiicierit-to moautate the activity of the polypeptide.
The invention also includes an isolated nucleic acid that encodes a NOVX
polypeptide, or a fragment, homolog, analog or derivative thereof. In a preferred embodiment, the nucleic acid molecule comprises the nucleotide sequence of a naturally occurring allelic nucleic acid variant. In another embodiment, the nucleic acid encodes a variant polypeptide, wherein the variant polypeptide has the polypeptide sequence of a naturally occurring polypeptide variant. In another embodiment, the nucleic acid molecule differs by a single nucleotide from a NOVX nucleic acid sequence. In one embodiment, the NOVX nucleic acid molecule hybridizes under stringent conditions to the nucleotide sequence selected from the group consisting of SEQ ID NO: 2n-1, wherein n is an integer between l and 73, or a complement of the nucleotide sequence. In one embodiment, the invention provides a nucleic acid molecule wherein the nucleic acid includes the nucleotide sequence of a naturally occurring allelic nucleic acid variant.
Also included in the invention is a vector containing one or more of the nucleic acids described herein, and a cell containing the vectors or nucleic acids described herein.
The invention is also directed to host cells transformed with a vector comprising any of the nucleic acid molecules described above.
In yet another aspect, the invention provides for a method for determining the presence or amount of a nucleic acid molecule in a sample by contacting a sample with a probe that binds a NOVX nucleic acid and determining the amount of the probe that is bound to the NOVX nucleic acid. For example the NOVX nucleic may be a marker for cell or tissue type such as a cell or tissue type that is cancerous.
In yet a further aspect, the invention provides a method for determining the presence of or predisposition to a disease associated with altered levels of a nucleic acid molecule in a first mammalian subject, wherein an alteration in the level of the nucleic acid in the first subject as compared to the control sample indicates the presence of or predisposition to the disease.
The invention further provides an antibody that binds immunospecifically to a NOVX polypeptide. The NOVX antibody may be monoclonal, humanized, or a fully human antibody. Preferably, the antibody has a dissociation constant for the binding of the NOVX polypeptide to the antibody less than 1 x 10-9 M. More preferably, the NOVX
antibody neutralizes the activity of the NOVX polypeptide.

In a further aspect, the invention provides for the use of a t~lierapeutic in the manufacture of a medicament for treating a syndrome associated with a human disease, associated with a NOVX polypeptide. Preferably the therapeutic is a NOVX
antibody.
In yet a further aspect, the invention provides a method of treating or preventing a NOVX-associated disorder, a method of treating a pathological state in a mammal, and a method of treating or preventing a pathology associated with a polypeptide by administering a NOVX antibody to a subject in an amount sufficient to treat or prevent the disorder.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In the case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be limiting.
Other features and advantages of the invention will be apparent from the following detailed description and claims.
DETAILED DESCRIPTION OF THE INVENTION
The present invention provides novel nucleotides and polypeptides encoded thereby. Included in the invention are the novel nucleic acid sequences, their encoded polypeptides, antibodies, and other related compunds. The sequences are collectively referred to herein as "NOVX nucleic acids" or "NOVX polynucleotides" and the corresponding encoded polypeptides are referred to as "NOVX polypeptides" or "NOVX
proteins." Unless indicated otherwise, "NOVX" is meant to refer to any of the novel sequences disclosed herein. Table 1 provides a summary of the NOVX nucleic acids and their encoded polypeptides.

TABLE 1. NOVX Polynucleotide and Polypeptide Sequences and Corresponding SEQ ID Numbers SEQ
Internal IdentificationID SEQ ID Homology NO NO
(nucleic(polypeptide) acid la CG100653-O1 1 2 Cadherin Associated Protein-like 2a CG100689-O1 3 4 Leucine Rich Repeat-like 3a CG100760-O1 5 6 Leucine Rich Repeat-like 4a 7 8 Leukocyte Surface Antigen CG 100851-02 CD53-like 5a CG101068-O1 9 10 Claudin-9-like 6a 11 12 Integral Membrane Protein CG 2 01231-O IsOform 1 2-like 6b 13 14 Integral Membrane Protein CG 101231-02 Isoform 2-like 7a CG101362-Oi 15 16 Prion Protein-like 8a 17 18 Von Willebrand Domain CG101458-O1 Containin Protein-like 9a CG101475-O1 19 20 Plasma Membrane Protein-like 9b CG 101475-02 21 22 Plasma Membrane Protein-like IOa CG101772-01 23 24 RAGE-like 11 a CG 102532-O1 25 26 Emerin-like 12a CG102575-O1 27 28 ATPase-like 12b CG102575-02 29 30 ATPase-like 13a 31 32 Mat8 (Mammary Tumor CG 102615-01 8 kDa) Protein-like 13b 33 34 MatB (Mammary Tumor CG 102615-04 8 kDa) Protein-like 14a CG102646-01 35 36 High Affinity Proline Permease-like 15a CG102878-Ol 37 38 Transmembrane-like 15b CG102878-02 39 40 Transmembrane-like 16a CG 103459-O 1 41 42 Pe tide/Histidine Transporter-like 17a CG104210-O1 43 44 Type III Membrane Protein-like 17b CG104210-02 45 46 Type III Membrane Protein-like 17c 272249075 47 48 Type III Membrane Protein-like 18a CG104251-Ol 49 50 Type III Membrane Protein-like 19a 51 52 Phospholipid-Transporting CG 104934-O1 ATPase IH-like 20a 53 54 Meningioma-Expressed CG105463-OI Antigen 6/11 (MEA6) (MEAI1)-like 20b 55 56 Meningioma-Expressed CG 105463-02 Antigen 6/ 1 I (MEA6) (MEA
11 )-like 21a CG105491-O1 57 58 Serine Protease-like 22a CG105954-O1 59 60 Neurofascin Precursor-like 23a CG105963-O1 61 62 Cadherin-like 24a CG 105973-O1 63 64 Integrin A1 ha 8-like 24b CG 105973-02 65 66 Inte rin Alpha 8-like 25a CG106915-O1 67 68 No o Rece for Isoform-1-like 26a CG 106924-O I 69 70 Nogo Receptor Isoform-2-Iike 26b 210062144 71 72 Nogo Receptor Isoform-2-like 27a CG106942-O1 73 74 NRAMP-like Membrane Protein 28a 75 76 Syntaxin Domain Containing CG 107513-01 Protein-like 29a CG107533-02 77 78 Tumor Necrosis Factor-like 30a CG107562-O1 ~ 79 80 Leucine-Rich Repeat Type III

Transmembrane-like 30b 81 82 Leucine-Rich Repeat Type III

CG 107562-02 Transmembrane-1 ike 30c 83 84 Leucine-Rich Repeat Type 11I

210086373 Transmembrane-like 30d 85 86 Leucine-Rich Repeat Type III

210086403 Transmembrane-like 30e 87 88 Leucine-Rich Repeat Type II1 210086422 Transmembrane-like 31 a CG 108184-O1 89 90 Transmembrane Protein Tm7-like 3I b CG 108184-02 91 92 Transmembrane Protein Tm7-like 31c CG108184-03 93 94 Transmembrane Protein Tm7-like 32a 95 96 Sialic Acid Binding CG 108238-O1 Immunoglobulin-like 33a CG108695-O1 97 98 OB binding rotein (SIGLEC)-like 34a CG109505-O1 99 100 Aldehyde Dehydro enase-like 35a 101 102 Latent Transforming Growth Factor CG109742-O1 Beta Bindin Protein 3-like 35b 103 104 Latent Transforming Growth Factor 207639410 Beta Bindin Protein 3-like 35c 105 106 Latent Transforming Growth Factor 207639427 Beta Binding Protein 3-like 35d 107 108 Latent Transforming Growth Factor 207639438 Beta Bindin~ Protein 3-like 35e 109 110 Latent Transforming Growth Factor 207639448 Beta Bindin Protein 3-like 36a CG109844-O1 11 112 C4B-Binding Protein-like I

37a CG110014-02 113 114 Colon Carcinoma kinase 4-like 37b CG 110014-03 115 1 I6 Colon Carcinoma kinase 4-like 37c CGl 10014-04 117 118 Colon Carcinoma kinase 4-like 38a CG110187-O1 119 120 AI ha Cl-like Protocadherin 38b CG110I87-03 121 122 Alpha C1-like Protocadherin 39a 123 124 Disintegrin-like l Metalloprotease (Reprolysin Type) with CG110205-O1 Tlu-ombospondin Type I Motif like 39b 125 126 Disintegrin-like /
Metalloprotease (Reprolysin Type) with CG110205-02 Thrombos ondin Type I Motif like 39c 127 128 Disintegrin-Iike l Metalloprotease (Reprolysin Type) with 207756942 Thrombospondin Type I Motif lilee 39d 129 130 Disintegrin-like /
Metalloprotease (Reprolysin Type) with 207756946 Thrombospondin Type I Motif like 39e 131 132 Disintegrin-like /
Metalloprotease (Reprolysin Type) with 207756950 Thrombospondin Type I Motif like 39f 133 134 Disintegrin-like l Metalloprotease (Reprolysin Type) with 207756966 Thrombospondin Type I Motif like 40a CGII0242-O1 135 136 Ebnerin-like 40b 207728344 137 138 Ebnerin-like 40c 207728348 139 140 Ebnerin-like 40d 207728354 141 142 Ebnerin-like 40e 207728365 143 144 Ebnerin-like 41a 145 146 Endosomal Glycoprotein CG99598-O 1 Precursor-like Table 1 indicates the homology of NOVX polypeptides ~o known protein families.
Thus, the nucleic acids and polypeptides, antibodies and related compounds according to the invention corresponding to a NOVX as identified in column 1 of Table 1 will be useful in therapeutic and diagnostic applications implicated in, for example, pathologies and disorders associated with the known protein families identified in column 5 of Table 1.
NOVX nucleic acids and their encoded polypeptides are useful in a variety of applications and contexts. The various NOVX nucleic acids and polypeptides according to the invention are useful as novel members of the protein families according to the presence of domains and sequence relatedness to previously described proteins.
Additionally, NOVX nucleic acids and polypeptides can also be used to identify proteins that are members of the family to which the NOVX polypeptides belong.
Consistent with other known members of the family of proteins, identified in column 5 of Table l, the NOVX polypeptides of the present invention show homology to, and contain domains that are characteristic of, other members of such protein families. Details of the sequence relatedness and domain analysis for each NOVX are presented in Example A.
The NOVX nucleic acids and polypeptides can also be used to screen for molecules, which inhibit or enhance NOVX activity or function. Specifically, the nucleic acids and polypeptides according to the invention may be used as targets for the identification of small molecules that modulate or inhibit diseases associated with the protein families listed in Table 1.
The NOVX nucleic acids and polypeptides are also useful for detecting specific cell types. Details of the expression analysis for each NOVX are presented in Example C.
Accordingly, the NOVX nucleic acids, polypeptides, antibodies and related compounds according to the invention will have diagnostic and therapeutic applications in the detection of a variety of diseases with differential expression in normal vs. diseased tissues, e.g.
detection of a variety of cancers.
Additional utilities for NOVX nucleic acids and polypeptides according to the invention are disclosed herein.
NOVX clones NOVX nucleic acids and their encoded polypeptides are useful in a variety of applications and contexts. The various NOVX nucleic acids and polypeptides according to the invention are useful as novel members of the protein families according to the presence of domains and sequence relatedness to previously descrilie-d prot~tris.
Acrctitionally;
NOVX nucleic acids and polypeptides can also be used to identify proteins that are members of the family to which the NOVX polypeptides belong.
The NOVX genes and their corresponding encoded proteins are useful for preventing, treating or ameliorating medical conditions, e.g., by protein or gene therapy.
Pathological conditions can be diagnosed by determining the amount of the new protein in a sample or by determining the presence of mutations in the new genes.
Specific uses are described for each of the NOVX genes, based on the tissues in which they are most highly expressed. Uses include developing products for the diagnosis or treatment of a variety of diseases and disorders.
The NOVX nucleic acids and proteins of the invention are useful in potential diagnostic and therapeutic applications and as research tools. These include serving as a specific or selective nucleic acid or protein diagnostic and/or prognostic marker, wherein the presence or amount of the nucleic acid or the protein are to be assessed, as well as potential therapeutic applications such as the following: (i) a protein therapeutic, (ii) a small molecule drug target, (iii) an antibody target (therapeutic, diagnostic, drug targeting/cytotoxic antibody), (iv) a nucleic acid useful in gene therapy (gene delivery/gene ablation), and (v) a composition promoting tissue regeneration in vitro and in vivo (vi) a biological defense weapon.
In one specific embodiment, the invention includes an isolated polypeptide comprising an amino acid sequence selected from the group consisting of: (a) a mature form of the amino acid sequence selected from the group consisting of SEQ ID
NO: 2n, wherein n is an integer between l and 73; (b) a variant of a mature form of the amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 73, wherein any amino acid in the mature form is changed to a different amino acid, provided that no more than 15% of the amino acid residues in the sequence of the mature form are so changed; (c) an amino acid sequence selected from the group consisting of SEQ ID NO: Zn, wherein n is an integer between 1 and 73; (d) a variant of the amino acid sequence selected from the group consisting of SEQ ID N0:2n, wherein n is an integer between 1 and 73 wherein any amino acid specified in the chosen sequence is changed to a different amino acid, provided that no more than 15% of the amino acid residues in the sequence are so changed; and (e) a fragment of any of (a) through (d).
In another specific embodiment, the invention includes an isolated nucleic acid molecule comprising a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence selected from the group consisting of (a)"a mature torrii o~-the amino acid sequence given SEQ ID NO: 2n, wherein n is an integer between 1 and 73; (b) a variant of a mature form of the amino acid sequence selected from the group consisting of SEQ ID
NO: 2n, wherein n is an integer between 1 and 73 wherein any amino acid in the mature form of the chosen sequence is changed to a different amino acid, provided that no more than 15% of the amino acid residues in the sequence of the mature form are so changed; (c) the amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 73; (d) a variant of the amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between I and 73, in which any amino acid specified in the chosen sequence is changed to a different amino acid, provided that no more than 15% of the amino acid residues in the sequence are so changed;
(e) a nucleic acid fragment encoding at least a portion of a polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 73 or any variant of said polypeptide wherein any amino acid of the chosen sequence is changed to a different amino acid, provided that no more than 10% of the amino acid residues in the sequence are so changed; and (f) the complement of any of said nucleic acid molecules.
In yet another specific embodiment, the invention includes an isolated nucleic acid molecule, wherein said nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of: (a) the nucleotide sequence selected from the group consisting of SEQ ID NO: 2n-l, wherein n is an integer between 1 and 73; (b) a nucleotide sequence wherein one or more nucleotides in the nucleotide sequence selected from the group consisting of SEQ ID NO: 2n-l, wherein n is an integer between l and 73 is changed from that selected from the group consisting of the chosen sequence to a different nucleotide provided that no more than 15% of the nucleotides are so changed; (c) a nucleic acid fragment of the sequence selected from the group consisting of SEQ ID NO:
2n-1, wherein n is an integer between 1 and 73; and (d) a nucleic acid fragment wherein one or more nucleotides in the nucleotide sequence selected from the group consisting of SEQ ID NO: 2n-1, wherein n is an integer between l and 73 is changed from that selected from the group consisting of the chosen sequence to a different nucleotide provided that no more than 15% of the nucleotides are so changed.

NOVX Nucleic Acids and Polypeptides One aspect of the invention pertains to isolated nucleic acid molecules that encode NOVX polypeptides or biologically active portions thereof. Also included in the invention are nucleic acid fragments suff cient for use as hybridization probes to identify NOVX-encoding nucleic acids (e.g., NOVX mRNA's) and fragments for use as PCR
primers for the amplification and/or mutation of NOVX nucleic acid molecules. As used herein, the term "nucleic acid molecule" is intended to include DNA molecules (e.g., cDNA
or genomic DNA), RNA molecules (e.g., mRNA), analogs of the DNA or RNA generated using nucleotide analogs, and derivatives, fragments and homologs thereof. The nucleic I O acid molecule may be single-stranded or double-stranded, but preferably is comprised double-stranded DNA. ' -A NOVX nucleic acid can encode a mature NOVX polypeptide. As used herein, a "mature" form of a polypeptide or protein disclosed in the present invention is the product of a naturally occurring polypeptide or precursor form or proprotein. The naturally occurring polypeptide, precursor or proprotein includes, by way of nonlimiting example, the full-length gene product encoded by the corresponding gene. Alternatively, it may be defined as the polypeptide, precursor or proprotein encoded by an ORF
described herein.
The product "mature" form arises, again by way of nonlimiting example, as a result of one or more naturally occurring processing steps as they may take place within the cell, or host cell, in which the gene product arises. Examples of such processing steps leading to a "mature" form of a polypeptide or protein include the cleavage of the N-terminal methionine residue encoded by the initiation codon of an ORF, or the proteolytic cleavage of a signal peptide or leader sequence. Thus a mature form arising from a precursor polypeptide or protein that has residues 1 to N, where residue 1 is the N-terminal methionine, would have residues 2 through N remaining after removal of the N-terminal methionine. Alternatively, a mature form arising from a precursor polypeptide or protein having residues 1 to N, in which an N-terminal signal sequence from residue 1 to residue M
is cleaved, would have the residues from residue M+1 to residue N remaining.
Further as used herein, a "mature" form of a polypeptide or protein may arise from a step of post-translational modification other than a proteolytic cleavage event. Such additional processes include, by way of non-limiting example, glycosylation, myristylation or phosphorylation. In general, a mature polypeptide or protein may result from the operation of only one of these processes, or a combination of any of them.

The term "probes", as utilized herein, refers to nucleic acid sequences of vamable length, preferably between at least about 10 nucleotides (nt), 100 nt, or as many as approximately, e.g., 6,000 nt, depending upon the specific use. Probes are used in the detection of identical, similar, or complementary nucleic acid sequences.
Longer length probes are generally obtained from a natural or recombinant source, are highly specific, and much slower to hybridize than shorter-length oligomer probes. Probes may be single- or double-stranded and designed to have specificity in PCR, membrane-based hybridization technologies, or ELISA-like technologies.
The term "isolated" nucleic acid molecule, as utilized herein, is one, which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid. Preferably, an "isolated" nucleic acid is free of sequences which naturally flank the nucleic acid (i. e., sequences located at the 5'- and 3'-termini of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived. Fpr example, in various embodiments, the isolated NOVX nucleic acid molecules can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cellltissue from which the nucleic acid is derived (e.g., brain, heart, Liver, spleen, etc.). Moreover, an "isolated" nucleic acid molecule, such as a cDNA molecule, can be substantially free of other cellular material or culture medium when produced by recombinant techniques, or of chemical precursors or other chemicals when chemically synthesized.
A nucleic acid molecule of the invention, e.g., a nucleic acid molecule having the nucleotide sequence of SEQ ID N0:2n-1, wherein n is an integer between 1-73, or a complement of this aforementioned nucleotide sequence, can be isolated using standard molecular biology techniques and the sequence information provided herein.
Using all or a portion of the nucleic acid sequence of SEQ ID N0:2h-l, wherein n is an integer between 1-73, as a hybridization probe, NOVX molecules can be isolated using standard hybridization and cloning techniques (e.g., as described in Sambrook, et al., (eds.), MOLECULAR CLONING: A LABORATORY MANUAL 2°a Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989; and Ausubel, et al., (eds.), CURRENT
PROTOCOLS IN
3O MOLECULAR BIOLOGY, John Wiley & Sons, New York, NY, 1993.) A nucleic acid of the invention can be amplified using cDNA, mRNA or alternatively, genomic DNA, as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques. The nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis.

Furthermore, oligonucleotides corresponding to NOVX~nuc~eotnte sequences can be prepared by standard synthetic techniques, e.g., using an automated DNA
synthesizer.
As used herein, the term "oligonucleotide" refers to a series of linked nucleotide residues, which oligonucleotide has a sufficient number of nucleotide bases to be used in a S PCR reaction. A short oligonucleotide sequence may be based on, or designed from, a genomic or cDNA sequence and is used to amplify, confirm, or reveal the presence of an identical, similar or complementary DNA or RNA in a particular cell or tissue.
Oligonucleotides comprise portions of a nucleic acid sequence having about 10 nt, SO nt, or 100 nt in length, preferably about 15 nt to 30 ntin length. In one embodiment of the invention, an oligonucleotide comprising a nucleic acid molecule less than 100 nt in length would further comprise at least 6 contiguous nucleotides of SEQ ID N0:2n-1, wherein n is an integer between 1-73, or a complement thereof. Oligonucleotides may be chemically synthesized and may also be used as probes.
In another embodiment, an isolated nucleic acid molecule of the invention 1 S comprises a nucleic acid molecule that is a complement of the nucleotide sequence SEQ ID
N0:2~c-l, wherein n is an integer between 1-73, or a portion of this nucleotide sequence (e.g., a fragment that can be used as a probe or primer or a fragment encoding a biologically-active portion of a NOVX polypeptide). A nucleic acid molecule that is complementary to the nucleotide sequence of SEQ ID N0:2n-I, wherein ~ is an integer between 1-73, is one that is sufficiently complementary to the nucleotide sequence of SEQ
ID N0:2n-l, wherein n is an integer between 1-73, that it can hydrogen bond with little or no mismatches to the nucleotide sequence of SEQ ID N0:2n-l, wherein h is an integer between 1-73, thereby forming a stable duplex.
As used herein, the term "complementary" refers to Watson-Crick or Hoogsteen 2S base pairing between nucleotides units of a nucleic acid molecule, and the term "binding"
means the physical or chemical interaction between two polypeptides or compounds or associated polypeptides or compounds or combinations thereof. Binding includes ionic, non-ionic, van der Waals, hydrophobic interactions, and the like. A physical interaction can be either direct or indirect. Indirect interactions may be through or due to the effects of another polypeptide or compound. Direct binding refers to interactions that do not take place through, or due to, the effect of another polypeptide or compound, but instead are without other substantial chemical intermediates.
Fragments provided herein are defined as sequences of at least 6 (contiguous) nucleic acids or at least 4 (contiguous) amino acids, a length sufficient to allow for specific hybridization in the case of nucleic acids or for specific recognition o~ an epitope in the case of amino acids, respectively,-and are at most some portion less than a full length sequence. Fragments may be derived from any contiguous portion of a nucleic acid or amino acid sequence of choice. Derivatives are nucleic acid sequences or amino acid sequences formed from the native compounds either directly or by modification or partial substitution. Analogs are nucleic acid sequences or amino acid sequences that have a structure similar to, but not identical to, the native compound but differs from it in respect to certain components or side chains. Analogs may be synthetic or from a different evolutionary origin and may have a similar or opposite metabolic activity compared to wild type. Homologs are nucleic acid sequences or amino acid sequences of a particular gene that are derived from different species.
A full-length NOVX clone is identified as containing an ATG translation start colon and an in-frame stop colon. Any disclosed NOVX nucleotide sequence lacking an ATG start colon therefore encodes a truncated C-terminal fragment of the respective NOVX polypeptide, and requires that the corresponding full-length cDNA extend in the 5' direction of the disclosed sequence. Any disclosed NOVX nucleotide sequence lacking an in-frame stop colon similarly encodes a truncated N-terminal fragment of the respective NOVX polypeptide, and requires that the corresponding full-length cDNA extend in the 3' direction of the disclosed sequence.
Derivatives and analogs may be full length or other than full length, if the derivative or analog contains a modified nucleic acid or amino acid, as described below.
Derivatives or analogs of the nucleic acids or proteins of the invention include, but are not limited to, molecules comprising regions that are substantially homologous to the nucleic acids or proteins of the invention, in various embodiments, by at least about 70%, 80%, or 95%
identity (with a preferred identity of 80-95°10) over a nucleic acid or amino acid sequence of identical size or when compared to an aligned sequence in which the alignment is done by a computer homology program known in the art, or whose encoding nucleic acid is capable of hybridizing to the complement of a sequence encoding the aforementioned proteins under stringent, moderately stringent, or low stringent conditions. See e.g.
Ausubel, et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley 8c Sons, New York, NY, 1993, and below.
A "homologous nucleic acid sequence" or "homologous amino acid sequence," or variations thereof, refer to sequences characterized by a homology at the nucleotide level or amino acid level as discussed above. Homologous nucleotide sequences encode those sequences coding for isoforms of NOVX polypeptides. -Isofoiins can be expressed in different tissues of the same organism as a result of, for example, alternative splicing of RNA. Alternatively, isoforms can be encoded by different genes. In the invention, homologous nucleotide sequences include nucleotide sequences encoding for a NOVX
polypeptide of species other than humans, including, but not limited to:
vertebrates, and thus can include, e.g., frog, mouse, rat, rabbit, dog, cat cow, horse, and other organisms.
Homologous nucleotide sequences also include, but are not limited to, naturally occurring allelic variations and mutations of the nucleotide sequences set forth herein.
A homologous nucleotide sequence does not, however, include the exact nucleotide sequence encoding human NOVX protein. Homologous nucleic acid sequences include those nucleic acid sequences that encode conservative amino acid substitutions (see below) in SEQ
ID
N0:2~-l, wherein h is an integer between 1-73, as well as a polypeptide possessing NOVX
biological activity. Various biological activities of the NOVX proteins are described below.
A NOVX polypeptide is encoded by the open reading frame ("ORF") of a NOVX
nucleic acid. An ORF corresponds to a nucleotide sequence that could potentially be translated into a polypeptide. A stretch of nucleic acids comprising an ORF is uninterrupted by a stop codon. An ORF that represents the coding sequence for a full protein begins with an ATG "start" codon and terminates with one of the three "stop"
codons, namely, TAA, TAG, or TGA. For the purposes of this invention, an ORF
may be any part of a coding sequence, with or without a start codon, a stop codon, or both. For an ORF to be considered as a good candidate for coding for a bona fide cellular protein, a minimum size requirement is often set, e.g., a stretch of DNA that would encode a protein of 50 amino acids or more.
The nucleotide sequences determined from the cloning of the human NOVX genes allows for the generation of probes and primers designed for use in identifying and/or cloning NOVX homologues in other cell types, e. g. from other tissues, as well as NOVX
homologues from other vertebrates. The probe/primer typically comprises substantially purified oligonucleotide. The oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12, 25, 50, 100, 150, 200, 250, 300, 350 or 400 consecutive sense strand nucleotide sequence of SEQ
ID NO:2n-l, wherein rz is an integer between 1-73; or an anti-sense strand nucleotide sequence of SEQ ID N0:2h-1, wherein ~ is an integer between 1-73; or of a naturally occurring mutant of SEQ ID NO:2n-l, wherein ~ is an integer between 1-73.

Probes based on the human NOVX nucleotide sequence's can be usea to etetect transcripts or genomic sequences encoding the same or homologous proteins. In various embodiments, the probe further comprises a label group attached thereto, e.g.
the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor.
Such probes can be used as a part of a diagnostic test kit for identifying cells or tissues which mis-express a NOVX protein, such as by measuring a level of a NOVX-encoding nucleic acid in a sample of cells from a subject e.g., detecting NOVX mRNA
levels or determining whether a genomic NOVX gene has been mutated or deleted.
"A polypeptide having a biologically-active portion of a NOVX polypeptide"
refers to polypeptides exhibiting activity similar, but not necessarily identical to, an activity of a polypeptide of the invention, including mature forms, as measured in a particular biological assay, with or without dose dependency. A nucleic acid fragment encoding a "biologically-active portion of NOVX" can be prepared by isolating a portion of SEQ ID N0:2n-1, wherein n is an integer between .l -73, that encodes a polypeptide having a NOVX
biological activity (the biological activities of the NOVX proteins are described below), expressing the encoded portion of NOVX protein (e.g., by recombinant expression i~ vitro) and assessing the activity of the encoded portion of NOVX.
NOVX Nucleic Acid and Polypeptide Variants The invention further encompasses nucleic acid molecules that differ from the 2Q nucleotide sequences of SEQ ID N0:2fz-l, wherein n is an integer between 1-73, due to degeneracy of the genetic code and thus encode the same NOVX proteins as that encoded by the nucleotide sequences of SEQ ID N0:2n-1, wherein ~ is an integer between 1-73. In another embodiment, an isolated nucleic acid molecule of the invention has a nucleotide sequence encoding a protein having an amino acid sequence of SEQ ID N0:2h, wherein n is an integer between 1-73.
In addition to the human NOVX nucleotide sequences of SEQ ID N0:2h-1, wherein ~ is an integer between 1-73, it will be appreciated by those skilled in the art that DNA
sequence polymorphisms that lead to changes in the amino acid sequences of the NOVX
polypeptides may exist within a population (e.g., the human population). Such genetic polymorphism in the NOVX genes may exist among individuals within a population due to natural allelic variation. As used herein, the terms "gene" and "recombinant gene" refer to nucleic acid molecules comprising an open reading frame (ORF) encoding a NOVX
protein, preferably a vertebrate NOVX protein. Such natural allelic variations can typically result in 1-5% variance in the nucleotide sequence of the NOVX genes. Any and all such nucleotide variations and resulting amino acid polymorphisms in the NOVX
polypeptides, which are the result of natural allelic variation and that do not alter the functional activity of the NOVX polypeptides, are intended to be within the scope of the invention.
Moreover, nucleic acid molecules encoding NOVX proteins from other species, and thus that have a nucleotide sequence that differs from any one of the human SEQ ID
N0:2h-1, wherein h is an integer between 1-73, are intended to be within the scope of the invention. Nucleic acid molecules corresponding to natural allelic variants and homologues of the NOVX cDNAs of the invention can be isolated based on their homology to the human NOVX nucleic acids disclosed herein using the human cDNAs, or a portion thereof, as a hybridization probe according to standard hybridization techniques under stringent hybridization conditions.
Accordingly, in another embodiment, an isolated nucleic acid molecule of the invention is at least 6 nucleotides in length and hybridizes under stringent conditions to the nucleic acid molecule comprising the nucleotide sequence of SEQ ID N0:2~c-l, wherein ~
is an integer between I-73. In another embodiment, the nucleic acid is at least 10, 25, 50, 100, 250, 500, 750, 1000, 1500, or 2000 or more nucleotides in length. In yet another embodiment, an isolated nucleic acid molecule of the invention hybridizes to the coding region. As used herein, the term "hybridizes under stringent conditions" is intended to describe conditions for hybridization and washing under which nucleotide sequences at least 60% homologous to each other typically remain hybridized to each other.
Homologs (i. e., nucleic acids encoding NOVX proteins derived from species other ' than human) or other related sequences (e.g., paralogs) can be obtained by low, moderate or high stringency hybridization with all or a portion of the particular human sequence as a probe using methods well known in the art for nucleic acid hybridization and cloning.
As used herein, the phrase "stringent hybridization conditions" refers to conditions under which a probe, primer or oligonucleotide will hybridize to its target sequence, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures than shorter sequences. Generally, stringent conditions are selected to be about 5 °C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength, pH and nucleic acid concentration) at which 50% of the probes complementary to the target sequence hybridize to the target sequence at equilibrium. Since the target sequences are generally present at excess, at Tm, 50% of the probes are occupied at equilitinurii. ' T'-ypical'Iy;"-Strut gent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30 °C for short probes, primers or oligonucleotides (e.g., 10 nt to 50 nt) and at least about 60 °C for longer probes, primers and oligonucleotides.
Stringent conditions may also be achieved with the addition of destabilizing agents, such as formamide.
Stringent conditions are known to those skilled in the art and can be found in Ausubel, et al., (eds.), CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley &
Sons, N.Y. (1989), 6.3.1-6.3.6. Preferably, the conditions are such that sequences at least about 65%, 70%, 75%, 85%, 90%, 95%, 98%, or 99% homologous to each other typically remain hybridized to each other. A non-limiting example of stringent hybridization conditions are hybridization in a high salt buffer comprising 6X SSC, 50 mM Tris-HCI (pH
7.5), 1 mM
EDTA, 0.02% PVP, 0.02% FicoII, 0.02% BSA, and 500 mg/ml denatured salmon sperm DNA at 65 °C, followed by one or more washes in 0.2X SSC, 0.01 % BSA at 50 °C. An isolated nucleic acid molecule of the invention that hybridizes under stringent conditions to any one of the sequences of SEQ ID N0:2n-1, wherein n is an integer between 1-73, corresponds to a naturally-occurring nucleic acid molecule. As used herein, a "naturally-occurring" nucleic acid molecule refers to an RNA or DNA molecule having a nucleotide sequence that occurs in nature (e.g., encodes a natural protein).
In a second embodiment, a nucleic acid sequence that is hybridizable to the nucleic acid molecule comprising the nucleotide sequence of SEQ ID N0:2n-l, wherein fZ
is an integer between 1-73, or fragments, analogs or derivatives thereof, under conditions of moderate stringency is provided. A non-limiting example of moderate stringency hybridization conditions axe hybridization in 6X SSC, SX Reinhardt's solution, 0.5% SDS
and 100 mg/ml denatured salmon sperm DNA at 55 °C, followed by one or more washes in 1X SSC, 0.1% SDS at 37 °C. Other conditions of moderate stringency that may be used are well-known within the art. See, e.g., Ausubel, et al. (eds.), 1993, CURRENT PROTOCOLS
IN MOLECULAR BIOLOGY, John Wiley & Sons, NY, and Krieger, I 990; GENE TRANSFER
AND EXPRESSION, A LABORATORY MANUAL, Stockton Press, NY.
In a third embodiment, a nucleic acid that is hybridizable to the nucleic acid molecule comprising the nucleotide sequences of SEQ ID NO:Zn-l, wherein n is an integer between 1-73, or fragments, analogs or derivatives thereof, under conditions of low stringency, is provided. A non-limiting example of low stringency hybridization conditions are hybridization in 35% formamide, 5X SSC, 50 mM Tris=HCI' (pT=I 7:5), 5- inM
EDTA, 0.02% PVP, 0.02% Ficoll, 0.2% BSA, 100 mg/m1 denatured salmon sperm DNA, IO%
(wt/volt) dextran sulfate at 40 °C, followed by one or more washes in 2X SSC, 25 mM
Tris-HCl (pH 7.4), 5 mM EDTA, and 0. I % SDS at 50 °C. Other conditions of low stringency that may be used are well known in the art (e.g., as employed for cross-species hybridizations). See, e.g., Ausubel, et al. (eds.), 1993, CURRENT PROTOCOLS IN
MOLECULAR BIOLOGY, John Wiley & Sons, NY, and Kriegler, 1990, GENE TRANSFER
AND
EXPRESSION, A LABORATORY MANUAL, Stockton Press, NY; Shilo and Weinberg, 1981.
Pt~oc Natl Acad Sci USA 78: 6789-6792.
Conservative Mutations In addition to naturally-occurring allelic variants of NOVX sequences that may exist in the population, the skilled artisan will further appreciate that changes can be introduced by mutation into the nucleotide sequences of SEQ ID N0:2~z-l, wherein h is an integer between 1-73, thereby leading to changes in the amino acid sequences of the encoded NOVX proteins, without altering the functional ability of said NOVX
proteins.
For example, nucleotide substitutions leading to amino acid substitutions at "non-essential"
amino acid residues can be made in the sequence of SEQ ID N0:2h, wherein h is an integer between I-73. A "non-essential" amino acid residue is a residue that can be altered from the wild-type sequences of the NOVX proteins without altering their biological activity, whereas an "essential" amino acid residue is required for such biological activity. For example, amino acid residues that are conserved among the NOVX proteins of the invention are particularly non-amenable to alteration. Amino acids for which conservative substitutions can be made are well-known within the art.
2S Another aspect of the invention pertains to nucleic acid molecules encoding NOVX
proteins that contain changes in amino acid residues that are not essential for activity. Such NOVX proteins differ in amino acid sequence from any one of SEQ ID NO:2h-l, wherein n is an integer between 1-73, yet retain biological activity. In one embodiment, the isolated nucleic acid molecule comprises a nucleotide sequence encoding a protein, wherein the protein comprises an amino acid sequence at least about 45% homologous to the amino acid sequences of SEQ ID N0:2~, wherein n is an integer between 1-73.
Preferably, the protein encoded by the nucleic acid molecule is at least about 60% homologous to SEQ ID
N0:2n, wherein v~ is an integer between 1-73; more preferably at least about 70%
homologous to SEQ ID N0:2n, wherein n is an integer between 1-73; still more preferably at least about 80% homologous to SEQ ID N0:2TZ, wherein ~ is an int'eger~~etween 1-73 even more preferably at least about 90% homologous to SEQ ID N0:2n, wherein to is an integer between 1-73; and most preferably at least about 95% homologous to SEQ
ID
N0:2n, wherein r~ is an integer between 1-73.
An isolated nucleic acid molecule encoding a NOVX protein homologous to the protein of SEQ ID N0:2~c, wherein n is an integer between 1-73, can be created by introducing one or more nucleotide substitutions, additions or deletions into the nucleotide sequence of SEQ ID N0:2n-1, wherein n is an integer between 1-73, such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein.
Mutations can be introduced into any of SEQ ID N0:2fz-1, wherein fZ is an integer between 1-73, by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Preferably, conservative amino acid substitutions are made at one or more predicted, non-essential amino acid residues. A "conservative amino acid substitution" is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined within the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolax side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, txyptophan, histidine).
Thus, a predicted non-essential amino acid residue in the NOVX protein is replaced with another amino acid residue from the same side chain family. Alternatively, in another embodiment, mutations can be introduced randomly along all or part of a NOVX coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for NOVX
biological activity to identify mutants that retain activity. Following mutagenesis of any one of SEQ ID N0:2rc-1, wherein n is an integer between 1-73, the encoded protein can be expressed by any recombinant technology known in the art and the activity of the protein can be determined.
The relatedness of amino acid families may also be determined based on side chain interactions. Substituted amino acids may be fully conserved "strong" residues or fully conserved "weak" residues. The "strong" group of conserved amino acid residues may be any one of the following groups: STA, NEQK, NHQK, NDEQ, QHRK, MILV, MILF, HY, FYW, wherein the single letter amino acid codes are grouped by those amino acids that may be substituted fox each other. Likewise, the "weak'j' group of conserved xesidues may be any one of the following: CSA, ATV, SAG, STNK, STPA, SGND, SNDEQK, NDEQHK, NEQHRK, HFY, wherein the letters within each group represent the single letter amino acid code.
In one embodiment, a mutant NOVX protein can be assayed for (i) the ability to form protein:protein interactions with other NOVX proteins, other cell-surface proteins, or biologically-active portions thereof, (ii) complex formation between a mutant NOVX
protein and a NOVX ligand; or (iii) the ability of a mutant NOVX protein to bind to an intracellular target protein or biologically-active portion thereof; (e.g.
avidin proteins).
In yet another embodiment, a mutant NOVX protein can be assayed for the ability to regulate a specific biological function (e.g., regulation of insulin release).
Antisense Nucleic Acids Another aspect of the invention pertains to isolated antisense nucleic acid molecules that are hybridizable to or complementary to the nucleic acid molecule comprising the nucleotide sequence of SEQ ID N0:2~-l, wherein n is an integer between 1-73, or fragments, analogs or derivatives thereof. An "antisense" nucleic acid comprises a nucleotide sequence that is complementary to a "sense" nucleic acid encoding a protein (e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence). In specific aspects, antisense nucleic acid molecules are provided that comprise a sequence complementary to at least about 10, 25, 50, 100, 250 or 500 nucleotides or an entire NOVX coding strand, or to only a portion thereof. Nucleic acid molecules encoding fragments, homologs, derivatives and analogs of a NOVX protein of SEQ ID N0:2n, wherein ~ is an integer between 1-73, or antisense nucleic acids complementary to a NOVX nucleic acid sequence of SEQ ID N0:2r~-l, wherein ~e is an integer between 1-73, are additionally provided.
In one embodiment, an antisense nucleic acid molecule is antisense to a "coding region" of the coding strand of a nucleotide sequence encoding a NOVX protein.
The term "coding region" refers to the region of the nucleotide sequence comprising codons which are translated into amino acid residues. In another embodiment, the antisense nucleic acid molecule is antisense to a "noncoding region" of the coding strand of a nucleotide sequence encoding the NOVX protein. The term "noncoding region" refers to 5' and 3' sequences which flank the coding region that are not translated into amino acids (i. e., also referred to as 5' and 3' untranslated regions).

Given the coding strand sequences encoding the NOVX protein disclosed herein, antisense nucleic acids of the invention cambe designed according to the rules of Watson and Crick or Hoogsteen base pairing. The antisense nucleic acid molecule can be complementary to the entire coding region of NOVX mRNA, but more preferably is an S oligonucleotide that is antisense to only a portion of the coding or noncoding region of NOVX mRNA. For example, the antisense .oligonucleotide can be complementary to the region surrounding the translation start site of NOVX mRNA. An antisense oligonucleotide can be, for example, about S, 10, 1S, 20, 2S, 30, 3S, 40, 4S
or SO
nucleotides in length. An antisense nucleic acid of the invention can be constructed using chemical synthesis or enzymatic Iigation reactions using procedures known in the art. For example, an antisense nucleic acid (e.g., an antisense oligonucleotide) can be chemically synthesized using naturally-occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids (e.g., 1 S phosphorothioate derivatives and acxidine substituted nucleotides can be used).
Examples of modified nucleotides that can be used to generate the antisense nucleic acid include: S-fluorouracil, S-bromouracil, S-chlorouracil, S-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, S-(carboxyhydroxylmethyl) uracil, S-carboxymethylaminomethyl-2-thiouridine, S-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, I-methylguanine, I-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, S-methylcytosine, N6-adenine, 7-methylguanine, S-methylaminomethyluracil, S-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, S'-methoxycarboxymethyluracil, S-methoxyuracil, 2S 2-methylthio-N6-isopentenyladenine, uracil-S-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, S-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, S-methyluracil, uracil-S-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), S-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).

The antisense nucleic acid molecules of the invention are typically administered to a subject or generated i~z situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a NOVX protein to thereby inhibit expression of the protein (e.g., by inhibiting transcription and/or translation). The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule that binds to DNA duplexes, through specific interactions in the major groove of the double helix. An example of a route of administration of antisense nucleic acid molecules of the invention includes direct injection at a tissue site.
Alternatively, antisense nucleic acid molecules can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface (e.g., by linking the antisense nucleic acid molecules to peptides or antibodies that bind to cell surface receptors or antigens). The antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve I 5 sufficient nucleic acid molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter axe preferred.
In yet another embodiment, the antisense nucleic acid molecule of the invention is an a-anomeric nucleic acid molecule. An cc-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual (3-units, the strands run parallel to each other. See, e.g., Gaultier, et al., 1987.
Nucl. Acids Res. 15:
6625-6641. The antisense nucleic acid molecule can also comprise a 2'-o-methylxibonucleotide (See, e.g., moue, et al. 1987. Nucl. Acids Res. 15:
6131-6148) or a chimeric RNA-DNA analogue (See, e.g., moue, et al., 1987. FEBS Lett. 215:
327-330.
Ribozymes and PNA Moieties Nucleic acid modifications include, by way of non-limiting example, modif ed bases, and nucleic acids whose sugar phosphate backbones are modified or derivatized.
These modifications are carried out at least in part to enhance the chemical stability of the modified nucleic acid, such that they may be used, for example, as antisense binding nucleic acids in therapeutic applications in a subject.
In one embodiment, an antisense nucleic acid of the invention is a ribozyme.
Ribozymes are catalytic RNA molecules with ribonuclease activity that are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes as described in Haselhoff and Gerlach 1988. Nature 334: 585-591) can be used to catalytically cleave NOVX mRNA transcripts to thereby inhibit translation of NOVX mRNA. A ribozyme having specificity for a NOVX-encoding nucleic acid can be designed based upon the nucleotide sequence of a NOVX cDNA disclosed herein (i.e., any one of SEQ ID
N0:2n-1, wherein rz is an integer between 1-73). For example, a derivative of a Tetrahynae~a L-19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in a NOVX-encoding mRNA.
See, e.g., U.S. Patent 4,987,071 to Cech, et al, and U.S. Patent 5,116,742 to Cech, et al.
NOVX mRNA can also be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel et al., (1993) Science 261:1411-1418.
Alternatively, NOVX gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of the NOVX nucleic acid (e.g., the NOVX promoter and/or enhancers) to form triple helical structures that prevent transcription of the NOVX gene in target cells. See, e.g., Helene, 1991.
Ahtica~zcer D~°ug Des. 6: 569-84; Helene, et al. 1992. Ar~~. N. Y. Acad. Sci. 660: 27-36; Maher, 1992.
Bioassays 14: 807-15. ' In various embodiments, the NOVX nucleic acids can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility of the molecule. For example, the deoxyribose phosphate backbone of the nucleic acids can be modified to generate peptide nucleic acids. See, e.g., Hyrup, et al., 1996. Bioorg Med Cl2eyvc 4: 5-23. As used herein, the terms "peptide nucleic acids" or "PNAs" refer to nucleic acid mimics (e.g., DNA mimics) in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleotide bases are retained. The neutral backbone of PNAs has been shown to allow for specific hybridization to DNA and RNA under conditions of low ionic strength.
The synthesis of PNA oligomer can be performed using standard solid phase peptide synthesis protocols as described in Hyrup, et al., 1996. supra; Perry-O'I~eefe, et al., 1996. Proc. Natl.
Acad. Sci. LISA 93: 14670-14675.
PNAs of NOVX can be used in therapeutic and diagnostic applications. For example, PNAs can be used as antisense or antigene agents for sequence-specific modulation of gene expression by, e.g., inducing transcription or translation arrest or inhibiting replication. PNAs of NOVX can also be used, for example, in the analysis of single base pair mutations in a gene (e.g., PNA directed"PC'R ctampmg; as araticiat restriction enzymes when used in combination with other enzymes, e.g., S~
nucleases (See, Hyrup, et al., 1996.supra); or as probes or primers for DNA sequence and hybridization (See, Hyrup, et al., 1996, supra; Perry-O'Keefe, et al., 1996. supra).
In another embodiment, PNAs of NOVX can be modified, e.g., to enhance their stability or cellular uptake, by attaching lipophilic or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known in the art. For example, PNA-DNA chimeras of NOVX can be generated that may combine the advantageous properties of PNA and DNA. Such chimeras allow DNA recognition enzymes (e.g., RNase H and DNA polymerises) to interact with the DNA
portion while the PNA portion would provide high binding affinity and specificity.
PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleotide bases, and orientation (see, Hyrup, et al., 1996. supra). The synthesis of PNA-DNA chimeras can be performed as described in Hyrup, et al., 1996. supra and Finn, et al., 1996. Nuel Acids Res 24: 3357-3363. For example, a DNA chain can be synthesized on a solid support using standard phosphoramidite coupling chemistry, and modified nucleoside analogs, e.g., 5'-(4-methoxytrityl)amino-S'-deoxy-thymidine phosphoramidite, can be used between the PNA and the 5' end of DNA. See, e.g., Mag, et al., 1989. Nucl Acid Res 17:
5973-5988.
PNA monomers are then coupled in a stepwise manner to produce a chimeric molecule with a 5' PNA segment and a 3' DNA segment. See, e.g., Finn, et al., 1996.
supra.
Alternatively, chimeric molecules can,be synthesized with a 5' DNA segment and a 3' PNA
segment. See, e.g., Petersen, et al., 1975. Bioorg. Med. Clzem. Lett. 5: 1119-11124.
In other embodiments, the oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors ire vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger, et al., 1989. Proc. Natl.
Acid. Sci. U.S.A. 86:
6553-6556; Lemaitre, et al., I 987. Proc. Natl. Acid. Sci. 84: 648-652; PCT
Publication No.
W088/09810) or the blood-brain barrier (see, e.g., PCT Publication No. WO
89110134). In addition, oligonucleotides can be modified with hybridization triggered cleavage agents (see, e.g., Krol, et al., 1988. BioTechuiques 6:958-976) or intercalating agents (see, e.g., Zon, 1988. PharMZ. Res. 5: 539-549). To this end, the oligonucleotide may be conjugated to another molecule, e.g., a peptide, a hybridization triggered cross-linking agent, a transport agent, a hybridization-triggered cleavage agent, and the like.

NOVX Polypeptides A polypeptide according to the invention includes a polypeptide including the amino acid sequence of NOVX polypeptides whose sequences are provided in any one of SEQ ID N0:2n, whexein n is an integex between 1-73. The invention also includes a mutant or variant protein any of whose residues may be changed from the corresponding residues shown in any one of SEQ ID N0:2n, wherein n is an integer between 1-73, while still encoding a protein that maintains its NOVX activities and physiological functions, or a functional fxagment thereof.
In general, a NOVX variant that preserves NOVX-like function includes any variant in which residues at a particular position in the sequence have been substituted by other amino acids, and further include the possibility of inserting an additional residue or residues between two residues of the parent protein as well as the possibility of deleting one or more residues from the parent sequence. Any amino acid substitution, insertion, or deletion is encompassed by the invention. In favorable circumstances, the substitution is a conservative substitution as defined above.
One aspect of the invention pertains to isolated NOVX proteins, and biologically-active portions thereof, ox derivatives, fragments, analogs or homologs thereof. Also provided are polypeptide fragments suitable for use as immunogens to raise anti-NOVX
antibodies. In one embodiment, native NOVX proteins can be isolated from cells or tissue sources by an appropriate purification scheme using standard protein purification techniques. In another embodiment, NOVX proteins are produced by recombinant DNA
techniques. Alternative to recombinant expression, a NOVX protein or polypeptide can be synthesized chemically using standard peptide synthesis techniques.
An "isolated" or "purified" polypeptide or protein or biologically-active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the NOVX protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized. The language "substantially free of cellular material" includes preparations of NOVX
proteins in which the protein is separated fxom cellular components of the cells from which it is isolated or recombinantly-produced. In one embodiment, the language "substantially free of cellular material" includes pxeparations of NOVX proteins having less than about 30%
(by dry weight) of non-NOVX proteins (also referred to herein as a "contaminating protein"), more preferably Iess than about 20% of non-NOVX proteins, still more preferably Less than about 10% of non-NOVX proteins, and most preferably less than about 5% of non-NUVX
proteins. When the NOVX protein or biologically-active portion thereof is recombinantly-produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of the NOVX protein preparation.
The language "substantially free of chemical precursors or other chemicals"
includes preparations of NOVX proteins in which the protein is separated from chemical precursors or other chemicals that are involved in the synthesis of the protein. In one embodiment, the language "substantially free of chemical precursors or other chemicals"
includes preparations of NOVX proteins having less than about 30% (by dry weight) of chemical precursors or non-NOVX chemicals, more preferably less than about 20%
chemical precursors or non-NOVX chemicals, still more preferably less than about 10%
chemical precursors or non-NOVX chemicals, and most preferably less than about 5%
chemical precursors or non-NOVX chemicals.
Biologically-active portions of NOVX proteins include peptides comprising amino acid sequences sufficiently homologous to or derived from the amino acid sequences of the NOVX proteins (e.g., the amino acid sequence of SEQ ID N0:2n, wherein n is an integer between 1-73) that include fewer amino acids than the full-length NOVX
proteins, and exhibit at least one activity of a NOVX protein. Typically, biologically-active portions comprise a domain or motif with at least one activity of the NOVX protein. A
biologically-active portion of a NOVX protein can be a polypeptide which is, for example, 10, 25, 50, 100 or more amino acid residues in length.
Moreover, other biologically-active portions, in which other regions of the protein are deleted, can be prepared by recombinant techniques and evaluated for one or more of the functional activities of a native NOVX protein.
In an embodiment, the NOVX protein has an amino acid sequence of SEQ ID
N0:2~, wherein h is an integer between 1-73. In other embodiments, the NOVX
protein is substantially homologous to SEQ ID N0:2n, wherein ~ is an integer between 1-73, and retains the functional activity of the protein of SEQ ID NO:2h, wherein n is an integer between 1-73, yet differs in amino acid sequence due to natural allelic variation or mutagenesis, as described in detail, below. Accordingly, in another embodiment, the NOVX protein is a protein that comprises an amino acid sequence at least about 45%
homologous to the amino acid sequence of SEQ ID NO:2n, wherein n is an integer between 1-73, and retains the functional activity of the NOVX proteins of S~~-'~D
~I~b:2n, wherein h is an integer between 1-73.
Determining Homology Between Two or More Sequences To determine the percent homology of two amino acid sequences or of two nucleic acids, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino or nucleic acid sequence). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are homologous at that position (i. e., as used herein amino acid or nucleic acid "homology" is equivalent to amino acid or nucleic acid "identity").
The nucleic acid sequence homology may be determined as the degree of identity between two sequences. The homology may be determined using computer programs known in the art, such as GAP software provided in the GCG program package.
See, Needleman and Wunsch, 1970. JMoI Biol 48: 443-453. Using GCG GAP software with the following settings for nucleic acid sequence comparison: GAP creation penalty of 5.0 and GAP extension penalty of 0.3, the coding region of the analogous nucleic acid sequences referred to above exhibits a degree of identity preferably of at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99%, with the CDS (encoding) part of the DNA
sequence of SEQ ID NO:2n-l, wherein ra is an integer between 1-73.
The term "sequence identity" refers to the. degree to which two polynucleotide or polypeptide sequences are identical on a residue-by-residue basis over a particular region of comparison. The term "percentage of sequence identity" is calculated by comparing two optimally aligned sequences over that region of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, U, or I, in the case of nucleic acids) 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 region of comparison (i.e., the window size), and multiplying the result by I00 to yield the percentage of sequence identity. The term "substantial identity" as used herein denotes a characteristic of a polynucleotide sequence, wherein the polynucleotide comprises a sequence that has at least 80 percent sequence identity, preferably at least 85 percent identity and often 90 to 95 percent sequence identity, mode it~u~lly a~-feast f9 percent sequence identity as compared to a reference sequence over a comparison region.
Chimeric and Fusion Proteins The invention also provides NOVX chimeric or fusion proteins. As used herein, a NOVX "chimeric protein" or "fusion protein" comprises a NOVX polypeptide operatively-linked to a non-NOVX polypeptide. An "NOVX polypeptide" refers to a polypeptide having an amino acid sequence corresponding to a NOVX protein of SEQ ID N0:2n, wherein n is an integer between 1-73, whereas a "non-NOVX polypeptide" refers to a polypeptide having an amino acid sequence corresponding to a protein that is not substantially homologous to the NOVX protein, e.g., a protein that is different from the NOVX protein and that is derived from the same or a different organism. Within a NOVX
fusion protein the NOVX polypeptide can correspond to all or a portion of a NOVX
protein. In one embodiment, a NOVX fusion protein comprises at least one biologically-active portion of a NOVX protein. In another embodiment, a NOVX fusion protein comprises at least two biologically-active portions of a NOVX protein. In yet another embodiment, a NOVX fusion protein comprises at Ieast three biologically-active portions of a NOVX protein. Within the fusion protein, the term "operatively-linked" is intended to indicate that the NOVX polypeptide and the non-NOVX polypeptide are fused in-frame with one another. The non-NOVX polypeptide can be fused to the N-terminus or C-terminus of the NOVX polypeptide.
In one embodiment, the fusion protein is a GST-NOVX fusion protein in which the NOVX sequences axe fused to the C-terminus of the GST (glutathione S-transferase) sequences. Such fusion proteins can facilitate the purification of recombinant NOVX
polypeptides.
In another embodiment, the fusion protein is a NOVX protein containing a heterologous signal sequence at its N-terminus. In certain host cells (e.g., mammalian host cells), expression and/or secretion of NOVX can be increased through use of a heterologous signal sequence.
In yet another embodiment, the fusion protein is a NOVX-immunoglobulin fusion protein in which the NOVX sequences axe fused to sequences derived from a member of the immunoglobulin protein family. The NOVX-immunoglobulin fusion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject to inhibit an interaction between a NOVX ligand and a NOVX protein on the surface of a cell, to thereby suppress NOVX-mediated sign'a'l trarisduction in vivo. The NOVX-immunoglobulin fusion proteins can be used to affect the bioavailability of a NOVX cognate ligand. Inhibition of the NOVX ligand/NOVX interaction may be useful therapeutically for both the treatment of proliferative and differentiative disorders, as well as modulating (e.g. promoting or inhibiting) cell survival. Moreover, the NOVX-immunoglobulin fusion proteins of the invention can be used as immunogens to produce anti-NOVX antibodies in a subject, to purify NOVX ligands, and in screening assays to identify molecules that inhibit the interaction of NOVX with a NOVX
ligand.
A NOVX chimeric or fusion protein of the invention can be produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, e.g., by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR
amplification of gene fragments can be carried out using anchor primers that give rise to complementary overhangs between two consecutive gene fragments that can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, e.g., Ausubel, et al.
(eds.) CURRENT
PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, 1992). Moreover, many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide). A NOVX-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the NOVX protein.
NOYX Agonists and Antagonists The invention also pertains to variants of the NOVX proteins that function as either NOVX agonists (i. e., mimetics) or as NOVX antagonists. Variants of the NOVX
protein can be generated by mutagenesis (e.g., discrete point mutation or truncation of the NOVX
protein). An agonist of the NOVX protein can retain substantially the same, or a subset of, the biological activities of the naturally occurring form of the NOVX protein.
An antagonist of the NOVX protein can inhibit one or more of the activities of the naturally occurring form of the NOVX protein by, for example, competitively binding to a downstream or upstream member of a cellular signaling cascade which includes the NOVX
protein. Thus, specific biological effects can be elicited by treatment with a variant of limited function. In one embodiment, treatment of a subject'vit'h a'"vai~ianf having a subset of the biological activities of the naturally occurring form of the protein has fewer side effects in a subject relative to treatment with the naturally occurring form of the NOVX
proteins.
Variants of the NOVX proteins that function as either NOVX agonists (i. e., mimetics) or as NOVX antagonists can be identified by screening combinatorial libraries of mutants (e.g., truncation mutants) of the NOVX proteins for NOVX protein agonist or antagonist activity. In one embodiment, a variegated library of NOVX variants is generated by combinatorial mutagenesis at the nucleic acid Level and is encoded by a variegated gene library. A variegated library of NOVX variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential NOVX sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display) containing the set of NOVX sequences therein. There are a variety of methods which can be used to produce libraries of potential NOVX variants from a degenerate oligonucleotide sequence. Chemical synthesis of a degenerate gene sequence can be performed in an automatic DNA synthesizer, and the synthetic gene then ligated into an appropriate expression vector. Use of a degenerate set of genes allows for the provision, in one mixture, of all of the sequences encoding the desired set of potential NOVX sequences.
Methods for synthesizing degenerate oligonucleotides are well-known within the art. See, e.g., Narang, 1983. Tetrahedron 39: 3; Itakura, et al., 1984. An~u. Rev.
Biochenz. 53: 323;
Itakura, et al., 1984. Science I98: 1056; Ike, et al., 1983. Nucl. Acids Res.
11: 477.
Polypeptide Libraries In addition, libraries of fragments of the NOVX protein coding sequences can be used to generate a variegated population of NOVX fragments for screening and subsequent selection of variants of a NOVX protein. In one embodiment, a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of a NOVX coding sequence with a nuclease under conditions wherein nicking occurs only about once per molecule, denaturing the double stranded DNA, renaturing the DNA to form double-stranded DNA that can include sense/antisense pairs from different nicked products, removing single stranded portions from reformed duplexes by treatment with S~
nuclease, and ligating the resulting fragment library into an expression vector. By this method, expression libraries can be derived which encodes N-terminal and internal fragments of various sizes of the NOVX proteins.
Various techniques are known in the art for screening gene products of combinatorial libraries made by point mutations or truncation, and for screening cDNA
libraries for gene products having a selected property. Such techniques are adaptable for rapid screening of the gene libraries generated by the combinatorial mutagenesis of NOVX
proteins. The most widely used techniques, which are amenable to high throughput analysis, for screening large gene libraries typically include cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates isolation of the vector encoding the gene whose product was detected. Recursive ensemble mutagenesis (REM), a new technique that enhances the frequency of functional mutants in the libraries, can be used in combination with the screening assays to identify NOVX variants. See, e.g., Arkin and Yourvan, 1992. Proc.
Natl. Acad. Sci. USA 89: 7811-7815; Delgrave, et al., 1993. Protein Engineering 6:327-331.
NOVX Antibodies The term "antibody" as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin (Ig) molecules, i.e., molecules that contain an antigen binding site that specifically binds (immunoreacts with) an antigen.
Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, Fab, Fab° and Ftab~)a fragments, and an Fab expression library.
In general, antibody molecules obtained from humans relates to any of the classes IgG, IgM, IgA, IgE and IgD, which differ from one another by the nature of the heavy chain present in the molecule.
Certain classes have subclasses as well, such as IgGi, IgG2, and others.
Furthermore, in humans, the light chain may be a kappa chain or a lambda chain. Reference herein to antibodies includes a reference to all such classes, subclasses and types of human antibody species.
An isolated protein of the invention intended to serve as an antigen, or a portion or fragment thereof, can be used as an immunogen to generate antibodies that immunospecifically bind the antigen, using standard techniques for polyclonal and monoclonal antibody preparation. The full-length protein can be used or, alternatively, the invention provides antigenic peptide fragments of the antigen for use as immunogens. An antigenic peptide fragment comprises at least 6 amino acid"residues"ot-~the ammo acid sequence of the full length protein, such as an amino acid sequence of SEQ ID
N0:2~, wherein rz is an integer between I-73, and encompasses an epitope thereof such that an antibody raised against the peptide forms a specific immune complex with the full length protein or with any fragment that contains the epitope. Preferably, the antigenic peptide comprises at least IO amino acid residues, or at least 15 amino acid residues, or at least 20 amino acid residues, or at least 30 amino acid residues. Preferred epitopes encompassed by the antigenic peptide are xegions of the protein that are located on its surface; commonly these are hydrophilic regions.
In certain embodiments of the invention, at least one epitope encompassed by the antigenic peptide is a region of NOVX that is located on the surface of the protein, e.g., a hydrophilic region. A hydrophobicity analysis of the human NOVX protein sequence will indicate which regions of a NOVX polypeptide are particularly hydrophilic and, therefore, encode surface residues useful for targeting antibody production. As a means for targeting antibody production, hydropathy plots showing regions of hydrophilicity and hydrophobicity may be generated by any method well known in the art, including, for example, the Kyte Doolittle or the Hopp Woods methods, either with or without Fourier transformation. See, e.g., Hopp and Woods, 1981, P~°oc. Nat. Acad. Sci.
USA 78: 3824-3828; Kyte and Doolittle 1982, J. Mol. Biol. 157: 105-I42, each incorporated herein by reference in their entirety. Antibodies that are specific for one or more domains within an antigenic protein, or derivatives, fragments, analogs or homologs thereof, are also provided herein.
The term "epitope" includes any protein determinant capable of specif c binding to an immunoglobulin or T-cell receptor. Epitopic determinants usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains and usually have specific three dimensional structural characteristics, as well as specific charge characteristics. A NOVX polyppeptide or a fragment thereof comprises at least one antigenic epitope. An anti-NOVX antibody of the present invention is said to specifically bind to antigen NOVX when the equilibrium binding constant (KD) is S1 ~.M, preferably 5 100 nM, more preferably <_ 10 nM, and most preferably _< 100 pM to about 1 pM, as measured by assays such as radioligand binding assays or similar assays known to those skilled in the art.
'34 A protein of the invention, or a derivative, fragment, analog, riomolog or ortholog thereof, may be utilized as an immunogen in the generation of antibodies that immunospecifically bind these protein components.
Various procedures known within the art may be used fox the production of polyclonal or monoclonal antibodies directed against a protein of the invention, or against derivatives, fragments, analogs homologs or orthologs thereof (see, for example, Antibodies: A Laboratory Manual, Harlow E, and Lane D, 1988, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, incorporated herein by reference).
Some of these antibodies are discussed below.
Polyclonal Antibodies For the production of polyclonal antibodies, various suitable host animals (e.g., rabbit, goat, mouse or other mammal) may be immunized by one or more injections with the native protein, a synthetic variant thereof, or a derivative of the foregoing. An appropriate immunogenic preparation can contain, for example, the naturally occurring immunogenic protein, a chemically synthesized polypeptide representing the irnmunogenic protein, or a recombinantly expressed immunogenic protein. Furthermore, the protein may be conjugated to a second protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. The preparation can further include an adjuvant. Various adjuvants used to increase the immunological response include, but are not limited to, Freund's (complete and incomplete), mineral gels (e.g., aluminum hydroxide), surface active substances (e.g., lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, dinitrophenol, etc.), adjuvants usable in humans such as Bacille Calmette-Guerin and Corynebacterium paxvum, or similar immunostimulatory agents. Additional examples of adjuvants which can be employed include MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).
The polyclonal antibody molecules directed against the immunogenic protein can be isolated from the mammal (e.g., from the blood) and further purified by well known techniques, such as affinity chromatography using protein A or protein G, which provide primarily the IgG fraction of immune serum. Subsequently, or alternatively, the specific antigen which is the target of the irrimunoglobulin sought, or an epitope thereof, may be immobilized on a column to purify the immune specific antibody by immunoaffinity chromatography. Purification of immunoglobulins is discu'~"sed,"ror example;
by'b.
Wilkinson (The Scientist, published by The Scientist, Inc., Philadelphia PA, VoI. 14, No. 8 (April I7, 2000), pp. 25-28).
Monoclonal Antibodies The term "monoclonal antibody" (MAb) or "monoclonal antibody composition", as used herein, refers to a population of antibody molecules that contain only one molecular species of antibody molecule consisting of a unique light chain gene product and a unique heavy chain gene product. In particular, the complementarity determining regions (CDRs) of the monoclonal antibody axe identical iri all the molecules of the population. MAbs thus contain an antigen binding site capable of immunoreacting with a particular epitope of the antigen characterized by a unique binding affinity for it.
Monoclonal antibodies can be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature, 256:495 (1975). In a hybridoma method, a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes can be immunized in vitro.
The immunizing agent will typically include the protein antigen, a fragment thereof or a fusion protein thereof. Generally, either peripheral blood lymphocytes are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non-human mammalian sources axe desired. The lymphocytes are then fused with an immortalized cell Line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding, Monoclonal Antibodies: Principles and Practice, Academic Press, (1986) pp. 59-103). Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovine and human origin. Usually, rat or mouse myeloma cell lines are employed. The hybridoma cells can be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells. For example, if the parental cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine ("HAT
medium"), which substances prevent the growth of HGPRT-deficient cells.

Preferred immortalized cell lines are those that ~use~ef~cieritly, support stable high level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are marine rnyeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, California and the American Type Culture Collection, Manassas, Virginia. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor, J.
Immunol., 133:3001 (1984); Brodeur et al., Monoclonal Antibody Production Techniques and Applications, Marcel Dekker, Inc., New York, (1987) pp. 51-63).
The culture medium in which the hybridoma cells are cultured can then be assayed for the presence of monoclonal antibodies directed against the antigen.
Preferably, the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). Such techniques and assays are known in the art. The binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollard, Anal. Biochem., 107:220 (1980). It is an objective, especially important in therapeutic applications of monoclonal antibodies, to identify antibodies having a high degree of specificity and a high binding affinity for the target antigen.
After the desired hybridoma cells are identified, the clones can be subcloned by limiting dilution procedures and grown by standard methods (Goding,1986).
Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium. Alternatively, the hybridoma cells can be grown in vivo as ascites in a mammal.
The monoclonal antibodies secreted by the subclones can be isolated or purified from the culture medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.
The monoclonal antibodies can also be made by recombinant DNA methods, such as those described in U.S. Patent No. 4,816,567. DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of marine antibodies). The hybridoma cells of the invention serve as a preferred source of such DNA. Once isolated, the DNA can be placed into expression vectors, which are then transfected into host 'cel'~s such as siiW
ari (:O'~lcells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. The DNA also can be modif ed, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous marine sequences (U.S. Patent No. 4,816,567; Morrison, Nature 368, (1994)) or by covalently joining to the immunoglobulin coding sequence aI1 or part of the coding sequence for a non-immunoglobulin polypeptide. Such a non-immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention, or I 0 can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody.
Humanized Antibodies The antibodies directed against the protein antigens of the invention can further comprise humanized antibodies or human antibodies. These antibodies are suitable for administration to humans without engendering an immune response by the human against the administered immunoglobulin. Humanized forms of antibodies are chimeric immunoglobulins, ilnmunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab')a or other antigen-binding subsequences of antibodies) that are principally comprised of the sequence of a human immunoglobulin, and contain minimal sequence derived from a non-human immunoglobulin. Humanization can be performed following the method of Winter and co-workers (Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science, 239:1534-1536 (1988)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody.
(See also U.S. Patent No. 5,225,539.) In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues.
Humanized antibodies can also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody will comprise substantially all of at Least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the framework regions are those of a human innmunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin (Jones et al., 1986; Riechmann et ~'t, '198$; and I~resla, Curr. Z7p.
Struct. Biol., 2:593-596 (1992)).
Human Antibodies Fully human antibodies essentially relate to antibody molecules in which the entire sequence of both the light chain and the heavy chain, including the CDRs, arise from human genes. Such antibodies are termed "human antibodies", or "fully human antibodies"
herein. Human monoclonal antibodies can be prepared by the trioma technique;
the human B-cell hybridoma technique (see I~ozbor, et al., 1983 Immunol Today 4: 72) and the EBV
hybridoma technique to produce human monoclonal antibodies (see Cole, et al., 1985 In:
MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc., pp. 77-96).
Human monoclonal antibodies may be utilized in the practice of the present invention and may be produced by using human hybridomas (see Cote, et al., 1983. Proc Natl Acad Sci USA 80:
2026-2030) or by transforming human B-cells with Epstein Barr Virus in vitro (see Cole, et aL, 1985 In: MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc., pp.
77-96).
In addition, human antibodies can also be produced using additional techniques, including phage display libraries (Hoogenboom and Winter, J. Mol. Biol., 227:381 (1991);
Marks et al., J. Mol. Biol., 222:581 (1991)). Similarly, human antibodies can be made by introducing human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin genes have been partially or completely inactivated.
Upon challenge, human antibody production is observed, which closely resembles that seen in humans in alI respects, including gene rearrangement, assembly, and antibody repertoire.
This approach is described, for example, in U.S. Patent Nos. 5,545,807;
5,545,806;
5,569,825; 5,625,126; 5,633,425; 5,661,016, and in Marks et al.
(Bio/Technology 10, 779-783 (1992)); Lonberg et al. (Nature 368 856-859 (1994)); Morrison ( Nature 368, 812-I3 (1994)); Fishwild et al,( Nature Biotechnology 14, 845-51 (1996)); Neuberger (Nature Biotechnology 14, 826 (1996)); and Lonberg and Huszar (Intern. Rev. Immunol.

(1995)).
Human antibodies may additionally be produced using transgenic nonhuman animals which are modified so as to produce fully human antibodies rather than the animal's endogenous antibodies in response to challenge by an antigen. (See PCT
publication W094/02602). The endogenous genes encoding the heavy and light immunoglobulin chains in the nonhuman host have been incapacitated, and active loci encoding human heavy and Iight chain immunogIobulins are inserted into the host's genome. The human genes are incorporated, for example, using yeast artificial chromosomes containing the requisite human DNA segments. An animal which provides all the desired modifications is then obtained as progeny by crossbreeding intermediate transgenic animals containing fewer than the full complement of the modifications. The preferred embodiment of such a nonhuman animal is a mouse, and is termed the xenomouseTM as disclosed in PCT publications WO 96/33735 and WO 96!34096. This animal produces B cells which secrete fully human immunoglobulins. The antibodies can be obtained directly from the animal after immunization with an immunogen of interest, as, for example, a preparation of a polyclonal antibody, or alternatively from immortalized B
cells derived from the animal, such as hybridomas producing monoclonal antibodies.
Additionally, the genes encoding the immunoglobulins with human variable regions can be recovered and expressed to obtain the antibodies directly, or can be further modified to 1 S obtain analogs of antibodies such as, for example, single chain Fv molecules.
An example of a method of producing a nonhuman host, exemplified as a mouse, lacking expression of an endogenous immunoglobulin heavy chain is disclosed in U.S.
Patent No. 5,939,598. It can be obtained by a method including deleting the J
segment genes from at least one endogenous heavy chain locus in an embryonic stem cell to prevent rearrangement of the locus and to prevent formation of a transcript of a rearranged immunoglobulin heavy chain locus, the deletion being effected by a targeting vector containing a gene encoding a selectable marker; and producing from the embryonic stem cell a transgenic mouse whose somatic and germ cells contain the gene encoding the selectable marker.
A method for producing an antibody of interest, such as a human antibody, is disclosed in U.S. Patent No. 5,916,771. It includes introducing an expression vector that contains a nucleotide sequence encoding a heavy chain into one mammalian host cell in culture, introducing an expression vector containing a nucleotide sequence encoding a light chain into another mammalian host cell, and fusing the two cells to form a hybrid cell. The hybrid cell expresses an antibody containing the heavy chain and the light chain.
In a further improvement on this procedure, a method for identifying a clinically relevant epitope on an immunogen, and a correlative method for selecting an antibody that binds immunospecifically to the relevant epitope with high affinity, are disclosed in PCT
publication WO 99/53049.

Fab Fragments and Single Chain Antibodies According to the invention, techniques can be adapted for the production of single-chain antibodies specific to an antigenic protein of the invention (see e.g., U.S.
Patent No. 4,946,778). In addition, methods can be adapted for the construction of Fab expression libraries (see e.g., Huse, et al., 1989 Science 246: 1275-1281) to allow rapid and effective identification of monoclonal Fab fragments with the desired specificity for a protein or derivatives, fragments, analogs or homologs thereof. Antibody fragments that contain the idiotypes to a protein antigen may be produced by techniques known in the art including, but not limited to: (i) an F(ab~~~ fragment produced by pepsin digestion of an antibody molecule; (ii) an Fab fragment generated by reducing the disulfide bridges of an F(ab')2 fragment; (iii) an Fab fragment generated by the treatment of the antibody molecule with papain and a reducing agent and (iv) F,, fragments.
Bispecific Antibodies Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. In the present case, one of the binding specificities is for an antigenic protein of the invention. The second binding target is any other antigen, and advantageously is a cell-surface protein or receptor or receptor subunit.
Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities (Milstein and Cuello, Nature, 305:537-539 (1983)). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO
93108829, published 13 May 1993, and in Traunecker et al., EMBO J., 10:3655-(1991).
Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to imrnunoglobulin constant domain sequences.
The fusion preferably is with an immunoglobulin heavy-chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant region (CH1) containing the site necessary for light-chain binding present in at least one of the fusions. L~NAs encoding the immunogiobuim heavy-chain iusions and, u-desired, the immunoglobulin light chain, are inserted into separate expression vectors, and are co-transfected into a suitable host organism. For further details of generating bispecific antibodies see, for example, Suresh et al., Methods in Enzymology, 121:210 (1986).
According to another approach described in WO 96/2701 l, the interface between a pair of antibody molecules can be engineered to maximize the percentage of heterodimers which are recovered from recombinant cell culture. The preferred interface comprises at least a part of the CH3 region of an antibody constant domain. In this method, one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains (e.g. tyrosine or tryptophan). Compensatory "cavities"
of identical or similar size to the large side chains) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones (e.g.
alanine or threonine). This provides a mechanism for increasing the yield of the heterodimer over other unwanted end-products such as homodimers.
Bispecific antibodies can be prepared as full length antibodies or antibody fragments.(e.g. F(ab')2 bispecific antibodies). Techniques for generating bispecific antibodies from antibody fragments have been described in the literature. For example, bispecif c antibodies can be prepared using chemical linkage. Brennan et al., Science 229:81 (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate F(ab')~, fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation. The Fab' fragments generated are then converted to thionitrobenzoate (TNB) derivatives. One of the Fab'-TNB derivatives is then reconverted to the Fab'-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab'-TNB derivative to form the bispecif c antibody. The bispecific antibodies produced can be used as agents for the selective immobilization of enzymes.
Additionally, Fab' fragments can be directly recovered from E. coli and chemically coupled to form bispecific antibodies. Shalaby et al., J. Exp. Med. 175:217-225 (1992) describe the production of a fully humanized bispecific antibody F(ab')2 molecule. Each Fab' fragment was separately secreted from E. coli and subjected to directed chemical coupling in vitro to form the bispecific antibody. The bispecific antibody thus formed was able to bind to cells overexpressing the ErbB2 receptor and normal human T
cells, as well as trigger the lytic activity of human cytotoxic lymphocytes against human breast tumor targets.

Various techniques for making and isolating bispecifac'antibody fragments directly from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers. Kostelny et al., J. Immunol.
148(5):1547-1553 (1992). The leucine zipper peptides from the Fos and Jun proteins were linked to the Fab' portions of two different antibodies by gene fusion. The antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers. This method can also be utilized for the production of antibody homodimers.
The "diabody" technology described by Hollinger et al., Proc. Natl. Acad. Sci.
USA
90:6444-6448 (1993) has provided an alternative mechanism for making bispecific antibody fragments. The fragments comprise a heavy-chain variable domain (Vu) connected to a light-chain variable domain (VL) by a linker which is too short to allow pairing between the two domains on the same chain. Accordingly, the VH and VL
domains of one fragment are forced to pair with the complementary VL and VH domains of another fragment, thereby forming two antigen-binding sites. Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) dimers has also been reported. See, Gruber et al., J. Immunol. 152:5368 (1994).
Antibodies with more than two valencies are contemplated. For example, trispecific antibodies can be prepared. Tutt et al., J. Immunol. 147:60 (1991).
Exemplary bispecific antibodies can bind to two different epitopes, at least one of which originates in the protein antigen of the invention. Alternatively, an anti-antigenic arm of an immunoglobulin molecule can be combined with an arm which binds to a triggering molecule on a leukocyte such as a T-cell receptor molecule (e.g.
CD2, CD3, CD28, or B7), or Fc receptors for IgG (FcyR), such as FcyRI (CD64), FcyRII
(CD32) and Fc7RIII (CD16) so as to focus cellular defense mechanisms to the cell expressing the particular antigen. Bispecific antibodies can also be used to direct cytotoxic agents to cells which express a particular antigen. These antibodies possess an antigen-binding arm and an arm which binds a cytotoxic agent or a radionuclide chelator, such as EOTUBE, DPTA, DOTA, or TETA. Another bispecific antibody of interest binds the protein antigen described herein and further binds tissue factor (TF).
Heteroconjugate Antibodies Heteroconjugate antibodies axe also within the scope of the present invention.
Heteroconjugate antibodies are composed of two covalently joined antibodies.
Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Patent No. 4,676,980), and for treatment of HIV''irifectiori ('W~C-9170036~0;-WO
92/200373; EP 03089). It is contemplated that the antibodies can be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents. For example, immunotoxins can be constructed using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S.
Patent No. 4,676,980.
Effector Function Engineering It can be desirable to modify the antibody of the invention with respect to effector function, so as to enhance, e.g., the effectiveness of the antibody in treating cancer. For example, cysteine residues) can be introduced into the Fc region, thereby allowing interchain disulfide bond formation in this region. The homodimeric antibody thus generated can have improved internalization capability and/or increased complement-mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See Caron et al., J. Exp Med., 176: 1191-1195 (1992) and Shopes, J. Immunol., 148: 2918-2922 (1992).
Homodimeric antibodies with enhanced anti-tumor activity can also be prepared using heterobifunctional cross-linkers as described in Wolff et al. Cancer Research, 53: 2560-2565 (1993). Alternatively, an antibody can be engineered that has dual Fc regions and can thereby have enhanced complement Iysis and ADCC capabilities. See Stevenson et al., Anti-Cancer Drug Design, 3: 219-230 (1989).
Immunoconjugates The invention also pertains to immunoconjugates comprising an antibody conjugated to a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i. e., a radioconjugate).
Chemotherapeutic agents useful in the generation of such immunoconjugates have been described above. Enzyrnatically active toxins and fragments thereof that can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A
chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A
chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes. A variety of radionuclides are available for flie prodizct'i~ori ~of~
radioconjugated antibodies. Examples include 212Bi, 1311, ~3iln, 9oY, and ~86Re.
Conjugates of the antibody and cytotoxic agent are made using a variety of bifunctional protein-coupling agents such as N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCL), active esters (such as disuccinimidyl suberate), aldehydes (such as glutareldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as tolyene 2,6-diisocyanate), and bis-active fluorine compounds (such as I,5-difluoro-2,4-dinitrobenzene). Fox example, a ricin immunotoxin can be prepared as described in Vitetta et al., Science, 238: 1098 (1987).
Carbon-I4-labeled 1-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See W094/11026.
In another embodiment, the antibody can be conjugated to a "receptor" (such streptavidin) for utilization in tumor pretargeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a "ligand"
(e.g., avidin) that is in turn conjugated to a cytotoxic agent.
Immunoliposomes The antibodies disclosed herein can also be formulated as immunoliposomes.
Liposomes containing the antibody are prepared by methods known in the art, such as described in Epstein et al., Proc. Natl. Acad. Sci. USA, 82: 3688 (1985);
Hwang et al., Proc. Natl Acad. Sci. USA, 77: 4030 (1980); and U.S. Pat. Nos. 4,485,045 and 4,544,545.
Liposomes with enhanced circulation time are disclosed in U.S. Patent No.
5,013,556.
Particularly useful liposomes can be generated by the reverse-phase evaporation method with a lipid composition comprising phosphatidylcholine, cholesterol, and PEG-derivatized phosphatidylethanolamine (PEG-PE). Liposomes are extruded through filters of defined pore size to yield liposomes with the desired diameter. Fab' fragments of the antibody of the present invention can be conjugated to the Iiposomes as described in Martin et al ., J. Biol. Chern., 257: 286-288 (1982) via a disulfide-interchange reaction. A
chemotherapeutic agent (such as Doxorubicin) is optionally contained within the liposome.
See Gabizon et al., J. National Cancer Inst., 81(19): 1484 (I989).

Diagnostic Applications of Antibodies Directed Against the Proteins of the Invention Antibodies directed against a protein of the invention may be used in methods known within the art relating to the localization and/or quantitation of the protein (e.g., for use in measuring levels of the protein within appropriate physiological samples, for use in diagnostic methods, for use in imaging the protein, and the like). In a given embodiment, antibodies against the proteins, or derivatives, fragments, analogs or homologs thereof, that contain the antigen binding domain, are utilized as pharmacologically-active compounds (see below).
An antibody specific for a protein of the invention can be used to isolate the protein by standard techniques, such as immunoaffinity chromatography or immunoprecipitation.
Such an antibody can facilitate the purification of the natural protein antigen from cells and of recombinantly produced antigen expressed in host cells. Moreover, such an antibody can be used to detect the antigenic protein (e.g., in a cellular Iysate or cell supernatant) in order to evaluate the abundance and pattern of expression of the antigenic protein.
Antibodies directed against the protein can be used diagnostically to monitor pxotein levels in tissue as part of a clinical testing procedure, e.g., to, for example, determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling (i. e., physically linking) the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, [3-galactosidase, or acetylcholinesterase;
examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes IuminoI;
examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include lash i3ih ass or 3H.
Antibody Therapeutics Antibodies of the invention, including polyclonaI;
rrioizdclorial;"liuiii'aiiized"arld' fully "~
human antibodies, may used as therapeutic agents. Such agents will generally be employed to treat or prevent a disease or pathology in a subject. An antibody preparation, preferably one having high specificity and high affinity for its target antigen, is administered to the subject and will generally have an effect due to its binding with the target.
Such an effect may be one of two kinds, depending on the specific nature of the interaction between the given antibody molecule and the target antigen in question. In the first instance, administration of the antibody may abrogate or inhibit the binding of the target with an endogenous Iigand to which it naturally binds. In this case, the antibody binds to the target and masks a binding site of the naturally occurring Iigand, wherein the ligand serves as an effector molecule. Thus the receptor mediates a signal transduction pathway for which ligand is responsible.
Alternatively, the effect may be one in which the antibody elicits a physiological result by virtue of binding to an effector binding site on the target molecule. In this case the target, a receptor having an endogenous ligand which may be absent or defective in the disease or pathology, binds the antibody as a surrogate effector ligand, initiating a receptor-based signal transduction event by the receptor.
A therapeutically effective amount of an antibody of the invention relates generally to the amount needed to achieve a therapeutic objective. As noted above, this may be a binding interaction between the antibody and its target antigen that, in certain cases, interferes with the functioning of the target, and in other cases, promotes a physiological response. The amount required to be administered will furthermore depend on the binding affinity of the antibody for its specific antigen, and will also depend on the xate at which an administered antibody is depleted from the free volume other subject to which it is administered. Common ranges for therapeutically effective dosing of an antibody or antibody fragment of the invention may be, by way of nonlimiting example, from about 0.1 mg/kg body weight to about 50 mg/kg body weight. Common dosing frequencies may range, for example, from twice daily to once a week.
Pharmaceutical Compositions of Antibodies Antibodies specifically binding a protein of the invention, as well as other molecules identified by the screening assays disclosed herein, can be administered for the treatment of various disorders in the form of pharmaceutical compositions.
Principles and considerations involved in preparing such compositions, as well as guidance in the choice of components are provided, for example, in Remington The science And Practice Of Pharmacy 19th ed. (Alfonso R. Gennaro, et al., editors) Mack Pub. Co., Easton, Pa. : 1995;
Drug Absorption Enhancement : Concepts, Possibilities, Limitations, And Trends, Harwood Academic Publishers, Langhorne, Pa., 1994; and Peptide And Protein Drug ~ Delivery (Advances In Parenteral Sciences, Vol. 4), 1991, M. Dekker, New York.
If the antigenic protein is intracellular and whole antibodies are used as inhibitors, internalizing antibodies are preferred. However, liposomes can also be used to deliver the antibody, or an antibody fragment, into cells. Where antibody fragments are used, the smallest inhibitory fragment that specifically binds to the binding domain of the target protein is preferred. For example, based upon the variable-region sequences of an antibody, peptide molecules can be designed that retain the ability to bind the target protein sequence. Such peptides can be synthesized chemically and/or produced by recombinant DNA technology. See, e.g., Marasco et al., Proc. Natl. Acad. Sci. LISA, 90:

(1993). The formulation herein can also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other. Alternatively, or in addition, the composition can comprise an agent that enhances its function, such as, for example, a cytotoxic agent, cytokine, chemotherapeutic agent, or growth-inhibitory agent.
Such molecules axe suitably present in combination in amounts that are effective for the purpose intended.
The active ingredients can also be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsules and poly-(methylmethacrylate) microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles, and nanocapsules) or in macroemulsions.
The formulations to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes.
Sustained-release preparations can be prepared. Suitable examples of sustained-release preparations include semipermeable matrices of solid hydrophobic polymers containing the antibody, which matrices are in the form of shaped articles, e.g., films, or microcapsules. Examples of sustained-release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides (U.S.
Pat. No. 3,773,919), copolymers of L-glutamic acid and y ethyl-L-glutamate, non-degradable ethylene-vinyl acetate, degradable lactic acid-~l~'c'~l~c°~aci~d ~~~~i~l7I~iriers«~s~c~~Fa~~°
the LUPRON DEPOT TM (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate), and poly-D-(-)-3-hydroxybutyric acid. While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogels release proteins for shorter time periods.
ELISA Assay An agent for detecting an analyte protein is an antibody capable of binding to an analyte protein, preferably an antibody with a detectable label. Antibodies can be polyclonal, or more preferably, monoclonal. An intact antibody, or a fragment thereof (e.g., Fab or F~ab~2) can be used. The term "labeled", with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled.
Examples of indirect labeling include detection of a primary antibody using a fluorescently-labeled secondary antibody and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently-labeled streptavidin. The term "biological sample"
is intended to include tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject. Included within the usage of the term "biological sample", therefore, is blood and a fraction or component of blood including blood serum, blood plasma, or lymph. That is, the detection method of the invention can be used to detect an analyte mRNA, protein, or genomic DNA in a biological sample in vitro as well as ivy vivo. For example, in vitro techniques for detection of an analyte mRNA
include Northern hybridizations and iu situ hybridizations. Ih vitro techniques for detection of an analyte protein include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations, and immunofluorescence. I~ vitro techniques for detection of an analyte genomic DNA include Southern hybridizations. Procedures for conducting immunoassays are described, for example in "ELISA: Theory and Practice:
Methods in Molecular Biology", Vol. 42, J. R. Crowther (Ed.) Human Press, Totowa, NJ, 1995;
"Immunoassay", E. Diamandis and T. Christopoulus, Academic Press, Inc., San Diego, CA, 1996; and "Practice and Thory of Enzyme Immunoassays", P. Tijssen, Elsevier Science Publishers, Amsterdam, 1985. Furthermore, in vivo techniques for detection of an analyte protein include introducing into a subject a labeled anti-an analyte protein antibody.

For example, the antibody can be labeled with a radioactme marker whose presence and location in a subject can be detected by standard imaging techniques.
NOVX Recombinant Expression Vectors and Host Cells Another aspect of the invention pertains to vectors, preferably expression vectors, containing a nucleic acid encoding a NOVX protein, or derivatives, fragments, analogs or homologs thereof. As used herein, the term "vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a "plasmid", which refers to a circular double stranded DNA loop into which additional DNA segments can be ligated. Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors).
Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome.
Moreover, certain vectors are capable of directing the expression of genes to which they are operatively-linked. Such vectors are referred to herein as "expression vectors". In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, "plasmid" and "vector" can be used interchangeably as the plasmid is the most commonly used form of vector. However, the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.
The recombinant expression vectors of the invention comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, that is operatively-linked to the nucleic acid sequence to be expressed. Within a recombinant expression vector, "operably-linked" is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequences) in a manner that allows for expression of the nucleotide sequence (e.g., in an irc vitro transcription/translation system or in a host cell when the vector is introduced into the host cell).

The term "regulatory sequence" is intended to includes promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel, GENE EXPRESSION TECHNOLOGY:
METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990).
Regulatory sequences include those that direct constitutive expression of a nucleotide sequence in many types of host cell and those that direct expression of the nucleotide sequence only in certain host cells (e.g., tissue-specific regulatory sequences). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, etc. The expression vectors of the invention can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein (e.g., NOVX proteins, mutant forms ofNOVX proteins, fusion proteins, etc.).
The recombinant expression vectors of the invention can be designed for expression of NOVX proteins in prokaryotic or eukaryotic cells. For example, NOVX
proteins can be expressed in bacterial cells such as Eschef~ichia coli, insect cells (using baculovirus expression vectors) yeast cells or mammalian cells. Suitable host cells are discussed further in Goeddel, GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990). Alternatively, the recombinant expression vector can be ~0 transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.
Expression of proteins in prokaryotes is most often carried out in Escherichia coli with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion proteins. Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus of the recombinant protein. Such fusion vectors typically serve three purposes: (i) to increase expression of recombinant protein; (ii) to increase the solubility of the recombinant protein; and (iii) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase.
Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith and Johnson, 1988. Gene 67: 31-40), pMAL (New England Biolabs, Beverly, Mass.) and SI

pRITS (Pharmacia, Piscataway, N.J.) that fuse glutathione 5-transterase (CJ5~1 ), maltose E
'binding protein, or protein A, respectively, to the target recombinant protein.
Examples of suitable inducible non-fusion E. coli expression vectors include pTrc (Amrann et al., (1988) Gene 69:301-315) and pET 1 1d (Studier et al., GENE
EXPRESSION
TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif.
(1990) 60-89).
One strategy to maximize recombinant protein expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein. See, e.g., Gottesman, GENE EXPRESSION TECHNOLOGY: METHODS
IN
1O ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990) 119-128. Another strategy is to alter the nucleic acid sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (see, e.g., Wada, et al., 1992. Nucl. Acids Res. 20: 211 I-2118). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.
In another embodiment, the NOVX expression vector is a yeast expression vector.
Examples of vectors for expression in yeast Sacchanornyces cef°ivisae include pYepSecl (Baldari, et al., 1987. EMBO J. 6: 229-234), pMFa (Kurjan and Herskowitz, 1982. Cell 30:
933-943), pJRY88 (Schultz et al., 1987. Gene 54: 113-123), pYES2 (Invitrogen Corporation, San Diego, Calif.), and picZ (InVitrogen Corp, San Diego, Calif.).
Alternatively, NOVX can be expressed in insect cells using baculovirus expression vectors. Baculovirus vectors available for expression of proteins in cultured insect cells (e.g., SF9 cells) include the pAc series (Smith, et al., 1983. Mol. Cell.
Biol. 3: 2156-2165) and the pVL series (Lucklow and Summers, 1989. Virology 170: 31-39).
In yet another embodiment, a nucleic acid of the invention is expressed in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDM8 (Seed, 1987. Nature 329: 840) and pMT2PC
(Kaufinan, et al., 1987. EMBO J. 6: 187-I 95). When used in mammalian cells, the expression vector's control functions are often provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, adenovirus 2, cytomegalovirus, and simian virus 40. For other suitable expression systems for both prokaryotic and eukaryotic cells see, e.g., Chapters 16 and 17 of Sambrook, et al., MOLECULAR CLONING: A LABORATORY
MANUAL. 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.

In another embodiment, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid).
Tissue-specific regulatory elements are known in the art. Non-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert, et al., 1987.
Genes Dev. 1:
268-277), lymphoid-specific promoters (Calaine and Eaton, 1988. Adv.
Imrrzunol. 43:
235-275), in particular promoters of T cell receptors (Winoto and Baltimore, 1989. EMBO
J. 8: 729-733) and immunoglobulins (Banerji, et al., 1983. Cell 33: 729-740;
Queen and Baltimore, 1983. Cell 33: 741-748), neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle, 1989. Proc. Natl. Acad Sci. USA 86: 5473-5477), pancreas-specific promoters (Edlund, et al., 1985. Sciefzce 230: 912-916), and mammary gland-specific promoters (e.g., milk whey promoter; U.S. Pat. No. 4,873,316 and European Application Publication No. 264,166). Developmentally-regulated promoters are also encompassed, e.g., the marine hox promoters (I~essel and Grass, 1990. Science 249:
374-379) and the a,-fetoprotein promoter (Camper and Tilghman, 1989. Genes Dev. 3:
537-546).
The invention further provides a recombinant expression vector comprising a DNA
molecule of the invention cloned into the expression vector in an antisense orientation.
That is, the DNA molecule is operatively-linked to a regulatory sequence in a manner that allows for expression (by transcription of the DNA molecule) of an RNA
molecule that is antisense to NOVX mRNA. Regulatory sequences. operatively linked to a nucleic acid cloned in the antisense orientation can be chosen that direct the continuous expression of the antisense RNA molecule in a variety of cell types, for instance viral promoters and/or enhancers, or regulatory sequences can be chosen that direct constitutive, tissue specific or cell type specific expression of antisense RNA. The antisense expression vector can be in the form of a recombinant plasmid, phagemid or attenuated virus in which antisense nucleic acids are produced under the control of a high efficiency regulatory region, the activity of which can be determined by the cell type into which the vector is introduced.
For a discussion of the regulation of gene expression using antisense genes see, e.g., Weintraub, et al., "Antisense RNA as a molecular tool for genetic analysis," Reviews-Trends in Genetics, Vol. 1(1) 1986.
Another aspect of the invention pertains to host cells into which a recombinant expression vector of the invention has been introduced. The terms "host cell"
and "recombinant host cell" are used interchangeably herein: lf~is understood that such terms refer not only to the particular subject cell but also to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.
A host cell can be any prokaryotic or eukaryotic cell. For example, NOVX
protein can be expressed in bacterial cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells). Other suitable host cells are known to those skilled in the art.
Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques. As used herein, the terms "transformation" and "transfection" are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, or electroporation. Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. (MOLECULAR CLONING: A LABORATORY MANUAL. 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989), and other laboratory manuals.
For stable transfection of mammalian cells, it is known that, depending upon the expression vector and transfection technique used, only a small fraction of cells may integrate the foreign DNA into their genome. In order to identify and select these integrants, a gene that encodes a selectable marker (~.g., resistance to antibiotics) is generally introduced into the host cells along with the gene of interest.
Various selectable markers include those that confer resistance to drugs, such as 6418, hygromycin and methotrexate. Nucleic acid encoding a selectable marker can be introduced into a host cell on the same vector as that encoding NOVX or can be introduced on a separate vector Cells stably transfected with the introduced nucleic acid can be identified by drug selection (e.g., cells that have incorporated the selectable marker gene will survive, while the other cells die).
A host cell of the invention, such as a prokaryotic or eukaryotic host cell in culture, can be used to produce (i. e., express) NOVX protein. Accordingly, the invention further provides methods for producing NOVX protein using the host cells of the invention. In one embodiment, the method comprises culturing the host cell of invention (into which a recombinant expression vector encoding NOVX protein has been introduced) in a suitable medium such that NOVX protein is produced. In another eimhodirrient, the method further comprises isolating NOVX protein from the medium or the host cell.
Transgenic NOVX Animals The host cells of the invention can also be used to produce non-human transgenic animals. For example, in one embodiment, a host cell of the invention is a fertilized oocyte or an embryonic stem cell into which NOVX protein-coding sequences have been introduced. Such host cells can then be used to create non-human transgenie animals in which exogenous NOVX sequences have been introduced into their genome or homologous recombinant animals in which endogenous NOVX sequences have been altered. Such animals are useful for studying the function and/or activity of NOVX protein and for identifying and/or evaluating modulators of NOVX protein activity. As used herein, a "transgenic animal" is a non-human animal, preferably a mammal, more preferably a rodent such as a rat or mouse, in wluch one or more of the cells of the animal includes a transgene. Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, amphibians, etc. A transgene is exogenous DNA that is integrated into the genome of a cell from which a transgenic animal develops and that remains in the genome of the mature animal, thereby directing the expression of an encoded gene product in one or more cell types or tissues of the transgenic animal. As used herein, a "homologous recombinant animal" is a non-human animal, preferably a mammal, more preferably a mouse, in which an endogenous NOVX gene has been altered by homologous recombination between the endogenous gene and an exogenous DNA
molecule introduced into a cell of the animal, e.g., an embryonic cell of the animal, prior to development of the animal.
A transgenic animal of the invention can be created by introducing NOVX-encoding nucleic acid into the male pronuclei of a fertilized oocyte (e.g., by microinjection, retroviral infection) and allowing the oocyte to develop in a pseudopregnant female foster animal. The human NOVX cDNA sequences, i. e., any one of SEQ ID
N0:2n-l, wherein n is an integer between 1-73, can be introduced as a transgene into the genome of a non-human animal. Alternatively, a non-human homologue of the human NOVX gene, such as a mouse NOVX gene, can be isolated based on hybridization to the human NOVX cDNA (described further supra) and used as a transgene. Intronic sequences and polyadenylation signals can also be included in the transgene to increase the efficiency of expression of the transgene. A tissue-specific regulatory sequences) can be operably-linked to the NOVX transgene to direct expressioi~~bf NO'~X"'protein to'particuTar~~
cells. Methods for generating transgenic animals via embryo manipulation and microinjection, particularly animals such as mice, have become conventional in the art and are described, for example, in U.S. Patent Nos. 4,736,866; 4,870,009; and 4,873,191; and Hogan, 1986. In: MANIPULATING THE MOUSE EMBRYO, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. Similar methods are used for production of other transgenic animals. A transgenic founder animal can be identified based upon the presence of the NOVX transgene in its genome and/or expression of NOVX mRNA in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals carrying the transgene. Moreover, transgenic animals carrying a transgene-encoding NOVX protein can further be bred to other transgenic animals carrying other transgenes.
To create a homologous recombinant animal, a vector is prepared which contains at least a portion of a NOVX gene into which a deletion, addition or substitution has been introduced to thereby alter, e.g., functionally disrupt, the NOVX gene. The NOVX gene can be a human gene (e.g., the cDNA of any one of SEQ ID N0:2~-1, wherein n is an integer between I-73), but more preferably, is a non-human homologue of a human NOVX
gene. For example, a mouse homologue of human NOVX gene of SEQ ID N0:2~-1, wherein h is an integer between 1-73, can be used to construct a homologous recombination vector suitable for altering an endogenous NOVX gene in the mouse genome. In one embodiment, the vector is designed such that, upon homologous recombination, the endogenous NOVX gene is functionally disrupted (i. e., no longer encodes a functional protein; also referred to as a "knock out" vector).
Alternatively, the vector can be designed such that, upon homologous recombination, the endogenous NOVX gene is mutated or otherwise altered but still encodes functional protein (e.g., the upstream regulatory region can be altered to thereby alter the expression of the endogenous NOVX protein). In the homologous recombination vector, the altered portion of the NOVX gene is flanked at its 5'- and 3'-termini by additional nucleic acid of the NOVX gene to allow for homologous recombination to occur between the exogenous NOVX gene carried by the vector and an endogenous NOVX
gene in an embryonic stem cell. The additional flanking NOVX nucleic acid is of suffcient length for successful homologous recombination with the endogenous gene.
Typically, several kilobases of flanking DNA (both at the S'- and 3'-termini) are included in the vector. See, e.g., Thomas, et al., 1987. Cell 51: 503 for a description of homologous recombination vectors. The vector is ten introduced into' aii°'~rlibryo'3ii'c"stein cell°"line ~e.g., by electroporation) and cells in which the introduced NOVX gene has homologously-recombined with the endogenous NOVX gene are selected. See, e.g., Li, et al., 1992. Cell 69: 915.
The selected cells are then injected into a blastocyst of an animal (e.g., a mouse) to form aggregation chimeras. See, e. g., Bradley, 1987. In: TERATOCARCINOMAS AND
EMBRYONIC STEM CELLS: A PRACTICAL APPROACH, Robertson, ed. IRL, Oxford, pp.
113-152. A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term. Progeny harboring the homologously-recombined DNA in their germ cells can be used to breed animals in which all cells of the animal contain the homologously-recombined DNA by germline transmission of the transgene. Methods for constructing homologous recombination vectors and homologous recombinant animals are described further in Bradley, 1991. Curr. Opin.
Biotechnol. 2:
823-829; PCT International Publication Nos.: WO 90/11354; WO 91/01140; WO
92/0968;
and WO 93/04169.
In another embodiment, transgenic non-humans animals can be produced that contain selected systems that allow for regulated expression of the transgene.
One example of such a system is the cre/loxP recombinase system of bacteriophage P1. For a description of the cre/loxP recombinase system, See, e.g., Lakso, et al., 1992. Proc.
Natl. Acad. Sci.
LISA 89: 6232-6236. Another example of a recombinase system is the FLP
recombinase system of Saccharomyces cerevisiae. See, O'Gorman, et al., 1991. Science 251:1351-1355.
If a cre/loxP recombinase system is used to regulate expression of the transgene, animals containing transgenes encoding both the Cre recombinase and a selected protein are required. Such animals can be provided through the construction of "double"
transgenic animals, e.g., by mating two transgenic animals, one containing a transgene encoding a selected protein and the other containing a transgene encoding a recombinase.
Clones of the non-human transgenic animals described herein can also be produced according to the methods described in Wilmut, et al., 1997. Nature 385: 810-813. In brief, a cell (e.g., a somatic cell) from the transgenic animal can be isolated and induced to exit the growth cycle and enter Go phase. The quiescent cell can then be fused, e.g., through the use of electrical pulses, to an enucleated oocyte from an animal of the same species from which the quiescent cell is isolated. The reconstructed oocyte is then cultured such that it develops to morula or blastocyte and then transferred to pseudopregnant female foster animal. The offspring borne of this female foster animal"will lie ~a crone of the aroma! from which the cell (e. g., the somatic cell) is isolated.
Pharmaceutical Compositions The NOVX nucleic acid molecules, NOVX proteins, and anti-NOVX antibodies (also referred to herein as "active compounds") of the invention, and derivatives, fragments, analogs and homologs thereof, can be incorporated into pharmaceutical compositions suitable for administration. Such compositions typically comprise the nucleic acid molecule, protein, or antibody and a pharmaceutically acceptable carrier. As used herein, "pharmaceutically acceptable carrier" is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. Suitable carriers are described in the most recent edition of Remington's Pharmaceutical Sciences, a standard reference text in the field, which is incorporated herein by reference.
Preferred examples of such carriers or diluents include, but are not limited to, water, saline, forger's solutions, dextrose solution, and 5% human serum albumin. Liposomes and non-aqueous vehicles such as fixed oils may also be used. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.
A pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (i.e., topical), transmucosal, and rectal administration. Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components:
a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as beaizyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfate;
chelating agents such as ethylenediaminetetraacetic acid (EDTA); buffers such as acetates, citrates or phosphates, and agents for the adjustment of tonicity such as sodium chloride or dextrose. The pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.

Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor ELT" (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringeability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example,, water, ethanol, polyol (fox example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as manitol, sorbitol, sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
Sterile injectable solutions can be prepared by incorporating the active compound (e.g., aNOVX protein or anti-NOVX antibody) in the required annount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, methods of preparation are vacuum drying and freeze-drying that yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
Oral compositions generally include an inert diluent ox an edible carrier.
They can be enclosed in gelatin capsules or compressed into tablets. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules. Oral compositions can also be prepared using a fluid carrier for use as a mouthwash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed. Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition. The tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes;
a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin;
or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.
For administration by inhalation, the compounds are delivered in the form of an aerosol spray from pressured container or dispenser which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.
Systemic administration can also be by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid' derivatives. Transmucosal administration can be accomplished through the use of nasal sprays or suppositories. For transdermal administration, the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.
The compounds can also be prepared in the form of suppositories (e.g., with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.
In one embodiment, the active compounds are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems.
Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. The materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc.
Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers.
These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Patent No. 4,522,811.
It is especially advantageous to formulate oral or parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique characteristics of the active compound and the particular therapeutic effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals.
The nucleic acid molecules of the invention can be inserted into vectors and used as gene therapy vectors. Gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (see, e.g., U.S. Patent No.
5,328,470) or by stereotactic injection (see, e.g., Chen, et al., 1994. Proc. Natl. Acad. Sci.
USA 91:
3054-3057). The pharmaceutical preparation of the gene therapy vector can include the gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded. Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can include one or more cells that produce the gene delivery system.
The pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.
Screening and Detection Methods The isolated nucleic acid molecules of the invention can be used to express NOVX
protein (e.g., via a recombinant expression vector in a host cell in gene therapy applications), to detect NOVX mRNA (e.g., in a biological sample) or a genetic lesion in a NOVX gene, and to modulate NOVX activity, as described further, below. In addition, the NOVX proteins can be used to screen drugs or compounds that modulate the NOVX
protein activity or expression as well as to treat disorders characterized by insufficient or excessive production of NOVX protein or production of NOVX protein forms that have decreased or aberrant activity compared to NOVX wild-type protein (e.g.;
diabetes (regulates insulin release); obesity (binds and transport lipids); metabolic disturbances associated with obesity, the metabolic syndrome X as well as anorexia and wasting disorders associated with chronic diseases and various cancers, and infectious disease(possesses anti-microbial activity) and the various dyslipidemias. In addition, the anti-NOVX antibodies of the invention can be used to detect and isolate NOVX
proteins and modulate NOVX activity. In yet a further aspect, the invention can be used in methods to influence appetite, absorption of nutrients and the disposition of metabolic substrates in both a positive and negative fashion.
The invention further pertains to novel agents identified by the screening assays described herein and uses thereof for treatments as described, supra.
Screening Assays The invention provides a method (also referred to herein as a "screening assay") for identifying modulators, i.e., candidate or test compounds or agents (e.g., peptides, peptidomimetics, small molecules or other drugs) that bind to NOVX proteins or have a stimulatory or inhibitory effect on, e.g., NOVX protein expression orNOVX
protein activity. The invention also includes compounds identified in the screening assays described herein.
In one embodiment, the invention provides assays for screening candidate or test compounds which bind to or modulate the activity of the membrane-bound form of a NOVX protein or polypeptide or biologically-active portion thereof. The test compounds of the invention can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the "one-bead one-compound" library method; and synthetic library methods using affinity chromatography selection. The biological library approach is limited to peptide libraries, while the other four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds. See, e.g., Lam, 1997.
A~tica~zcer Drug Design 12: 145.
A "small molecule" as used herein, is meant to refer to a composition that has a molecular weight of less than about 5 kD and most preferably less than about 4 kD. Small molecules can be, e.g., nucleic acids, peptides, polypeptides, peptidomimetics, carbohydrates, lipids or other organic or inorganic molecules. Libraries of chemical and/or biological mixtures, such as fungal, bacterial, or algal extracts, are known in the art and can be screened with any of the assays of the invention.
Examples of methods for the synthesis of molecular libraries can be found in the art, for example in: DeWitt, et al., 1993. Pi°oc. Natl. Acad. Sci.
U.S.A. 90: 6909; Erb, et al., 1994. Proc. Natl. Acad. Sci. U.S.A. 9I: 11422; Zuckermann, et al., 1994. J.
Med. Chem. 37:
2678; Cho, et al., 1993. Seience 261: 1303; Carrell, et al., 1994. Angew.
Clzenz. Int. Ed.

Engl. 33: 2059; Carell, et al., 1994. Angew. Chem. Int. Ed. Engl. 33: 2061;
and Gallop, et al., 1994. J. Med. Chern. 37: 1233.
Libraries of compounds may be presented in solution (e.g., Houghten, 1992.
Biotechniques 13: 412-421), or on beads (Lam, 1991. Nature 354: 82-84), on chips (Fodor, 1993. Nature 364: 555-556), bacteria (Ladner, U.S. Patent No. 5,223,409), spores (Ladner, U.S. Patent 5,233,409), plasmids (Cull, et al., 1992. P~oc. Natl. Acad. Sci.
USA 89:
1865-1869) or on phage (Scott and Smith, 1990. Science 249: 386-390;
Devlin,1990.
Science 249: 404-406; Cwirla, et al., 1990. Proc. Natl. Acad. Sci. U.SA. 87:
6378-6382;
Felici, 1991. J. Mol. Biol. 222: 301-310; Ladner, U.S. Patent No. 5,233,409.).
In one embodiment, an assay is a cell-based assay in which a cell which expresses a membrane-bound form of NOVX protein, or a biologically-active portion thereof, on the cell surface is contacted with a test compound and the ability of the test compound to bind to a NOVX protein determined. The cell, for example, can of mammalian origin or a yeast cell. Determining the ability of the test compound to bind to the NOVX protein can be accomplished, for example, by coupling the test compound with a radioisotope or enzymatic label such that binding of the test compound to the NOVX protein or biologically-active portion thereof can be determined by detecting the labeled compound in a complex. For example, test compounds can be labeled with 1251, 3sS, iaC, or 3H, either directly or indirectly, and the radioisotope detected by direct counting of radioemission or by scintillation counting. Alternatively, test compounds can be enzymatically-labeled with, for example, horseradish peroxidase, alkaline phosphatase, or luciferase, and the enzymatic label detected by determination of conversion of an appropriate substrate to product. In one embodiment, the assay comprises contacting a cell which expresses a membrane-bound form of NOVX protein, or a biologically-active portion thereof, on the cell surface with a known compound which binds NOVX to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with a NOVX protein, wherein determining the ability of the test compound to interact with a NOVX protein comprises determining the ability of the test compound to preferentially bind to NOVX protein or a biologically-active portion thereof as compared to the known compound.
In another embodiment, an assay is a cell-based assay comprising contacting a cell expressing a membrane-bound form of NOVX protein, or a biologically-active portion thereof, on the cell surface with a test compound and determining the ability of the test compound to modulate (e.g., stimulate or inhibit) the activity of the NOVX
protein or biologically-active portion thereof. Determining the ability of the test compound to modulate the activity of NOVX or a biologically-active portion thereof can be accomplished, for example, by determining the ability of the NOVX protein to bind to or interact with a NOVX target molecule. As used herein, a "target molecule" is a molecule with which a NOVX protein binds or interacts in nature, for example, a molecule on the suxface of a cell which expresses a NOVX interacting protein, a molecule on the surface of a second cell, a molecule in the extracellular milieu, a molecule associated with the internal surface of a cell membrane or a cytoplasmic molecule. A NOVX target molecule can be a non-NOVX molecule or a NOVX protein or polypeptide of the invention. In one embodiment, a NOVX target molecule is a component of a signal transduction pathway that facilitates transduction of an extracellular signal (e.g. a signal generated by binding of a compound to a membrane-bound NOVX molecule) through the cell membrane and into the cell. The target, for example, can be a second intercellular protein that has catalytic activity or a protein that facilitates the association of downstream signaling molecules with NOVX.
Determining the ability of the NOVX protein to bind to or interact with a NOVX
target molecule can be accomplished by one of the methods described above for determining direct binding. In one embodiment, determining the ability of the NOVX
protein to bind to or interact with a NOVX target molecule can be accomplished by determining the activity of the target molecule. For example, the activity of the target molecule can be determined by detecting induction of a cellular second messenger of the target (i.e. intracellular Ca2+, diacylglycerol, IP3, etc.), detecting catalytic/enzymatic activity of the target an appropriate substrate, detecting the induction of a reporter gene (comprising a NOVX-responsive regulatory element operatively linked to a nucleic acid encoding a detectable marker, e.g., luciferase), or detecting a cellular response, for example, cell survival, cellular differentiation, or cell proliferation.
In yet another embodiment, an assay of the invention is a cell-free assay comprising contacting a NOVX protein or biologically-active portion thereof with a test compound and determining the ability of the test compound to bind to the NOVX protein or biologically-active portion thereof. Binding of the test compound to the NOVX protein can be determined either directly or indirectly as described above. In one such embodiment, the assay comprises contacting the NOVX protein or biologically-active portion thereof with a known compound which binds NOVX to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with a NOVX protein, wherein determining the ability of the test compound to interact with a NOVX protein comprises determining the ability of the test compound to preferentially bind to NOVX or biologically-active portion thereof as compared to the known compound.
In still another embodiment, an assay is a cell-free assay comprising contacting NOVX protein or biologically-active portion thereof with a test compound and determining the ability of the test compound to modulate (e.g. stimulate or inhibit) the activity of the NOVX protein or biologically-active portion thereof. Determining the ability of the test compound to modulate the activity of NOVX can be accomplished, for example, by determining the ability of the NOVX protein to bind to a NOVX target molecule by one of the methods described above for determining direct binding. In an alternative embodiment, determining the ability of the test compound to modulate the activity of NOVX
protein can be accomplished by determining the ability of the NOVX protein further modulate a NOVX target molecule. For example, the catalytic/enzymatic activity of the target molecule on an appropriate substrate can be determined as described, supra.
In yet another embodiment, the cell-free assay comprises contacting the NOVX
protein or biologically-active portion thereof with a known compound which binds NOVX
protein to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with a NOVX protein, wherein determining the ability of the test compound to interact with a NOVX protein comprises determining the ability of the NOVX protein to preferentially bind to or modulate the activity of a NOVX target molecule.
The cell-free assays of the invention axe amenable to use of both the soluble form or the membrane-bound form of NOVX protein. In the case of cell-free assays comprising the membrane-bound form of NOVX protein, it may be desirable to utilize a solubilizing agent such that the membrane-bound form of NOVX protein is maintained in solution.
Examples of such solubilizing agents include non-ionic detergents such as n-octylglucoside, n-dodecylglucoside, n-dodecylmaltoside, octanoyl-N-methylglucamide, decanoyl-N-methylglucamide, Triton° X-100, Triton~ X-114, Thesit°, Isotridecypoly(ethylene glycol ether)", N-dodecyl--N,N-dimethyl-3-ammonio-1-propane sulfonate, 3-(3-cholamidopropyl) dimethylamminiol-1-propane sulfonate (CHAPS), or 3-(3-cholamidopropyl)dimethylamminiol-2-hydroxy-1-propane sulfonate (CHAPSO).
In more than one embodiment of the above assay methods of the invention, it may be desirable to immobilize either NOVX protein or its target molecule to facilitate separation of complexed from uncomplexed forms of one or both of the proteins, as well as to accommodate automation of the assay. Binding of a test' coiizpound'to NOVX'protein, or interaction of NOVX protein with a target molecule in the presence and absence of a candidate compound, can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtiter plates, test tubes, and micro-centrifuge tubes. In one embodiment, a fusion protein can be provided that adds a domain that allows one or both of the proteins to be bound to a matrix. For example, GST-NOVX fusion proteins or GST-target fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, MO) or glutathione derivatized microtiter plates, that are then combined with the test compound or the test compound and either the non-adsorbed target protein or NOVX protein, and the mixture is incubated under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH). Following incubation, the beads or microtiter plate wells are washed to remove any unbound components, the matrix immobilized in the case of beads, complex determined either directly or indirectly, for example, as described, supra.
Alternatively, the complexes can be dissociated from the matrix, and the level of NOVX protein binding or activity determined using standard techniques.
Other techniques for immobilizing proteins on matrices can also be used in the screening assays of the invention. For example, either the NOVX protein or its target molecule can be immobilized utilizing conjugation of biotin and streptavidin.
Biotinylated NOVX protein or target molecules can be prepared from biotin-NHS
(N-hydroxy-succinimide) using techniques well-known within the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, Ill.), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical). Alternatively, antibodies reactive with NOVX
protein or target molecules, but which do not interfere with binding of the NOVX protein to its target molecule, can be derivatized to the wells of the plate, and unbound target or NOVX protein trapped in the wells by antibody conjugation. Methods for detecting such complexes, in addition to those described above for the GST-immobilized complexes, include immunodetection of complexes using antibodies reactive with the NOVX protein or target molecule, as well as enzyme-linked assays that rely on detecting an enzymatic activity associated with the NOVX protein or target molecule.
In another embodiment, modulators of NOVX protein expression are identified in a method wherein a cell is contacted with a candidate compound and the expression of NOVX mRNA or protein in the cell is determined. The level of expression of NOVX
mRNA or protein in the presence of the candidate compound is compared to the level of expression of NOVX mRNA or protein in the absence of the candidate compound.
The candidate compound can then be identified as a modulator of NOVX mRNA or protein expression based upon this comparison. For example, when expression of NOVX
mRNA
or protein is greater (i. e., statistically significantly greater) in the presence of the candidate compound than in its absence, the candidate compound is identified as a stimulator of NOVX mRNA or protein expression. Alternatively, when expression of NOVX mRNA
or protein is less (statistically significantly less) in the presence of the candidate compound than in its absence, the candidate compound is identified as an inhibitor of NOVX mRNA
or protein expression. The level of NOVX mRNA or protein expression in the cells can be determined by methods described herein for detecting NOVX mRNA or protein.
In yet another aspect of the invention, the NOVX proteins can be used as "bait proteins" in a two-hybrid assay or three hybrid assay (see, e.g., U.S. Patent No. 5,283,3I7;
Zervos, et al., 1993. Cell 72: 223-232; Madura, et al., 1993. J. Biol. Chem.
268:
12046-12054; Bartel, et al., 1993. Bioteehnigues 14: 920-924; Iwabuchi, et al., 1993.
O~cogeue 8: 1693-1696; and Brent WO 94/10300), to identify other proteins that bind to or interact with NOVX ("NOVX-binding proteins" or "NOVX-by") and modulate NOVX
activity. Such NOVX-binding proteins are also involved in the propagation of signals by the NOVX proteins as, for example, upstream or downstream elements of the NOVX
pathway.
The two-hybrid system is based on the modular nature of most transcription factors, which consist of separable DNA-binding and activation domains. Briefly, the assay utilizes two different DNA constructs. In one construct, the gene that codes for NOVX
is fused to a gene encoding the DNA binding domain of a known transcription factor (e.g., GAL-4). In the other construct, a DNA sequence, from a library of DNA sequences, that encodes an unidentified protein ("prey" or "sample") is fused to a gene that codes for the activation domain of the known transcription factor. If the "bait" and the "prey"
proteins are able to interact, in vivo, forming a NOVX-dependent complex, the DNA-binding and activation domains of the transcription factor are brought into close proximity. This proximity allows transcription of a reporter gene (e.g., LacZ) that is operably linked to a transcriptional regulatory site responsive to the transcription factor. Expression of the reporter gene can be detected and cell colonies containing the functional transcription factor can be isolated and used to obtain the cloned gene that encodes the protein which interacts with NOVX.
The invention further pertains to novel agents identified by the aforementioned screening assays and uses thereof for treatments as described herein.

Detection Assays Portions or fragments of the cDNA sequences identified herein (and the corresponding complete gene sequences) can be used in numerous ways as polynucleotide reagents. By way of example, and not of limitation, these sequences can be used to: (i) map their respective genes on a chromosome; and, thus, locate gene regions associated with genetic disease; (ii) identify an individual from a minute biological sample (tissue typing);
and (iii) aid in forensic identification of a biological sample. Some of these applications are described in the subsections, below.
Chromosome Mapping Once the sequence (or a portion of the sequence) of a gene has been isolated, this sequence can be used to map the location of the gene on a chromosome. This process is called chromosome mapping. Accordingly, portions or fragments of the NOVX
sequences of SEQ ID NO:2n-l, wherein n is an integer between 1-73, or fragments or derivatives thereof, can be used to map the location of the NOVX genes, respectively, on a chromosome. The mapping of the NOVX sequences to chromosomes is an important first step in correlating these sequences with genes associated with disease.
Briefly, NOVX genes can be mapped to chromosomes by preparing PCR primers (preferably 15-25 by in length) from the NOVX sequences. Computer analysis of the NOVX, sequences can be used to rapidly select primers that do not span more than one exon in the genomic DNA, thus complicating the amplification process. These primers can then be used for PCR screening of somatic cell hybrids containing individual human chromosomes. Only those hybrids containing the human gene corresponding to the NOVX
sequences will yield an amplified fragment.
Somatic cell hybrids are prepared by fusing somatic cells from different mammals (e.g., human and mouse cells). As hybrids of human and mouse cells grow and divide, they gradually lose human chromosomes in random order, but retain the mouse chromosomes.
By using media in which mouse cells cannot grow, because they lack a particular enzyme, but in which human cells can, the one human chromosome that contains the gene encoding the needed enzyme will be retained. By using various media, panels of hybrid cell lines can be established. Each cell line in a panel contains either a single human chromosome or a small number of human chromosomes, and a full set of mouse chromosomes, allowing easy mapping of individual genes to specific human chromosomes. See, e.g., D'Eustachio, et al., 1983. Science 220: 919-924. Somatic cell hybrids containing only fragments of human chromosomes can also be produced by using human chromosomes with translocations and deletions.
PCR mapping of somatic cell hybrids is a rapid procedure for assigning a particular sequence to a particular chromosome. Three or more sequences can be assigned per day using a single thermal cycler. Using the NOVX sequences to design oligonucleotide . primers, sub-localization can be achieved with panels of fragments from specific chromosomes.
Fluorescence in situ hybridization (FISH) of a DNA sequence to a metaphase chromosomal spread can further be used to provide a precise chromosomal location in one step. Chromosome spreads can be made using cells whose division has been blocked in metaphase by a chemical like colcemid that disrupts the mitotic spindle. The chromosomes can be treated briefly with trypsin, and then stained with Giemsa. A pattern of light and dark bands develops on each chromosome, so that the chromosomes can be identified individually. The FISH technique can be used with a DNA sequence as short as 500 or 600 bases. However, clones larger than 1,000 bases have a higher likelihood of binding to a unique chromosomal location with sufficient signal intensity for simple detection.
Preferably 1,000 bases, and more preferably 2,000 bases, will suffice to get good results at a reasonable amount of time. For a review of this technique, see, Verma, et al., HUMAN
CHROMOSOMES: A MANUAL OF BASIC TECHNIQUES (Pergamon Press, New York 1988).
Reagents for chromosome mapping can be used individually to mark a single chromosome or a single site on that chromosome, or panels of reagents can be used for marking multiple sites and/or multiple chromosomes. Reagents corresponding to noncoding regions of the genes actually are preferred for mapping purposes.
Coding sequences are more likely to be conserved within gene families, thus increasing the chance of cross hybridizations during chromosomal mapping.
Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be correlated with genetic map data. Such data are found, e.g., in McKusick, MENDELIAN INHERITANCE IN MAN, available on-line through Johns Hopkins University Welch Medical Library). The relationship between genes and disease, mapped to the same chromosomal region, can then be identified through linkage analysis (co-inheritance of physically adjacent genes), described in, e.g., Egeland, et al., 1987. Nature, 325: 783-787.

Moreover, differences in the DNA sequences between individuals affected and unaffected with a disease associated with the NOVX gene, can be determined. If a mutation is observed in some or all of the affected individuals but not in any unaffected individuals, then the mutation is likely to be the causative agent of the particular disease.
Comparison of affected and unaffected individuals generally involves first looking for structural alterations in the chromosomes, such as deletions or translocations that are visible from chromosome spreads or detectable using PCR based on that DNA
sequence.
Ultimately, complete sequencing of genes from several individuals can be performed to confirm the presence of a mutation and to distinguish mutations from polymorphisms.
Tissue Typing The NOVX sequences of the invention can also be used to identify individuals from minute biological samples. In this technique, an individual's genomic DNA is digested with one or more restriction enzymes, and probed on a Southern blot to yield unique bands for identification. The sequences of the invention are useful as additional DNA markers for RFLP ("restriction fragment length poIymorphisrns," described in U.S. Patent No.
5,272,057).
Furthermore, the sequences of the invention can be used to provide an alternative technique that determines the actual base-by-base DNA sequence of selected portions of an individual's genome. Thus, the NOVX sequences described herein can be used to prepare two PCR primers from the 5'- and 3'-termini of the sequences. These primers can then be used to amplify an individual's DNA and subsequently sequence it.
Panels of corresponding DNA sequences from individuals, prepared in this manner, can provide unique individual identifications, as each individual will have a unique set of such DNA sequences due to allelic differences. The sequences of the invention can'be used to obtain such identification sequences from individuals and from tissue. The NOVX
sequences of the invention uniquely represent portions of the human genome.
Allelic variation occurs to some degree in the coding regions of these sequences, and to a greater degree in the noncoding regions. It is estimated that allelic variation between individual humans occurs with a frequency of about once per each 500 bases. Much of the allelic variation is due to single nucleotide polyrnorphisms (SNPs), which include restriction fragment length polymorphisms (RFLPs).
Each of the sequences described herein can, to some degree, be used as a standard against which DNA from an individual can be compared for identification purposes.

Because greater numbers of polymorphisms occur in the noncocling regions, fewer sequences are necessary to differentiate individuals. The noncoding sequences can comfortably provide positive individual identification with a panel of perhaps 10 to 1,000 primers that each yield a noncoding amplified sequence of 100 bases. If coding sequences, such as those of SEQ ID N0:2tZ-l, wherein n is an integer between 1-73, are used, a more appropriate number of primers for positive individual identification would be 500-2,000.
Predictive Medicine The invention also pertains to the field of predictive medicine in which diagnostic assays, prognostic assays, pharmacogenomics, and monitoring clinical trials are used for prognostic (predictive) purposes to thereby treat an individual praphylactically.
Accordingly, one aspect of the invention relates to diagnostic assays for determining NOVX protein and/or nucleic acid expression as well as NOVX activity, in the context of a biological sample (e.g., blood, serum, cells, tissue) to thereby determine whether an individual is afflicted with a disease or disorder, or is at risk of developing a disorder, associated with aberrant NOVX expression or activity. The disorders include metabolic disorders, diabetes, obesity, infectious disease, anorexia, cancer-associated cachexia, cancer, neurodegenerative disorders, Alzheimer's Disease, Parkinson's Disorder, immune disorders, and hematopoietic disorders, and the various dyslipidemias, metabolic disturbances associated with obesity, the metabolic syndrome X and wasting disorders associated with chronic diseases and various cancers. The invention also provides for prognostic (or predictive) assays fox determining whether an individual is at risk of developing a disorder associated with NOVX protein, nucleic acid expression or activity.
For example, mutations in a NOVX gene can be assayed in a biological sample.
Such assays can be used for prognostic or predictive purpose to thereby prophylactically treat an individual prior to the onset of a disorder characterized by or associated with NOVX
protein, nucleic acid expression, or biological activity.
Another aspect of the invention provides methods for determining NOVX protein, nucleic acid expression or activity in an individual to thereby select appropriate therapeutic or prophylactic agents for that individual (referred to herein as "pharmacogenomics").
Pharmacogenomics allows far the selection of agents (e.g., drugs) for therapeutic or prophylactic treatment of an individual based on the genotype of the individual (e.g., the genotype of the individual examined to determine the ability of the individual to respond to a particular agent.) Yet another aspect of the invention pertains to monitoring the influence of agents (e.g., drugs, compounds) on the expression or activity of NOVX in clinical trials.
These and other agents are described in further detail in the following sections.
Diagnostic Assays An exemplary method for detecting the presence or absence of NOVX in a biological sample involves obtaining a biological sample from a test subject and contacting the biological sample with a compound or an agent capable of detecting NOVX
protein or nucleic acid (e.g., mRNA, genomic DNA) that encodes NOVX protein such that the presence of NOVX is detected in the biological sample. An agent for detecting NOVX
mRNA or genomic DNA is a labeled nucleic acid probe capable of hybridizing to NOVX
mRNA or genomic DNA. The nucleic acid probe can be, for example, a full-length NOVX
nucleic acid, such as the nucleic acid of SEQ ID N0:2n-l, wherein ~ is an integer between 1-73, or a portion thereof, such as an oligonucleotide of at least 15, 30, 50, 100, 250 or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to NOVX mRNA or genomic DNA. Other suitable probes for use in the diagnostic assays of the invention are described herein.
An agent for detecting NOVX protein is an antibody capable of binding to NOVX
protein, preferably an antibody with a detectable label. Antibodies can be polyclonal, or more preferably, monoclonal. An intact antibody, or a fragment thereof (e.g., Fab or F(ab')2) can be used. The term "labeled", with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i. e. , physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled. Examples of indirect labeling include detection of a primary antibody using a fluorescently-labeled secondary antibody and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently-labeled streptavidin. The term "biological sample" is intended to include tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject. That is, the detection method of the invention can be used to detect NOVX mRNA, protein, or genomic DNA in a biological sample ivy vitro as well as i~ vivo. For example, i~ vitro techniques for detection of NOVX mRNA include Northern hybridizations and in situ hybridizations. Ih vitro techniques for detection of NOVX
protein include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations, and immunofluorescence. l~ vitro techniques for detection of NOVX genomic DNA include Southern hybridizations. Furthermore, in vivo techniques for detection of NOVX protein include introducing into a subject a labeled anti NOVX
antibody. For example, the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques.
In one embodiment, the biological sample contains protein molecules from the test subject. Alternatively, the biological sample can contain mRNA molecules from the test subject or genomic DNA molecules from the test subject. A preferred biological sample is a peripheral blood leukocyte sample isolated by conventional means from a subject.
In another embodiment, the methods further involve obtaining a control biological sample from a control subject, contacting the control sample with a compound or agent capable of detecting NOVX protein, mRNA, or genomic DNA, such that the presence of NOVX protein, mRNA or genomic DNA is detected in the biological sample, and comparing the presence of NOVX protein, mRNA or genomic DNA in the control sample with the presence of NOVX protein, mRNA or genomic DNA in the test sample.
The invention also encompasses kits for detecting the presence of NOVX in a biological sample. For example, the kit can comprise: a labeled compound or agent capable of detecting NOVX protein or mRNA in a biological sample; means for determining the amount of NOVX in the sample; and means for comparing the amount of NOVX in the sample with a standard. The compound or agent can be packaged in a suitable container. The kit can further comprise instructions for using the kit to detect NOVX protein or nucleic acid.
Prognostic Assays The diagnostic methods described herein can furthermore be utilized to identify subjects having or at risk of developing a disease or disorder associated with aberrant NOVX expression or activity. For example, the assays described herein, such as the preceding diagnostic assays or the following assays, can be utilized to identify a subject having or at risk of developing a disorder associated with NOVX protein, nucleic acid expression or activity. Alternatively, the prognostic assays can be utilized to identify a subject having or at risk for developing a disease or disorder. Thus, the invention provides a method for identifying a disease or disorder associated with aberrant NOVX
expression or activity in which a test sample is obtained from a subject and NOVX protein or nucleic acid (e.g., mRNA, genomic DNA) is detected, wherein the presence of NOVX
protein or nucleic acid is diagnostic for a subject having or at risk of developing a disease or disorder associated with aberrant NOVX expression or activity. As used herein, a "test sample"
refers to a biological sample obtained from a subject of interest. For example, a test sample can be a biological fluid (e.g., serum), cell sample, or tissue.
Furthermore, the prognostic assays described herein can be used to determine whether a subject can be administered an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate) to treat a disease or disorder associated with aberrant NOVX expression or activity. For example, such methods can be used to determine whether a subject can be effectively treated with an agent for a disorder. Thus, the invention provides methods for determining whether a subject can be effectively treated with an agent for a disorder associated with aberrant NOVX expression or activity in which a test sample is obtained and NOVX
protein or nucleic acid is detected (e.g., wherein the presence of NOVX
protein or nucleic acid is diagnostic for a subject that can be administered the agent to treat a disorder associated with aberrant NOVX expression or activity).
The methods of the invention can also be used to detect genetic lesions in a NOVX
gene, thereby determining if a subject with the lesioned gene is at risk for a disorder characterized by aberrant cell proliferation and/or differentiation. In various embodiments, the methods include detecting, in a sample of cells from the subject, the presence or absence of a genetic lesion characterized by at least one of an alteration affecting the integrity of a gene encoding a NOVX-protein, or the misexpression of the NOVX
gene.
For example, such genetic lesions can be detected by ascertaining the existence of at least one of-. (i) a deletion of one or more nucleotides from a NOVX gene; (ii) an addition of one or more nucleotides to a NOVX gene; (iii) a substitution of one or more nucleotides of a NOVX gene, (iv) a chromosomal rearrangement of a NOVX gene; (v) an alteration in the level of a messenger RNA transcript of a NOVX gene, (vi) aberrant modification of a NOVX gene, such as of the methylation pattern of the genomic DNA, (vii) the presence of a non-wild-type splicing pattern of a messenger RNA transcript of a NOVX gene, (viii) a non-wild-type level of a NOVX protein, (ix) allelic loss of a NOVX gene, and (x) inappropriate post-translational modification of a NOVX protein. As described herein, there are a large number of assay techniques known in the art which can be used for detecting lesions in a NOVX gene. A preferred biological sample is a peripheral blood leukocyte sample isolated by conventional means from a subject. However, any biological sample containing nucleated cells may be used, including, for example, buccal mucosal cells.

In certain embodiments, detection of the lesion involves the use of a probe/primer in a polymerase chain reaction (PCR) (see, e.g., U.S. Patent Nos. 4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see, e.g., Landegran, et al., 1988. Science 241: 1077-1080; and Nakazawa, et al., 1994.
Pr~oc. Natl. Acad Sci. USA 91: 360-364), the latter of which can be particularly useful for detecting point mutations in the NOVX-gene (see, Abravaya, et al., 1995. Nucl.
Acids Res.
23: 675-682). This method can include the steps of collecting a sample of cells from a patient, isolating nucleic acid (e.g., genomic, mRNA or both) from the cells of the sample, contacting the nucleic acid sample with one or more primers that specifically hybridize to a NOVX gene under conditions such that hybridization and amplification of the NOVX gene (if present) occurs, and detecting the presence or absence of an amplification product, or detecting the size of the amplification product and comparing the length to a control sample. It is anticipated that PCR and/or LCR may be desirable to use as a preliminary amplification step in conjunction with any of the techniques used for detecting mutations described herein.
Alternative amplification methods include: self sustained sequence replication (see, Guatelli, et al., 1990. Pr~oc. Natl. Acaa'. Sci. USA 87: 1874-1878), transcriptional amplification system (see, Kwoh, et al., 1989. Proc. Natl. Acad. Sei. USA 86:
1173-1177);
Qj3 Replicase (see, Lizardi, et al, 1988. BioTechf2ology 6: 1197), or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers.
In an alternative embodiment, mutations in a NOVX gene from a sample cell can be identified by alterations in restriction enzyme cleavage patterns. For example, sample and control DNA is isolated, amplified (optionally), digested with one or more restriction endonucleases, and fragment length sizes are determined by gel electrophoresis and compared. Differences in fragment length sizes between sample and control DNA
indicates mutations in the sample DNA. Moreover, the use of sequence specific ribozymes (see, e.g., U.S. Patent No. 5,493,531) can be used to score for the presence of specific mutations by development or loss of a ribozyme cleavage site.
In other embodiments, genetic mutations in NOVX can be identified by hybridizing a sample and control nucleic acids, e.g., DNA or RNA, to high-density arrays containing hundreds or thousands of oligonucleotides probes. See, e.g., Cronin, et al., 1996. Human Mutation 7: 244-255; Kozal, et al., 1996. Nat. Med. 2: 753-759. For example, genetic mutations in NOVX can be identified in two dimensional arrays containing light-generated DNA probes as described in Cronin, et al., supra. Briefly, a first hybridization array of probes can be used to scan through Long stretches of DNA in a sample and control to identify base changes between the sequences by making linear arrays of sequential overlapping probes. This step allows the identification of point mutations.
This is followed by a second hybridization array that allows the characterization of specific mutations by using smaller, specialized probe arrays complementary to all variants or mutations detected. Each mutation array is composed of parallel probe sets, one complementary to the wild-type gene and the other complementary to the mutant gene.
In yet another embodiment, any of a variety of sequencing reactions known in the art'can be used to directly sequence the NOVX gene and detect mutations by comparing the sequence of the sample NOVX with the corresponding wild-type (control) sequence.
Examples of sequencing reactions include those based on techniques developed by Maxim and Gilbert, 1977. Proc. Natl. Acad. Sci. USA 74: 560 or Sanger, 1977. Proc.
Natl. Acad.
Sci. USA 74: 5463. It is also contemplated that any of a variety of automated sequencing procedures can be utilized when performing the diagnostic assays (see, e.g., Naeve, et al., 1995. Biotech~iques 19: 448), including sequencing by mass spectrometry (see, e.g., PCT
International Publication No. WO 94/16101; Cohen, et al., 1996. Adv.
Chromatography 36:
127-162; and Griffin, et al., 1993. Appl. Biochem. Biotechhol. 38: 147-159).
Other methods for detecting mutations in the NOVX gene include methods in which protection from cleavage agents is used to detect mismatched bases in RNA/RNA
or RNA/DNA heteroduplexes. See, e.g., Myers, et al., 1985. Science 230: 1242. In general, the art technique of "mismatch cleavage" starts by providing heteroduplexes of formed by hybridizing (labeled) RNA or DNA containing the wild-type NOVX sequence with potentially mutant RNA or DNA obtained from a tissue sample. The double-stranded duplexes axe treated with an agent that cleaves single-stranded regions of the duplex such as which will exist due to basepair mismatches between the control and sample strands.
For instance, RNA/DNA duplexes can be treated with RNase and DNA/DNA hybrids treated with S~ nuclease to enzymatically digesting the mismatched regions. In other embodiments, either DNA/DNA or RNA/DNA duplexes can be treated with hydroxylamine or osmium tetroxide and with piperidine in order to digest mismatched regions. After digestion of the mismatched regions, the resulting material is then separated by size on denaturing polyacrylamide gels to determine the site of mutation.
See, e.g., Cotton, et al., 1988. Proc. Natl. Acad. Sci. USA 85: 4397; Saleeba, et al., I
992. Methods Enzynzol. 217: 286-295. In an embodiment, the contxol DNA or RNA can be labeled for detection.
In still another embodiment, the mismatch cleavage reaction employs one or more proteins that recognize mismatched base pairs in double-stranded DNA (so called "DNA
mismatch xepair" enzymes) in defined systems for detecting and mapping point mutations in NOVX cDNAs obtained from samples of cells. For example, the mutt enzyme of E.
coli cleaves A at G/A mismatches and the thymidine DNA glycosylase from HeLa cells I O cleaves T at G/T mismatches. See, e.g., Hsu, et al., 1994.
Ca~cirzoge~zesis I5: 1657-I662.
According to an exemplary embodiment, a probe based on a NOVX sequence, e.g., a wild-type NOVX sequence, is hybridized to a cDNA or other DNA product from a test cell(s). The duplex is treated with a DNA mismatch repair enzyme, and the cleavage products, if any, can be detected from electrophoresis protocols or the like.
See, e.g., U.S.
Patent No. 5,459,039.
In other embodiments, alterations in electrophoretic mobility will be used to identify mutations in NOVX genes. For example, single strand conformation polymorphism (SSCP) may be used to detect differences in electrophoretic mobility between mutant and wild type nucleic acids. See, e.g., Orita, et al., 1989.
Proc. Natl. Acad.
Sci. USA: 86: 2766; Cotton, 1993. Mutat. Res. 285: 125-144; Hayashi, 1992.
Genet. Anal.
Tech. Appl. 9: 73-79. Single-stranded DNA fragments of sample and control NOVX
nucleic acids will be denatured and allowed to renature. The secondary structure of single-stranded nucleic acids varies according to sequence, the resulting alteration in electrophoretic mobility enables the detection of even a single base change.
The DNA
fragments may be labeled or detected with labeled probes. The sensitivity of the assay may be enhanced by using RNA (rather than DNA), in which the secondary structure is more sensitive to a change in sequence. In one embodiment, the subject method utilizes heteroduplex analysis to separate double stranded hetexoduplex molecules on the basis of changes in electrophoretic mobility. See, e.g., Keen, et al., 1991. Trefzds Gefzet. 7: 5.
In yet another embodiment, the movement of mutant or wild-type fragments in polyacrylamide gels containing a gxadient of denaturant is assayed using denaturing gradient gel electrophoresis (DGGE). See, e.g., Myers, et al., 1985. Nature 313: 495.
When DGGE is used as the method of analysis, DNA will be modified to insure that it does not completely denature, for example by adding a GC clamp of approximately 40 by of high-melting GC-rich DNA by PCR. In a further embodirrierit; a temperature gradient is used in place of a denaturing gradient to identify differences in the mobility of control and sample DNA. See, e.g., Rosenbaum and Reissner, 1987. Biophys. Cl~e~rz. 265:
12753.
Examples of other techniques fox detecting point mutations include, but are not limited to, selective oligonucleotide hybridization, selective amplification, or selective primer extension. For example, oligonucleotide primers may be prepared in which the known mutation is placed centrally and then hybridized to target DNA under conditions that permit hybridization only if a perfect match is found. See, e.g., Saiki, et al., 1986.
Nature 324: 163; Saiki, et al., 1989. Proc. Natl. Acad Sci. USA 86: 6230. Such allele specific oligonucleotides are hybridized to PCR amplified target DNA or a number of different mutations when the oligonucleotides are attached to the hybridizing membrane and hybridized with labeled target DNA.
Alternatively, allele specific amplification technology that depends on selective PCR amplification may be used in conjunction with the instant invention.
Oligonucleotides used as primers for specific amplification may carry the mutation of interest in the center of the molecule (so that amplification depends on differential hybridization;
see, e.g., Gibbs, et al., 1989. Nucl. Acids Res. 17: 2437-2448) or at the extreme 3'-terminus of one primer where, under appropriate conditions, mismatch can prevent, or reduce polymerase extension (see, e.g., Prossner, 1993. Tibtech. 11: 238). In addition it may be desirable to introduce a novel restriction site in the region of the mutation to create cleavage-based detection. See, e.g., Gasparini, et al., 1992. Mol. Cell Probes 6: 1. It is anticipated that in certain embodiments amplification may also be performed using Taq ligase for amplification. See, e.g., Barany, 1991. Proc. Natl. Acad. Sci. USA 88: 189. In such cases, ligation will occur only if there is a perfect match at the 3'-terminus of the 5' sequence, making it possible to detect the presence of a known mutation at a specific site by looking for the presence or absence of amplification.
The methods described herein may be performed, for example, by utilizing pre-packaged diagnostic kits comprising at least one probe nucleic acid or antibody reagent described herein, which may be conveniently used, e.g., in clinical settings to diagnose patients exhibiting symptoms or family history of a disease or illness involving a NOVX
gene.
Furthermore, any cell type or tissue, preferably peripheral blood leukocytes, in which NOVX is expressed may be utilized in the prognostic assays described herein.

However, any biological sample containing nucleated cells may be used, including, for example, buccaI mucosaI cells.
Pharmacogenomics Agents, or modulators that have a stimulatory or inhibitory effect on NOVX
activity (e.g., NOVX gene expression), as identified by a screening assay described herein can be administered to individuals to treat (prophylactically or therapeutically) disorders (The disorders include metabolic disorders, diabetes, obesity, infectious disease, anorexia, cancer-associated cachexia, cancer, neurodegenerative disorders, Alzheimer's Disease, Parkinson's Disorder, immune disorders, and hematopoietic disorders, and the various dyslipidemias, metabolic disturbances associated with obesity, the metabolic syndrome X
and wasting disorders associated with chronic diseases and various cancers.) In conjunction with such treatment, the pharmacogenomics (i. e., the study of the relationship between an individual's genotype and that individual's response to a foreign compound or drug) of the individual may be considered. Differences in metabolism of therapeutics can lead to severe toxicity or therapeutic failure by altering the relation between dose and blood concentration of the pharmacologically active drug. Thus, the pharmacogenomics of the individual permits the selection of effective agents (e.g., drugs) for prophylactic or therapeutic treatments based on a consideration of the individual's genotype.
Such pharmacogenornics can further be used to determine appropriate dosages and therapeutic regimens. Accordingly, the activity of NOVX protein, expression of NOVX
nucleic acid, or mutation content of NOVX genes in an individual can be determined to thereby select appropriate agents) for therapeutic or prophylactic treatment of the individual.
Pharmacogenomics deals with clinically significant hereditary variations in the response to drugs due to altered drug disposition and abnormal action in affected persons.
See e.g., Eichelbaum, 1996. Clin. Exp. Phc~rmacol. Physiol., 23: 983-985;
Linden 1997.
Clin. Chem.; 43: 254-266. In general, two types of pharmacogenetic conditions can be differentiated. Genetic conditions transmitted as a single factor altering the way drugs act on the body (altered drug action) or genetic conditions transmitted as single factors altering the way the body acts on drugs (altered drug metabolism). These pharmacogenetic conditions can occur either as rare defects or as polymorphisms. For example, glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common inherited enzymopathy in which the main clinical complication is hemolysis after ingestion of oxidant drugs (anti-malarials, sulfonamides, analgesics, nits~furans) and consumption of fava beans.
As an illustrative embodiment, the activity of drug metabolizing enzymes is a major determinant of both the intensity and duration of drug action. The discovery of genetic polymorphisms of drug metabolizing enzymes (e.g., N-acetyltransferase 2 (NAT
2) and cytochrome pregnancy zone protein precursor enzymes CYP2D6 and CYP2C 19) has provided an explanation as to why some patients do not obtain the expected drug effects or show exaggerated drug response and serious toxicity after taking the standard and safe dose of a drug. These polymorphisms are expressed in two phenotypes in the population, the extensive metabolizer (EM) and poor metabolizer (PM). The prevalence of PM is different among different populations. For example, the gene coding for CYP2D6 is highly polymorphic and several mutations have been identified in PM, which all lead to the absence of functional CYP2D6. Poor metabolizers of CYP2D6 and CYP2C19 quite frequently experience exaggerated drug response and side effects when they receive standard doses. If a metabolite is the active therapeutic moiety, PM show no therapeutic response, as demonstrated for the analgesic effect of codeine mediated by its CYP2D6-formed metabolite morphine. At the other extreme are the so called ultra-rapid metabolizers who do not respond to standard doses. Recently, the molecular basis of ultra-rapid metabolism has been identified to be due to CYP2D6 gene amplifcation.
Thus, the activity of NOVX protein, expression of NOVX nucleic acid, or mutation content of NOVX genes in an individual can be determined to thereby select appropriate agents) for therapeutic or prophylactic treatment of the individual. In addition, pharmacogenetic studies can be used to apply genotyping of polymorphic alleles encoding drug-metabolizing enzymes to the identification of an individual's drug responsiveness phenotype. This knowledge, when applied to dosing or drug selection, can avoid adverse reactions or therapeutic failure and thus enhance therapeutic_or prophylactic efficiency when treating a subject with a NOVX modulator, such as a modulator identified by one of the exemplary screening assays described herein.
Monitoring of Effects During Clinical Trials Monitoring the influence of agents (e.g., drugs, compounds) on the expression or activity ofNOVX (e.g., the ability to modulate aberrant cell proliferation and/or differentiation) can be applied not only in basic drug screening, but also in clinical trials.
For example, the effectiveness of an agent determined by a screening assay as described herein to increase NOVX gene expression, protein levels, or upregulate NOVX
activity, can be monitored in clinical trails of subjects exhibiting decreased NOVX gene expression, protein levels, or downregulated NOVX activity. Alternatively, the effectiveness of an agent determined by a screening assay to decrease NOVX gene expression, protein levels, or downregulate NOVX activity, can be monitored in clinical trails of subjects exhibiting increased NOVX gene expression, protein levels, or upregulated NOVX activity.
In such clinical trials, the expression or activity of NOVX and, preferably, other genes that have been implicated in, for example, a cellular proliferation or immune disorder can be used as a "read out" or markers of the immune responsiveness of a particular cell.
By way of example, and not of limitation, genes, including NOVX, that are modulated in cells by treatment with an agent (e.g., compound, drug or small molecule) that modulates NOVX activity (e.g., identified in a screening assay as described herein) can be identified. Thus, to study the effect of agents on cellular proliferation disorders, for example, in a clinical trial, cells can be isolated and RNA prepared and analyzed for the levels of expression of NOVX and other genes implicated in the disorder. The levels of gene expression (i.e., a gene expression pattern) can be quantified by Northern blot analysis or RT-PCR, as described herein, or alternatively by measuring the amount of protein produced, by one of the methods as described herein, or by measuring the levels of activity of NOVX or other genes. In this manner, the gene expression pattern can serve as a marker, indicative of the physiological response of the cells to the agent.
Accordingly, this response state may be determined before, and at various points during, treatment of the individual with the agent.
In one embodiment, the invention provides a method for monitoring the effectiveness of treatment of a subject with an agent (e.g., an agonist, antagonist, protein, peptide, peptidomimetic, nucleic acid, small molecule, or other drug candidate identified by the screening assays described herein) comprising the steps of (i) obtaining a pre-administration sample from a subject prior to administration of the agent;
(ii) detecting the level of expression of a NOVX protein, mRNA, or genomic DNA in the preadministration sample; (iii) obtaining one or more post-administration samples from the subject; (iv) detecting the level of expression or activity of the NOVX
protein, mRNA, or genomic DNA in the post-administration samples; (v) comparing the level of expression or activity of the NOVX protein, mRNA, or genomic DNA in the pre-administration sample with the NOVX protein, mRNA, or genomic DNA in the post administration sample or samples; and (vi) altering the administration of the agent to the subject accordingly. For example, increased administration of the agent may be desirable to increase the expression or activity of NOVX to higher levels than detected, i. e., to increase the effectiveness of the agent. Alternatively, decreased administration of the agent may be desirable to decrease expression or activity of NOVX to lower levels than detected, i.e., to decrease the effectiveness of the agent.
Methods of Treatment The invention provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) a disorder or having a disorder associated with aberrant NOVX expression or activity. The disorders include cardiomyopathy, atherosclerosis, hypertension, congenital heart defects, aortic stenosis, atrial septal defect (ASD), atrioventricular (A-V) canal defect, ductus arteriosus, pulmonary stenosis, subaortic stenosis, ventricular septal defect (VSD), valve diseases, tuberous sclerosis, scleroderma, obesity, transplantation, adrenoleukodystrophy, congenital adrenal hyperplasia, prostate cancer, neoplasm; adenocarcinorna, lymphoma, uterus cancer, fertility, hemophilia, hypercoagulation, idiopathic thrombocytopenic purpura, immunodeficiencies, graft versus host disease, AIDS, bronchial astluna, Crohn's disease; multiple sclerosis, treatment of Albright Hereditary Ostoeodystrophy, and other diseases, disorders and conditions of the like.
These methods of treatment will be discussed more fully, below.
Disease and Disorders Diseases and disorders that are characterized by increased (relative to a subject not suffering from the disease or disorder) levels or biological activity may be treated with Therapeutics that antagonize (i.e., reduce or inhibit) activity. Therapeutics that antagonize activity may be administered in a therapeutic or prophylactic manner.
Therapeutics that may be utilized include, but are not limited to: (i) an aforementioned peptide, or analogs, derivatives, fragments or homologs thereof; (ii) antibodies to an aforementioned peptide;
(iii) nucleic acids encoding an aforementioned peptide; (iv) administration of antisense nucleic acid and nucleic acids that axe "dysfunctional" (i. e., due to a heterologous insertion within the coding sequences of coding sequences to an aforementioned peptide) that axe utilized to "knockout" endogenous function of an aforementioned peptide by homologous recombination (see, e.g., Capecchi, 1989. Science 244: 1288-1292); or (v) modulators ( i.e., inhibitors, agonists and antagonists, including additional peptide mimetic of the invention or antibodies specific to a peptide of the invention) that alter the interaction between an aforementioned peptide and its binding partner.
Diseases and disorders that are characterized by decreased (relative to a subject not suffering from the disease or disorder) levels or biological activity may be treated with Therapeutics that increase (i.e., are agonists to) activity. Therapeutics that upregulate activity may be administered in a therapeutic or prophylactic manner.
Therapeutics that may be utilized include, but are not limited to, an aforementioned peptide, or analogs, derivatives, fragments or homologs thereof; or an agonist that increases bioavailability.
Increased or decreased levels can be readily detected by quantifying peptide and/or RNA, by obtaining a patient tissue sample (e.g., from biopsy tissue) and assaying it in vitro for RNA or peptide levels, structure and/or activity of the expressed peptides (or mRNAs of an aforementioned peptide). Methods that are well-known within the art include, but are not limited to, immunoassays (e.g., by Western blot analysis, immunoprecipitation followed by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis, immunocytochemistry, etc.) and/or hybridization assays to detect expression of mRNAs (e.g., Northern assays, dot blots, in situ hybridization, and the like).
Prophylactic Methods In one aspect, the invention provides a method for preventing, in a subject, a disease or condition associated with an aberrant NOVX expression or activity, by administering to the subject an agent that modulates NOVX expression or at least one NOVX
activity.
Subjects at risk for a disease that is caused or contributed to by aberrant NOVX expression or activity can be identified by, for example, any or a combination of diagnostic or prognostic assays as described herein. Administration of a prophylactic agent can occur prior to the manifestation of symptoms characteristic of the NOVX aberrancy, such that a disease or disorder is prevented or, alternatively, delayed in its progression. Depending upon the type of NOVX abenrancy, for example, a NOVX agonist or NOVX
antagonist agent can be used for treating the subject. The appropriate agent can be determined based on screening assays described herein. The prophylactic methods of the invention are further discussed in the following subsections.
Therapeutic Methods Another aspect of the invention pertains to methods of modulating NOVX
expression or activity for therapeutic purposes. The modulatory method of the invention involves contacting a cell with an agent that modulates one or more of the activities of NOVX protein activity associated with the cell. An agent that modulates NOVX
protein activity can be an agent as described herein, such as a nucleic acid or a protein, a naturally-occurring cognate ligand of a NOVX protein, a peptide, a NOVX ' peptidomimetic, or other small molecule. In one embodiment, the agent stimulates one or more NOVX protein activity. Examples of such stimulatory agents include active NOVX
protein and a nucleic acid molecule encoding NOVX that has been introduced into the cell.
In another embodiment, the agent inhibits one or more NOVX protein activity.
Examples of such inhibitory agents include antisense NOVX nucleic acid molecules and anti-NOVX
antibodies. These modulatory methods can be performed in vitro (e.g., by culturing the cell with the agent) or, alternatively, in vivo (e.g., by administering the agent to a subject). As such, the invention provides methods of treating an individual afflicted with a disease or disorder characterized by aberrant expression or activity of a NOVX protein or nucleic acid molecule. In one embodiment, the method involves administering an agent (e.g, an agent identified by a screening assay described herein), or combination of agents that modulates (e.g., up-regulates or down-regulates) NOVX expression or activity. In another embodiment, the method involves administering a NOVX protein or nucleic acid molecule as therapy to compensate for reduced or aberrant NOVX expression or activity.
Stimulation of NOVX activity is desirable in situations in which NOVX is abnormally downregulated andlor in which increased NOVX activity has a beneficial effect. One example of such a situation is where a subject has a disorder characterized by aberrant cell proliferation and/or differentiation (e.g., cancer or immune associated disorders). Another example of such a situation is where the subj ect has a gestational disease (e.g., preclampsia).
Determination of the Biological Effect of the Therapeutic In various embodiments of the invention, suitable in vitro or irc vivo assays are performed to determine the effect of a specific Therapeutic and whether its administration is indicated for treatment of the affected tissue.
In various specific embodiments, in vitro assays may be performed with representative cells of the types) involved in the patient's disorder, to determine if a given Therapeutic exerts the desired effect upon the cell type(s). Compounds for use in therapy may be tested in suitable animal model systems including, but not limited to rats, mice, chicken, cows, monkeys, rabbits, and the like, prior to testing in human subjects. Similarly, for in vivo testing, any of the animal model system known in the art may be used prior to administration to human subjects.
Prophylactic and Therapeutic Uses of the Compositions of the Invention The NOVX nucleic acids and proteins of the invention are useful in potential prophylactic and therapeutic applications implicated in a variety of disorders including, but not limited to: metabolic disorders, diabetes, obesity, infectious disease, anorexia, cancer-associated cancer, neurodegenerative disorders, Alzheimer's Disease, Parkinson's Disorder, immune disorders, hematopoietic disorders, and the various dyslipidemias, metabolic disturbances associated with obesity, the metabolic syndrome X and wasting disorders associated with chronic diseases and various cancers.
As an example, a cDNA encoding the NOVX protein of the invention may be useful in gene therapy, and the protein may be useful when administered to a subject in need thereof. By way of non-limiting example, the compositions of the invention will have efficacy for treatment of patients suffering from: metabolic disorders, diabetes, obesity, infectious disease, anorexia, cancer-associated cachexia, cancer, neurodegenerative disorders, Alzheimer's Disease, Parkinson's Disorder, immune disorders, hematopoietic disorders, and the various dyslipidemias.
Both the novel nucleic acid encoding the NOVX protein, and the NOVX protein of the invention, or fragments thereof, may also be useful in diagnostic applications, wherein the presence or amount of the nucleic acid or the protein are to be assessed.
A further use could be as an anti-bacterial molecule (i. e., some peptides have been found to possess anti-bacterial properties). These materials are further useful in the generation of antibodies, which immunospecifically-bind to the novel substances of the invention for use in therapeutic or diagnostic methods.
~5 EXAMPLES
Example A: Polynucleotide and Polypeptide Sequences, and Homology Data Example 1.
The NOV 1 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table I A.
Table 1A. NOVl Sequence Analysis SEQ ID NO: 1 3430 by NOVla, ,GGGCTGCAGGAATTCCCCCACAGAGGGAGCATGACTTCGGCAACTTCACCTATCATTC
CG100653-Ol TGAAATGGGACCCCAAAAGTTTGGAAATCCGGACGCTAACAGTGGAAAGGCTGTTGGA
DNA Se 118nC~ GCCACTTGTTACACAGGTGACTACACTTGTCAACACAAGCAACAAAGGCCCATCTGGT
AAAAAGAAAGGGAGGTCAAAGAAAGCCCATGTACTAGCTGCCTCTGTAGAGCAAGCCA
CTCAGAATTTCCTGGAAAAGGGTGAACAGATCGCTAAGGAGAGTCAAGATCTCAAAGA
AGAGTTGGTGGCTGCTGTAGAGGATGTGCGCAAACAAGGTGAGACGATGCGGATCGCC
CGGCAAGGGCTTTGCTCTCCGCGGTGACACGCTTACTCATCCTGGCGGACATGGCAGA
TGTCATGAGACTTTTATCCCATCTGAAAATTGTGGAAGAGGCCCTGGAAGCTGTCAAA
AATGCTACAAATGAGCAAGACCTTGCAAACCGTTTTAAAGAGTTTGGGAAAAAGATGG
GGATGAGATGGCAGCCGCCCGAGGGGCTCTGAAGAAGAATGCCACAATGCTGTACACG
GCCTCTCAAGCATTTCTCCGCCACCCAGATGTCGCCGCTACGAGAGCCAACCGAGATT
ATGTGTTCAAACAAGTCCAGGAGGCCATCGCCGGCATCTCCAATGCTGCTCAAGCTAC
CTCGCCCACTGACGAAGCCAAGGGCCACACGGGCATCGGCGAGCTGGCTGCGGCTCTT
AATGAGTTTGACAATAAGATTATCCTGGACCCCATGACGTTCAGCGAGGCCAGGTTCC
GGCCGTCCCTGGAGGAGAGGCTGGAGAGCATCATCAGCGGCGCAGCGCTGATGGCCGA
CTCCTCCTGCACGCGAGACGACCGGCGCGAGAGGATCGTGGCGGAGTGCAACGCCGTG
CGGCAGGCGCTCCAGGACCTGCTCAGCGAGTACATGAATAATACTGGAAGGAAAGAAA
AAGGAGATCCTCTCAACATTGCGATTGATAAGATGACTAAGAAAACAAGAGATCTAAG
GAGACAGCTTCGGAAAGCAGTGATGGATCACATATCTGACTCTTTCCTGGAAACCAAT
GTTCCTTTGCTAGTTCTCATTGAGGCTGCAAAGAGCGGAAATGAAAAGGAAGTGAAAG
AATATGCCCAAGTTTTCCGTGAGCATGCCAACAAACTGGTAGAGGTTGCCAATTTGGC
CTGTTCCATCTCCAACAATGAAGAAGGGGTGAAATTAGTTCGGATGGCAGCCACCCAG
ATTGACAGCCTGTGTCCCCAGGTCATCAATGCCGCTCTGACACTGGCTGCCCGGCCAC
. AGAGCAAAGTTGCTCAGGATAACATGGACGTCTTCAAAGACCAGTGGGAGAAGCAGGT
CCGAGTGTTGACAGAGGCCGTGGATGACATCACCTCAGTGGATGACTTCCTCTCTGTC
TCAGAAAATCACATCTTGGAGGATGTGAACAAGTGTGTGATAGCCCTCCAAGAGGGCG
ATGTGGACACTCTGGACCGGACTGCAGGGGCCATCAGGGGCCGGGCAGCTCGAGTCAT
ACACATCATCAATGCTGAGATGGAGAACTATGAAGCTGGGGTTTATACTGAGAAGGTG
~TTGGAAGCTACAAAATTGCTTTCTGAAACAGTGATGCCACGCTTCGCTGAACAAGTAG
CATCGATGCCTCTCGCCTGGTGTATGATGGCGTTCGGGACATCAGAAAGGCTGTGCTG
ATGATCAGGACCCCAGAAGAACTAGAGGATGATTCTGACTTTGAGCAGGAAGATTATG
ATGTGCGTAGAGGGACAAGTGTTCAGACTGAGGATGACCAGCTCATTGCAGGGCAGAG
CGCACGGGCCATCATGGCGCAACTACCGCAGGAGGAGAAGGCAAAAATAGCTGAGCAG
GTGGAGATATTCCATCAAGAGAAAAGCAAGCTGGATGCAGAAGTGGCCAAATGGGACG
ATCATTGTACTGGCCAAGCAGATGTGTATGATCATGATGGAAAT
GACAGACTTCACAAGAGGCAAAGGCCCATTGAAAAATACATCTGATGTCATTAATGCT
GCCAAGAAAATTGCCGAAGCAGGTTCTCGAATGGACAAATTAGCTCGTGCTGTGGCTG
ATCAGCTGGACAGTGCCACATCGCTTATCCAGGCAGCTAAAAACCTGATGAATGCTGT
TGTCCTCACGGTGAAAGCATCCTATGTGGCCTCAACCAAATACCAGAAGGTCTATGGG
~6 CCCTTGTGAAGAGAGAAA.AGCCTGAAGAATTCCAGACACGAGTTCGACGAGGTTCTCA
GAAGAAACACATTTCGCCTGTACAGGCTTTAAGTGAATTCAAAGCAATGGATTCCTTC

TAGGACGATAGGTTTTAACAAGAAAGCTTTTTCTTTCTTTTCTTTCTTTCTTTTTCTT

TTTAATTCCATTTTTGTATGCATACCTGCCAGCTCGTATGCCTCTGGCATGGGGAAAT

TAAGGGAACAGTGTCTGTTTGCATGTAAGATGAGATGAGATCAATACTACTGATCCAT

CTGTAGCCTGGGAAGGAGACAGGACATTCCTGTACTAAGGTGGCACAGAGCTGTCCTT

TGCAACATTCTCATAAA.ATTGGGCACAGAGTTCGCATTGGCGCAATATTTATGGGAGT

GGGAGGGATGGGGAAAATAAACTTAACTCTACAAA.AGCAAACTCTAATGCATGCAAGA

ATCATTAGGTTGGCAGGTATATGCATAAGTGAAAAATCTGGAAGTGTAATGGTAGAAC

ATAAAACTTGTATTGCTTCTGTTTCAGTGCAAAAATGTACTAGCCAATACGCTTAAGT

GTGTGGCCCATGAATTGAACAATTTAACCTTGAAGTCTATATCCGTGATATTATGTCG

ATTTTTAACTGAGGGGAAATTAACTAGTCCAGCCTAAAATGCTTCTTTTAATCTGCAT

TCTGTTTCCTCTTCTAGTTGTGCCATTACTAGTGATCATGTTTTTTTCCCCCCTTTAA

TGAAA.ACAATAAACATCTATTTGAGACAATTAAAATCCTTCTGGGGGCACTGGAAGCA

CAATACGGTGACCAATCTTGCTTTCATTTTTTTTTCTTTTTAATTTGAACCATGATTT

TGCTAGAAATAGAAGGCCCAGTGGTGGAATATTAGAGGGAAGGAAACTGACAACGTGT

GAAAGTTA

ORF Start: ATG at 31 ORF Stop: TAG at 2611 SEQ ID NO: 2 860 as MW at 9SS2S.9kD

NOVIa, MTSATSPIILKWDPKSLEIRTLTVERLLEPLVTQVTTLVNTSNKGPSGKKKGRSKKAH

CGIOO6S3-OI V~SVEQATQNFLEKGEQIAKESQDLKEELVAAVEDVRKQGETMRIASSEFADDPCS

Protein SequenceSVKRGTMVRAARALLSAVTRLLILADMADVMRLLSHLKIVEEALEAVKNATNEQDLAN

RFKEFGKKMVKLNYVAARRQQELKDPHCRDEMAAARGALKKNATMLYTASQAFLRHPD

VAATRANRDYVFKQVQEAIAGISNAAQATSPTDEAKGHTGIGELAAALNEFDNKIILD

PMTFSEARFRPSLEERLESIISGAALMADSSCTRDDRRERIVAECNAVRQALQDLLSE

YMNNTGRKEKGDPLNIAIDKMTKKTRDLRRQLRKAVMDHISDSFLETNVPLLVLIEAA

KSGNEKEVKEYAQVFREHANKLVEVANLACSISNNEEGVKLVRMAATQIDSLCPQVIN

AALTLAARPQSKVAQDNMDVFKDQWEKQVRVLTEAVDDITSVDDFLSVSENHILEDVN

KCVIALQEGDVDTLDRTAGAIRGRAARVIHIINAEMENYEAGVYTEKVLEATKLLSET

VMPRFAEQVEVAIEALSANVPQPFEENEFIDASRLVYDGVRDIRKAVLMIRTPEELED

DSDFEQEDYDVRRGTSVQTEDDQLIAGQSARAIMAQLPQEEKAKIAEQVEIFHQEKSK

LDAEVAKWDDSGNDIIVLAKQMCMIMMEMTDFTRGKGPLKNTSDVINAAKKIAEAGSR

MDKLARAVADQLDSATSLIQAAKNLMNAVVLTVKASYVASTKYQKVYGTAAVNSPVVS

WKMKAPEKKPLVKREKPEEFQTRVRRGSQKKHISPVQALSEFKAMDSF

Further analysis of the NOV 1 a protein yielded the following properties shown in Table 1 B.
Table 1B. Protein Sequence Properties NOVla PSort 0.3600 probability located in mitochondrial matrix space; 0.3000 probability analysis: located in microbody (peroxisome); 0.1000 probability located in lysosome (lumen); 0.0000 probability located in endoplasmic reticulum (membrane) SignalP No Known Signal Sequence Predicted analysis:
A search of the NOV 1 a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 1 C.

Table 1C. Geneseq Results for NOVla NOVla Identities/

Geneseq Protein/Organism/Length [PatentResidues!Similarities Expect for Identifier ~ #, Date] Match the Matched Value ResiduesRegion AAR58778 ~ Neural alpha-catenin protein1..860 8511906 (93%)0.0 -Homo Sapiens, 906 aa. 1..906 855/906 (93%) [JP06211898-A, 02-AUG-1994]

T

AAY07060 a Renal cancer associated 8..859 694/899 (77%)0.0 antigen precursor sequence - Homo Sapiens, 9..905 773/899 (85%) '~ 906 aa. [W09904265-A2, 28-JAN-1999]

AAU32945 Novel human secreted protein8..769 611/766 (79%)0.0 #3436 - Homo sapiens, 932 aa. 10..773 683/766 (88%) [W0200179449-A2, 25-OCT-2001]

ABG10622 i Novel human diagnostic 8..769 610/766 (79%)0.0 protein #10613 - Homo Sapiens, 932 aa. 10..773 682/766 (88%) j [WO200175067-A2, 11-OCT-2001]

ABGI 0622 Novel human diagnostic 8..769 610/766 (79%)0.0 protein #10613 - Homo Sapiens, 932 aa. 10..773 682/766 (88%) [WO200175067-A2, 11-OCT-2001]

In a BLAST search of public sequence databases, the NOV 1 a protein was found to have homology to the proteins shown in the BLASTP data in Table 1D.

Table 1D. Public BLASTP Results for NOVla ~OVIa Identities/

Protein f Residues/Similarities' Expect for AccessionProtein/Organism/Length Match the Matched Value Number Residues Portion P30997 ~ Alpha-2 catenin (Alpha 1..860 8511906 (93%)~ 0.0 N-catenin) (Neural alpha-catenin) 1..906 855/906 (93%) - Gallus '~ gallus (Chicken), 906 .
aa.

I49499 alpha N-catenin I - mouse,~ 1..860 850/905 (93%)0.0 905 aa.

_ .
l ..
505 854/905 (93 /) A45011 ~ alpha-catenin 2 - human,1..769 768/770 (99%)0.0 945 aa.

1..770 7681770 (99%) P26232 ' Alpha-2 catenin (Alpha-catenin~ 1..769 768/770 (99%)~ 0.0 related protein) (Alpha 1..770 768/770 (99%) N-catenin) -Homo Sapiens (Human), 953 aa.

Q61301 ; Alpha-2 catenin (Alpha-catenin1..769 759/770 (98%)~ 0.0 related protein) (Alpha 1..770 762/770 (98%) N-catenin) -Mus musculus (Mouse), 953 aa.

PFam analysis predicts that the NOV 1 a protein contains the domains shown in the Table 1 E.
Table 1E. Domain Analysis of NOVla Identities/
Pfam Domain NOVIa Match Re ion : Similarities Ex ect Value P
for the Matched Region Vinculin 18..765 424/948 (45%) ~ 0 736/948 (78°l°) Vinculin 766..821 ~ 32/57 (56%) 5.4e-30 ~~~.w,.,.,.__~.~~,....~._~..~ ~, . 56/57 (98%) ~~_~
Example 2.
The NOV2 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 2A.
Table 2A. NOV2 Seguence Analysis SEQ ID NO: 3 2883 by NOV2a, CGTGAATGGTGTAGTGAGTTCTAATGAAACTTTATTTACAAGAGGAGACTGACCAGGT~
CG100689-O1 ~Z'TGGCCTGGGGGCCACAGTGTGTAGACCCCTGGAAAGATACATCCTGAGAAGAAAAAA

DNA SeCjLteriCe AGAATATATGCAGGAATGCTTAACTTTGTGGGTTTTCTCTCCTCTTGCCCTCACTGAC
TCAGGATACACAAAGACCTATCAAGCTCACGCAAAGCAGAAATTCAGCCGCTTATGGT
CCAGCAAGTCTGTCACTGAGATTCACCTATACTTTGAGGAGGAAGTCAAGCAAGAAGA
ATGTGACCATTTGGACCGCCTTTTTGCTCCCAAGGAAGCTGGGAAACAGCCACGTACA
GTGATCATTCAAGGACCACAAGGAATTGGAAAAACGACACTCCTGATGAAGCTGATGA
TGGCCTGGTCGGACAACAAGATCTTTCGGGATAGGTTCCTGTACACGTTCTATTTCTG
CTGCAGAGAACTGAGGGAGTTGCCGCCAACGAGTTTGGCTGACTTGATTTCCAGAGAG
TGGCCTGACCCCGCTGCTCCTATAACAGAGATCGTGTCTCAACCGGAGAGACTCTTGT
TCGTCATCGACAGCTTCGAAGAGCTGCAGGGCGGCTTGAACGAACCCGATTCGGATCT
GTGTGGTGACTTGATGGAGAAACGGCCGGTGCAGGTGCTTCTGAGCAGTTTGCTGAGG
AAGAAGATGCTCCCGGAGGCCTCCCTGCTCATCGCTATCAAACCCGTGTGCCCGAAGG
AGCTCCGGGATCAGGTGACGATCTCAGAAATCTACCAGCCCCGGGGATTCAACGAGAG
TGATAGGTTAGTGTATTTCTGCTGTTTCTTCAAAGACCCGAAAAGAGCCATGGAAGCC
TTCAATCTTGTAAGAGAAAGTGAACAGCTGTTTTCCATATGCCAAATCCCGCTCCTCT
GCTGGATCCTGTGTACCAGTCTGAAGCAAGAGATGCAGAAAGGAAAAGACCTGGCCCT
GACCTGCCAGAGCACTACCTCTGTGTACTCCTCTTTCGTCTTTAACCTGTTCACACCT
GAGGGTGCCGAGGGCCCGACTCCGCAAACCCAGCACCAGCTGAAGGCCCTGTGCTCCC
TGGCTGCAGAGGGTATGTGGACAGACACATTTGAGTTTTGTGAAGACGACCTCCGGAG
AAATGGGGTTGTTGACGCTGACATCCCTGCGCTGCTGGGCACCAAGATACTTCTGAAG
TACGGGGAGCGTGAGAGCTCCTACGTGTTCCTCCACGTGTGTATCCAGGAGTTCTGTG
CCGCCTTGTTCTATTTGCTCAAGAGCCACCTTGATCATCCTCACCCAGCTGTGAGATG
TGTACAGGAATTGCTAGTTGCCAATTTTGAAAAAGCAAGGAGAGCACATTGGATTTTT
TTGGGGTGTTTTCTAACTGGCCTTTTAAATAAAAAGGAACAAGAAAAACTGGATGCGT
TTTTTGGCTTCCAACTGTCCCAAGAGATAAAGCAGCAAATTCACCAGTGCCTGAAGAG
CTTAGGGGAGCGTGGCAATCCTCAGGGACAGGTGGATTCCTTGGCGATATTTTACTGT
CTCTTTGAAATGCAGGATCCTGCCTTTGTGAAGCAGGCAGTGAACCTCCTCCAAGAAG
CTAACTTTCATATTATTGACAACGTGGACTTGGTGGTTTCTGCCTACTGCTTAAAATA
CTGCTCCAGCTTGAGGAAACTCTGTTTTTCCGTTCAAAATGTCTTTAAGAAAGAGGAT
GAACACAGCTCTACGTCGGATTACAGCCTCATCTGTTGGCATCACATCTGCTCTGTGC
TCACCACCAGCGGGCACCTCAGAGAGCTCCAGGTGCAGGACAGCACCCTCAGCGAGTC
GACCTTTGTGACCTGGTGTAACCAGCTGAGGCATCCCAGCTGTCGCCTTCAGAAGCTT
GGAATAAATAACGTTTCCTTTTCTGGCCAGAGTGTTCTGCTCTTTGAGGTGCTCTTTT
CAGGTCCCTCTGTGATGCCTTGAACTACCCAGCAGGCAACGTCAAAGAGCTAGCGCTG
GTAAATTGTCACCTCTCACCCATTGATTGTGAAGTCCTTGCTGGCCTTCTAACCAACA
ACAAGAAGCTGACGTATCTGAATGTATCCTGCAACCAGTTAGACACAGGCGTGCCCCT
TTTGTGTGAAGCCCTGTGCAGCCCAGACACGGTCCTGGTATACCTGATGTTGGCTTTC
TGCCACCTCAGCGAGCAGTGCTGCGAATACATCTCTGAAATGCTTCTGCGTAACAAGA
GCGTGCGCTATCTAGACCTCAGTGCCAATGTCCTGAAGGACGAAGGACTGAAAACTCT
CTGCGAGGCCTTGAAACATCCGGACTGCTGCCTGGATTCACTGTGTTTGGTAAAATGT
TTTATCACTGCTGCTGGCTGTGAAGACCTCGCCTCTGCTCTCATCAGCAATCAAAACC
TGAAGATTCTGCAAATTGGGTGCAATGAAATCGGAGATGTGGGTGTGCAGCTGTTGTG
TCGGGCTCTGACGCATACGGATTGCCGCTTAGAGATTCTTGGGTTGGAAGAATGTGGG
TTAACGAGCACCTGCTGTAAGGATCTCGCGTCTGTTCTCACCTGCAGTAAGACCCTGC
AGCAGCTCAACCTGACCTTGAACACCTTGGACCACACAGGGGTGGTTGTACTCTGTGA
GGCCCTGAGACACCCAGAGTGTGCCCTGCAGGTGCTCGGGCTGAGAAAAACT'GATTTT
GATGAGGAAACCCAGGCACTTCTGACGGCTGAGGAAGAGAGAAATCCTAACCTGACCA
TCACAGACGACTGTGACACAATCACAAGGGTAGAGATCTGA
ORF Start ATG at 124 ORF Stop: TGA at 2881 ~ 919 as _ . . .. _.."~,:
SE ID NO. 4 MW at 103966.7kD
NOV2a, MQECLTLWVFSPLALTDSGYTKTYQAHAKQKFSRLWSSKSVTEIHLYFEEEVKQEECD

Protein SeCjlleriCe ELRELPPTSLADLISREWPDPAAPITEIVSQPERLLFVIDSFEELQGGLNEPDSDLCG
DLMEKRPVQVLLSSLLRKKMLPEASLLIAIKPVCPKELRDQVTISEIYQPRGFNESDR
LVYFCCFFKDPKRAMEAFNLVRESEQLFSICQIPLLCWILCTSLKQEMQKGKDLALTC
QSTTSVYSSFVFNLFTPEGAEGPTPQTQHQLKALCSLAAEGMWTDTFEFCEDDLRRNG

ELLVANFEKARRAHWIFLGCFLTGLLNKKEQEKLDAFFGFQLSQEIKQQIHQCLKSLG
ERGNPQGQVDSLAIFYCLFEMQDPAFVKQAVNLLQEANFHIIDNVDLVVSAYCLKXCS

SLRKLCFSVQNVFKKEDEHSSTSDYSLICWHHICSVLTTSGHLRELQVQDSTLSESTF
VTWCNQLRHPSCRLQKLGINNVSFSGQSVLLFEVLFYQPDLKYLSFTLTKLSRDDIRS
LCDALNYPAGNVKELALVNCHLSPIDCEVLAGLLTNNKKLTYLNVSCNQLDTGVPLLC
EALCSPDTVLVYLMLAFCHLSEQCCEYISEMLLRNKSVRYLDLSANVLKDEGLKTLCE
ALKHPDCCLDSLCLVKCFITAAGCEDLASALISNQNLKILQIGCNEIGDVGVQLLCRA
LTHTDCRLEILGLEECGLTSTCCKDLASVLTCSKTLQQLNLTLNTLDHTGVVVLCEAL
RHPECALQVLGLRKTDFDEETQALLTAEEERNPNLTITDDCDTITRVEI
Further analysis of the NOV2a protein yielded the following properties shown in Table 2B.
Table 2B. Protein Sequence Properties NOV2a PSort 0.6000 probability located in nucleus; 0.3000 probability located in microbody analysis: (peroxisome); 0.2000 probability located in endoplasmic reticulum (membrane); 0.1000 probability located in mitochondria! inner membrane SignalP Cleavage site between residues 17 and 18 analysis.
A search of the NOV2a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 2C.
Table 2C. Geneseq Results for NOV2a NOVZa Identities/

Geneseq Protein/OrganismlLength Residues!SimilaritiesExpect [Patent ~ for Identifier#, Date] Match the lYlatchedValue Residues Region AAM50328 Human nucleotide binding 33..882 849/850 (99%)0.0 site protein NBS-5 - Homo Sapiens,1..850 850/850 (99%) aa. [WO200183753-A2, 08-NOV-2001]

_ __ ~ _____ AAU07878 Polypeptide sequence for 165..907 375/743 (50%): 0.0 mammalian Spg65 - Mammalia,5..744 528/743 (70%) ~

748 aa. [WO200166752-A2, _SEP.-2001]. ~ ~

.... .....
AAE07514 Human PYRIN-1 protein - 20..907~~320/926 (34%)e-146 Homo ' i sapiens, 1034 aa. [W0200161005-134..1028491/926 (52%) p'2' ~3-AUG-2001 ] ...
. . [

___ AAG65895 Amino acid sequence of ~75..907 301/849 (35%)e-137 GSI~ gene ~~

Id 97078 - Homo Sapiens, 208..1043460/849 (53%) 1062 aa. ~

[WO200172961-A2, 04-OCT-2001]

AAE07513 Human nucleotide binding 75..907 299/849 (35%)e-134 site 1 (NBS-1) protein - Homo 180..1014459/849 (53%) Sapiens, 1033 aa. [W0200I61005-A2, AUG-2001] _. _.

In a BLAST search of public sequence databases, the NOV2a protein was found to have homology to the proteins shown in the BLASTP data in Table 2D.
Table 2D. Public BLASTP Results for NOV2a NOV2a Identities/

Protein , SimilaritiesExpect Residues/

AccessionProtein/OrganismlLength for the Number es Matched ~ Value R Portion idues __ Q96MN2 ' CDNA FLJ32126 FIS, CLONE 1..919 918/919 (99%)0.0 ~

PEBLM2000112, WEAKLY 1..919 918/919 (99%) SIMILAR TO HOMO SAPIENS

NUCLEOTIDE-BINDING SITE

PROTEIN 1 MRNA - Homo Sapiens (Human), 919 aa.

.~~. ..._._..~.._....-~......-...-,.~..",~.-..,..-..,...,_ Q96MN2 NACHT-, LRR- and PYD-containing18..919 900/902 (99%)_ ~ 0.0 protein 4 (PAAD and NACHT- 93..994 901/902 (99%) containing protein 2) (PYRIN-containing APAF 1-like protein 4) (Ribonuclease inhibitor 2) - Homo Sapiens (Human), 994 aa.

AAL88672 RIBONUCLEASE INHIBITOR 2 18..919 894/902 (99%)0.0 - ~

Homo Sapiens (Human), 916 15..916 897/902 (99%) aa.

CAD19386 SEQUENCE 7 FROM PATENT 33..882 849/850 (99%)0.0 ~

W00183753 - Homo Sapiens 1..850 850/850 (99%) (Human), ~

858 as (fragment).

Q99MW0 RIBONUCLEASE/ANGIOGENIN 165..907374/743 (50%)0.0 =

INHIBITOR 2 - Mus musculus 5..744 528/743 (70%) (Mouse), 748 aa.

PFam analysis predicts that the NOV2a protein contains the domains shown in the Table 2E.
Table 2E. Domain Analysis of NOV2a Identities/
Pfam Domain NOVZa Match Region Similarities Expect Value for the Matched Region SRP54 71..93 11/23 (48%) ~~~ 0.1 g.. .
. . . ~. _. .17/23...(74%) Exanipte 3.
The NOV3 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 3A.
Table 3A. NOV3 Sequence Analysis SEQ ID NO: 5 2142 by NOV3a, ~TATTATTCAGCAAACAATCTCAATGTGTTCCTGATGGGAGAGAGAGCATCTGGAAAAA
CG100760-Ol CTATTGTTAT.AAATCTGGCTGTGTTGAGGTGGATCAAGGGTGAGATGTGGCAGAACAT
DNA Se ueriCe GATCTCGTACGTCGTTCACCTCACTGCTCACGAAATAAACCAGATGACCAACAGCAGC
TTGGCTGAGCTAATCGCCAAGGACTGGCCTGACGGCCAGGCTCCCATTGCAGACATCC
TGTCTGATCCCAAGAAACTCCTTTTCATCCTCGAGGACTTGGACAACATAAGATTCGA
GTTAAATGTCAATGAAAGTGCTTTGTGTAGTAACAGCACCCAGAAAGTTCCCATTCCA
GTTCTCCTGGTCAGTTTGCTGAAGAGAAAAATGGCTCCAGGCTGCTGGTTCCTCATCT
CCTCAAGGCCCACACGTGGGAATAATGTAAAAACGTTCTTGAAAGAGGTAGATTGCTG
CACGACCTTGCAGCTGTCGAATGGGAAGAGGGAGATATATTTTAACTCTTTCTTTAAA
~GACCGCCAGAGGGCGTCGGCAGCCCTCCAGCTTGTACATGAGGATGAAATACTCGTGG
GGACAAGGGGCGTGACTTCCAGCTCTGCTGCCAAACACCCACTGATCTACATGCCCAC
TTTCTTGCTGATGCGTTGACATCAGAGGCTGGACTTACTGCCAATCAGTATCACCTAG
TTTCAGTGGTGAAGACCTCAGATGTGTTGGGTTTACTGAGGCTGATGTCTCTGTGTTG
CAGGCCGCGAATATTCTTTTGCCGAGCAACACTCATAAAGACCGTTACAAGTTCATAC
ACTTGAACGTCCAGGAGTTTTGTACAGCCATTGCATTTCTGATGGCAGTACCCAACTA
TCTGATCCCCTCAGGCAGCAGAGAGTATAAAGAGAAGAGAGAACAATACTCTGACTTT
AGACATCCTTTGGATACCAGCTACCGATGGTAGACAGCTTCAAGTGGTACTCGGTGGG
ATACATGAAACATTTGGACCGTGACCCGGAAAAGTTGACGCACCATATGCCTTTGTTT
TACTGTCTCTATGAGAATCGGGAAGAAGAATTTGTGAAGACGATTGTGGATGCTCTCA
TGGAGGTTACAGTTTACCTTCAATCAGACAAGGATATGATGGTCTCATTATACTGTCT
GGATTACTGCTGTCACCTGAGGACACTTAAGTTGAGTGTTCAGCGCATCTTTCAAAAC
CCAGCATCCAACACGTAACTCGATTGTGCCTGGGATTTAATCGGCTCCAAGATGATGG
CATAAAGCTATTGTGTGCGGCCCTGACTCACCCCAAGTGTGCCTTAGAGAGACTGGAG
CTCTGGTTTTGCCAGCTGGCAGCACCCGCTTGCAAGCACTTGTCAGATGCTCTCCTGC
AGAACAGGAGCCTGACACACCTGAATCTGAGCAAGAACAGCCTGAGAGACGAGGGAGT
CAAGTTCCTGTGTGAGGCCTTGGGTCGCCCAGATGGTAACCTGCAGAGCCTGAGTTTG
TCAGGTTGTTCTTTCACAAGAGAGGGCTGTGGAGAGCTGGCTAATGCCCTCAGCCATA
ATCATAATGTGAAAATCTTGGATTTGGGAGAAAATGATCTTCAGGATGATGGAGTGAA
GCTACTGTGTGAGGCTCTGAAACCACATCGTGCATTGCACACACTTGGGTTGGCGAAA
GCCTGGTCAATCTGAACCTTCTAGGCAATGAATTGGATACTGATGGTGTCAAGATGCT
ATGTAAGGCTTTGAAAAAGTCGACATGCAGGCTGCAGAAACTCGGGTAAACCTCACTG
ORF Start: ATG at 34 ORF Stop: TAA at 2077 SEQ ID NO: 6 X681 as MW at 76724.1kD
NOV3a, MGERASGKTIVINLAVLRWIKGEMWQNMISYVVHLTAHEINQMTNSSLAELIAKDWPD

CGlOO76O-O1 GQAPIADILSDPKKLLFILEDLDNIRFELNVNESALCSNSTQKVPIPVLLVSLLKRKM

Protein SeqilenCe'nPGCWFI'ISSRPTRGNNVKTFLKEVDCCTTLQLSNGKREIYFNSFFKDRQRASAALQL

VHEDEILVGLCRVAILCWITCTVLKRQMDKGRDFQLCCQTPTDLHAHFLADALTSEAG

LTANQYHLGLLKRLCLLAAGGLFLSTLNFSGEDLRCVGFTEADVSVLQAANILLPSNT

HKDRYKFIHLNVQEFCTAIAFLMAVPNYLIPSGSREYKEKREQYSDFNQVFTFIFGLL

NANRRKILETSFGYQLPMVDSFKWYSVGYMKHLDRDPEKLTHHMPLFYCLYENREEEF

VKTIVDALMEVTVYLQSDKDMMVSLYCLDYCCHLRTLKLSVQRIFQNKLEKCNLSAAS

CQDLALFLTSIQHVTRLCLGFNRLQDDGIKLLCAALTHPKCALERLELWFCQLAAPAC
KHLSDALLQNRSLTHLNLSKNSLRDEGVKFLCEALGRPDGNLQSLSLSGCSFTREGCG
ELANALSHNHNVKILDLGENDLQDDGVKLLCEALKPHRALHTLGLAKCNLTTACCQHL
FSVLSSSKSLVNLNLLGNELDTDGVKMLCKALKKSTCRLQKLG
Further analysis of the NOV3a protein yielded the following properties shown in Table 3B.
y4 ~~~~~~ Table 3B. Protein Sequence~Properties NOV3a PSort ; 0.8200 probability located in endoplasmic reticulum (membrane); 0.1900 analysis: . probability located in plasma membrane; 0.1000 probability located in endoplasmic reticulum (lumen); 0.1000 probability located in outside SignalP Cleavage site between residues 23 and 24 analysis:
A search of the NOV3a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 3C.
Table 3C. Geneseq Results for NOV3a NOV3a Identities) Geneseq Protein/Organism/Length Residues/Similarities Expect [Patent for Identifier#, Date) Match the Matched Value ~ Residueslegion . ..
. .

AAM50330 Human nucleotide binding 1..681 539/745 (72%)0.0 site protein NBS-3 - Homo Sapiens,116..859587/745 (78%) aa. [W0200183753-A2, 08 NOV-2001 ]

AAM50326 Human nucleotide binding 1..510 469/517 (90%)0.0 site protein NBS-3 - Homo sapiens,116..631479/517 (91%) aa. [W0200183753-A2, 08-NOV-AAM50328 Human nucleotide binding 2..681 247/750 (32%)e-1 site OS

protein NBS-5 - Homo sapiens,48..792 381/750 (49%) aa. [WO200183753-A2, OS-NOV-2001 ]
~.. 3 . ._...

AAE07514 Human PYRIN-1 protein - 2..680 238/729 (32%)e-100 Homo Sapiens, 1034 aa. [W0200161005-224..944362/729 (49%) A2, 23-AUG-2001 ]

ABG03924 Novel human diagnostic 2..680 228/741 (30%)7e-78 protein #3915 - Homo sapiens, 952 178..908334/741 (44%) aa.

[WO200175067-A2, 11-OCT-2001 ]

In a BLAST search of public sequence databases, the NOV3a protein was found to have homology to the proteins shown in the BLASTP data in Table 3D.

Table 3D. Public BLASTP
Results for NOV3a Protein NOV3a Identities/

Accession Protein/Organism/Length Residues/SimilaritiesExpect for Number Match the Matched Value ResiduesPortion CAD19388 SEQUENCE 15 FROM PATENT 1..681 539/745 (72%)0.0 W00183753 - Homo Sapiens 116..859587/745 (78%) (Human), 875 aa.

CAD 193 SEQUENCE 3 FROM PATENT 1..510 469/517 (90%)0.0 W00183753 - Homo Sapiens 116..631479/517 (91%) (Human), 631 as (fragment).

CAD19386 SEQUENCE 7 FROM PATENT ~ 2..681247/750 (32%)e-104 W00183753 - Homo Sapiens 48..792 3811750 (49%) (Human), 858 as (fragment).

Q96MN2 CDNA FLJ32126 FIS, CLONE 2..681 247/750 (32%)e-104 PEBLM2000112, WEAKLY ~ 381/750 (49%) 80..824 SIMILAR TO HOMO SAPIENS

NUCLEOTIDE-BINDING SITE

PROTEIN 1 MRNA - Homo sapiens (Human), 919 aa.

Q96MN2 NACHT-, LRR- and PYD-containing2..681 247/750 (32%)e-104 protein 4 (PAAD and NACHT- 155..899381/750 (49%) containing protein 2) (PYR1N-containing APAF1-like protein 4) (Ribonuclease inhibitor 2) - Homo _ .. .... Sapiens (Human), 994. aa... _...

Example 4.
The NOV4 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 4A.
Table 4A. NOV4 Sequence Analysis SEQ ID NO: 7 X782 by NOV4a, ;TCTCAAGGGATAATCACTAAATTCTGCCGAAAGGACTGAGGAACGGTGCCTGGAAAAG

DNA Sequence ~TTTCTTCAACTTGCTCTTTTGGATCTGTGGCTGCTGCATTTTGGGCTTTGGGATCTAC
[[CTGCTGATCCACAACAACTTCGGAGTGCTCTTCCATAACCTCCCCTCCCTCACGCTGG
GCAATGTGTTTGTCATCGTGGGCTCTATCAAGGAAAACAAGTGTCTGCTTATGTCGTT
CTTCATCCTGC'Z'GCTGATTATCCTCCTTGCTGAGGTGACCTTGGCCATCCTGCTCTTT
GTATATGAACAGAAGCTGAATGAGTATGTGGCTAAGGGTCTGACCGACAGCATCCACC
GTTACCACTCAGACAATAGCACCAAGGCAGCGTGGGACTCCATCCAGTCATTTCTGCA
GTGTTGTGGTATAAATGGCACGAGTGATGGGACCAGTGGCCCACCAGCATCTTGCCCC
TCAGATCGAAAAGTGGAGGGTTGCTATGCGAAAGCAAGACTGTGGTTTCATTCCAATT
TCCTGTATATCGGAATCATCACCATCTGTGTATGTGTGATTGAGGTGTTGGGGATGTC
CTTTGCACTGACCCTGAACTGCCAGATTGACAAAACCAGCCAGACCATAGGGCTATGA

TCTGCAGTAGTTCTGTGGTGAAGAGACTTGTTTCATCTCCTGGAAATGCAAAACCATT
~TATAGCATGAGCCCTACATGATCATCAG
ORF Start: ATG at 76 ORF Stop: TGA at 694 SEQ ID NO: 8 206 as MW at 22888.8kD
NOV4a, MGMSSLKLLKYVLFFFNLLFWTCGCCILGFGIYLLIHNNFGVLFHNLPSLTLGNVFVI

PPOteln Se uenCe STKAAWDSIQSFLQCCGINGTSDGTSGPPASCPSDRKVEGCYAKARLWFHSNFLYIGI
q ITICVCVIEVLGMSFALTLNCQIDKTSQTIGL
Further analysis of the NOV4a protein yielded the following properties shown in Table 4B.
Table 4B. Protein Sequence Properties NOV4a PSort 0.6400 probability located in plasma membrane; 0.4600 probability located in analysis: Golgi body; 0.3700 probability located in endoplasmic reticulum (membrane);
0.1000 probability located in endoplasmic reticulum (lumen) SignalP Cleavage site between residues 32 and 33 analysis:
A search of the NOV4a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 4C.
Table 4C. Geneseq Results for NOV4a NOV4a Identities/
~ ~

Geneseq Protein/Organism/Length Residues/SimilaritiesExpect [Patent ~ for Identifier~ #, Date] Match the Matched Value Residues Region AAY96I41 Human haematopoietic CD53 I ..206 205/2I9 (93%)e-I

Homo sapiens, 219 aa. 1..219 205/219 (93%) [US6111093-A, 29-AUG-2000]

AAB58136 s Lung cancer associated 1..206 205/219 (93%)e-1 polypeptide I
S

sequence SEQ ID 474 - Homo13..231 205/219 (93%) sapiens, 231 aa. [W0200055180-A2, 21-SEP-2000]

AAW89152 Human CD53 antigen - Homo 1..206 205/219 (93%)e-115 sapiens, 219 aa. [IJS5849898-A,1..219 205/219 (93%) 15- ~

DEC-1998]

AAW80455 Human CD53 antigen - Homo 1..206 205/219 (93%)e-1 i IS

Sapiens, 219 aa. [US5830731-A,1..219 205/219 (93%) 03-' NOV-1998]

AAR91446 . Human CD53 antigen - 1..206 2051219 (93%)e-115 Homo ' sapiens, 219 aa. [LTS5506126-A,1..219 205/219 (93%) APR-1996]. . _ . . .. ...._ . _..
~. .

In a BLAST search of public sequence databases, the NOV4a protein was found to have homology to the proteins shown in the BLASTP data in Table 4D.
Table 4D. Public BLASTP Results for NOV4a Protein NOV4a Identities/

AccessionProtein/Organism/Length Residues/SimilaritiesExpect for Number Match the Matched Value Residues Portion P19397 ~ Leukocyte surface antigen1..206 205/219 (93%)e-115 (Cell surface glycoprotein1..219 205/219 (93%) CD53) -Homo Sapiens (Human), 219 aa.

AAH21310 CD53 ANTIGEN - Mus musculus1..206 168/219 (76%)6e-95 (Mouse), 219 aa. 1..219 183/219 (82%) Q61451 Leukocyte surface antigen 2..206 167/218 (76%)2e-94 (Cell surface glycoprotein1..218 182/218 (82%) CD53) -Mus musculus (Mouse), 218 aa.

A39574 leukocyte antigen OX-44 1..206 164/219 (74%~7e-94 - rat, 219 aa. 1..219 183/219 (82%) P24485 Leukocyte surface antigen 2..206 163/218 (74%)3e-93 (Cell surface glycoprotein1..218 182/218 (82%) CD53) (Leukocyte antigen MRC
OX-44) -- ' Rattus norvegicus (Rat),~~-218 aa~x :.:..,..~."-..~

PFam analysis predicts that the NOV4a protein contains the domains shown in the Table 4E.
Table 4E. Domain Analysis of NOV4a Identities/
Pfam Domain NOV4a Match Region Similarities Expect Value for the Matched Region transmembrane4 10..36 17/27 (63%) 4.4e-08 27/27 (100%) transmembrane4 58..197 52/202 (26%) 1.2e-44 _._ __ _ .____ ~.. _ _ _._ __~.. _. _~ _ _....._120/202'(59%) n.___. -Example 5.
The NOVS clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 5A.

Table SA. NOVS Sequence Analysis SEQ ID NO: 9 1719 by NOVSa, ATGCGGACGCCGGTGGTGATGACGCTGGGCATGGTGTTGGCGCCCTGCGGGCTCCTGC

CG101068-OlTCAACCTGACCGGCACCCTGGCGCCCGGCTGGCGGCTGGTGAAGGGCTTCCTGAACCA

DNA SeClilenCeGCCAGTGGACGTGGAGTTGTACCAGGGCCTGTGGGACATGTGTCGCGAGCAGAGCAGC

CGCGAGCGCGAGTGCGGCCAGACGGACCAGTGGGGCTACTTCGAGGCCCAGCCCGTGC

TGGTGGCGCGGGCACTCATGGTCACCTCGCTGGCCGCCACGGTCCTGGGGCTTCTGCT

GGCGTCGCTGGGCGTGCGCTGCTGGCAGGACGAGCCCAACTTCGTGCTGGCAGGGCTC

TCGGGCGTCGTGCTCTTCGTCGCTGGCCTCCTCGGCCTCATCCCGGTGTCCTGGTACA

GGTCAGCTACAGCCTGGTCCTGGGCTACCTGGGCAGCTGCCTCCTGCTGCTGGGCGGC
TTCTCGCTGGCGCTCAGCTTCGCGCCCTGGTGCGACGAGCGTTGTCGCCGCCGCCGCA
AGGGACCCTCCGCCGGGCCTCGCCGCAGCAGCGTCAGCACCATCCAAGTGGAGTGGCC
CGAGCCCGACCTGGCGCCCGCCATCAAGTACTACAGCGACGGCCAGCACCGACCGCCG
CCTGCCCAGCACCGCAAGCCCAAGCCCAAGCCCAAGGTCGGCTTCCCCATGCCGCGGC
CGCGGCCCAAGGCCTACACCAACTCGGTGGACGTCCTCGACGGGGAGGGGTGGGAGTC
CCAGGACGCTCCCTCGTGCAGCACCCACCCCTGCGACAGCTCGCTGCCCTGCGACTCC
GACCTCTAGACGCTTGTAGAGCCTGGGGGGCGCCGGGTGGCAAAGGACTCACCCCCGC
ACAGGCCCGCCTGGCTTCGAGTTGGAACCCGGACACTTGCCCCTCACTGGTGTGGATG
GAAATCTGCCTTTCGTGGGACCAAACAGGACTCCTTGGACGATTAGTTCAGGTTGGGT
TTGGTTTTCTTCTTAAAGAGTTTAGTTTTCCTCTCCAGAGGGATCAGGGTCCTCTTAG
GGAGTGACGGGCTTTTCATATATTTTTGCTGAAGAATATATGGAAAGGGTGGCATTTG
CGTCACGTGGACCAGGGACAGTGCTGAAATCAGCAGTGCTCAGAAACAATTTAACATG
TTGAAACGACAATATTCTAAAATACTGATGAATCTTGCATCAATATAATTATTGGGTT
TTTTTTCTTTTTCCTGCTGTATAACTCCTTGCCATGCAAACTCTCAAGAGGCCAATAT
ATTCCTGGCCATGTTTGAATGAGCCTCTTAAAATAAACTTAGAGCCATGCAAATGCCA
GCAGCTTAATGGATTTCATGGAATGAAATACCGTGATTAACTCATAGCTACATATCAT
TGCATAAATGGGATTTATCTTTTTTCTCACTTATTTTTGCGGTGAAAGTCGAGGGCAT
GCAAGAGTTTCTCTTCCAGAAGCCAAGAGGAGAACAAAGGTCCTAATGCTGTACTATT
CCACCCTTTGGACGCCTCATCCAGGACGCAGAGGACTCTAGGTTTAACATTTTGTACA
AAATGGAACCTGTTAATCATATTAAAGCACATATGTATATATCTTTTATTTATAAATA
AAATTTTAAAACAATAGTTTCAGTATAGCCACAAAAA
ORF Start: ATG at 1 ORF Stop: TAG at 877 SEQ ID NO: 10 292 as MW at 31914.SkD
NOVSa, MRTPVVMTLGMVLAPCGLLLNLTGTLAPGWRLVKGFLNQPVDVELYQGLWDMCREQSS
CG101068-Ol RERECGQTDQWGYFEAQPVLVARALMVTSLAATVLGLLLASLGVRCWQDEPNFVLAGL
PTOteln SeCluenCe SGVVLFVAGLLGLTPVSWYNfiFLGDRDVLPAPASPVTVQVSYSLVLGYLGSCLLLLGG
FSLALSFAPWCDERCRRRRKGPSAGPRRSSVSTIQVEWPEPDLAPAIKYYSDGQHRPP
PAQHRKPKPKPKVGFPMPRPRPKAYTNSVDVLDGEGWESQDAPSCSTHPCDSSLPCDS
Further analysis of the NOVSa protein yielded the following properties shown in Table SB.
Table 5B. Protein Sequence Properties NOVSa PSort 0.6400 probability located in plasma membrane; 0.4600 probability located in analysis: ~ Golgi body; 0.3700 probability located in endoplasmic reticulum (membrane);
0.1000 probability located in endoplasmic reticulum (lumen) SignalP Cleavage site between residues 28 and 29 analysis:

A search of the NOVSa protein against the Geneseq dafabase; a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table SC.
Table SC. Geneseq Results for NOVSa NOVSa Identities/

Geneseq Protein/Organism/Length Residues/SimilaritiesExpect [Patent for Identifier'; #, Date] Match the Matched Value Residues Region :

AAB64401 Amino acid sequence of 9..206 74/206 (35%)1e-16 human intracellular signalling 9..209 101/206 (48%) molecule INTRA33 - Homo sapiens, 217 aa.

[WO200077040-A2, 21-DEC-2000]

AAG75467 Human colon cancer antigen6..187 59/188 (31%)2e-13 protein SEQ ID N0:6231 - Homo Sapiens,7..192 92/188 (48%) 210 aa. [W0200122920-A2, OS-~R-Zoo 1 J ~

__ ABB50278 Claudin 4 ovarian tumour 6..187 59/188 (31%)2e-13 marker protein, SEQ ID N0:45 - 6..191 92/188 (48%) Homo Sapiens, 209 aa. [WO200175177-A2, 11-OCT-2001]

AAB43133 6..187 59/188 (31%)2e-13 Human ORFX

polypeptide sequence SEQ 6..191 92/I88 (48%) ID

N0:5794 - Homo Sapiens, 209 aa.

[WO200058473-A2, OS-OCT-2000]

ABB50396 Human secreted protein 9..187 59/185 (3I%)Ze-I3 encoded by ~

gene 96 SEQ ID N0:344 - 1..183 91/185 (48%) Homo Sapiens, 202 aa. [WO200162891-A2, In a BLAST search of public sequence databases, the NOVSa protein was found to have homology to the proteins-shown in the BLASTP data in Table SD.

Table SD Public BLASTP
Results for NOVSa Protein NOVSa Identities/

Accession Protein/Organism/Length Residues/ SimilaritiesExpect for Number Match the Matched Value Residues Portion Q96B33 SIMILAR TO RIKEN CDNA 28..292 252/267 (94%)e-147 2310014808 GENE - Homo 2..268 254!267 (94%) sapiens (Human), 268 as (fragment).

Q9D7D7 2310014B08RIK PROTEIN 1..292 230/296 (77%)e-135 (RIKEN CDNA 2310014808 1..296 248/296 (83%) GENE) - Mus musculus (Mouse), 296 aa.

095484 Claudin 9 - Homo Sapiens9..206 74!206 (35%)4 16~

(Human), 217 aa. 9..209 101/206 (48%) Q9ZOS7 Claudin-9 - Mus musculus9..206 71/206 (34%)1e-14 (Mouse), 217 aa. ~ 9..209 991206 (47%) Q98SR2 CLAUDIN-3 - Gallus gallus10..206 64/202 (31%)!e-13 (Chicken), 214 aa. 9..207 99/202 (48%) PFam analysis predicts that the NOVSa protein contains the domains shown in the Table SE.
Table 5E. Domain Analysis of NOVSa Identities/
Pfam Domain ~ NOVSa Match Region Similarities Expect Value fox the Matched Region PMP22 Claudin 3..177 40/194 (21%) 0.00018 108/194 (56%) _._ ......__ . . .... ....... .. ..._.....~ ........... _._... .........._ ..
..................... ............... ....... ._... ... _...
................... ..................... . ... .....~~........ .... ....
..._.. .
Example 6.
The NOV6 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 6A.
Table 6A. NOV6 Sequence Analysis SEQ ID NO: 11 X2369 by NOV6a, CGGCCGGAGCGCCGAGGCCCGGCCATGGCCACCACCAGCACCACGGGCTCCACCCTGC
CG101231-Ol TGCAGCCCCTCAGCAACGCCGTGCAGCTGCCCATCGACCAGGTCAACTTTGTAGTGTG
DNA Sequence CCAACTCTTTGCCTTGCTAGCAGCCATTTGGTTTCGAACTTATCTACATTCAAGCAAA
ACTAGCTCTTTTATAAGACATGTAGTTGCTACCCTTTTGGGCCTTTATCTTGCACTTT

TTTGCTTTGGATGGTATGCCTTACACTTTCTTGTACAAAGTGGAATTTCCTACTGTAT

CATGATCATCATAGGAGTGGAGAACATGCACAATTACTGCTTTGTGTTTGCTCTGGGA

TACCTCACAGTGTGCCAAGTTACTCGAGTCTATATCTTTGACTATGGACAATATTCTG

CTGATTTTTCAGGCCCAATGATGATCATTACTCAGAAGATCACTAGTTTGGCTTGCGA

AATTCATGATGGGATGTTTCGGAAGGATGAAGAACTGACTTCCTCACAGAGGGATTTA

GCTGTAAGGCGCATGCCAAGCTTACTGGAGTATTTGAGTTACAACTGTAACTTCATGG

GGATCCTGGCAGGCCCACTTTGCTCTTACAAAGACTACATTACTTTCATTGAAGGCAG

ATCATACCATATCACACAATCTGGTGAAAATGGAAAAGAAGAGACACAGTATGAAAGA

ACAGAGCCATCTCCAAATAGTGCGGTTGTTCAGAAGCTCTTAGTTTGTGGGCTGTCCT

TGTTATTTCACTTGACCATCTGTACAACATTACCTGTGGAGTACAACATTGATGAGCA

TTTTCAAGCTACAGCTTCGTGGCCAACAAAGATTATCTATCTGTATATCTCTCTTTTG

GCTGCCAGACCCAAATACTATTTTGCATGGACGCTAGCTGATGCCATTAATAATGCTG

CAGGCTTTGGTTTCAGAGGGTATGACGAAAATGGAGCAGCTCGCTGGGACTTAATTTC

CAATTTGAGAATTCAACAAATAGAGATGTCAACAAGTTTCAAGATGTTTCTTGATAAT

TGGAATATTCAGACAGCTCTTTGGCTCAAAAGGGTGTGTTATGAACGAACCTCCTTCA

GTCCAACTATCCAGACGTTCATTCTCTCTGCCATTTGGCACGGGGTATACCCAGGATA

TTATCTAACGTTTCTAACAGGGGTGTTAATGACATTAGCAGCAAGAGCTGTAAGAAAT

AACTTTAGACATTATTTCATTGAACCTTCCCAACTGAAATTATTTTATGATGTTATAA

CATGGATAGTAACTCAAGTAGCAATAAGTTACACAGTTGTGCCATTTGTGCTTCTTTC

TATAAAACCATCACTCACGTTTTACAGCTCCTGGTATTATTGCCTGCACATTCTTGGT

ATCTTAGTATTATTGTTGTTGCCAGTAAAAAAAACTCAAAGAAGAAAGAATACACATG

AAAACATTCAGCTCTCACAATCCAAAAAGTTTGATGAAGGAGAAAATTCTTTGGGACA

GAACAGTTTTTCTACAACAAACAATGTTTGCAATCAGAATCAAGAAATAGCCTCGAGA

CATTCATCACTAAAGCAGTGATCGGGAAGGCTCTGAGGGCTGTTTTTTTTTTTTGATG

TTAACAGAAACCAATCTTAGCACCTTTTCAAGGGGTTTGAGTTTGTTGGAAAAGCAGT

TAACTGGGGGGAAATGGACAGTTATAGATAAGGAATTTCCTGTACACCAGATTGGAAA

TGGAGTGAAACAAGCCCTCCCATGCCATGTCCCCGTGGGCCACGCCTTATGTAAGAAT

ATTTCCATATTTCAGTGGGCACTCCCAACCTCAGCACTTGTCCGTAGGGTCACACGCG

TGCCCTGTTGCTGAATGTATGTTGCGTATCCCAAGGCACTGAAGAGGTGGAAAAATAA

TCGTGTCAATCTGGATGATAGAGAGAAATTAACTTTTCCAAATGAATGTCTTGCCTTA

AACCCTCTATTTCCTAAAATATTGTTCCTAAATGGTATTTTCAAGTGTAATATTGTGA

GAACGCTACTGCAGTAGTTGATGTTGTGTGCTGTAAAGGATTTTAGGAGGAATTTGAA

ACAGGATATTTAAGAGTGTGGATATTTTTAAAATGCAATAAACATCTCAGTATTTGAA

GGGTTTTCTTAAAGTATGTCAAATGACTACAATCCATAGTGAAACTGTAAACAGTAAT

GGACGCCAAATTATAGGTAGCTGATTTTGCTGGAGAGTTTAATTACCTTGTGCAGTCA

AAGAGCGCTTCCAGAAGGAATCTCTTAAAACATAATGAGAGGTTTGGTAATGTGATAT

TTTAAGCTTACTCTTTTTCTTAAAAGAGAGAGGTGACGAAGGAAGGCAG

~ORF Start: ATG at 25 ORF Stop: TGA at 1585 SEQ ID NO: 12 ~ 520 as MW at 59480.OkD

NOVC7a, MATTSTTGSTLLQPLSNAVQLPIDQVNFWCQLFALLAAIWFRTYLHSSKTSSFIRHV

Protein SeCllleriCeR~IFDYGQYSADFSGPMMIITQKITSLACEIHDGMFRKDEELTSSQRDLAVRRMPSL

LEYLSYNCNFMGILAGPLCSYKDYITFIEGRSYHITQSGENGKEETQYERTEPSPNSA

VVQKLLVCGLSLLFHLTICTTLPVEYNIDEHFQATASWPTKIIYLYISLLAARPKYYF

AWTLADAINNAAGFGFRGYDENGAARWDLISNLRIQQIEMSTSFKMFLDNWNIQTALW

LKRVCYERTSFSPTIQTFILSAIWHGVYPGYYLTFLTGVLMTLAARAVRNNFRHYFIE

PSQLKLFYDVITWIVTQVAISYTVVPFVLLSIKPSLTFYSSWYYCLHILGILVLLLLP

VKKTQRRKNTHENIQLSQSKKFDEGENSLGQNSFSTTNNVCNQNQEIASRHSSLKQ

SEQ ID NO: 13 2270 by NOVE)b, CGGCCGGAGCGCCGAGGCCCGGCCATGGCCACCACCAGCACCACGGGCTCCACCCTGC

ACTAGCTCTTTTATAAGACATGTAGTTGCTACCCTTTTGGGCCTTTATCTTGCACTTT

TTTGCTTTGGATGGTATGCCTTACACTTTCTTGTACAAAGTGGAATTTCCTACTGTAT

CATGATCATCATAGGAGTGGAGAACATGCAGCCAATGATGATCATTACTCAGAAGATC

ACTAGTTTGGCTTGCGAAATTCATGATGGGATGTTTCGGAAGGATGAAGAACTGACTT

CCTCACAGAGGGATTTAGCTGTAAGGCGCATGCCAAGCTTACTGGAGTATTTGAGTTA

CAACTGTAACTTCATGGGGATCCTGGCAGGCCCACTTTGCTCTTACAAAGACTACATT

ACTTTCATTGAAGGCAGATCATACCATATCACACAATCTGGTGAAAATGGAAAAGAAG

AGACACAGTATGAAAGAACAGAGCCATCTCCAAATAGTGCGGTTGTTCAGAAGCTCTT

AGTTTGTGGGCTGTCCTTGTTATTTCACTTGACCATCTGTACAACATTACCTGTGGAG

TACAACATTGATGAGCATTTTCAAGCTACAGCTTCGTGGCCAACAAAGATTATCTATC

TGTATATCTCTCTTTTGGCTGCCAGACCCAAATACTATTTTGCATGGACGCTAGCTGA

TGCCATTAATAATGCTGCAGGCTTTGGTTTCAGAGGGTATGACGAAAATGGAGCAGCT

CGCTGGGACTTAATTTCCAATTTGAGAATTCAACAAATAGAGATGTCAACAAGTTTCA

AGATGTTTCTTGATAATTGGAATATTCAGACAGCTCTTTGGCTCAAAAGGGTGTGTTA

TGAACGAACCTCCTTCAGTCCAACTATCCAGACGTTCATTCTCTCTGCCATTTGGCAC

GGGGTATACCCAGGATATTATCTAACGTTTCTAACAGGGGTGTTAATGACATTAGCAG

CAAGAGCTGTAAGAAATAACTTTAGACATTATTTCATTGAACCTTCCCAACTGAAATT

ATTTTATGATGTTATAACATGGATAGTAACTCAAGTAGCAATAAGTTACACAGTTGTG

CCATTTGTGCTTCTTTCTATAAAACCATCACTCACGTTTTACAGCTCCTGGTATTATT

GCCTGCACATTCTTGGTATCTTAGTATTATTGTTGTTGCCAGT~~AAAAAAACTCAAAG

AAGAAAGAATACACATGAAAACATTCAGCTCTCACAATCCAAAAAGTTTGATGAAGGA

GAAAATTCTTTGGGACAGAACAGTTTTTCTACAACAAACAATGTTTGCAATCAGAATC

AAGAAATAGCCTCGAGACATTCATCACTAAAGCAGTGATCGGGAAGGCTCTGAGGGCT

GTTTTTTTTTTTTGATGTTAACAGAAACCAATCTTAGCACCTTTTCAAGGGGTTTGAG

TTTGTTGGAAAAGCAGTTAACTGGGGGGAAATGGACAGTTATAGATAAGGAATTTCCT

GTACACCAGATTGGAAATGGAGTGAAACAAGCCCTCCCATGCCATGTCCCCGTGGGCC

ACGCCTTATGTAAGAATATTTCCATATTTCAGTGGGCACTCCCAACCTCAGCACTTGT

CCGTAGGGTCACACGCGTGCCCTGTTGCTGAATGTATGTTGCGTATCCCAAGGCACTG

AAGAGGTGGAAAAATAATCGTGTCAATCTGGATGATAGAGAGAAATTAACTTTTCCAA

ATGAATGTCTTGCCTTAAACCCTCTATTTCCTAAAATATTGTTCCTAAATGGTATTTT

CAAGTGTAATATTGTGAGAACGCTACTGCAGTAGTTGATGTTGTGTGCTGTAAAGGAT

TTTAGGAGGAATTTGAAACAGGATATTTAAGAGTGTGGATATTTTTAAAATGCAATAA

ACATCTCAGTATTTGAAGGGTTTTCTTAAAGTATGTCAAATGACTACAATCCATAGTG

AAACTGTAAACAGTAATGGACGCCAAATTATAGGTAGCTGATTTTGCTGGAGAGTTTA

ATTACCTTGTGCAGTCAAAGAGCGCTTCCAGAAGGAATCTCTTAAAACATAATGAGAG

GTTTGGTAATGTGATATTTTAAGCTTACTCTTTTTCTTAAAAGAGAGAGGTGACGAAG

GAAGGCAG

ORF Start: ATG at 25 ORF Stop: TGA at 1486 SEQ ID NO: 14 487 as MW at 55677.7kD

NOV6b, MATTSTTGSTLLQPLSNAVQLPIDQVNFVVCQLFALLAAIWFRTYLHSSKTSSFIRHV

PTOte2n SequenceDGMFRKDEELTSSQRDLAVRRMPSLLEYLSYNCNFMGILAGPLCSYKDYITFIEGRSY

HITQSGENGKEETQYERTEPSPNSAWQKLLVCGLSLLFHLTICTTLPVEYNIDEHFQ

ATASWPTKIIYLYISLLAARPKYYFAWTLADAINNAAGFGFRGYDENGAARWDLISNL

RIQQIEMSTSFKMFLDNWNIQTALWLKRVCYERTSFSPTIQTFILSAIWHGVYPGYYL

TFLTGVLMTLAARAVRNNFRHYFIEPSQLKLFYDVITWIVTQVAISYTVVPFVLLSIK

PSLTFYSSWYYCLHILGILVLLLLPVKKTQRRKNTHENIQLSQSKKFDEGENSLGQNS

FSTTNNVCNQNQEIASRHSSLKQ

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 6B.
Table 6B. Comparison of NOV6a against NOV6b.
NOV6a Residues/ ~ Identities/
Protein Sequence Match Residues Similarities for the Matched Region NOV6b ~ 1..520 = 474/520 (91%) . 1..487 4741520 (91%) Further analysis .of the NOV6a protein yielded the following properties shown in Table 6C.

Table 6C. Protein Sequence Properties NOV6a PSort ' 0.6000 probability located in plasma membrane; 0.4000 probability located in analysis: GoIgi body; 0.3406 probability located in mitochondria) intermembrane space;
0.3384 probability located in mitochondria) inner membrane SignalP , Cleavage site between residues 44 and 45 analysis:
A search of the NOV6a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 6D.
Table 6D. Geneseq Results for NOV6a NOV6a Identities/

Geneseq Protein/Organism/Length Residues/SimilaritiesExpect [Patent for Identifier#, Date] Match the Matched Value Residues Region AAG81345 Human AFP protein sequence98..520 419/423 (99%)0.0 SEQ

ID N0:208 - Homo Sapiens, 1..423 421/423 (99%) 423 aa.

[W0200129221-A2, 26-APR-2001]
v AAB93797 ~ Human protein sequence 102..520 416/419 (99%)0.0 SEQ ID

N0:13560 - Homo Sapiens, 14..432 419/419 (99%) 432 aa.

[EP 1074617-A2, 07-FEB-2001 ]

AAM93974 ~ Human stomach cancer 102..520 416/419 (99%)0.0 expressed polypeptide SEQ ID NO 17 14..432 419/419 (99%) - Homo : .

Sapiens, 432 aa. [W0200109317-Al, 08-FEB-2001]

ABG04835 Novel human diagnostic 50..297 243/248 (97%)e-143 protein #4826 - Homo Sapiens, 371 23..270 246/248 (98%) aa.

[WO200175067-A2, 11-OCT-2001]

ABG04835 Novel human diagnostic 50..297 243/248 (97%)e-143 protein #4826 - Homo Sapiens, 371 23..270 2461248 (98%) aa.

T~;~___....~[W0200175067-A2, 1.1-OCT-2001]......_._..__.~..~_~x,~,~.,~_ __. __" ~ _ . ._ ~_.w~x In a BLAST search of public sequence databases, the NOV6a protein was found to have homology to the proteins shown in the BLASTP data in Table 6E.

Table 6E. Public BLASTP Results for NOV6a Protein '~ NOV6a Identities/

Accession Protein/Organism/Length Residues/ Similarities Expect for Number Match the Matched Value Residues Portion ~

AAH25429 SIMILAR TO RIKEN CDNA 1..520 451/520 (86%)0.0 2810049606 GENE - Mus 1..519 479/520 (91 %) musculus (Mouse), 519 aa.

CAC38595 SEQUENCE 207 FROM 98..520 419/423 (99%)0.0 PATENT W00129221 - Homo ~ 1..423 421/423 (99%) Sapiens (Human), 423 aa.

AAH25020 RIKEN CDNA 2810049606 ~ 1..520 422/520 (81%)0.0 GENE - Mus musculus (Mouse),1..487 449/520 (86%) 487 aa.

Q9CZ73 2810049G06RIK PROTEIN 1..520 421/520 (80%)0.0 -Mus musculus (Mouse), 1..487 448/520 (85%) 487 aa.

Q96KY4 SIMILAR TO RIKEN CDNA ~ 171..520348/350 (99%)0.0 2810049606 GENE - Homo 1..350 350/350 (99%) Sapiens (Human), 350 ~
aa.

t PFam analysis predicts that the NOV6a protein contains the domains shown in the Table 6F.
Table 6F. Domain Analysis of NOV6a Identities/
Pfam Domain NOV6a Match Region Similarities Expect Value for the Matched Region Adeno_Penton_B 204..222 8/20 (40%) 0.54 17/20 (85%) MBOAT 148..442 108/334 (32%) ~ 4.1e-89 225/334 (67%) _ .. _ . .. _... .
Example 7.
The NOV7 clone was analyzed, and the nucleotide and encoded polypeptide sequences axe shown in Table 7A.
Table 7A. NOV7 Sequence Analysis __~~" ,.~~Q ID.NO.~.15 ... . ... w,~ 537 by ,~ . ..~ ,..:-NOV7a, ATTAGCAACGGCTCATGATGAACTCAATCAAAGGGGGCTTGACCAGCATCTCAGGTCT

DNA Sequence ~GAGAGAAGAAAGAGTGAGACACCACCACTAAAAGGGCTGCAGGTGGATACCGCCTC
CCTCAAGCTGGAAAAAGATTAGAAAGATGGTGAAAACAGGAAGACCTTCCTCATCCCA
CTATCAGGAAGATGAGGAAAGAGATCAGGAGGATCACAGGTGGAGAGGAGAAGAGGAC
CATGCTCGATCCTCTCTGGTAATAGGCCTGAGATTCCCTCTCGTACTGGGTGATACAC
ATCTGCTCCCAGTGTTCCATCCTCCAGGCTTCGGGCGCTTCTTGCAGAGGCCCAGGTC
ACTCCATGTGGCCACAAAGAGAACCAGCATCCAGCAGCCAAGGTTCGCCATAATGACT
GCTCTGCCTCGGTCGTGAGGAGAGGAGAAGCTCGCGGCGCCGCGGCTGTCAGCGACTG
GCTCGGAGGACAGGC
ORF StarE: ATG at 201 ORF Stop:_TGA at 4_80___ SEQ ID N0~16. a 93 as ~MW at 10769.1kD
NOV7a, MVKTGRPSSSHYQEDEERDQEDHRWRGEEDHARSSLVIGLRFPLVLGDTHLLPVFHPP
CG101362-Ol GFGRFLQRPRSLHVATKRTSIQQPRFAIMTALPRS
Protein Sequence Further analysis of the NOV7a protein yielded the following properties shown in Table 7B.
Table 7B. Protein Sequence Properties NOV7a PSort ~ 0.6400 probability located in microbody (peroxisome); 0.4500 probability analysis: ~ located in cytoplasm; 0.2288 probability located in lysosome (lumen); 0.1000 probability located in mitochondrial matrix space SignalP No Known Signal Sequence Predicted ~alysis: ~ .. _.. _ . _. ~.~u.-~,~..,~- ~.....~~~,:~. W _..~_ _W~.~;._~:,~"...
.. ..._...._.
A search of the NOV7a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 7C.

Table 7C.'Geneseq Results for NOV7a NOV7a Identities/

Geneseq Protein/Organism/Length Residues/ SimilaritiesExpect [Patent #, IdentifierDate] Match for the Value Residues Matched Region AAY19678 SEQ ID NO 396 from W099222431..30 24/30 (46%)0.94 -Homo Sapiens, 133 aa. [W09922243-63..91 19/30 (62%) Al, 06-MAY-1999]

AAB92467 Human protein sequence SEQ 2..90 24/90 (26%)1.2 ID

N0:10527 - Homo Sapiens, 318..398 41/90 (44%) 563 aa.

[EP1074617-A2, 07-FEB-2001]

AAU16292 Human novel secreted protein,2..90 24/90 (26%)1.2 Seq ID

1245 - Homo sapiens, 564 319..399 41/90 (44%) aa.

[W0200155322-A2, 02-AUG-2001]
___ _______-____ -__ _ _ ABB50224 Human transcription factor 2..90 24/90 (26%)1.2 - Homo sapiens, 596 aa. 351..431 41/90 (44%) [WO200172777-A2, 04-OCT-2001]

AAM33060 Peptide #7097 encoded by 5..30 13/26 (50%)1.6 probe for measuring placental gene 1..25 18/26 (69%) expression -Homo Sapiens, 49 aa.

[W0200157272-A2, 09-AUG-2001]

In a BLAST search of public sequence databases, the NOV7a protein was found to have homology to the proteins shown in the BLASTP data in Table 7D.

Table 7D. Public BLASTP
Results for NOV7a ~_~

~ 7a Identities/

Protein ' Similarities Residues/ Expect Accession Protein/Organism/Length for the Match Value Number Matched Residues Portion Q9D3A0 6330414C15RIK PROTEIN - ~ 1..30 14/30 (46%)2.2 Mus musculus (Mouse), 150 aa. 51..79 19/30 (62%) Q9Y269 Protein HSPC020 - Homo 1..30 14/30 (46%); 2.2 Sapiens (Human), and, 121 aa. 51..79 19/30 (62%) . ~ .

Q9UKD0 _ _ 24/90 (26%)2.9 DNA BINDING PROTEIN P96PIF2..90 (GLUCOCORTICOID 318..398 41/90 (44%) MODULATORY ELEMENT

BINDING PROTEIN 1 ) - Homo Sapiens (Human), 563 aa.

Q9NWH1 HYPOTHETICAL 61.4 KDA 2..90 24/90 (26%)2.9 PROTEIN - Homo Sapiens 318..398 41/90 (44%) (Human), 563 aa.

Q9Y692 GLUCOCORTICOID 2..90 24/90 (26%)3.8 MODULATORY ELEMENT 328..408 40190 (43%) BINDING PROTEIN-1 - Homo sapiens (Human), 573 aa.

Examine 8.
The NOV8 clone was analyzed, and the nucleotide and.encoded polypeptide sequences are shown in Table 8A.
Table 8A. NOV8 Sequence Analysis SEQ ID NO: 17 3653 by NOV8a, CGGGATGCCCGGCTTGCTGAATTGGATCACGGGGGCAGCCCTGCCCCTCACCGCGTCT
CG101458-Ol GATGTTACCTCCTGTGTCAGCGGTTATGCCCTGGGCCTAACTGCCTCCCTCACCTATG
DNA SBqueriCe GCAACCTGGAAGCCCAGCCCTTCCAGGGTCTCTTCGTGTACCCCCTGGATGAGTGCAC
CACGGTGATCGGCTTTGAGGCAGTCATTGCCGACCGTGTCGTGACAGTACAGATCAAG
GACAAAGCCAAGCTGGAGAGCGGCCACTTCGATGCCTCCCATGTTCGATCCCCAACAG
GGATTTGGAGCGGATCCTGTTCGTGGCCAACCTGGGGACCATTGCCCCCATGGAGAAT
GGGTCCTTCTGCCTGCTGTCTGTGCCCCAACCGTGCCCCAGTTCTGCACCAAGAGCAC
TGGCACCTCCAACCAACAGGCCCAGGGGAAAGACAGGCACTGCTTCGGTGCCTGGGCC
CCGGGCTCCTGGAATAAGTTGTGCCTGGCGACTCTCCTGAACACCGAAGTGTCCAACC
CCATGGAGTATGAGTTCAACTTCCAGCTGGAGATCCGTGGGCCATGTCTGCTCGCAGG
TGTGGAGAGTCCCACTCATGAGATTCGTGCCGACGCCGCCCCATCTGCCCGCTCGGCC
TCATCCACCCCAGCGAGCCCCATATGCCCCATGTCCTGATAGAGAAAGGGGACATGAC

CCTGGGAGAGTTTGACCAGCACTTGAAGGGAAGAACAGATTTCATTAAAGGGATGAAG
TTCCCCACCACTCCGTCATCATGCTCAACTTCTGTCCCGACCTCCAGTCAGTCCAGCC
GTGCCTGAGAAAGGCCCACGGGGAGTTCATCTTCCTCATTGACAGGAGCAGCAGCATG
AGCGGGATCAGCATGCACCGAGTCAAGGATGCCATGTTGGTGGCCCTTAAGAGCCTCA
TGCCAGCCTGCCTCTTCAATATCATTGGGTTTGGATCCACATTTAAGAGCCTTTTTCC
TTCCAGCCAGACCTACAGTGAGGACAGCTTGGCCATGGCTTGTGATGACATCCAGAGA
ATGAAGGCCGACATGGGTGGGACCAACATCCTTTCCCCTCTCAAGTGGGTCATCAGGC
AGCCAGTGCACCGAGGCCACCCGCGGCTCCTCTTCGTGATCACAGATGGCGCTGTCAA
CAACACAGGGAAGGTGCTGGAGCTGGTGCGAAATCACGCCTTCTCCACCAGGTGCTAT
AGCTTTGGAATTGGACCCAACGTCTGCCACAGACTGGTGAAAGGACTGGCATCTGTGT
CCGAGGGCAGTGCTGAGCTCCTGATGGAGGGGGAGCGGCTGCAACCCAAGATGGTCAA
ATCCTTGAAGAAGGCCATGGCCCCAGTCCTGAGCGATGTGACTGTGGAGTGGATCTTC
CCTGAGACCACTGAGGTCCTGGTCTCACCCGTCAGCGCCAGCTCCCTCTTCCCTGGAG
AACGGCTGGTGGGGTATGGCATTGTATGTGATGCTTCTTTGCACATCTCCAATCCCAG
ATCTGACAAGAGGCGCCGGTACAGCATGCTGCACTCTCAGGAGTCTGGCAGCTCTGTC
TTCTACCACTCTCAGGATGACGGACCCGGGCTGGAAGGTGGAGACTGTGCCAAGAACT
CGGGGGCACCCTTCATCCTAGGGCAGGCCAAAAATGCCCGGCTAGCCAGCGGAGACTC
TACCACCAAGCACGGTCTGAACCTCTCTCAGCGACGGAGGGCATACAGCACCAACCAG
ATCACCAATCACAAGCCCCTCCCAAGAGCCACCATGGCAAGTGACCCCATGCCAGCTG
CCAAGAGATACCCACTGCGGAAAGCCAGGCTGCAGGACCTCACCAACCAGACCAGCCT
GGATGTCCAGCGGTGGCAGATTGATTTGCAGGTATTGCTGAACAGTGGTCAGGACCTG
GCTGCCAGCCCTTCCTGCCCTGGGGCCAGGAGACCCAGGCCTGGAGCCCTGTGAGAGA
GCGGACTTCTGACAGCCGAAGCCCTGGAGATCTGCCCGCAGAGCCGTCCCACCATCCC
TCTGCCTTCGAGACAGAGACGTCCTCGGACTGGGACCCCCCAGCCGAGTCCCAGGAGC
GAGCCAGTCCCAGCAGGCCCGCCACCCCGGCCCCGGTGCTGGGCAAGGCCCTGGTCAA
AGGCCTGCACGACAGCCAACGCCTGCAGTGGGAGGTGAGCTTCGAGCTGGGGACCCCT
GGACCGGAGCGGGGCGGCGCGCAGGATGCCGACCTATGGAGCGAGACCTTCCACCACC
TGGCGGCCCGCGCCATCATCCGCGACTTCGAGCAGCTGGCGGAGCGCGAGGGCGAGAT
CGAGCAGGGTTCCAACCGCCGCTACCAAGTGAGCGCCTTGCACACCAGCAAGGCCTGC
TTAGCAAATACACAGCCTTCGTGCCTGTGGACGTGAGCAAGAGCCGGTACC
TGCCCACCGTGGTGGAGTACCCCAACTCTGGTCGTATGCTTGGCTCTCGGGCCCTGGC
GATTCGGCACCAGGAAATGGTAAATTTCAGGTCCTAGACATGGAGGCAAGTCCCACTG
CTCTCTTCAGCGAGGCCAGGTCCCCCGGCCGCGAGAAGCACGGTGCTTCTGAAGGTCC
CCAGCGCAGCCTGGCTACAAATACTCTTTCTTCCATGAAGGCCTCAGAGAATCTCTTT
GGATCCAGGCTAAATCTCAACAAGTCCAGGCTACTGACGCGAGCAGCCAAGGGCTTCC
TGAGCAAGCCACTGATCAAAGCTGTGGAGTCGACCTCCGGGAACCAGAGCTTCGACTA
CATACCTCTGGTGTCTCTGCAGCTGGCCTCCGGAGCCTTCCTGCTCAACGAAGCCTTC
TGTGAGGCCACGCACATCCCCATGGAGAAGCTCAAGTGGACGTCCCCCTTCACCTGCC
ATCGAGTGTCCCTCACCACCCGCCCGTCTGAGTCCAAGACCCCGAGTCCCCAGCTGTG
CACCAGCTCCCCGCCTAGGCACCCGTCCTGTGACAGCTTCTCCCTGGAGCCTCTGGCC
AAGGGCAAGCTGGGCCTGGAGCCGAGGGCAGTGGTGGAGCACACTGGGAAGCTGTGGG
CCACGGTGGTGGGGCTGGCATGGCTGGAGCACAGTTCGGCCTCCTACTTCACTGAGTG
GGAGTTGGTGGCTGCCAAGGCCAACTCATGGCTGGAGCAGCAGGAAGTACCCGAGGGC
CGCACGCAGGGCACACTCAAGGCCGCTGCCCGCCAGCTGTTTGTGCTTCTGCGGCACT
GGGATGAGAATCTCGAGTTCAATATGCTCTGCTATAACCCGAATTATGTGTAGTTGA
ORF Start: ATG at 5 ~ORF Stop: TAG at 3647_ SEQ ID NO: 18 1214 as MW at 1331 lB.OkD
NOVBa, MPGLLNWITGAALPLTASDVTSCVSGYALGLTASLTYGNLEAQPFQGLFWPLDECTT

Protein S8 Lt~rlCe LERILFVANLGTIAPMENVTIFISTSSELPTLPSGAVRVLLPAVCAPTVPQFCTKSTG
TSNQQAQGKDRHCFGAWAPGSWNKLCLATLLNTEVSNPMEYEFNFQLEIRGPCLLAGV
ESPTHEIRADAAPSARSAKSIIITLANKHTFDRPVEILIHPSEPHMPHVLTEKGDMTL
GEFDQHLKGRTDFIKGMKKKSRAERKTEIIRKRLHKDIPHHSVIMLNFCPDLQSVQPC
LRKAHGEFIFLIDRSSSMSGISMHRVKDAMLVALKSLMPACLFNIIGFGSTFKSLFPS
SQTYSEDSLAMACDDIQRMKADMGGTNILSPLKWVIRQPVHRGHPRLLFVITDGAVNN
TGKVLELVRNHAFSTRCYSFGIGPNVCHRLVKGLASVSEGSAELLMEGERLQPKMVKS

LKKAMAPVLSDVTVEWIFPETTEVLVSPVSASSLFPGERLVGYGIVCDASLHISNPRS
DKRRRYSMLHSQESGSSVFYHSQDDGPGLEGGDCAKNSGAPFILGQAKNARLASGDST
TKHGLNLSQRRRAYSTNQITNHKPLPRATMASDPMPAAKRYPLRKARLQDLTNQTSLD
VQRWQIDLQVLLNSGQDLNQGPKLRGPGARRPSLLPQGCQPFLPWGQETQAWSPVRER
TSDSRSPGDLPAEPSHHPSAFETETSSDWDPPAESQERASPSRPATPAPVLGKALVKG
LHDSQRLQWEVSFELGTPGPERGGAQDADLWSETFHHLAARAIIRDFEQLAEREGEIE
QGSNRRYQVSALHTSKACNIISKYTAFVPVDVSKSRYLPTVVEYPNSGRMLGSRALAQ
QWRGTSSGFGRPQTMLGEDSAPGNGKFQVLDMEASPTALFSEARSPGREKHGASEGPQ
RSLATNTLSSMKASENLFGSRLNLNKSRLLTRAAKGFLSKPLIKAVESTSGNQSFDYI
PLVSLQLASGAFLLNEAFCEATHIPMEKLKWTSPFTCHRVSLTTRPSESKTPSPQLCT
SSPPRHPSCDSFSLEPLAKGKLGLEPRAVVEHTGKLWATVVGLAWLEHSSASYFTEWE
LVAAKANSWLEQQEVPEGRTQGTLKAAARQLFVLLRHWDENLEFNMLCYNPNYV
Further analysis of the NOVBa protein yielded the following properties shown in Table 8B.
Table 8B. Protein Sequence Properties NOVBa"
PSort 0.8700 probability located in nucleus; 0.8500 probability located in analysis: endoplasmic reticulum (membrane); 0.7900 probability located in plasma membrane; 0.3325 probability located in microbody (peroxisome) SignalP Cleavage site between residues 19 and 20 analysis:
A search of the NOV 8a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 8C.

~. . ~ ... . Table 8C. _........
Geneseq .Results for NOVBa . ~... .

NOVBa Identities/

Geneseq Protein/Organism/Length Residues/Similarities Expect [Patent ~ for ~

Identifier#, Datej Match the Matched Value i Residues Region AAB82047 Human mast cell surface 13..565 168/565 (29%)2e-59 antigen - ~

Homo Sapiens, 786 aa. 15:.500 269/565 (46%) [JP2001025388-A, 30-JAN-2001]

AAY82530 Human neurotransmitter 1034..121182/194(42%) 1e-32 associated protein sequence SEQ ID 16..207 105/194 (53%) N0:6 - 3 Homo Sapiens, 210 aa.

[W0200012685-A2, 09-MAR-2000] _ AAU33242 Novel human secreted protein36..568 120/537 (22%)4e-23 ~

#3?33 - Homo Sapiens, 1730650..1096214/537 (39%) aa. ' [W0200179449-A2, 25-OCT-2001]

AAB51022 Human minor vault protein 36..568 120/537 (22%)6e-23 p193 - ~

Homo Sapiens, 1724 aa. 644..1090214/537 (39%) [US6156879-A, OS-DEC-2000]

.
~.

AAY54373 cDNA sequence encoding 36..568 120/537 (22%)6e-23 the ~ ~ ~

human minor vault protein 644..1090214/537 (39%) p193 -Homo sa iens 1724 aa.
p [W09962547-Al, 09-DEC-1999] t In a BLAST search of public sequence databases, the NOVBa protein was found to nave homology to the proteins shown in the BLASTP data in Table 8D.

Table 8D. Public BLASTP
Results for NOVBa NOVBa ~ Identities/
Protein Residues/ SimilaritiesExpect AccessionProtein/Organism/Length for ' Match the Matched Value Number Residues Portion Q9CUE8 4931403E03RIK PROTEIN 1..1208 883/1218 0.0 - Mus ~ (72%) musculus (Mouse), 1209 1..1209 1012/1218 as (82%) ', (fragment).

Q96M7I CDNA FLJ32784 FIS, CLONE588..953 362/369 (98%)0.0 ~

TESTI2002245 - Homo Sapiens1..367 362/369 (98%) (Human), 424 aa. ~

:

Q9BVH8 HYPOTHETICAL 106.2 KDA 274..1211 31111047 e-106 ~ (29%) PROTEIN - Homo Sapiens 32..998 467/1047 ~ (43%) (Human), 1001 as (fragment).

075668 DJ745E8.1 (BREAST CANCER~ 417..564148/148 (100%)4e-80 SUPPRESSOR CANDIDATE 1..148 148/148 (100%) (BCSC-1) LIKE) - Homo sapiens (Human), 148 as (fragment).

Q9CTV9 5830475I06RII~ PROTEIN 13..565 165/567 (29%) - Mus ~ Se-57 musculus (Mouse), 565 15..500 259/567 (45%) as ~fragment).

_._. .. __...._ ~ .. .. . ..... ...
~- .-y_...~

PFam analysis predicts that the NOVBa protein contains the domains shown in the Table 8E.
Table 8E. Domain Analysis of NOVBa Identities/
Pfam Domain NOVBa Match Region Similarities Expect Value for the Matched Region wwa 355 523 ~ 37/203 (18%) 0.021 107/203 (53°1°) Example 9.
The NOV9 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 9A.
Table 9A. NOV9 Sequence Analysis SEQ ID NO: 19 868 by NOV9a, CGTTTTCTTCTACAATGTCTGAAGAAGTGACCTACGCGACACTCACATTTCAGGATTC
TGCTGGAGCAAGGAATAACCGAGATGGAAATAACCTAAGAAAAAGAGGTCATCCAGCT

CG101475-Ol CCATCTCCCATTTGGCGTCATGCTGCTCTGGGTCTGGTAACTCTTTGCCTGATGTTGC

DNA Sequence TGATTGGGCTGGTGACATTGGGGATGATGTGTTTGCAGATATCTAATGACATTAACTC

AGATTCAGAGAAATTGAGTCAACTTCAGAAAACCATCCAACAGCAGCAGGATAACTTA

TCCCAGCAACTGGGCAACTCCAACAACTTGTCCATGGAGGAGGAATTTCTCAAGTCAC

AGATCTCCAGTGTACTGAAGAGGCAGGAACAAATGGCCATCAAACTGTGCCAAGAGCT

AATCATTCATTTTTCAGACCACAGATG'T'AATCCATGTCCTAAGATGTGGCAATGGTAC

CAAAATAGTTGCTACTATTTTACAACAAATGAGGAGAAAACCTGGGCTAACAGTAGAA

AGGACTGCATAGACAAGAACTCCACCC'I'AGTGAAGATAGACAGTTTGGAAGAAAAGGA

TTTTCTTATGTCACAGCCATTACTCATGTTTTCGTTCTTTTGGCTGGGATTATCATGG

GACTCCTCTGGCAGAAGTTGGTTCTGGGAAGATGGCTCTGTTCCCTCTCCATCCTTGA

GTAC'Z'ARAGAACTTGACCAGATCAATGGATCCAAAGGATGTGCTTATTTTCAAAAAGG

AAATATTTATATTTCTCGCTGTAGTGCTGAAATTTTTTGGATTTGCGAGAAGACAGCT

GCCCCAGTGAAGACTGAGGA'T'TTGGATTAGTATGCTTCTTCCAAATTCTCCAAGAA
_.
..
-~

0~
..
0~ Start: ATG at l s Stop. TAG at 840 SEQ ID NO: 20 X275 as MW at 31470.4kD

NOV9a, MSEEVTYATLTFQDSAGARNNRDGNNLRKRGHPAPSPIWRHAALGLVTLCLMLLTGLV

CG101475-Ol TLGMMCLQISNDINSDSEKLSQLQKTIQQQQDNLSQQLGNSNNLSMEEEFLKSQISSV

Protein SeqLleriCeL~'QEQMAIICLCQELIIHFSDHRCNPCPKMWQWYQNSCYYFTTNEEKTWANSRKDCID

KNSTLVKIDSLEEKDFLMSQPLLMFSFFWLGLSWDSSGRSWFWEDGSVPSPSLSTKEL

DQINGSKGCAYFQKGNIYISRCSAEIFWICEKTAAPVKTEDLD

SEQ ID NO: 21 819 by NOV9b, ACACTCACATTTCAGGATTCTGCTGGAGCAAGGAATAACCGAGATGGAAATAACCTAA

CGIOI47S-O2 G~GAGGGCATCCAGCTCCATCTCCCATTTGGCGTCATGCTGCTCTGGGTCTGGT

'DNA SeqLlenCe~CTCTTTGCCTGATGTTGCTGATTGGGCTGGTGACGTTGGGGATGATGTTTTTGCAG

ATATCTAATGACATTAACTCAGATTCAGAGAAATTGAGTCAACTTCAGAAAACCATCC

AACAGCAGCAGGATAACTTATCCCAGCAACTGGGCAACTCCAACAACTTGTCCATGGA

GGAGGAATTTCTCAAGTCACAGATCTCCAGTGTACTGAAGAGGCAGGAACAAATGGCC

ATCAAACTGTGCCAAGAGCTAATCATTCATACTTCAGACCACAGATGTAATCCATGTC

CTAAGATGTGGCAATGGTACCAAAATAGTTGCTACTATTTTACAACAAATGAGGAGAA

AACCTGGGCTAACAGTAGAAAGGACTGCATAGACAAGAACTCCACCCTAGTGAAGATA

GACAGTTTGGAAGAAAAGGATTTTCTTATGTCACAGCCATTACTCATGTTTTCGTTCT

TTTGGCTGGGATTATCATGGGACTCCTCTGGCAGAAGTTGGTTCTGGGAAGATGGCTC

TGTTCCCTCTCCATCCTTATTTAGTACTAAAGAACTTGACCAGATCAATGGATCCAAA

GGATGTGCTTATTTTCAAAAAGGAAATATTTATATTTCTCGCTGTAGTGCTGAAATTT

TTTGGATTTGCGAGAAGACAGCTGCCCCAGTGAAGACTGAGGATTTGGATTAGAAGGG

CGATTCC

ORF Start: at 1 ORF Stop: TAG at 80S

SEQ ID NO: 22 ~ 268 aa. ~MW at 30704 SkD

NOV9b, TLTFQDSAGARNNRDGNNLRKRGHPAPSPIWRHAALGLVTLCLMLLIGLVTLGMMFLQ

Protein SeqLlenCeIKLCQELIIHTSDHRCNPCPKMWQWYQNSCYYFTTNEEKTWANSRKDCIDKNSTLVKI

DSLEEKDFLMSQPLLMFSFFWLGLSWDSSGRSWFWEDGSVPSPSLFSTKELDQINGSK

GCAYFQKGNIYISRCSAEIFWICEKTAAPVKTEDLD

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 9B.

Table 9B. Comparison of NOV9a against NOV9b.
Protein Sequence NOV9a Residues/ ~ Identities/
Match Residues Similarities for the Matched Region NOV9b 9..275 241/268 (89%) 1..268 ' 241/268 (89%) Further analysis of the NOV9a protein yielded the following properties shown in Table 9C.
. J~~_~ ........_ Table 9C. Protein Sequence Properties NOV9a~
PSort 0.7900 probability located in plasma membrane; 0.3000 probability located in analysis: Golgi body; 0.2000 probability located in endoplasmic reticulum (membrane);
0.1000 probability located in mitochondria) inner membrane SignalP Cleavage site between residues 62 and 63 analysis:
A search of the NOV9a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 9D.

Table 9D. Geneseq Results for NOV9a NOV9a Identities!

Geneseq Protein/Organism/Length Residues/SimilaritiesExpect [Patent for Identifier#, Date] Match the Matched Value Residues Region AAU29320 Human PRO polypeptide 1..227 224/227 (98%)e-131 sequence #297 - Homo Sapiens, 232 1..227 225/227 (98%) aa.

[W0200168848-A2, 20-SEP-2001]

AAM79324 Human protein SEQ ID NO 1..270 91/270 (33%)3e-37 Homo Sapiens, 289 aa. 25..280 147/270 (53%) [W0200157190-A2, 09-AUG-2001]

ABB11776 Human macrophage Ag homologue,1..270 91/270 (33%)3e-37 SEQ ID N0:2146 - Homo 25..280 147/270 (53%) Sapiens, 289 aa. [W0200157188-A2, AUG-2001 ]

AAM78340 Human protein SEQ ID NO 1..270 88/270 (32%)!e-35 Homo sapiens, 265 aa. 1..256 147/270 (53%) [WO200157190-A2, 09-AUG-2001 ]

AAY02283 Secreted protein clone 1..270 88/270 (32%)!e-35 br342_11 polypeptide sequence - 1..256 147/270 (53%) Homo Sapiens, 265 aa. [W09918127-Al, 15-APR-1999]

In a BLAST search of public sequence databases, the NOV9a protein was found to have homology to the proteins shown in the BLASTP data in Table 9E.

Table 9E. Public BLASTP
Results for NOV9a Protein NOV9a Identities/

AccessionProtein/OrganismlLength Residues!SimilaritiesExpect ' for Number Match the Matched Value Residues Portion ' Q9D403 4933425B16RIK PROTEIN - 1..275 197/276 (71%)e-113 Mus ~

musculus (Mouse), 275 aa. 1..275 227/276 (81 ~ %) AAL95693 C-TYPE LECTIN PROTEIN 1..270 88/270 (32%)2e-35 CLL-1 - Homo Sapiens (Human),1..256 147/270 (53%) ~

265 aa.

..... .. ............. ................ .... .... ........
.. ......... .... . ........ ..... ... ... . .
.... ... ~.. ... ... .....

Q9NZH3 C-TYPE LECTIN-LIKE 28..274 83/249 (33%)Se-33 ~

RECEPTOR-1 - Homo sapiens 36..269 131/249 (52%) (Human), 280 aa.

Q9~TA8 LECTIN-LIKE OXIDIZED LDL 36..272 79/247 (31%)Y~Se-27 3 ~

RECEPTOR - Oryctolagus 36..278 124/247 (49%) cuniculus (Rabbit), 278 3 aa.

P78380 LECTIN-LIKE OXIDIZED LDL 36..266 79/245 (32%)3e-24 ~

RECEPTOR - Homo Sapiens 32..268 124/245 (50%) (Human), 273 aa.

PFam analysis predicts that the NOV9a protein contains the domains shown in the Table 9F.
Table 9I'. Domain Analysis of NOV9a Identities/
Pfam Domain NOV9a Match Region ~ Similarities ' Expect Value for the Matched Region Iectin_c 161..264 29/125 (23%) ~ 7.4e-06 61/125 (49%) _..... ....
Example 10, The NOV 10 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 1 OA.
Table 10A. NOV10 Sequence Analysis SEQ ID NO: 23 516 by NOVIOa, CACTGCGCATGCTATTTGGGCGCCCACCTCAGTGCACATGTTCACTGGGCGTCTTCTA
CG101772-Ol CTCTACCCCTTCGCCCTCGTGGGGGTGTGAGGGTCGCGTTCCTGCTGTCTGGACTTTT
DNA Sequence TCTGTCCCACTGAGACGCAATGTATCGATAACAAAACTTTTTATCTGCACACACACAC
ACACACACACACACCCCTGGTTCCAGGAGCCCGGTGATGAGGAGCCTCAGCAAGAGGA

ACCACCAACTGAAAGTCGGGATCCTGCACCTGGTCAGGAGAGAGAAGAAGATCAGGGT
GCAGCTGAGACTCAATGCCTGACCTGGAAGCTGATCTCCAGGAGCTGTCTCAGTCAAA
GACTGGGGGTGAATGTGGAAATGAAGATTCTGCCAAAATCAGAACAATTTAAAATGCC
AGAAGGAGGTATGCTATCCATTATTATGTGCTTTCTGTTTTCCACAATATTATACTTT
TGATAATAAAAGAGAACATTACTATCCCTTTAAAATCAGAGTTCAAATGCAG
ORF Start: ATG at 9 ORF Stop: TGA at 465 SEQ ID NO: 24 152 as MW at 17265.6kD
NOVIOa, MLFGRPPQCTCSLGVFYSTPSPSWGCEGRVPAVWTFSVPLRRNVSITKLFICTHTHTH
CG101772-Ol THPWFQEPGDEEPQQEEPPTESRDPAPGQEREEDQGAAETQCLTWKLISRSCLSQRLG
~UNVEMKILPKSEQFKMPEGGMLSIIMCFLFSTILYF
Protein Sequence Further analysis of the NOV 10a protein yielded the following properties shown in Table 10B.
Table 10B. Protein Sequence Properties NOVlOa PSort 0.9190 probability located in plasma membrane; 0.2000 probability located in analysis: lysosome (membrane); 0.1021 probability located in microbody (peroxisome);
0.1000 probability located in endoplasmic reticulum (membrane) SignalP No Known Signal Sequence Predicted analysis:
A search of the NOV 1 Oa protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table l OC.

Table 10C. Geneseq Results for NOVlOa NOVlOa Identities) ' Geneseq ProteinlOrganism/Length Residues/SimilaritiesExpect [Patent ' Identifier#, Date] Match for the Value Residues Matched Region AAM39588 Human polypeptide SEQ ID 65..136 51/78 (65%)4e-20 NO

2733 - Homo Sapiens, 111 28..105 56/78 (71%) aa.

[W0200153312-Al, 26-JUL-2001]

AAM41374 Human polypeptide SEQ ID 65..135 52/77 (67%)2e-19 NO

6305 - Homo sapiens, 106 29..105 57/77 (73%) aa.

[W0200153312-Al, 26-JUL-2001]

ABG05297 Novel human diagnostic 65..136 48/78 (61%)8e-19 protein #5288 - Homo Sapiens, 112 29..106 56178 (71 aa. %) [W0200175067-A2, 11-OCT-2001]

ABG05297 Novel human diagnostic 65..136 48/78 (61%)8e-19 protein #5288 - Homo Sapiens, 112 29..106 56/78 (71 aa. %) [W0200175067-A2, 11-OCT-2001]

ABG27048 Novel human diagnostic 64..135 45/78 (57%)5e-15 protein #27039 - Homo Sapiens, 70..147 53/78 (67%) 249 aa. ~

[W0200175067 A2, 1 l -OCT
2001 ]

.. . .... . _ ....
. . . . .
. ... ...
.. ._..
~ .

In a BLAST search of public sequence databases, the NOV 10a protein was found to have homology to the proteins shown in the BLASTP data in Table )OD.

Table !OD Public BLASTP Results for NOVlOa ~~
Protein . NOVlOa Identities/
Residues/ Similarities for ; Expect Accession Protein/Organism/Length Match the Matched ~ Value Number Residues Portion Q8WTP9 RAGE-3 PROTEIN - Homo 65..136 51/78 (65%) ~ 1e-19 Sapiens (Human)~111 aa. 28..105 56/78 (71%) Q8WYS9 ! HYPOTHETICAL 12.3-KDAy y 65..136 51/78 (65%) ~ 1e-19 PROTEIN -Homo sapiens ~ 28..105 56178 (71%) ' (Human), 111 aa.
Q9HD64 , G antigen family D 2 protein 1..136 59/149 (39%) ~ 3e-18 (RAGE-1) - Homo Sapiens 1..140 76/149 (50%) (Human), 146 aa.
Q8WWM1 ' RAGE-5 PROTEIN - Homo 65..136 45/78 (57%) 9e-15 sapiens (Human), 108 aa. 25..102 53/78 (67%) Q96GT9 ~ SIMILAR TO G ANTIGEN 8 65..136 39/78 (50%) ~ 7e-13 ~ (XAGE-2 PROTEIN) - Homo 28..105. 53/78 (67%) sapiens (Human), 111 aa.
Example 11.
The NOV 11 clone waS analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 1 1A.
Table 11A. NOVll Sequence Analysis SEQ ID NO: 25 709 by NOVlla, CGGCCGGTTTTGGTAGGCCCGGGCCGCCGCCAGGCCTCCGCCTGAGCCCGCACCCGCC

DNA SequeriCeACATCCCGCACGGGCCTGTAGTAGGATCAACTCGTAGGCTTTACGAGAAGAAGATCTT

CGAGTACGAGACCCAGAGGCGGCGGCTCTCGCCCCCCAGCTCGTCCGCCGCCTCCTCT

TATAGCTTCTCTGACTTGAATTCGACTAGAGGGGATGCAGATATGTATGATCTTCCCA

AGAAAGAGGACGCTTTACTCTACCAGAGCAAGGGCTACAATGACGATCTTTTGTCTTC

TTCTGAAGAGGAGTGCAAGGATAGGGAACGCCCCATGTACGGCCGGGACAGTGCCTAC

CAGAGCATCACGCACTACCGCCCTGTTTCAGCCTCCAGGAGCTCCCTGGACCTGTCCT

ATTATCCTACTTCCTCCTCCACCTCTTTTATGTCCTCCTCATCATCTTCCTCTTCATG

GCTCACCCGCCGTGCCATCCGGCCTGAAAACCGTGCTCCTGGGGCTGGGCTGGGCCAG

GATCGCCAGGTCCCGCTCTGGGGCCAGCTGCTGCTTTTCCTGGTCTTTGTGATCGTCC

TCTTCTTCATTTACCACTTCATGCAGGCTGAAGAAGGCAACCCCTTCTGACTGCAGCC

AAGCTAATTCCGG

ORF Start: ATG at 59 ORF Stop: TGA at 686 SEQ ID NO: 26 209 as MW at 23844.1kD

,.,...,.~:.,.~..., ~.,.~..,~,....~.~.... .~,.w....-.,..~.~........J
NOVlla, MDNYADLSDTELTTLLRRYNIPHGPWGSTRRLYEKKIFEYETQRRRLSPPSSSAASS

QSITHYRPVSASRSSLDLSYYPTSSSTSFMSSSSSSSSWLTRRAIRPENRAPGAGLGQ

PrOteln SeqllenCe DRQVPLWGQLLLFLVFVIVLFFIYHFMQAEEGNPF
Further analysis of the NOV 11 a protein yielded the following properties shown in Table 11B.
Table 11B. Protein Sequence Properties NOVlla PSort 0.8500 probability located in endoplasmic reticulum (membrane); 0.6000 analysis: probability located in nucleus; 0.4400 probability located in plasma membrane; 0.2323 probability located in microbody (peroxisome) SignalP No Known Signal Sequence Predicted analysis:
A search of the NOV 11 a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 11 C. . .
Table 11C. Geneseq Results for NOVlla NOVlla Identities/ 1 ~

Geneseq ~ Protein/Organism/LengthResidues/SimilaritiesExpect for Identifier(Patent #, Date) Match the Matched ~ Value Residues Region rc AAY41294 ~ Human emerin sequence 1..209 209/254 (82%)~ e-112 (EMD HU) - Homo Sapiens, 1..254 209/254 (82%) aa. [W09954468-Al, 28-OCT-~

1999] ~ rt AAG02346 ~ Human secreted protein,1..51 51/51 (100%)2e-23 SEQ ID

NO: 6427 - Homo Sapiens, 1..51 51 /51 ( 51 aa. 100%) [EP 1033401-A2, 06-SEP-2000]

AAY41297 ~ Human thymopoietin gamma6..209 60/231 (25%)7e-10 ~

sequence - Homo Sapiens, 114..333 107/231 (45%) 345 aa.

[WO9954468-A1, 28-OCT-1999]

AAR93188 ~ Thymopoietin-gamma - 6..209 60/231 (2S%)~ 7e-10 Homo Sapiens, 345 aa. [W09609526-Al,114..333 107/231 (45%) 28-MAR-1996]

AAR76499 Human thymopoietin-gamma 6..209 60/231 (25%)~ 7e-10 -Homo Sapiens, 345 aa. 114..333 107/231 (45%) ~ [W09517205-A1, 29-JUN-1995]

In a BLAST search of public sequence databases, the NOV 11 a protein was found to have homology to the proteins shown in the BLASTP data in Table I 1 D.

~.. ~.... . . . ~_. _..~
.. ....... . .. ~_...
__, .
Table 11D. Public BLASTP
Results for NOVlla Protein NOVlla Identities/

Accession Protein/Organism/Length Residues/ Similarities~ Expect ~ for Number Match the Matched Value Residues Portion P50402 ' Emerin - Homo Sapiens 1..209 209/254 (82%)e-111 (Human), 254 aa. 1..254 209/254 (82%) Q63190 Emerin - Rattus norvegicus1..209 162/256 (63%)1e-81 ~ ~

(Rat), 260 aa. 1..256 182/256 (70%) ~

008579 Emerin - Mus musculus 1..209 162/255 (63%)1e-81 (Mouse), 259 aa. ~ 1..255 182/255 (70%) Q61032 THYMOPOIETIN GAMMA - 6..209 66/231 (28%)2e-l l Mus musculus (Mouse), 112..331 106/231 (45%) 342 aa. ~ ~

AAC25390 THYMOPOIETIN GAMMA - 6..209 60/231 (25%). 2e-09 ~

Homo sapiens (Human), 114..333 107/231 (45%) 345 aa. s, .. ... . _ . h _ ~ ._ PFam analysis predicts that the NOV 11 a protein contains the domains shown in the Table 11E.
Table 11E. Domain Analysis of NOVlla Identities/
Pfam Domain NOVlla Match Region' Similarities Expect Value for the Matched Region LEM 1..44 22/47 (47%) 4.4e-24 43/47 (91 %) Example 12.
The NOV 12 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 12A.
Table 12A. NOV12 Sequence Analysis SEQ ID N0: 27 2812 by NOVl2a, CATTGAGTCGGCTTTTCTACTGCTTCGGCTAGGGTACCTTGTGACCATGTCTTCCAAG
CG102575-Ol ~G~TAGAAAGCGGTTGAACCAAAGCGCGGAAAATGGTTCGTCCTTGCCCTCTGCTG
DNA SBqLlenCe CTTCCTCTTGTGCGGAGGCACGGGCTCCTTCTGCTGGATCAGACTTCGCGGCAACCTC
CGGGACTCTGACGGTGACCAACTTATTAGAAAAGGGTAAAATTCCTAAAACATTCCAG
AATTCCCTTATTCATCTTGGACTCAACACTATGAAGTCTGCAAATATATGTATAGGTC
GACCAGTGTTGCTTACTAGTTTGAACGGAAAGCAAGAGGTATATACAGCCTGGCCTAT
GGCAGGATTTCCTGGAGGCAAGGTCGGCCTGAGTGAAATGGCACAGAAAAATGTGGGT
GTGAGGCCTGGTGATGCCATCCAGGTCCAGCCTCTTGTGGGTGCTGTGCTACAGGCTG
AGGAAATGGATGTGGCACTGAGTGACAAAGATATGGAAATTAATGAAGAAGAACTGAC

TGGTTGTATCCTGAGAAAACTAGATGGCAAGATTGTTTTACCAGGCAACTTTCTGTAT
TGTACATTCTATGGACGACCGTACAAGCTGCAAGTATTGCGAGTGAAAGGGGCAGATG
GCATGATATTGGGAGGGCCTCAGAGTGACTCTGACACTGATGCCCAAAGAATGGCCTT
TGAACAGTCCAGCATGGAAACCAGTAGCCTGGAGTTATCCTTACAGCTAAGCCAGTTA
GATCTGGAGGATACCCAGATCCCAACATCAAGAAGTACTCCTTATAAACCAATTGATG
ACAGAATTACAAATAAAGCCAGTGATGTTTTGCTGGATGTTACACAGAGCCCTGGAGA
TGGCAGTGGACTTATGCTAGAGGAAGTCACAGGTCTTAAATGTAATTTTGAATCTGCC
AGAGAAGGAAATGAGCAACTTACTGAAGAAGAGAGACTGCTAAAGTTCAGCATAGGAG
CAAAGTGCAATACTGATACTTTTTATTTTATTTCTTCAACAACAAGAGTCAATTTTAC
AGAGATTGATAAAAATTCAAAAGAGCAAGACAGTGATGTTAAAAGTAACTATGACCAT
GATAGAGGATTAAGTAGCCAGCTGAA.AGCAATTAGAGAAATAATTGAATTGCCCCTCA
AAATTCCTGCCCCTAGAGGATTGTTACTTTATGGTCCTCCATGTACTGGAAAAACAAT
GATCGCCAGGGCTGTTGCTAATGAATTTGGAGCCTATGTTTCTGTAATTAATGGTCCT
GAAATTATAAGCAAGTTCTATGGTGAGACTGAAGCAAAGTTACGTCAGATATTTGCTG
AAGCCACTCTAAGACACCCATCAATTATTTTTATTGATGAGCTGGATGCACTTTGTCC
GAAAAGAGAGGGGGCCCAGAATGAAGTGGAAAAAAGAGTTGTGGCTTCACTCTTAACA
CTGATGGATGGCATTGGTTCAGAAGTAAGTGAAGGACAAGTGTTGGTTCTTGGGGCCA
CAAATCGCCCTCATGCCTTGGATGCTGCTCTCCGAAGACCTGGGCGATTTGATAAAGA' GATTGAGATTGGAGTTCCCAATGCTCAGGACCGGCTAGATATTCTCCAGAAACTGCTT' CGAAGGGTACCCCATTTGCTCACTGAGGCTGAGCTGCTGCAGCTGGCAAATAGTGCTC
ATGGATACGTTGGAGCAGACTTGAAAGTCTTGTGTAATGAAGCAGGTCTCTGTGCCTT' GCGGAGAATCCTGAAAAAACAGCCTAACCTCCCTGATGTCAAGGTGGCTGGACTGGTG'' AAGATTACTCTGAAGGATTTCTTGCAGGCAATGAATGATATCAGACCCAGTGCCATGA!
GGGAAATAGCAATTGATGTCCCAAATGTAAGTTATGATGATGTTGGTGGAGTTAGAAAi GCAAATGGCCCAAATCAGAGAGCTTGTTGAGCTTCCACTACGCCATCCTCAACTTTTC
AAATCTATTGGTATTCCTGCCCCTAGAGGATTGTTACTTTATGGTCCTCCATGTACTG
GAAAAACAATGATCGCCAGGGCTGTTGCTAATGAATTTGGAGCCTATGTTTCTGTAAT
TAATGGTCCTGAAATTATAAGCAAGTATGTTGGTGAGAGTGAACGTGCTGTGCGACAA
GTTTTTCAACGAGCCAAGAACTCAGCACCATCAATTATTTTTATTGATGAGCTGGATG
CACTTTGTCCGAAAAGAGAGGGGGCCCAGAATGAAGTGGAAAAAAGAGTTGTGGCTTC
ACTCTTAACACTGATGGATGGCATTGGTTCAGTAAGTATAGTGTTGGTTCTTGGGGCC
ACAAATCGCCCTCATGCCTTGGATGCTGCTCTCCGAAGACCTGGGCGATTTGATAAAG
TCGAAGGGTACCCCATTTGCTCACTGAGGCTGAGCTGCTGCAGCTGGCAAATAGTGCT
CATGGATACGTTGGAGCAGACTTGAAAGTCTTGTGTAATGAAGCAGGTGAGTGTGGTT
TGCTATGGGACATTCAAGCCAATCTCATCATGAAAAGACATTTCACTCAGGCCTTGAG
CACTGTGACACCTAGAATTCCTGAGTCATTGAGACGTTTTTATGAAGATTATCAAGAG
AAGAGTGGGCTGCATACACTCTGAGAAAATATATATATTCAAGATGCTGAAAATCCTT
TCCAGAGAAAATTGTTTCTTTTTAAAATTTTTGAGAGTGTTAAAAAAAATTTTACTAG
GCAAAATGTTTGAAGTATGTTCAGTAGA
ORF Start: ATG at 47 ORF Stop: TGA at 2690 SEQ ID NO: 28 881 as MW at 96419.SkD
NOVl2a, MSSKKNRKRLNQSAENGSSLPSAASSCAEARAPSAGSDFAATSGTLWTNLLEKGKIP

Frotein Se lleriCe ~G~PGDAIQVQPLVGAVLQAEEMDVALSDKDMEINEEELTGCILRKLDGKIVLPG, NFLYCTFYGRPYKLQVLRVKGADGMILGGPQSDSDTDAQRMAFEQSSMETSSLELSLQ', LSQLDLEDTQIPTSRSTPYKPIDDRITNKASDVLLDVTQSPGDGSGLMLEEVTGLKCN':
FESAREGNEQLTEEERLLKFSIGAKCNTDTFYFISSTTRVNFTEIDKNSKEQDSDVKSI
NYDHDRGLSSQLKAIREIIELPLKIPAPRGLLLYGPPCTGKTMIARAVANEFGAYVSV:
INGPEIISKFYGETEAKLRQIFAEATLRHPSIIFIDELDALCPKREGAQNEVEKRWA' SLLTLMDGIGSEVSEGQVLVLGATNRPHALDAALRRPGRFDKEIEIGVPNAQDRLDIL) QKLLRRVPHLLTEAELLQLANSAHGWGADLKVLCNEAGLCALRRILKKQPNLPDVKV
AGLVKITLKDFLQAMNDIRPSAMREIAIDVPNVSYDDVGGVRKQMAQIRELVELPLRH
PQLFKSIGIPAPRGLLLYGPPCTGKTMIARAVANEFGAYVSVINGPEIISKWGESER
SIIFIDELDALCPKREGAQNEVEKRWASLLTLMDGIGSVSIVL
LRRPGRFDKEIEIGVPNAQDRLDILQKLLRRVPHLLTEAELLQL
LCNEAGECGLLWDIQANLIMKRHFTQALSTVTPRIPESLRRFYE
DYQEKSGLHTL

~ SEQ ID NO: 29 2789 by fNOVl2b, CAGAGTTCGCCCTTCATTGAGTCGGCTTTTCTACTGCTTCGGCTAGGGTACCTTGTGA

CG102S7S-02 _CCATGTCTTCCAAGAAGAATAGAAAGCGGTTGAACCAAAGCGCGGAAAATGGTTCGTC

DNA SeCILIeriCeCTTGCCCTCTGCTGCTTCCTCTTGTGTGGAGGCACGGGCTCCTTCTGCTGGATCAGAC

E TTCGCGGCAACCTCCGGGACTCTGACGGTGACCAACTTATTAGAAAAGGTAGATGACA' AAATTCCTAAAACATTCCAGAATTCCCTTATTCATCTTGGACTCAACACTATGAAGTC

TGCAAATATATGTATAGGTCGACCAGTGTTGCTTACTAGTTTGAACGGAAAGCAAGAGI

GTGTATACAGCCTGGCCTATGGCAGGATTTCCTGGAGGCAAGGTCGGCCTGAGTGAAA', TGGCACAGAAAAATGTGGGTGTGAGGCCTGGTGATGCCATCCAGGTCCAGCCTCTTGT'' GGGTGCTGTGCTACAGGCTGAGGAAATGGATGTGGCACTGAGTGACAAAGATATGGAA

ATTAATGAAGAAGAACTGACTGGTTGTATCCTGAGAAAACTAGATGGCAAGATTGTTT

TACCAGGCAACTTTCTGTATTGTACATTCTATGGACGACCGTACAAGCTGCAAGTATT

GCGAGTGAAAGGGGCAGATGGCATGATATTGGGAGGGCCTCAGAGTGACTCTGACACT

GATGCCCAAAGAATGGCCTTTGAACAGTCCAGCATGGAAACCAGTAGCCTGGAGTTAT

CCTTACAGCTAAGCCAGTTAGATCTGGAGGATACCCAGATCCCAACATCAAGAAGTAC

TCCTTATAAACCAATTGATGACAGAATTACAAATAAAGCCAGTGATGTTTTGCTGGAT

GTTACACAGAGCCCTGGAGATGGCAGTGGACTTATGCTAGAGGAAGTCACAGGTCTTA

AATGTAATTTTGAATCTGCCAGAGAAGGAAATGAGCAACTTACTGAAGAAGAGAGACT

GCTAAAGTTCAGCATAGGAGCAAAGTGCAATACTGATACTTTTTATTTTATTTCTTCA

ACAACAAGAGTCAATTTTACAGAGATTGATAAAAATTCAAAAGAGCAAGACAACCAAT

TTAAAGTAACTTATGACATGATAGGAGGATTAAGTAGCCAGCTGAAAGCAATTAGAGA

AATAATTGAATTGCCCCTCAAACAGCCTGAGCTTTTCAAGAGTTATGGAATTCCTGCC

CCTAGAGGAGTGTTACTTTATGGTCCTCCAGGTACTGGAAAAACAATGATCGCCAGGG

CTGTTGCTAATGAAGTTGGAGCCTATGTTTCTGTAATTAATGGTCCTGAAATTATAAG

CAAATTCTATGGTGAGACTGAAGCAAAGTTACGTCAGATATTTGCTGAAGCCACTCTA

CGACACCCATCAATTATTTTTATTGATGAGCTGGATGCACTTTGTCCGAAAAGAGAGG

GGGCCCAGAATGAAGTGGAA.AAAAGAGTTGTGGCTTCACTCTTAACACTGATGGATGG

CATTGGTTCAGAAGTAAGTGAAGGACAAGTGTTGGTTCTTGGGGCCACAAATCGCCCT

CATGCCTTGGATGCTGCTCTCCGAAGACCTGGGCGATTTGATAAAGAGATTGAGATTG

GAGTTCCCAATGCTCAGGACCGGCTAGATATTCTCCAGAAACTGCTTCGAAGGGTACC

CCATTTGCTCACTGAGGCTGAGCTGCTGCAGCTGGCAAATAGTGCTCATGGATACGTT

GGAGCAGACTTGAAAGTCTTGTGTAATGAAGCAGGTCTCTGTGCCTTGCGGAGAATCC

GAAGGATTTCTTGCAGGCAATGAATGATATCAGACCCAGTGCCATGAGGGAAATAGCA

ATTGATGTCCCAAATGTATCCTGGTCAGATATAGGAGGACTGGAAAGTATCAAACTGA

AGTTGGAACAGGCTGTGGAATGGCCCTTAAAACATCCAGAGTCTTTCATTCGAATGGG

TATTCAGCCACCTAAAGGAGTTCTTCTCTATGGGCCACCTGGGTGCTCTAAAACAATG

ATAGCAAAGGCTTTGGCCAATGAGAGTGGACTGAATTTTCTAGCTATAAAGGGGCCTG

AATTAATGAATAAATATGTTGGTGAATCTGAAAGAGCAGTTAGAGAGACCTTCCGAAA

AGCAAGAGCAGTGGCGCCTTCCATTATTTTCTTTGATGAACTGGATGCCTTAGCAGTT

GAAAGGGGCAGTTCTTTAGGTGCTGGGAATGTAGCCGATCGTGTTTTGGCTCAGCTCT

TAACAGAAATGGATGGGATTGAACAGCTAAAGGATGTGACCATTTTGGCAGCTACTAA

CCGTCCAGATAGGATAGACAAGGCTTTGATGCGGCCTGGAAGAATTGATAGAATCATC

TATGTGCCTTTACCGGATGCAGCAACAAGAAGGGAAATATTTAAGCTGCAGTTTCACT

CCATGCCTGTCAGTAATGAAGTTGACCTGGATGAACTCATCCTTCAAACCGACGCATA

~CTCAGGAGCAGAGATTGTAGCTGTCTGCAGAGAGGCAGCTCTTCTGGCTCTGGAAGAA

GACATTCAAGCCAATCTCATCATGAAAACACATmTCACTCACGCCmm(iACzC'At'mCmrA

CACCTAGAATTCCTGAGTCATTGAGACGTTTTTATGAAGATTATCAAGAGAAGAGTGG
GCTGCATACACTCTGAGAAAATATATATATTCAAGATGCTGAAAATCCTTTCCAGAGA
ORF Start: ATG at 61 ORF Stop: TGA at 2740 SEQ ID NO: 30 X893 as MW at 97931.2kD
'NOVl2b, MSSKKNRKRLNQSAENGSSLPSAASSCVEARAPSAGSDFAATSGTLTVTNLLEKVDDK

PTOtelri S8CILIeriCe AQ~GVRPGDAIQVQPLVGAVLQAEEMDVALSDKDMEINEEELTGCILRKLDGKIVL
PGNFLYCTFYGRPYKLQVLRVKGADGMTLGGPQSDSDTDAQRMAFEQSSMETSSLELS
LQLSQLDLEDTQIPTSRSTPYKPIDDRITNKASDVLLDVTQSPGDGSGLMLEEVTGLK
CNFESAREGNEQLTEEERLLKFSIGAKCNTDTFYFISSTTRVNFTEIDKNSKEQDNQF

KVTYDMIGGLSSQLKAIREIIELPLKQPELFKSYGIPAPRGVLLYGPPGTGKTMIARA
VANEVGAYVSVINGPEIISKFYGETEAKLRQIFAEATLRHPSIIFIDELDALCPKREG
AQNEVEKRVVASLLTLMDGIGSEVSEGQVLVLGATNRPHALDAALRRPGRFDKEIEIG
VPNAQDRLDILQKLLRRVPHLLTEAELLQLANSAHGYVGADLKVLCNEAGLCALRRIL
KKQPNLPDVKVAGLVKITLKDFLQAMNDIRPSAMREIAIDVPNVSWSDIGGLESIKLK
LEQAVEWPLKHPESFIRMGIQPPKGVLLYGPPGCSKTMTAKALANESGLNFLAIKGPE
LMNKYVGESERAVRETFRKARAVAPSIIFFDELDALAVERGSSLGAGNVADRVLAQLL
TEMDGIEQLKDVTILAATNRPDRIDKALMRPGRIDRIIYVPLPDAATRREIFKLQFHS
MPVSNEVDLDELILQTDAYSGAEIVAVCREAALLALEEDIQANLIMKRHFTQALSTVT
PRIPESLRRFYEDYQEKSGLHTL
Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 12B.
Table 12B. Comparison of NOVl2a against NOVl2b.
Protein Sequence NOVl2a Residues/ Identities/
Match Residues Similarities for the Matched Region NOV 12b 1..881 724/895 (80%) ~.... _...~ . ....... . ..... . ....... ......... .._... 1..893, .._.._. .....
.. . ~.. .. . ~... .64/895. (84%).
Further analysis of the NOV 12a protein yielded the following properties shown in Table 12C.
Table 12C. Protein Sequence Properties NOVl2a PSort 0.7000 probability located in plasma membrane; 0.3000 probability located in analysis: microbody (peroxisome); 0.2000 probability located in endoplasmic reticulum (membrane); 0.1000 probability located in mitochondrial inner membrane SignalP No Known Signal Sequence Predicted analysis:
A search of the NOV 12a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 12D.

Table 12D. Geneseq Results for NOVl2a f NOVl2a Identities/
~

Geneseq Protein/Organism/Length Residues!SimilaritiesExpect [Patent ~ for Identifier#, Date] Match the Matched Value ~

Residues Region ~

AAU17209 Novel signal transduction 261..823 442/575 (76%)0.0 pathway ~

protein, Seq ID 774 - Homo2..574 481/575 (82%) Sapiens, ~

574 aa. [W0200154733-A1, [

AUG-2001 ]

AAB59399 Protein tyrosine phosphatase337..848 229/527 (43%)e-120 related sequence - Unidentified, 190..711 340/527 (64%) 806 aa.

[W0200075339-A1, 14-DEC-2000]

AAE09327 Human intracellular regulatory337..848 229/527 (43%)e-120 molecule, VCP - Homo sapiens,190..711 340/527 (64%) 806 ~

aa. [US6274312-B1, 14-AUG-2001]

AAB05879 Human transitional endoplasmic337..848 229/527 (43%)e-120 ~

reticulum ATPase protein 190..711 340/527 (64%) sequence j - Homo Sapiens, 806 aa. 1 [W0200034470-A1, 15-JI1N-2000]
. . .. . .... . .. ... . .. ... .. . .. . . .. . ..
..,... .. .. . .. ;f ..
. ..

ABB59038 Drosophila melanogaster 322..844 228/540 (42%)e-117 [

polypeptide SEQ ID NO 3906170..704 342/540 (63%) - [

Drosophila melanogaster, a 801 aa.

[W0200171042-A2, 27-SEP-2001]

In a BLAST search of public sequence databases, the NOV 12a protein was found to have homology to the proteins shown in the BLASTP data in Table 12E.

Table 12E. Public BLASTP Results for NOVl2a Protein NOVl2a Identities/

Accession Protein/Organism/Length Residues/Similarities Expect for :
~

Match the Matched Value Number Residues Portion AAM00262 SPERMATOGENESIS 1..881 7451895 (83%)0.0 ASSOCIATED FACTOR - Homo I ..893 7851895 (87%) sapiens (Human), 893 aa.

Q9Z2K7 SPAF - Mus musculus (Mouse),1..881 6401895 (71 0.0 %) 892 aa. 1..892 721/895 (80%) Q9CXZ7 2510048F20RIK PROTEIN 1..881 640/896 (71%)X0.0 - Mus musculus (Mouse), 893 1..893 721/896 (80%) aa.

Q8ZYN4 AAA FAMILY ATPASE, 356..876 265!537 (49%)e-136 ' POSSIBLE CELL DIVISION 184..714 358!537 (66%) -Pyrobaculum aerophilum, 731 aa.

Q58556 Cell division cycle protein309..855 271/578 (46%)e-136 48 ~

homolog MJ1156 - Methanococcus127..697 378!578 (64%) jannaschii, 903 aa.

PFam analysis predicts that the NOV 12a protein contains the domains shown in the Table 12F.
Table 12F. Domain Analysis of NOVl2a Identities) Pfam Domain NOVl2a Match Region ' Similarities . Expect Value for the Matched Region AAA 378..566 9S/217 (44%) 3.3e-75 1651217 (76%) AAA 652..837 98/217 (45%) 2e-77 165/217 (76%) Example 13.
The NOV 13 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 13A.
Table 13A. NOVl3 Sequence Analysis SEQ ID NO. 31 420 by NOVl3a, TGCAGAAGGTGACCCTGGGCCTGCTTGTGTTCCTGGCAGGCTTTCCTGTCCTGGACGC

CG102615-Ol CAATGACCTAGAAGATAA.AAACAGTCCTTTCTACTATGACTGGCACAGCCTCCAGGTT

DNA Sequence GGCGGGCTCATCTGCGCTGGGGTTCTGTGCGCCATGGGCATCATCATCGTCATGAGTG

CAAAATGCAAATGCAAGTTTGGCCAGAAGTCCGGTCACCATCCAGGGGAGACTCCACC

TCTCATCACCCCAGGCTCAGCCCAAAGCTGATGAGGACAGACCAGCTGAAATTGGGTG

GAGGACCGTTCTCTGTCCCCAGGTCCTGTCTCTGCACAGAAACTTGAACTCCAGGATG

GAATTCTTCCTCCTCTGCTGGGACTCCTTTGCATGGCAGGGCCTCATCTCACCTCTCG

CAAGAGGGTCTCTT

ORF Start: at 3 ORF Stop: TGA at 261 SEQ ID NO: 32 86 as MW at 9131.6kD

NOVl3a, QKVTLGLLVFLAGFPVLDANDLEDKNSPFYYDWHSLQVGGLICAGVLCAMGIIIVMSA

Protein Sequence ~SEQ ID NO: 33 462 by NOVl3b, TCAGCCTGGTGAACCACACAGAGGCTGGGGCGAGGAGGATACCATCTGTCAGTCTTGG

DNA Se uenCe AGGAGCCCCTGGAAAGAGGCTTAAGAGGCCAGCGCTCTGACATGCAGAAGGTGACCCT
q GGGCCTGCTTGTGTTCCTGGCAGGCTTTCCTGTCCTGGACGCCAATGACCTAGAAGAT

AAAAACAGTCCTTTCTACTATGACTGGCACAGCCTCCAGGTTGGCGGGCTCATCTGCG

CTGGGGTTCTGTGCGCCATGGGCATCATCATCGTCATGAGTGCAAAATGCAAATGCAA

GTTTGGCCAGAAGTCCGGTCACCATCCAGGGGAGACTCCACCTCTCATCACCCCAGGC

TCAGCCCAAAGCTGATGAGGACAGACCAGCTGAAATTGGGTGGAGGACCGTTCTCT

ORF Start: ATG at 71 ORF Stop: TGA at 419 SEQ ID NO: 34 116 as BMW at 12362.2kD
i ' NOVl3b, MGRGYSGALQARGGLEEPLERGLRGQRSDMQKVTLGL,LVFLAGFPVLDANDLEDKNSP

CG102615-04 F~~SLQVGGLICAGVLCAMGIIIVMSAKCKCKFGQKSGHHPGETPPLITPGSAQS

Protein Sequence Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 13B.
Table 13B. Comparison of NOVl3a against NOVl3b.
Protein Sequence NOVl3a Residues/ Identities/
Match Residues Similarities for the Matched Region NOVl3b 1..86 86/86 (100%) ...,~~~... ~ _~.. ...."~" 31 1.16 _~T:.~~~.~.....86/86 (100%) _... . ...
Further analysis of the NOVl3a protein yielded the following properties shown in Table 13C.
Table 13C. Protein Sequence Properties NOVl3a PSort 0.4600 probability located in plasma membrane; 0.2000 probability located in analysis: lysosome (membrane); 0.1000 probability located in endoplasmic reticulum (membrane); 0.1000 probability located in endoplasmic reticulum (lumen) SignalP Cleavage site between residues 20 and 21 analysis:

A search of the NOV 13 a protein against the Geneseq database, a proprietary dafa'~ase that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 13D.
Table 13D. Geneseq Results for NOVl3a NOV.l3a Identities/

Geneseq Protein/Organism/Length Residues/SimilaritiesExpect (Patent for Identifier#, Date] Match the Matched Value ResiduesRegion AAM23962 Human EST encoded protein 1..86 86/86 (100%)7e-47 SEQ

ID NO: 1487 - Homo Sapiens,2..87 86/86 (100%) 87 aa.

~W0200154477-A2, 02-AUG-2001]

_.~~ .. ...
AAW92959 1..86 86/86 (1.00%)7e-47 Human protein - Homo Sapiens, 87 aa. [W09905276-Al,2..87 86/86 (100%) 04-FEB-1999]
~",,~.. _._. . .

AAY48304 Human prostate cancer-associated1..86 86/86 (100%)7e-47 protein 1 - Homo sapiens, 2..87 86/86 (100%) 87 aa.

[DE19811194-Al, 16-SEP-1999]

.. . .

AAR90990 Human Mat-8 polypeptide 1..86 86/86 (100%)7e-47 - Homo ~

sapiens, 87 aa. [WO9605322-A1,2..87 86/86 (100%) 22-FEB-1996]

AAB53415 Human colon cancer antigen 1..86 86/112 (76%)2e-42 protein sequence SEQ ID N0:955 - 39..150 86/112 (76%) Homo Sapiens, 150 aa. [W0200055351-A1, t ..
21-SEP-2000]

In a BLAST search of public sequence databases, the NOV 13 a protein was found to have homology to the proteins shown in the BLASTP data in Table 13E.

Table 13E. Public BLASTP Results for NOVl3a NOVl3a Identities/
' Protein Similarities1 Residues/ f Expect AccessionProtein/Organism/Length Match for the ~ Value Number Residues Matched !

Portion Q14802 FXYD domain-containing ion I..86 86/86 (100%)2e-46 transport regulator 3 precursor (Chloride2..87 86/86 (100%) conductance inducer protein Mat-8) (Mammary tumor 8 kDa protein) (Phospholernman-Like) - Homo Sapiens (Human), 87 aa.

Q61835 FXYD domain-containing ion 1..86 63/86 (73%)2e-33 transport regulator 3 precursor (Chloride2..87 72/86 (83%) conductance inducer protein Mat-8) (Mammary tumor 8 kDa protein) (Phospholemman-like) - Mus musculus (Mouse}, 88 aa.
;.

....
097797 FXYD domain-containing ion 2..84 60/83 (72%)~ 8e-32 transport regulator 3 precursor (Chloride3..85 68/83 (81%)f conductance inducer protein Mat-8) (Mammary tumor 8 kDa protein) - Sus scrofa (Pig), 88 aa.

Q9D2W0 FXYD domain-containing ion I ..86 45/86 (S2%)4e-21 transport regulator 4 precursor (Channel2..87 59/86 (68%) inducing factor) (CHIF) -Mus musculus (Mouse), 88 aa.

Q631 I FXYD domain-containing ion .' 3..86 44/84 (52%)7e-20 3 transport regulator 4 precursor (Channel4..87 55/84 (65%) inducing factor) (CHIF) (Corticosteroid-induced protein) -LRattus norvegicus (Rat), 87 as PFam analysis predicts that the NOV 13a protein contains the domains shown in the Table 13F.

Table 13F. Domain Analysis of NOVl3a Identities!
Pfam Domain NOVl3a Match Similarities Expect Region . for the Matched Value Region ATP1G1_PLM_MAT8 19..74 27/57 (47%) 2.7e-35 55/57 (96%) Example 14.
The NOV 14 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 14A.
Table 14A. NOV14 SEQ ID NO: 35 1638 by NOVl4a, ~TTATCTAATATGTTTGTTTTAGCTACATCTTTATCAAGCCAAGTGAATCCTGACTGGC
CG102646-Ol G~CATATATCATGCTTGCAGTATATTTTCTAATTTTACTTGTTATTGGATATTATGG
DNA Se LlenCe TTATAAGCAAGCAACCGGAGATTTAAGTGAATATATGCTTGGCGAAAGAAATATTGGT
q CCATATGTCACTGCCTTATCTGCCGGAGCTTCAGATATGAGCGGTTGGATGATTATGG
GATTACCTGGAGAAGTTTATACTACAGGTTTATCAGCAGCATGGTTAGCTATTGGGTT
AACTATCGGAGCTTATGTTAACTACATACTTGTAGCACCAAGACTTCGTGTGTACACT
GAAAAAGCCAATGACTCAATTACATTGCCTAATTACTTTACACATCGTCTTAATGATA
ATTCCAATATTATTAAAATTATCTCTGGTGGTATCATTGTTGTATTTTTTACACTCTA
TACTCATTCAGGTATGGTATCAGGTGGTAAATTATTTGATAGTGCTTTTGGTTTAGAC
TATCATATTGGACTTATTTTAATCTCTGTCATTGTAATTTTATATACTTTTTTTGGTG
GCTATTTAGCAGTGTCGTTAACTGACTTTTTCCAAGGGGTTGTCATGTTAATTGCGAT
GGTTATGGTACCTATTGTAGCCATGATGCAGCTCGGAGGTATGGATGCTTTTTCACAA
GCAGCAACATTAAAACCTACTAATTTAGATTTATTTAAAGGAACAACTATTATAGGCA
TCATTTCATTCTTTGCTTGGGGATTAGGCTATTTTGGCCAGCCTCATATCATTGTACG
ATTTATGTCTATCAAATCCGTACGACAATTAAAAACGTCTAGAAGATTTGGTATTAGT
TGGATGGCTATTAGTTTAATCGGTGCAGTATGTGTTGGATTAATTGGCATTTCGTTTG
TACAAGATAAAGGTGTTGAATTAAAAGATCCAGAAACACTATTTATTTTAATGGGACA
CATCCTCTTGTAGGTGGGTTCCTACTTGCAGCCATTTTGGCAGCAATT
TTTCTTCCCAATTACTTGTGACTTCAAGTTCACTTACAGAAGATTTTT
GGGTCGATTATCTGTTGTAGTCGTTGCGATTATCTCCATCCTCATTGCATGGACGCCA
AATGACACTATCTTAAATCTTGTTGGTAACGCTTGGGCTGGATTCGGTGCAGCATTTG
GTCCACTGGTATTATTATCTCTCTATTCGAAAGGTTTAAGTCGTACTGGAGCTATTTC
TGGAATGTTATCAGGAGCAATTGTCGTCATTCTTTGGATTGTGTTTGTTAAACCATTA
GGAGCATATAATGATTTCTTTAATTTATATGAAATTATTCCTGGTTTCTTAACAAGTC
TTATTGTGACATATGTAGTGAGTCTTGTAACTAAAAAGCCAGATCTCAATGTTCAAAA
AGATTTAGAAGACGTCAAACGTATTGTAAAAGGACAATAAATTAATAATATTCAACGA
TGCTTAATGTCAATATTATTTCAATTAGTGCATTACTCTTATAATATGAAACACAAAT
AAATTTTTATACAT
ORF Start: ATG at 10 ORF Stop: TAA at 1546 SEQ ID NO: 36 512 as ~MW at 55813.4kD
NOVl4a, MFVLATSLSSQVNPDWRTYIMLAVYFLILLVIGYYGYKQATGDLSEYMLGERNIGPYV
CG102646-O1 T~'SAGASDMSGWMIMGLPGEVYTTGLSAAWLAIGLTIGAYVNYILVAPRLRVYTEKA
NDSITLPNYFTHRLNDNSNIIKIISGGIIVVFFTLYTHSGMVSGGKLFDSAFGLDYHI

Protein SeqLtenCe GLILISVIVTLYTFFGGYLAVSLTDFFQGVVMLIAM~JM~IPhVAMMQLGGMDAFSQAAT
LKPTNLDLFKGTTIIGIISFFAWGLGYFGQPHITVRFMSTKSVRQLKTSRRFGISWMA
ISLIGAVCVGLIGISFVQDKGVELKDPETLFILMGQILFHPLVGGFLLAAILAAIMST
ISSQLLVTSSSLTEDFYKLIRGEEAAKQHKKEFLLVGRLSWWAIISILIAWTPNDT
ILNLVGNAWAGFGAAFGPLVLLSLYSKGLSRTGAISGMLSGAIWILWIVFVKPLGAY
NDFFNLYEIIPGFLTSLIVTYWSLVTKKPDLNVQKDLEDVKRIVKGQ
Further analysis of the NOV 14a protein yielded the following properties shown in Table 14B.
Table 14B. Protein Sequence Properties NOVl4a PSort 0.8200 probability located in plasma membrane; 0.4600 probability located in analysis: Golgi body; 0.3700 probability located in endoplasmic reticulum (membrane);
0.1000 probability located in endoplasmic reticulum (lumen) SignaIP ~ Cleavage site between residues 37 and 38 analysis:
A search of the NOV 14a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table I4C.

Table 14C. Geneseq Results for NOVl4a NOVl4a Identities/

Geneseq Protein/Organism/Length Residues/SimilaritiesExpect [Patent for Identifier#, Date] Match the Matched Value Residues Region AAB767S7 ~ Co~bacteriurn glutamicum20..506 233/502 (46%)e-127 MCT

protein SEQ ID N0:496 - 9..499 339/502 (67%) E Corynebacterium glutamicum, ~ aa. [W0200100805-A2, 04-JAN- j 2001 ) AAG93195 C glutamicum protein fragment20..506 2331502 (46%)e-127 SEQ

' ID NO: 6949 - Corynebacterium9_.499 339/502 (67%) glutamicum, 524 aa. [EPl A2, 20-JLTN-2001 z AAW20806 ~ H. pylori transporter 64..506 2081450 (46%)e-I
protein, I2 09ap20802orf27 - Helicobacter5..445 306/450 (67%) ~

~ pylori, 446 aa. [W09640893-Al, 19-DEC-1996]

AAG82S96 ~ S. epidermidis open reading266..510 171/245 (69%)1e-94 frame protein sequence SEQ ID 163..407 208I245 (84%) NO:2286 -Staphylococcus epidermidis, 408 aa.

[WO200I34809-A2, I7-MAY-_.

AAB96626 ~ Putative P. abyssi permease24..508 174/503 (34%)4e-83 #22 -Pyrococcus abyssi, 537 I I ..507275/503 (S4%) aa.

a [FR2792651-A1, 27-OCT-2000]

In a BLAST search of public sequence databases, the NOV 14a protein was found to have homology to the proteins shown in the BLASTP data in Table 14D.

Table 14D. Public BLASTP Results for NOVl4a Protein NOVl4a Identities/ ~

Residues/Similarities Expect AccessionProtein/Organism/Length for ' Match the Matched Value Number ResiduesPortion ' Q99SY5 HIGH AFFINITY PROLINE 1..510 378/510 (74%)0.0 PERMEASE - Staphylococcus I ..510 443/5I0 (86%) aureus (strain Mu50 / ATCC

~ 700699), and, 512 aa.

030986 HIGH AFFINITY PROLINE ~ 1..494 366/494 (74%)0.0 PERMEASE - Staphylococcus 1..493 431/494 (87%) aureus, 497 aa.

Q53584 PROLINE PERMEASE ~ 1..494 366/494 (74%)0.0 HOMOLOG - Staphylococcus 1..493 430/494 (86%) ~
aureus, 497 aa.

006493 Osmoregulated proline transporter20..494 268/478 (56%)e-I58 ~

_ 7..473 371/478 (77%) (Sodium/proline symporter) - ~

Bacillus subtilis, 492 aa.

P94392 HOMOLOGUE OF PROLINE ~ 54..504 243/452 (53%)e-142 PERMEASE OF E. COLI - Bacillus1..442 336/452 (73%) ~

subtilis, 449 aa.

~ .

PFaxn analysis predicts that the NOV 14a protein contains the domains shown in the Table 14E.
Table 14E. Domain Analysis of NOVl4a Identities/
Pfam Domain NOVl4a Match Region Similarities Expect Value for the Matched Region SSF 47..447 134/449 (30%) 5.7e-121 318/449 (71 %) Example 15.
The NOV 1 S clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 15A.
Table 15A. NOV15 Seque_nce_Analysis ..-...__.._.......--.,~,~......_..~SEQ..ID~~NO: 37 .'~°"'~'~...,..- l 146 bp "'""..~..~....~......-_.~_..r....~......._~.~..,-~.............",..~..
NOVISa, ~CTAGCTCGACAGCTTCCCGGCGGCTGCGCGATGGACAGCCCCGAGGTGACCTTCACTC
TCGCCTATCTGGTGTTCGCCGTGTGCTTCGTGTTCACGCCCAACGAGTTCCACGCGGC

GGGGCTCACGGTGCAGAACCTGCTGTCGGGCTGGC"T~GtG~~A~C'G2~'~GA~~~GCCG~CTTC~F

DNA SCCILteriCeGTGCCCTTCCACTTGCGCCGCACGGCCGCCACGCTGTTGTGCCACTCGCTGCTGCCGC

TCGGCTACTATGTGGGCATGTGCCTTGCGGCTTCAGAAAAGCGGCTCCACGCCCTCAG

CCAGGCCCCTGAGGCCTGGCGGCTCTTCCTGCTGCTGGCCGTGACCCTCCCCTCCATC

GCCTGCATCCTGATCTACTACTGGTCCCGTGACCGGTGGGCCTGCCACCCACTGGCGC

GCACCCTGGCCCTCTACGCCCTCCCACAGTCTGGCTGGCAGGCTGTTGCCTCCTCTGT

CAACACTGAGTTCCGGCGGATTGACAAGTTTGCCACCGGTGCACCAGGTGCCCGTGTG

ATTGTGACAGACACGTGGGTGATGAAGGTAACCACCTACCGAGTGCACGTGGCCCAGC

AGCAGGACGTGCACCTGACTGTGACGGAGTCTCGGCAGCATGAGCTCTCGCCAGACTC

GAACTTGCCCGTGCAGCTCCTCACCATCCGTGTGGCCAGCACCAACCCTGCTGTGCAG

GCCTTTGACATCAGGCTGAACTCCACTGAGTACGGGGAGCTCTGCGAGAAGCTCCGGG

CACCCATCCGCAGGGCAGCCCATGTGGTCATCCACCAGAGCCTGGGCGACCTGTTCCT

GGAGACATTTGCCTCCCTGGTAGAGGTCAACCCGGCCTACTCAGTGCCCAGCAGCCAG

GAGCTGGAGGCCTGCATAGGCTGCATGCAGACACGTGCCAGCGTGAAGCTGGTGAAGA

CCTGCCAGGAGGCAGCCACAGGCGAGTGCCAGCAGTGTTACTGCCGCCCCATGTGGTG

CCTCACCTGCATGGGCAAGTGGTTCGCCAGCCGCCAGGACCCCCTGCGCCCTGACACC

TGGCTGGCCAGCCGCGTGCCCTGCCCCACCTGCCGCGCACGCTTCTGCATCCTGGATG

TGTGCACCGTGCGCTGAGTGGGCTGGGGCCTTGAGGTGACTCTG

ORF Start: ATG at 31 ORF Stop: TGA at 1117 SEQ ID NO: 38 . 362 as MW at 40433.3kD

NOVISa, MDSPEVTFTLAYLVFAVCFVFTPNEFHAAGLTVQNLLSGWLGSEDAAFVPFHLRRTAA

P1'Otelri DRWACHPLARTLALYALPQSGWQAVASSVNTEFRRIDKFATGAPGARVIVTDTWVMKV
Se LleriCe TTYRVHVAQQQDVHLTVTESRQHELSPDSNLPVQLLTIRVASTNPAVQAFDIRLNSTE

YGELCEKLRAPIRRAAHWIHQSLGDLFLETFASLVEVNPAYSVPSSQELEACIGCMQ

TRASVKLVKTCQEAATGECQQCYCRPMWCLTCMGKWFASRQDPLRPDTWLASRVPCPT

CRARFCILDVCTVR

SEQ ID NO: 39 1115 by NOVISb, TTCGCCCTTGGCTGCGCGATGGACAGCCCCGAGGTGACCTTCACTCTCGCCTATCTGG

DNA Se LleriCBGCAGAACCTGCTGTCGGGCTGGCTGGGCAGCGAGGACGCCGCCTTCGTGCCCTTCCAC

TTGCGCCGCACGGCCGCCACGCTGTTGTGCCACTCGCTGCTGCCGCTCGGCTACTACG

TGGGCATGTGCCTTGCGGCTTCAGAAAAGCGGCTCCACGCCCTCAGCCAGGCCCCTGA

GGCCTGGCGGCTCTTCCTGCTGCTGGCCGTGACCCTCCCCTCCATTGCCTGCATCCTG

ATCTACTACTGGTCCCGTGACCGGTGGGCCTGCCACCCACTGGCGCGCACCCTGGCCC

TCTACGCCCTCCCACAGTCTGGCTGGCAGGCTGTTGCCTCCTCTGTCAACACTGAGTT

CCGGCGGATTGACAAGTTTGCCACCGGTGCACCAGGTGCCCGTGTGATTGTGACAGAC

ACGTGGGTGATGAAGGTAACCACCTACCGAGTGCACGTGGCCCAGCAGCAGGACGTGC

ACCTGACTGTGACGGAGTCTCGGCAGCATGAGCTCTCGCCAGACTCGAACTTGCCCGT

GCAGCTCCTCACCATCCGTGTGGCCAGCACCAACCCTGCTGTGCAGGCCTTTGACATC

TGGCTGAACTCCACTGAGTACGGGGAGCTCTGCGAGAAGCTCCGGGCACCCATCCGCA

GGGCAGCCCATGTGGTCATCCACCAGAGCCTGGGCGACCTGTTCCTGGAGACATTTGC

CTCCCTGGTAGAGGTCAACCCGGCCTACTCAGTGCCCAGCAGCCAGGAGCTGGAGGCC

TGCATAGGCTGCATGCAGACACGTGCCAGCGTGAAGCTGGTGAAGACCTGCCAGGAGG

CAGCCACAGGCGAGTGCCAGCAGTGTTACTGCCGCCCCATGTGGTGCCTCACCTGCAT

GGGCAAGTGGTTCGCCAGCCGCCAGGACCCCCTGCGCCCTGACACCTGGCTGGCCAGC

CGCGTGCCCTGCCCCACCTGCCGCGCACGCTTCTGCATCCTGGATGTGTGCACCGTGC

GCTGATGTGGCGG

ORF Start: ATG at 19 ORF Stop: TGA at 110S

SEQ ID NO: 40 362 as MW at 40463.4kD
.
~

NOVISb, ....,..~..".-".y,.~.,., .
MDSPEVTFTLAYLVFAVCFVFTPNEFHAAGLTVQNLLSGWLGSEDAAFVPFHLRRTAA

PrOtelri SeClLl2riCeDRWACHPLARTLALYALPQSGWQAVASSVNTEFRRIDKFATGAPGARVIVTDTWVMKV

TTYRVHVAQQQDVHLTVTESRQHELSPDSNLPVQLLTIRVASTNPAVQAFDIWLNSTE

YGELCEKLRAPZRRAAHV(TIHQSLGDLFLETFASLVEVNPAYSVPSSQELEACIGCMQ

TRASVKLVKTCQEAATGECQQCYCRPMWCLTCMGKWFASRQDPLRPDTWLASRVPCPT

CRARFCILDVCTVR
Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 15B.
Table 15B. Comparison of NOVlSa against NOVlSb.
Protein Sequence' NOVlSa Residues/'3 Identities/
Match Residues Similarities for the Matched Region NOVlSb 1..362 361/362 (99%) 1..362 361/362 (99%) Further analysis of the NOV 15a protein yielded the following properties shown in Table 15C.
Table 15C. Protein Sequence Properties NOVlSa PSort ' 0.6760 probability located in plasma membrane; 0.1000 probability located in analysis: ° endoplasmic reticulum (membrane); 0.1000 probability located in endoplasmic reticulum (lumen); 0.1000 probability located in outside SignalP Cleavage site between residues 29 and 30 analysis:
A search of the NOV 1 Sa protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 15D.

Table 15D. Geneseq Results for NOVlSa NOVlSa Identities/

Geneseq Protein/Organism/Length Residues!Similarities Expect [Patent for Identifier' #, Date] Match the Matched Value ResiduesRegion AAG81377 Human AFP protein sequence 1..362 360/362 (99%)0.0 SEQ

ID N0:272 - Homo Sapiens, 1..362 360/362 (99%) 362 aa.

[W0200129221-A2, 26-APR-2001 ABB69639 Drosophila melanogaster 1..358 122/389 (31%)7e-60 polypeptide SEQ ID NO 357091..383 200/389 (51%) -Drosophila melanogaster, 409 aa.

[W0200171042-A2, 27-SEP-2001]

AAG23427 Arabidopsis thaliana protein337..36213/26 (50%) 2.8 fragment SEQ ID NO: 26729 77..102 16/26 (61 - %) Arabidopsis thaliana, 284 aa.

[EP1033405-A2, 06-SEP-2000]

AAG23426 Arabidopsis thaliana protein337..36213/26 (50%) 2.8 fragment SEQ ID NO: 26728 206..23116/26 (61 - %) Arabidopsis thaliana, 413 aa.

[EP1033405-A2, 06-SEP-2000]

ABGl 1786~ Novel human diagnostic 285..35423/89 (25%) 3.6 protein #11777 - Homo Sapiens, 198 54..141 37/89 (40%) aa.

[W0200175067-A2, 11-OCT-2001) In a BLAST search of public sequence databases, the NOV 15a protein was found to have homology to the proteins shown in the BLASTP data in Table 15E.

Table 15E. Public BLASTP Results for NOVlSa ~~~~~NOVlSa Identities/

Protein Residues/Similarities ' Expect for Accession Protein/Organism/Length Match the Matched Value Number Residues Portion CAC38627 SEQUENCE 271 FROM 1..362 361/362 (99%~0.0 PATENT W00129221 - Homo 1..362 361/362 (99%) Sapiens (Human), 362 aa.

Q9DCF3 ?; .0610039G24RIK PROTEIN1..362 323/362 (89%)0.0 -~ Mus musculus (Mouse), 1..362 341/362 (93%) 362 aa. ~
~..

Q96GP5 SIMILAR TO RIKEN CDNA 1..226 226/226 (I00%)' e-129 0610039624 GENE - Homo 1..226 226/226 (100%) sapiens (Human), 232 aa.

Q9VN16 CG14646 PROTEIN - Drosophila1..358 122/389 (31%)2e-59 ~

melanogaster (Fruit fly),1..383 200/389 (51 409 aa. , ~ %) Q95TM4 LD39811P - Drosophila 20..358 116/370 (31%)1e-55 melanogaster (Fruit fly),4..367 190/370 (51%) _........ 393 aa. .. . ~ ....... ...............
_..... _ _..~ ....... _...~ .. . . _ _.._....
.

Example 16.
The NOV16 clone Was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 16A.
Table 16A. NOV16 Sequence Analysis SEQ ID NO: 41 X2765 by NOVl6a, -°~CTGGCGGCGTCGCATGGAGGGCTCTGGGGGCGGTGCGGGCGAGCGGGCGCCGCTGCTG
CG103459-Ol GGCGCGCGGCGGGCGGCGGCGGCCGCGGCGGCGGCTGGGGCGTTCGCGGGCCGGCGCG
DNA SequenCB CGGCGTGCGGGGCCGTGCTGCTGACGGAGCTGCTGGAGCGCGCCGCTTTCTACGGCAT
CACGTCCAACCTGGTGCTATTCCTGAACGGGGCGCCGTTCTGCTGGGAGGGCGCGCAG
GCCAGCGAGGCGCTGCTGCTCTTCATGGGCCTCACCTACCTGGGCTCGCCGTTCGGAG
~GCTGGCTGGCCGACGCGCGGCTGGGCCGGGCGCGCGCCATCCTGCTGAGCCTGGCGCT
CTACCTGCTGGGCATGCTGGCCTTCCCGCTGCTGGCCGCGCCCGCCACGCGAGCCGCG
CTCTGCGGTTCCGCGCGCCTGCTCAACTGCACGGCGCCTGGTCCCGACGCCGCCGCCC
GCTGCTGCTCACCGGCCACCTTCGCGGGGCTGGTGCTGGTGGGCCTGGGCGTGGCCAC
CGTCAAGGCCAACATCACGCCCTTCGGCGCCGACCAGGTTAAAGATCGAGGTCCGGAA
GCCACTAGGAGATTTTTTAATTGGTTTTATTGGAGCATTAACCTGGGAGCGATCCTGT
CGTTAGGTGGCATTGCCTATATTCAGCAGAACGTCAGCTTTGTCACTGGTTATGCGAT
CCCCACTGTCTGCGTCGGCCTTGCTTTTGTGGCCTTCCTCTGTGGCCAGAGCGTTTTC
ATCACCAAGCCTCCTGATGGCAGTGCCTTCACCGATATGTTCAAGATACTGACGTATT
CCTGCTGTTCCCAGAAGCGAAGTGGAGAGCGCCAGAGTAATGGTGAAGGCATTGGAGT
CTTTCAGCAATCTTCTAAACAAAGTCTGTTTGATTCATGTAAGATGTCTCATGGTGGG
CCATTTACAGAAGAGAAAGTGGAAGATGTGAAAGCTCTGGTCAAGATTGTCCCTGTTT
TCTTGGCTTTGATACCTTACTGGACAGTGTATTTCCAAATGCAGACAACATATGTTTT
ACAGAGTCTTCATTTGAGGATTCCAGAAATTTCAAATATTACAACCACTCCTCACACG
CTCCCTGCAGCCTGGCTGACCATGTTTGATGCTGTGCTCATCCTCCTGCTCATCCCTC
TGAAGGACAAACTGGTCGATCCCATTTTGAGAAGACATGGCCTGCTCCCATCCTCCCT

GAAGAGGATCGCCGTGGGCATGTTCTTTGTCATGTGCTCAGCCTTTGCTGCAGGAATT

TTGGAGAGTAAAAGGCTGAACCTTGTTAAAGAGAA.AACCATTAATCAGACCATCGGCA

ACGTCGTCTACCATGCTGCCGATCTGTCGCTGTGGTGGCAGGTGCCGCAGTACTTGCT

GATTGGGATCAGCGAGATCTTTGCAAGTATCGCAGGCCTGGAATTTGCATACTCAGCT

GCCCCCAAGTCCATGCAGAGTGCCATAATGGGCTTGTTCTTTTTCTTCTCTGGCGTCG

GGTCGTTCGTGGGTTCTGGACTGCTGGCACTGGTGTCTATCAAAGCCATCGGATGGAT

GAGCAGTCACACAGACTTTGGTAATATTAACGGCTGCTATTTGAACTATTACTTTTTT

CTTCTGGCTGCTATTCAAGGAGCTACCCTCCTGCTTTTCCTCATTATTTCTGTGAAAT

ATGACCATCATCGAGACCATCAGCGATCAAGAGCCAATGGCGTGCCCACCAGCAGGAG

GGCCTGACCTTCCTGAGGCCATGTGCGGTTTCTGAGGCTGACATGTCAGTAACTGACT

GGGGTGCACTGAGAACAGGCAAGACTTTAAATTCCCATAAAATGTCTGACTTCACTGA

AACTTGCATGTTGCCTGGATTGATTTCTTCTTTCCCTCTATCCAAAGGAGCTTGGTAA

GTGCCTTACTGCAGCGTGTCTCCTGGCACGCTGGGCCCTCCGGGAGGAGAGCTGCAGA

TTTCGAGTATGTCGCTTGTCATTCAAGGTCTCTGTGAATCCTCTAGCTGGGTTCCCTT

TTTTACAGAAACTCACAAATGGAGATTGCAAAGTCTTGGGGAACTCCACGTGTTAGTT

GGCATCCCAGTTTCTTAAACAAATAGTATCACCTGCTTCCCATAGCCATATCTCACTG

T TTAATAAACTGTTACTTATATTTAAGAAAGTGAGGATTTTTTTTTT

TTAAAGATAAAAGCATGGTCAGATGCTGCAAGGATTTTACATAAATGCCATATTTATG

GTTTCCTTCCTGAGAACAATCTTGCTCTTGCCATGTTCTTTGATTTAGGCTGGTAGTA

AACACATTTCATCTGCTGCTTCAAA.AAGTACTTACTTTTTAAACCATCAACATTACTT

TTCTTTCTTAAGGCAAGGCATGCATAAGAGTCATTTGAGACCATGTGTCCCATCTCAA

GCCACAGAGCAACTCACGGGGTACTTCACACCTTACCTAGTCAGAGTGCTTATATATA

GCTTTATTTTGGTACGATTGAGACTAAAGACTGATCATGGTTGTATGTAAGGAAAACA

TTCTTTTGAACAGAAATAGTGTAATTAAA.AATAATTGAAAGTGTTAAATGTGAACTTG

AGCTGTTTGACCAGTCACATTTTTGTATTGTTACTGTACGTGTATCTGGGGCTTCTCC

GTTTGTTAATACTTTTTCTGTATTTGTTGCTGTATTTTTGGCATAACTTTATTATAAA

AAGCATCTCAAATGCG

ORF Start: ATG at 14 ORF Stop: TGA at 1745 ~,. ,NO
~ 42 .
SEQ"IIO
~7~
aa~MW at 62004~6kD
. ~

.
16a, ~..
NO .~
.
y ~
"y.."r,~.,....
Z''iEGSGGGAGERAPLLGARRP~~AAAAAAGAFAGRRAACGAVLLTELLERAAFYGITSNL
V

PPOtelri SequenceM~FPLLAAPATRAALCGSARLLNCTAPGPDAAA12CCSPATFAGLVLVGLGVATVKAN

ITPFGADQVKDRGPEATRRFFNWFYWSINLGAILSLGGIAYIQQNVSFVTGYAIPTVC

VGLAFVAFLCGQSVFITKPPDGSAFTDMFKILTYSCCSQKRSGERQSNGEGIGVFQQS

SKQSLFDSCKMSHGGPFTEEKVEDVKALVKIVPVFLALIPYWTVYFQMQTTYVLQSLH

LRIPEISNITTTPHTLPAAWLTMFDAVLILLLIPLKDKLVDPILRRHGLLPSSLKRIA

VGMFFVMCSAFAAGILESKRLNLVKEKTINQTIGNVVYHA.ADLSLWWQVPQYLLIGIS

EIFASIAGLEFAYSAAPKSMQSAIMGLFFFFSGVGSFVGSGLLALVSIKAIGWMSSHT

DFGNINGCYLNYYFFLLAAIQGATLLLFLIISVKYDHHRDHQRSRANGVPTSRRA

Further analysis of the NOV 16a protein yielded the following properties shown in Table 16B.
Table 16B. Protein Sequence Properties NOVl6a PSort 0.6000 probability located in plasma membrane; 0.4000 probability located in analysis: Golgi body; 0.3000 probability located in endoplasmic reticulum (membrane);
0.3000 probability located in microbody (peroxisome) SignalP No Known Signal Sequence Predicted analysis:
A search of the NOV 16a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 16C.

Table 16C. Geneseq Results for NOVl6a NOVl6a ~ Identities/

Geneseq Protein/Organism/Length Residues/Similarities Expect [Patent for Identifier#, Date] Match ~ the Matched Value Residues~ Region AAU12071 Human PHT1 variant protein1..577 577/577 (100%)0.0 from Caco-2 cells - Homo Sapiens,1..577 577/577 (100%) aa. [WO200I92468-A2, 06-DEC-2001 ]

AAU12068 Human PHT1 protein isolated1..577 577/577 (100%)~ 0.0 from Caco-2 cells - Homo Sapiens,1..577 ~ 577/577 (100%) aa. [W0200192468-A2, 06-DEC-2001 ]

AAU12070 Human PHT1 variant protein1..577 ~ 575/577 (99%)0.0 from BeWo cells - Homo Sapiens,1..577 ~ 576/577 (99%) aa. [W0200192468-A2, 06-DEC-2001 ]

AAE16771 Human transporter and 1..577 ~ 576/577 (99%)0.0 ion channel-' 8 (TRICH-8) protein - 1..576 ~ 576/577 (99%) Homo Sapiens, 576 aa. [W0200192304-A2, 06-DEC-2001]

AAB82821 Human proton/oligonucleotide22..577 ~ 555/556 (99%)0.0 transporter hPHTI polypeptide1..556 ~ 555/556 (99%) -Homo Sapiens, 556 aa.

[W0200160854-Al, 23-AUG-_. . . _ ~ _ . _. .. ~.. ~ . .. . _ .. _. _._ _. .
.

In a BLAST search of public sequence databases, the NOV 16a protein was found to have homology to the proteins shown in the BLASTP data in Table 16D.

Table 16D. Public BLASTP
Results for NOVl6a' Protein , NOVl6a Identities) AccessionProtein/Organism/Length Residues/ SimilaritiesExpect for Number Match the Matched Value Residues Portion 009014 ~ PEPTIDE/HISTIDINE 9..576 500/578 (86%)0.0 TRANSPORTER - Rattus 3..571 531/578 (91%) ' norvegicus (Rat), 572 aa.

Q91 W98 SIMILAR TO PEPTIDE 9..576 496/578 (85%)0.0 TRANSPORTER 3 - Mus 3..573 531/578 (91%) musculus (Mouse), 574 aa.

AAH28394 SIMILAR TO PEPTIDE 117..577 460/461 (99%)0.0 TRANSPORTER 3 - Homo 1..461 460/461 (99%) sapiens (Human), 461 aa.

Q9P2X9 i PEPTIDE TRANSPORTER 9..558 289/570 (50%)e-152 3 - ~

Homo Sapiens (Human), 14..564 379/570 (65%) 581 aa.

Q9WU80 3 CAMP INDUCIBLE 1 8..567 279/577 (48%)e-144 ~

PROTEIN - Mus musculus 6..570 366/577 (63%) ~

(Mouse), 578 aa.

PFam analysis predicts that the NOV 16a protein contains the domains shown in the Table 16E.
Table 16E. Domain Analysis of NOVl6a Identities/
Pfam Domain NOVl6a Match Region Similarities Expect Value for the Matched Region PTR2 ( 103..496 ~ 109/448 (24%) 6.7e-103 ..._ _.... .. 310/448. (69%)y .. _. ~ ._ . ... . . ........
Example 17.
The NOV 17 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table I7A.
Table 17A. NOV17 Sequence Analysis ~SEQ ID NO: 43 1393 by NOVI7a, CCCATGGAGGCTCCGGGACCCCGCGCCTTGCGGACTGCGCTCTGTGGCGGCTGTTGCT
CG104210-Ol GCCTCCTCCTATGTGCCCAGCTGGCTGTGGCTGGTAAAGGAGCTCGAGGCTTTGGGAG
DNA Sequence GGGAGCCCTGATCCGCCTGAATATCTGGCCGGCGGTCCAAGGGGCCTGCAAACAGCTG
GAGGTCTGTGAGCACTGCGTGGAGGGAGACAGAGCGCGCAATCTCTCCAGCTGCATGT

GGGAGCAGTGCCGGCCAGAGGAGCCAGGTCACTGTGTGGCCCAATCTGAGGTGGTCAA

GGAAGGTTGCTCCATCTACAACCGCTCAGAGGCATGTCCAGCTGCTCACCACCACCCC

ACCTATGAACCGAAGACAGTCACAACAGGTAGCCCCCCAGTCCCTGAGGCCCACAGCC

CTGGATTTGACGGGGCCAGCTTTATCGGAGGTGTCGTGCTGGTGTTGAGCCTACAGGC

GGTGGCTTTCTTTGTGCTGCACTTCCTCAAGGCCAAGGACAGCACCTACCAGACGCTG

TGAGTACCTGGCCAGCAGCAAGTACCTGAGTCCCAGCTCACCTCCTGGTTCCTGCCCC

ACCGTTCCCCTTCAGTACCCAGGGTGCTGTCTTCTCCACTGGCAAGCCCTCAGGACGG

TGACAGCGTGCTCCATGTGAGCCACACCCCTTTTGTCTCCTCCAGTTGGGGTGTTTCC

TTTGTCAGATGTTGGCTGGGACCAGGACTCAGCCTGGGCCAGTCTAGGAGCCCAGCTG

AGCCCTCCTGTGTCTTTTCCCTTCATGCTGCCAGCAGGGAAGAGAACCAGTAGGTGCC

AGCCCAGCAACCTGTGGCCCGCGTTTCTGTGGCTGTGGGCAGGAGCTGGGCCTTGTGT

CTAGTTGGGTTTTGCTCTGAGAAGGGGAGCTGTGCTGAGGCCCTCTGTGTGCCGTGTG

TGCTGTGGGGCGGGTCGCCACAGCCTGTGTTAAAGTGTTTGCTCTTCCTCTGCTGCCT

CCTCTCGAGGCAGGGGGTCCTTGGCTGGCTGAGGCAGTGTCACCTTCCTGAGTGTCCT

CTTTGGCCTCTGCAGAATCTGACCCCTTTGGGCCTGGACTCCATCCTGAGGGGAAAGG

AGGATGCAGAGGGTGGCCTCTGGGCACCCTTGTGGGTAAGCGGGGGGCGGGGGCGGGA

AAAACTCTGGCCGCCAGTTTTTGGCTCCTGCGGGCACCAAGCAGGCTCAGTGTCTGAT

GCTTGACATCTCCTCCTGTCCTGGGCCTGGAACCTGCAGCTGAGAAAATCCCTCAACC

ACCTCGTCTCCTCCATCGCCCCTGCTGGGCCCCCCAGCCTGACAGTGGGTTGTATGCC

TGCCTCTTTCCACCAACTGGCCTGGGCACTGCCCCCAAATAAAGGAACTCTGCACTGC

A

ORF Start: ATG at 4 ORF Stop: TGA at 523 SEQ ID N0: 44 173 as ~MWat 18421.OkD
~.
w..~

NOVI7a, .
MEAPGPRALRTALCGGCCCLLLCAQLAVAGKGARGFGRGALIRLNIWPAVQGACKQLE

CG104210-Ol VCEHCVEGDRARNLSSCMWEQCRPEEPGHCVAQSEVVKEGCSIYNRSEACPAAHHHPT

P1'Otelri YEPKTVTTGSPPVPEAHSPGFDGASFIGGWLVLSLQAVAFFVLHFLKAKDSTYQTL
Sequence SEQ ID NO: 4S X561 by NOVl7b, CCCATGGAGGCTCCGGGACCCCGCGCCTTGCGGACTGCGCTCTGTGGCGGCTGTTGCT

DNA SeqlleriCeGGGAGCCCTGA'T'CCGCCTGAATATCTGGCCGGCGGTCCAAGGGGCCTGCAAACAGCTG

GAGGTCTGTGAGCACTGCGTGGAGGGAGACAGAGCGCGCAATCTCTCCAGCTGCGTGT

GGGAGCAGTGCCGGCCAGAGGAGCCAGGACACTGTGTGGCCCAATCTGAGGTGGTCAA

GGAAGGTTGCTCCATCTACAACCGCTCAGAGGCATGTCCAGCTGCTCACCACCACCCC

ACCTATGAACCGAAGACAGTCACAACAGGGAGCCCCCCAGTCCCTGAGGCCCACAGCC

CTGGATTTGACGGGGCCAGCTTTATCGGAGGTGTCGTGCTGGTGTTGAGCCTACAGGC

GGTGGCTTTCTTTGTGCTGCACTTCCTCAAGGCCAAGGACAGCACCTACCAGACGCTG

TGAGTACCTGGCCAGCAGCAAGTACCTGAGTCCCAGCTC

ORF Start: ATG at 4 ORF Stop: TGA at S23 SEQ ID NO: 46 173 as MW at 18389.OkD

NOVI7b, MEAPGPRALRTALCGGCCCLLLCAQLAVAGKGARGFGRGALIRLNIWPAVQGACKQLE

PT'Otelri YEPKTVTTGSPPVPEAHSPGFDGASFTGGVVLVLSLQAVAFFVLHFLKAKI3STYQTL
Sequence SEQ ID NO: 47 349 by NOVI7C, _CACCGGATCCGGTAAAGGAGCTCGAGGCTTTGGGAGGGGAGCCCTGATCCGCCTGAAT

DNA

AGGGAGACAGAGCGCGCAATCTCTCCAGCTGCATGTGGGAGCAGTGCCGGCCAGAGGA
Sequence GCCAGGACACTGTGTGGCCCAATCTGAGGTGGTCAAGGAAGGTTGCTCCATCTACAAC

CGCTCAGAGGCATGTCCAGCTGCTCACCACCACCCCACCTATGAACCGAAGACAGTCA

CAACAGGGAGCCCCCCAGTCCCTGAGGCCCACAGCCCTGGATTTGACGGGGTCGACGG

C

ORF Start: at 2 ORF Stop: end of sequence SEQ ID NO: 48 l I6 as MW at 12383.7kD

NOV17C, TGSGKGARGFGRGALIRLNIWPAVQGACKQLEVCEHCVEGDRARNLSSCMWEQCRPEE

Protein Sequence Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 17B.
Table 17B. Comparison of NOVl7a against NOVl7b and NOVl7c.
Protein Sequence NOVl7a Residues/ Identities/
Match Residues ~ Similarities for the Matched Region NOV 17b 1..173 139/173 (80%) 1..173 140/173 (80%) NOV 17c 41..139 99/99 (100%) 15..113 99/99 (100%) Further analysis of the NOV 17a protein yielded the following properties shown in Table 17C.
Table 17C. Protein Sequence Properties NOVl7a PSort 0.6850 probability located in endoplasmic reticulum (membrane); 0.6400 analysis: probability located in plasma membrane; 0.4600 probability located in Golgi body; 0.1000 probability located in endoplasmic reticulum (lumen) SignalP ~ Cleavage site between residues 30 and 31 ~~~
analysis:
S A search of the NOV 17a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 17D.

Table 17D. Geneseq Results for NOVl7a NOVl7a Identities/

Geneseq Protein/Organism/Length Residues!Similarities Expect jPatent for Identifier,'' #, Date] Match the Matched Value ResiduesRegion AAE03827Human gene 10 encoded secreted1..173 173/173 (100%)e-103 protein HBINS58, SEQ ID 1..173 173/173 (100%) NO: 73 - Homo Sapiens, 173 aa.

[W0200136440-A1, 25-MAY-2001]

AAE03852Human gene l0.encoded secreted1..160 159/160 (99%)5e-94 protein HBINS58, SEQ ID 1..160 159/160 (99%) N0:98 -Homo Sapiens, 210 aa.

[W0200136440-Al, 25-MAY-AAB58415Lung cancer associated polypeptide73..173 41/124 (33%) 8e-10 sequence SEQ ID 753 - Homo 95..214 56/124 (45%) sapiens, 214 aa. [W0200055180-A2, 21-SEP-2000) AAG03771Human secreted protein, 73..173 38/124 (30%) 1e-07 SEQ ID

NO: 7852 - Homo Sapiens, 78..197 52/124 (41%) 197 aa.

[EP1033401-A2, 06-SEP-2000 _..

ABB65987: Drosophila melanogaster 116..17329160 (48%) 9e-05 ~

polypeptide SEQ ID NO 24753127..18335/60 (58%) -Drosophila melanogaster, 183 aa.

[WO200171042-A2, 27-SEP-2001]

In a BLAST search of public sequence databases, the NOV 17a protein was found to have homology to the proteins shown in the BLASTP data in Table 17E.

Table 17E. Public BLASTP Results for NOVl7a NOVl7a Identities/
Protein ' Residues/Similarities Expect Accession Protein/Organism/Length for Match the Matched Value Number Residues Portion Q9D6W7 2310047NO1RII~ PROTEIN 1..173 1401173 (80%)1e-82 -Mus musculus (Mouse), 1..17I 150/173 (85%) 172 aa.

Q9BPV0 CD164 ISOFORM DELTA 4 73..173 41/111 (36%) 6e-11 -Homo sapiens (Human), ~ 561111 (49%) ~
184 aa. ~
78..184 Q9CVT7 CDI64 ANTIGEN - Mus 25..173 51/173 (29%) 2e-10 musculus (Mouse), 161 5..161 67/173 (38%) as (fragment).

Q9QX82 ENDOLYN PRECURSOR - 54..173 41/140 (29%) 4e-10 Rattus norvegicus (Rat),57..195 59/140 (41%) I95 aa.

Q9Z317 MGC-24V - Mus musculus 54..173 44/I44 (30%) 7e-10 _.. .._~..._,..~Mouse), 197 aa.,~ 58..197 __rv58/144 ~..........~v .. _ (39%) Example 18.
The NOV 18 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table I 8A.
Table 18A. NOV18 Sequence Analysis SEQ ID N049 788 by NOVlBa, CTTTTGCCTTTATGCAACCAACATGGAGATTTTGTACCATGTCCTGTTCTTAGTGCTT

CG104251-Ol G~TGTCCTAACCTGAAGCTGAAGAAGCCGCCCTGGCTGCACATGCTGTCGGCCATGA

DNA Se ueriCBCTGTATGCTCTGGTGGTGGTGTCTTCCTCATTACCGGAGGAATCATTTATGATGTTAT
q TGTTGAACCTCCAAGTGTTGGCTCTATGACTGATGAACATGGGCATCAGAGGCCAGTA

GCTTTCTTTGCCTATAGAGTAAATGGACAATATATTATGGAAGGACTTGCATCCAGCT

TCCTGTTTACAATGGGAGGTTTAGGTTTCATAATCCTGGACCAATTGAATGCACCAAA

TATCCCAAAACTCAATAGATTTCTTCTTCTATTCATTGGATTTGTCTGTGTTCTATTG

AGTATTTTCATGGCTAGAGTATTCATGAGAATGAAACTGCCGAGCTATCTGATGGGTT

AGAGTGCCTTTGAGAAGAAATCAGTGGATACTGGATTTTTTCTTGTCAATGAAGTTTT

AAAGGCTGTACCAATCCTCTAATATGAAATGTGGAAAAGAATGAAGAGCAGCAGTAAA

AGAAATATCTAGTGAAAAAACAGGAAGCGTATTGAAGCTTGGACTAGAATTTCTTCTT

GGTATTAAAGAGACAAGTTTATCACAGAATTTTTTTTCCTGCTGGCCTATTGCTATAC

CAATGATGTTGAGTGGCATTTTCTTTTTAGTTTTTCATTAAAATATATTCCATATCTA

CAACTATAATATCAAATAAAGTGATTATTTTTTA

ORF Start: ATG at 23 ORF Stop: TAG at 464 SEQ ID NO: 50 147 as MW at 16447.7kD

NOVIBa, MEILYHVLFLVLECPNLKLKKPPWLHMLSAMTVCSGGGVFLITGGIIYDVIVEPPSVG

CG104251-Ol SMTDEHGHQRPVAFFAYRVNGQYIMEGLASSFLFTMGGLGFIILDQLNAPNTPKLNRF

LLLFIGFVCVLLSIFMARVFMRMKLPSYLMG
Protein Sequence Further analysis of the NOV 18a protein yielded the following 'properties shown m Table 18B.
Table 18B. Protein Sequence Properties NOVl8a PSort 0.6400 probability located in plasma membrane; 0.4600 probability located in analysis: Golgi body; 0.3700 probability located in endoplasmic reticulum (membrane);
0.1000 probability located in endoplasmic reticulum (lumen) SignalP Cleavage site between residues 42 and 43 analysis:
A search of the NOV 18a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 18C.
Table 18C. Geneseq Results for NOVlBa NOVl8a Identities/

Geneseq Protein/Organism/Length Residues/SimilaritiesExpect [Patent ' for Identifier#, Date) Match the Matched Value ResiduesRegion AAY53631 A bone marrow secreted protein1..147 133/149 (89%)1 e-69 =

designated BMS155 - Homo 1..149 135/149 (90%) ~

Sapiens, 149 aa. [W09933979-A2, 08-JUL-1999]

AAY53042 Human secreted protein clone1..147 133/I49 (89%)1e-69 ~ ~

pu282_10 protein sequence 1..149 135/149 (90%) SEQ ID ;

N0:90 - Homo Sapiens, 149 aa.

[W09957132-A1, 11-NOV-1999]

AAB12143 Hydrophobic domain protein 1..147 133/149 (89%)1e-69 ~

isolated from WERI-RB cells1..149 135/149 (90%) -Homo sapiens, 149 aa. t [WO200029448-A2, 25-MAY-2000]

AAY59670 Secreted protein 108-005-5-0-F6-FL1..147 133/149 (89%)1e-69 - Homo Sapiens, 149 aa. 1..149 135/149 (90%) [W09940189-A2, I2-AIIG-1999]

AAY60146 Human endometrium tumour 1..147 133/149 (89%)1 e-69 EST :

encoded protein 206 - Homo 23..171 135/149 (90%) Sapiens, 171 aa. [DE19817948-A1, 2.1-~CT-1999]
_..........

In a BLAST search of public sequence databases, the NOV I 8a protein was found to have homology to the proteins shown in the BLASTP data in Table 18D.

Table 18D. Public BLASTP Results for NOVlBa Protein NOVl8a Identities/

Residues/ SimilaritiesExpect Accession Protein/Organism/Length for ~ Match the MatchedValue Number ' Residues Portion Q9NRP0 DC2 (HYDROPHOBIC PROTEIN 1..147 133/149 3e-69 (89%) HSF-28) (HYPOTHETICAL 1..149 135/149 16.8 (90%) I~IDA PROTEIN) - Homo sapiens (Human), 149 aa.

Q9P075 HSPC307 - Homo sapiens 1..147 133/149 3e-69 (89%) (Human), 167 as (fragment).19..167 135/149 ~ (90%) Q9CPZ2 2310008MlORII~ PROTEIN 1..147 132/149 6e-69 (88%) (RIKEN CDNA 2310008M10 1..149 135/149 (90%) GENE) - Mus musculus (Mouse), 149 aa.

Q9P1R4 HDCMD45P - Homo Sapiens ~ 1..147 132/149 2e-68 ~ (88%) (Human), 160 as (fragment).~ 12..160 134/149 (89%) AAH24224 SIMILAR TO DC2 PROTEIN 40..147 96/108 (88%)7e-50 - ~

Homo Sapiens (Human), 12..119 100/108 119 aa. (91%) ~

Examine 19.
The NOV 19 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 19A.
Table 19A. NOV19 Sequence Analysis SEQ ID NO: 51 3761 by NOVl9a, GGGCGCGCCGAGCCGGGCGCGGGGGCGCTGAACGGCGGAGCGGGAGCGGCCGGAGGAG

CG104934-O1 _CCATGGACTGCAGCCTCGTGCGGACGCTCGTGCACAGATACTGTGCAGGAGAAGAGAA

DNA Se uenCeTTGGGTGGACAGCAGGACCATCTACGTGGGACACAGGGAGCCACCTCCGGGCGCAGAG
q GCCTACATCCCACAGAGATACCCAGACAACAGGATCGTCTCGTCCAAGTACACATTTT

GGAACTTTATACCCAAGAATTTATTTGAACAATTCAGAAGAGTAGCCAACTTTTATTT

CCTTATCATATTTCTGGTGCAGTTGATTATTGATACACCCACAAGTCCAGTGACAAGC

GGACTTCCACTCTTCTTTGTCATTACTGTGACGGCTATCAAACAGGGTTATGAAGACT

GGCTTCGACATAAAGCAGACAATGCCATGAACCAGTGTCCTGTTCATTTCATTCAGCA

CGGCAAGCTCGTTCGGAAACAAAGTCGAAAGCTGCGAGTTGGGGACATTGTCATGGTT

AAGGAGGACGAGACCTTTCCCTGCGACTTGATCTTCCTTTCCAGCAACCGGGGAGATG

GGACGTGCCACGTCACCACCGCCAGCTTGGATGGAGAATCCAGCCATAAAACGCATTA

CGCGGTCCAGGACACCAAAGGCTTCCACACAGAGGAGGATATCGGCGGACTTCACGCC

ACCATCGAGTGTGAGCAGCCCCAGCCCGACCTCTACAAGTTCGTGGGTCGCATCAACG

TTTACAGTGACCTGAATGACCCCGTGGTGAGGCCCTTAGGATCGGAAAACCTGCTGCT

TAGAGGAGCTACACTGAAGAACACTGAGAAAATCTTTGGTGTGGCTATTTACACGGGA

ATGGAAACCAAGATGGCATTAAATTATCAATCAAAATCTCAGAAGCGATCTGCCGTGG

AAA.AATCGATGAATGCGTTCCTCATTGTGTATCTCTGCATTCTGATCAGCAAAGCCCT

GATAAACACTGTGCTGAAATACATGTGGCAGAGTGAGCCCTTTCGGGATGAGCCGTGG

TATAATCAGAAAACGGAGTCGGAAAGGCAGAGGAATCTGTTCCTCAAGGCATTCACGG
ACTTCCTGGCCTTCATGGTCCTCTTTAACTACATCATCCCTGTGTCCATGTACGTCAC
GGTCGAGATGCAGAAGTTCCTCGGCTCTTACTTCATCACCTGGGACGAAGACATGTTT
GACGAGGAGACTGGCGAGGGGCCTCTGGTGAACACGTCGGACCTCAATGAAGAGCTGG
GACAGGTGGAGTACATCTTCACAGACAAGACCGGCACCCTCACGGAAAACAACATGGA
GTTCAAGGAGTGCTGCATCGAAGGCCATGTCTACGTGCCCCACGTCATCTGCAACGGG
CAGGTCCTCCCAGAGTCGTCAGGAATCGACATGATTGACTCGTCCCCCAGCGTCAACG
GGAGGGAGCGCGAGGAGCTGTTTTTCCGGGCCCTCTGTCTCTGCCACACCGTCCAGGT
GAAAGACGATGACAGCGTAGACGGCCCCAGGAAATCGCCGGACGGGGGGAAATCCTGT
GTGTACATCTCATCCTCGCCCGACGAGGTGGCGCTGGTCGAAGGTGTCCAGAGACTTG
GCTTTACCTACCTAAGGCTGAAGGACAATTACATGGAGATATTAAACAGGGAGAACCA
CATCGAAAGGTTTGAATTGCTGGAAATTTTGAGTTTTGACTCAGTCAGAAGGAGAATG
AGTGTAATTGTAAAATCTGCTACAGGAGAAATTTATCTGTTTTGCAAAGGAGCAGATT
CTTCGATATTCCCCCGAGTGATAGAAGGCAAAGTTGACCAGATCCGAGCCAGAGTGGA
GCGTAACGCAGTGGAGGGGCTCCGAACTTTGTGTGTTGCTTATAAAAGGCTGATCCAA
GAAGAATATGAAGGCATTTGTAAGCTGCTGCAGGCTGCCAAAGTGGCCCTTCAAGATC
GAGAGAAA.AAGTTAGCAGAAGCCTATGAGCAAATAGAGAAAGATCTTACTCTGCTTGG
TGCTACAGCTGTTGAGGACCGGCTGCAGGAGAAAGCTGCAGACACCATCGAGGCCCTG
CAGAAGGCCGGGATCAAAGTCTGGGTTCTCACGGGAGACAAGATGGAGACGGCCGCGG
CCACGTGCTACGCCTGCAAGCTCTTCCGCAGGAACACGCAGCTGCTGGAGCTGACCAC
CAAGAGGATCGAGGAGCAGAGCCTGCACGACGTCCTGTTCGAGCTGAGCAAGACGGTC
CTGCGCCACAGCGGGAGCCTGACCAGAGACAACCTGTCCGGACTTTCAGCAGATATGC
AGGACTACGGTTTAATTATCGACGGAGCTGCACTGTCTCTGATAATGAAGCCTCGAGA
AGACGGGAGTTCCGGCAACTACAGGGAGCTCTTCCTGGAAATCTGCCGGAGCTGCAGC
GCGGTGCTCTGCTGCCGCATGGCGCCCTTGCAGAAGGCTCAGATTGTTAAATTAATCA
AATTTTCAAAAGAGCACCCAATCACGTTAGCAATTGGCGATGGTGCAAATGATGTCAG
CATGATTCTGGAAGCGCACGTGGGCATAGGTGTCATCGGCAAGGAAGGCCGCCAGGCT
TTCACGGGCATTTTTATTACATTAGGATCTCTGAGCTCGTGCAGTACTTCTTCTATAA
GAACGTCTGCTTCATCTTCCCTCAGTTTTTATACCAGTTCTTCTGTGGGTTTTCACAA
CAGACTTTGTACGACACCGCGTATCTGACCCTCTACAACATCAGCTTCACCTCCCTCC
CCATCCTCCTGTACAGCCTCATGGAGCAGCATGTTGGCATTGACGTGCTCAAGAGAGA
CCCGACCCTGTACAGGGACGTCGCCAAGAATGCCCTGCTGCGCTGGCGCGTGTTCATC
TACTGGACGCTCCTGGGACTGTTTGACGCACTGGTGTTCTTCTTTGGTGCTTATTTCG
TGTTTGAAAATACAACTGTGACAAGCAACGGGCAGATATTTGGAAACTGGACGTTTGG
AACGCTGGTATTCACCGTGATGGTGTTCACAGTTACACTAAAGCTTGCATTGGACACA
TCTTTTCGCTTCTCTGGGGAGGAGTGATCTGGCCGTTCCTCAACTACCAGAGGATGTA
CTACGTGTTCATCCAGATGCTGTCCAGCGGGCCCGCCTGGCTGGCCATCGTGCTGCTG
GTGACCATCAGCCTCCTTCCCGACGTCCTCAAGAAAGTCCTGTGCCGGCAGCTGTGGC
ATTCACCCCTCTTGCCTCTCTGCAGAGCCCAGGCTACCAGAGCACCTGTCCCTCGGCC
GCCTGGTACAGCTCCCACTCTCAGCAGGTGACACTCGCGGCCTGGAAGGAGAAGGTGT
CCACGGAGCCCCCACCCATCCTCGGCGGTTCCCATCACCACTGCAGTTCCATCCCAAG
TCACAGCTGCCCTAGGTCCCGTGTGGGAATGCTCGTGTGATGGATGGTCCTAAGCCTG
TGGAGACTGTGCACGTGCCTCTTCCTGGCCCCCAGCAGGCAAGGAGGGG
CCTTGCCCTCGAGCATGGCACCCTGGCCGCCTGGACCCAGCACTGTGGT
ORF Start: ATG at 61 ORF Stop: TGA at 3634 SEQ ID NO: 52 1191 as MW at 135846.OkD
NOVl9a, MDCSLVRTLVHRYCAGEENWVDSRTIYVGHREPPPGAEAYIPQRYPDNRIVSSKYTFW

PPOtelri LRHKADNAMNQCPVHFIQHGKLVRKQSRKLRVGDIVMVKEDETFPCDLIFLSSNRGDG
Sequence TCHVTTASLDGESSHKTHYAVQDTKGFHTEEDIGGLHATIECEQPQPDLYKFVGRTNV

YSDLNDPVVRPLGSENLLLRGATLKNTEKIFGVAIYTGMETKMALNYQSKSQKRSAVE

KSMNAFLIVYLCILISKALINTVLKYMWQSEPFRDEPWYNQKTESERQRNLFLKAFTD

FLAFMVLFNYIIPVSMYVTVEMQKFLGSYFITWDEDMFDEETGEGPLVNTSDLNEELG

QVEYIFTDKTGTLTENNMEFKECCIEGHVYVPHVICNGQVLPESSGIDMIDSSPSVNG

REREELFFRALCLCHTVQVKDDDSVDGPRKSPDGGKSCVYISSSPDEVALVEGVQRLG

FTYLRLKDNYMEILNRENHIERFELLEILSFDSVRRRMSVIVKSATGEIYLFCKGADS

SIFPRVIEGKVDQIRARVERNAVEGLRTLCVAYKRLIQEEYEGICKLLQAAKVALQDR
EKKLAEAYEQIEKDLTLLGATAVEDRLQEKAADTIEALQKAGIKVWVLTGDKMETAAA
TCYACKLFRRNTQLLELTTKRIEEQSLHDVLFELSKTVLRHSGSLTRDNLSGLSADMQ
DYGLIIDGAALSLIMKPREDGSSGNYRELFLEICRSCSAVLCCRMAPLQKAQIVKLIK
FSKEHPITLAIGDGANDVSMILEAHVGIGVIGKEGRQAARNSDYAIPKFKHLKKMLLV
HGHFYYTRISELVQYFFYKNVCFIFPQFLYQFFCGFSQQTLYDTAYLTLYNISFTSLP
ILLYSLMEQHVGIDVLKRDPTLYRDVAKNALLRWRVFIYWTLLGLFDALVFFFGAYFV
FENTTVTSNGQIFGNWTFGTLVFTVMVFTVTLKLALDTHYWTWINHFVIWGSLLFYVV
FSLLWGGVIWPFLNYQRMYYVFIQMLSSGPAWLAIVLLVTISLLPDVLKKVLCRQLWP
TATERVQNGCAQPRDRDSEFTPLASLQSPGYQSTCPSAAWYSSHSQQVTLAAWKEKVS
TEPPPILGGSHHHCSSIPSHSCPRSRVGMLV
Further analysis of the NOV 19a protein yielded the following properties shown in Table 19B.
YTabIeYl9B. Protein Sequence Properties NOVI9a PSort 0.6000 probability located m plasma membrane, 0.4000 probability located in analysis: ~ Golgi body; 0.3000 probability located in endoplasmic reticulum (membrane);
0.0300 probability located in mitochondria) inner membrane SignaIP No Known Signal Sequence Predicted analysis:
A search of the NOV 19a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 19C.

Table 19C. Geneseq Results for NOVl9a NOVl9a Identities/

Geneseq ProteinlOrganism/Length Residues/Similarities Expect for Identifier(Patent #, Date) Match the Matched Value Residues Region .

AAO14200 ~ Human transporter and 1..1191 1190/1192 0.0 ion (99%) channel TRICH-17 - Homo 1..l 192 1191/1192 (99%) Sapiens, 1192 aa. [W0200204520-A2, 17-JAN-2002]

AAB42368 Human ORFX ORF2132 338..1109770/772 (99%)0.0 polypeptide sequence SEQ 1..772 772/772 (99%) ID ~

N0:4264 - Homo sapiens, 797 aa.

[W0200058473-A2, OS-OCT- ' , .

2000]

AAG67546 Amino acid sequence of 22..1109 657/1119 (58%)0.0 a human transporter protein - 18..1106 833/1119 (73%) Homo Sapiens, 1177 aa. [W0200164878-A2, 07-SEP-2001 AA014203 Human transporter and 22..1109 583/1119 (52%)0.0 ion channel TRICH-20 - Homo 18..1040 755/I 119 a (67%) Sapiens, 1096 aa. [WO200204520-A2, 17-JAN-2002]

AAM39290 Human polypeptide SEQ 370..1109424/771 (54%)0.0 ID NO ' 2435 - Homo Sapiens, 815 1..744 544/771 (69%) aa.

[W0200153312-Al, 26-JUL-In a BLAST search of public sequence databases, the NOV 19a protein was found to have homology to the proteins shown in the BLASTP data in Table 19D.

....Table , .
19D. . .....
a - . .
lic BLA
. TP
Results a ....
.
P b S
for ~

Protein ~ NOVl9a Identities/

AccessionProtein/Organism/Length ' Residues/Similarities Expect for Number Match the Matched Value s Residues Portion P98197 Potential phospholipid- ~ 1..l 1074/1195 (89%)0.0 transporting ATPase IH I..1185 1117/1195 (92%) (EC

3.6.3.1 ) - Mus musculus (Mouse), 1187 aa.

P98196 Potential phospholipid- 338..1109772/772 (100%)0.0 transporting ATPase IS ~ I..772 772/772 (100%) (EC

3 .6.3.1 ) - Homo Sapiens (Human), 797 as (fragment).

...... .~ m ,~.., 14..997 633/992 (63%) 0.0 BB206I21.1 (ATPASE, CLASS

VI, TYPE 11C ) - Homo 1..962 770/992 (76%) sapienS

Human), 962.aa (fragment).. ..

Q9NOZ4 RING-FINGER BINDING ~ 22..1109574/1123 (51%)0.0 PROTEIN - Oryctolagus ~ 10..1036752/1123 (66%) cuniculus (Rabbit), 1107 as (fragment).

Q9Y2G3 Potential phospholipid- ~ 486..1109358/625 (57%) 0.0 transporting ATPase IR 1..601 462/625 (73%) (EC

3.6.3.1 ) - Homo sapiens x (Human), 672 as (fragment).

PFam analysis predicts that the NOV I 9a protein contains the domains shown in the Table 19E.
Table 19E. Domain Analysis of NOVl9a Identities/
Pfam Domain NOVl9a Match Region Similarities Expect Value for the Matched Region Hydrolase 408..846 46/448 (10%) 0.0058 _. __ ~~_ _ 258/448 (58%) _. _.._ . .. _.. _... _ ._ _____ . __ ____ _ _ .. _... .__.
Example 20.
The NOV20 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 20A.

Table 20A. NOV20 Sequence SEQ ID NO: 532588 by NOV2Oa, ~AGTTCCGAACAGAAGGCTGTGTATTCTCTGCCGCTTATTGTGGCCTCGACAGGCCATG

DNA Se tl0riC8 TCAGCTGTACTTGGGGCTGGTCCTGCAGTTGCTACCCAGGGTTATGGCAGCACTGCCT
GAAGGTGTGAGACCAAATTCGAATCCTTATGGTTTTCCATGGGAATTGGTGATATGTG
CAGCTGTCCTTGGATTTGTTGCTGTTCCCTTTTTTTTGTGGAGAAGTTTTAGATCGGT
TAGGAGTCGGCTTTATGTGGGAAGAGAGAAAGAGCTTGCTATAGCGCTTTCTGGACTA
ATTGAAGAAAAATGTAGACTACTTGAAAAATTTAGCCTTGTTCAAAAAGAGTATGAAG
GCTATGAAGTAGAGTCATCTTTAGAGGATGCCAGCTTTGAGAAGGAGGCAACAGAAGC
ACAAAGTCTGGAGGCAAACTGTGAAAAGCTGAACAGGTCCAATTCTGAACTGGAGCAT
GAAATACTCTGTCTAGAAAAGGGGATAAAAGAAGAGAAATCTAAACATTCTGAACAAG
ATGAGGTGATGGCAGATATTTCCAAAAAGATACAGTCTCTAGAAGATGAGTCAAAATC
CCTCAAATCACTACTAACTGAAGCCAAAATGACCTTCAAGGGATTTCAAATGAATGAA
GAAAA.ACTGGAGATAGGAATACAAGATGCTTCGAGTGAAAATTGTCAACTTCAGGAAA
GCCAGAAACAGCTTTTGCAAGAAGCTGAAGTATGGAAAGAACAAGTGAGTGAACTTAA
TAAACAGAAAATAACATTTGAAGACTCCAA.AGTACACGCAGAACAAGTTCTAAATGAT
AAAGAAAATCACATCGAGACTCTGACTGAACGCTTGCTAAAGATCAAAGATCAGGCTG
CTGTGCTGGAAGAAGACATAACGGATGATGGTAACTTGGAATTAGAAATGAACAGTGA
ATTGAAAGATGGTGCTTACTTAGATAATCCTCCAAAAGGAGCTTTGAAGAAACTGATT
CATGCTGCTAAGTTAAATGCTTCTTTAACAACCTTAGAAGGAGAAAGAAACCAATTTA
TATTCAGTTATCTGAAGTTGATAA.AACCAAGGAAGAGCTTAGAGAGCATATTAAAAAT
CTTCAGACGGAACAAGCATCTTTGCAGTCGGAA.AACACACATTTTGAAAGTGAGAATC
AGAAACTTCAACAGAAAGTTAATGACTGAGTTATATCAAGAAAATGAAATGAAACTCT
ACAGGAAATTAATAGTAGAGGAAAATAACCGGTTAGAGAAAGAGAAACTTTCTAAAGT
AGACGAAATGATCAGCCATGCCACTGAAGAGCTGGAGACCTGCAGAAAGCGAGCCAAA
GATCTTGAAGAAGAACTTGAGAGAACTATTCTTTTTTATCAAGGGAAGATTATATACC
ATGAGAAAAA.AGCACATGATAATTGTTTGGCAGCATGGACTGCTGAAAGAAACCTCAA
~TGATTTAAGGAAAGAAAATGCTCACAAAAGACAAAAATTAGCTGAAACAGAGTTTAAA
ATTAAACTTTTAGAAAAAGATCCTTATGCACTTGATGTTCCAAATACAGCATTTGGCA
GAGAGCATTCCTCATATGGTCCCTCACCATTGGGTCGGCCTTCATCTGAAACGAGAGC
TTTTCTCTATCTTCCGACTTTGTTGGAGGGTCCACTGAGACTCTCACCTTTGCTTCCA
GGGGGAGGAGGAAGAGACCCAAGAGGCCCAGGGAATCCTCTGGACCACCAGATTACCA
CACTGGGCCCCTGTCACCTCCGTGGGAACAGGACCGTAGGATGATGTTTC
GGACAATCATATCCTGATTCAGCTCTTCCTCCACAAAGGCAAGACAGATT
TAAAATGGATGGGTCAATGCCTTCAGAAATGGAATCCAGTGGAAATGATACCAAAGAT
AATCTTGGTAATTTAAATGTGGCTGATTCATCTCTCCCTGCTGGAAATGAAGTGAGTG
GCCCTGGCTTTGTTCCTCCACCTCTTGCTTCAATCAGAGGTCCATTGTTTCCAGTGGA
TACGAGGGGCCCGTTCATGAGAAGAGGACCTCCTTTCCCTCCACCTCCTCCAGGAACC
ATGTTTGGAGCTTCTCCAGATTATTTTCCACCAAGGGATGTCCCAGGTCCACCACGTG
CTCCATTTGCAATGAGAAATGTCTGTCCACCGAGGGGTTTTCCTCCTTACCTTCCCCC
AAGACCTGGATTTTGCCCCCACCCCCACCCCCACAGTGAGTTCCCTTTAGGGTTGAGT
CTGCCTTCAAATGAGCCTGCTGCTGAAGATCCAGAACCACGGCAAGAAACCTGATAAT
ATTTTTGCTGTCTTCAAAAGTCATTTTGACTATTCTCATTTTCAGTTGAAGTAACTGC
TGTTACTTCAGTGATTACACTTTTGCTCAAATTGAA
ORF Start ATG at 94 ORF Stop TGA at 2488 ~.. ID N . _.. ...... . 7 . . ~ ..

SEQ O. 54 98 as MW at 90383.6kD
NOVZOa, MEEPRATPQLYLGLVLQLLPRVMAALPEGVRPNSNPYGFPWELVICAAVLGFVAVPFF

Protein Se lleriCB FEKEATEAQSLEANCEKLNRSNSELEHEILCLEKGIKEEKSKHSEQDEVMADISKKIQ
SLEDESKSLKSLLTEAKMTFKGFQMNEEKLEIGIQDASSENCQLQESQKQLLQEAEVW
KEQVSELNKQKITFEDSKVHAEQVLNDKENHIETLTERLLKIKDQAAVLEEDITDDGN
LELEMNSELKDGAYLDNPPKGALKKLIHAAKLNASLTTLEGERNQFIFSYLKLIKPRK

SLESILKIFRRNKHLCSRKTHILKVRIRNFNRKLMTELYQENEMKLYRKLIVEENNRL

EKEKLSKVDEMISHATEELETCRKRAKDLEEELERTILFYQGKIIYHEKKAHDNCLAA

WTAERNLNDLRKENAFiKRQKLAETEFKIKLLEKDPYALDVPNTAFGREHSSYGPSPLG

RPSSETRAFLYLPTLLEGPLRLSPLLPGGGGRDPRGPGNPLDHQITKERGESSCDRFT

DPHKAPSDTGPLSPPWEQDRRMMFPPPGQSYPDSALPPQRQDRFYSNSARRSGLAELR

SFNIPSLDKMDGSMPSEMESSGNDTKDNLGNLNVADSSLPAGNEVSGPGFVPPPLASI

RGPLFPVDTRGPFMRRGPPFPPPPPGTMFGASPDYFPPRDVPGPPRAPFAMRNVCPPR

GFPPYLPPRPGFCPHPHPHSEFPLGLSLPSNEPAAEDPEPRQET

SEQ ID NO: SS 2483 by NOV2Ob, AGCTGGAATTCGCCCTTCTCGACAGGCCATGGTTACTTTGGCCACTGCCAGAGCAGCC

DNA Se tleriCeGTTGCTACCCAGGGTTATGGCAGCACTGCCTGAAGGTGTGAGACCAAATTCGAATCCT

TATGGTTTTCCATGGGAATTGGTGATATGTGCAGCTGTCCTTGGATTTGTTGCTGTTC

CCTTTTTTTTGTGGAGAAGTTTTAGATCGGTTAGGAGTCGGCTTTATGTGGGAAGAGA

GAAAGAGCTTGCTATAGCGCTTTCTGGACTAATTGAAGAAAAATGTAGACTACTTGAA

AAATTTAGCCTTGTTCAA.AAAGAGTATGAAGGCTATGAAGTAGAGTCATCTTTAGAGG

ATGCCAGCTTTGAGAAGGAGGCAACAGAAGCACAAAGTCTGGAGGCAAACTGTGAAAA

GCTGAACAGGTCCAATTCTGAACTGGAGCATGAAATACTCTGTCTAGAAAAGGGGATA

AAAGAAGAGAAATCTAAACATTCTGAACAAGATGAGGTGATGGCAGATATTTCCAAAA

AGATACAGTCTCTAGAAGATGAGTCAAAATCCCTCAAATCACTACTAACTGAAGCTAA

AATGACCTTCAAGGGATTTCAAATGAATGAAGAAAAACTGGAGATAGGAATACAAGAT

GCTTCGAGTGAAAATTGTCAACTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAAGCTG

AAGTATGGAAAGAACAAGTGAGTGAACTTAATAAACAGAAAATAACATTTGAAGACTC

CAAAGTACACGCAGAACAAGTTCTAAATGATAAAGAAAATCACATCGAGACTCTGACT

GAACGCTTGCTAAAGATCAAAGATCAGGCTGCTGTGCTGGAAGAAGACATAACGGATG

ATGGTAACTTGGAATTAGAAATGAACAGTGAATTGAAAGATGGTGCTTACTTAGATAA

TCCTCCAAAAGGAGCTTTGAAGAAACTGATTCATGCTGCTAAGTTAAATGCTTCTTTA

ACAACCTTAGAAGGAGAAAGAAACCAATTTATATTCAGTTATCTGAAGTTGATAAAAC

CAAGGAAGAGCTTAGAGAGCATATTAAAAATCTTCAGACGGAACAAGCATCTTTGCAG

TCGGAAAACACACATTTTGAAAGTGAGAATCAGAAACTTCAACAGAAAGTTAATGACT

GAGTTATATCAAGAAAATGAAATGAAACTCTACAGGAAATTAATAGTAGAGGAAAATA

ACCGGTTAGAGAAAGAGAAACTTTCTAAAGTAGACGAAATGATCAGCCATGCCACTGA

AGAGCTGGAGACCTGCAGAAAGCGAGCCAAAGATCTTGAAGAAGAACTTGAGAGAACT

ATTCTTTTTTATCAAGGGAAGATTATATACCATGAGAAAAAAGCACATGATAATTGTT

TGGCAGCATGGACTGCTGAAAGAAACCTCAATGATTTAAGGAAAGAAAATGCTCACAA

AAGACAAAAATTAGCTGAAACAGAGTTTAAAATTAAACTTTTAGAAAAAGATCCTTAT

GCACTTGATGTTCCAAATACAGCATTTGGCAGAGAGCATTCCTCATATGGTCCCTCAC

CATTGGGTCGGCCTTCATCTGAAACGAGAGCTTTTCTCTATCTTCCGACTTTGTTGGA

GGGTCCACTGAGACTCTCACCTTTGCTTCCAGGGGGAGGAGGAAGAGGCCCAAGAGGC

CCAGGGAATCCTCTGGACCACCAGATTACCAAGGAAAGAGGAGAATCAAGCTGTGATA

GGTTTACTGATCCTCACAAGGCTCCTTCTGACACTGGGCCCCTGTCACCTCCGTGGGA

ACAGGACCGTAGGATGATGTTTCCTCCACCAGGACAATCATATCCTGATTCAGCTCTT

CCTCCACAAAGGCAAGACAGATTTTATTCTAATTCTGCTAGACGCTCTGGACTAGCAG

AACTCAGAAGTTTT.AATATACCTTCTTTGGATAAAATGGATGGGTCAATGCCTTCAGA

AATGGAATCCAGTGGAAATGATACCAAAGATAATCTTGGTAATTTAAATGTGGCTGAT

TCATCTCTCCCTGCTGGAAATGAAGTGAGTGGCCCTGGCTTTGTTCCTCCACCTCTTG

CTCCAATCAGAGGTCCGTTGTTTCCAGTGGATACGAGGGGCCCGTTCATGAGAAGAGG

ACCTCCTTTCCCTCCACCTCCTCCAGGAACCATGTTTGGAGCTTCTCCAGATTATTTT

CCACCAAGGGATGTCCCAGGTCTACCACGTGCTCCATTTGCAATGAGAAATGTCTGTC

CACCGAGGGGTTTTCCTCCTTACCTTCCCCCAAGACCTGGATTTTGCCCCCACCCCCA

CCCCCACATTCTGAAGATAGAGTGAGTTCCCTTTAGGGTTGAGTGCCTTCAAATGAGC

CTGCTGCTGAAGATCCAGAACCACGGCAAGAAACCTGATAATATTTT

ORF Start: ATG at 67 ORF Stop: TGA at 2401 SEQ ID NO: S6 778 as MW at 882SS.SkD

NOV2Ob, MEEPRATPQLYLGLVLQLLPRVMAALPEGVRPNSNPYGFPWELVICAAVLGFVAVPFF

P1'Otelri FEKEATEAQSLEANCEKLNRSNSELEHEILCLEKGIKEEKSKHSEQDEVMADTSKKIQ
SeCllleriCe SLEDESKSLKSLLTEAKMTFKGFQMNEEKLEIGIQDASSENCQLQESQKQLLQEAEVW

KEQVSELNKQKITFEDSKVHAEQVLNDKENHIETLTERLLKIKDQAAVLEEDITDDGN
LELEMNSELKDGAYLDNPPKGALKKLIHAAKLNASLTTLEGERNQFIFSYLKLIKPRK
SLESTLKIFRRNKHLCSRKTHT~LKVRIRNFNRKLMTELYQENEMKLYRKLIVEENNRL
EKEKLSKVDEMISHATEELETCRK.RAKDLEEELERTILFYQGKI IYHEKI~AIiDNCLA.A
WTAERNLNDLRKENAHKRQKLAETEFKIKLLEKDPYALDVPNTAFGREHSSYGPSPLG
RPSSETRAFLYLPTLLEGPLRLSPLLPGGGGRGPRGPGNPLDHQITKERGESSCDRFT
DPHKAPSDTGPLSPPWEQDRRMMFPPPGQSYPDSALPPQRQDRFYSNSARRSGLAELR
SFNIPSLDKMDGSMPSEMESSGNDTKDNLGNLNVADSSLPAGNEVSGPGFVPPPLAPI
RGPLFPVDTRGPFMRRGPPFPPPPPGTMFGASPDYFPPRDVPGLPRAPFAMRNVCPPR
GFPPYLPPRPGFCPHPHPHILKIE
Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 20B.
Table 20B. Comparison of NOV20a against NOV20b.
Protein Sequence NOV20a Residues/ Identities/
Match Residues Similarities for the Matched Region ~~ .. ....~. .. . .
NOV20b ~ I..750 662/750 (88%) 1..750 662/750 (88%) _... . _.... _.. . ..
Further analysis of the NOV20a protein yielded the following properties shown in Table 20C.
Table 20C. Protein Sequence Properties NOV20a PSort a 0.4600 probability located in plasma membrane; 0.1000 probability located in analysis: endoplasmic reticulum (membrane); 0.1000 probability located in endoplasmic reticulum (lumen); 0.1000 probability located in outside SignalP ; Cleavage site between residues 25 and 26 analysis:
A search of the NOV20a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 20D.

Table 20D. Geneseq Results for NOV20a NOV20a Identities/
~

Geneseq Protein/Organism/Length Residues/Similarities Expect [Patent for Identifier#, Datej Match the Matched Value Residues~ Region AAY77574 Human cytoskeletal protein1..798 ~63 8/812 0.0 (78%) (HCYT) (clone 3768043) I ..806 683/812 (83%) - Homo Sapiens, 806 aa. [W0200006730-A2, 10-FEB-2000]

ABG05280 Novel human diagnostic 1..797 639/814 (78%)0.0 protein ~

#5271 - Homo Sapiens, 881 59..867 ~ 684/814 aa. (83%) x [W0200175067-A2, II-OCT-2001]

ABG05280 Novel human diagnostic 1..797 639/814 (78%)0.0 protein #5271 - Homo Sapiens, 881 59..867 ~ 684/814 aa. (83%) [W0200175067-A2, 11-OCT-2001]

ABG20258 Novel human diagnostic 1..797 634/814 (77%)0.0 protein #20249 - Homo sapiens, 59..867 681/814 (82%) 881 aa.

[W0200175067-A2, 11-OCT-2001] ~

ABG20258 Novel human diagnostic 1..797 ~ 634/814 0.0 protein (77%) #20249 - Homo sapiens, 59..867 681/814 (82%) 881 aa.

[W02001.75067.,A2, 1l-OCT-2001]..... . .. ~ _.. .. . ...
_.. .
...
_~

In a BLAST search of public sequence databases, the NOV20a protein Was found to have homology to the proteins shown in the BLASTP data in Table 20E.

Table 20E. Public BLASTP
Results for NOV20a Protein NOV20a Identities/

Accession Protein/Organism/Length Residues/Similarities for , Expect Number Match the Matched Value Residues Portion 015320 Meningioma-expressed antigen1..798 653/810 (80%) 0.0 (MEA6) (MEA11) - Homo Sapiens1..804 696/810 (85%) (Human), 804 aa.

Q96SG9 BASOOG10.2 (NOVEL PROTEIN 1..798 616/805 (76%) 0.0 SIMILAR TO MENINGIOMA 15..816 670/805 (82%) EXPRESSED ANTIGEN 6 (MEA6) AND 11 (MEA 11 )) - Homo Sapiens (Human), 825 as (fragment).
~~~

Q96RT6 CTAGE-2 - Homo Sapiens 30..775 605/749 (80%) 0.0 (Human), o~

754 aa. 1..746 6421749 84/
( )~

095046 WUGSC:H_DJ0988G15.3 1..770 570/775 (73%) 0.0 PROTEIN (DJ1005H11.2) 1..775 633/775 (8I%) (WUGSC:H DJ0988G15.3 PROTEIN) - Homo Sapiens (Human), 777 aa.

AAH26864 SIMILAR TO MENINGIOMA 30..796 5201783 (66%) ~
~ 0.0 EXPRESSED ANTIGEN 6 1..778 600/783 (76%) (COILED-COIL PROLINE-RICH) -Mus musculus (Mouse), 779 aa.

PFam analysis predicts that the NOV20a protein contains the domains shown in the Table 20F.
Table 20F. Domain Analysis of NOV20a Identities/
Pfam Domain NOV20a Match Region : Similarities Expect Value for the Matched Region No Significant Matches Found Example 21.
The NOV21 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 21A.

Table 21A. NOV21 Sequence Analysis SEQ ID NO: 57 1269 by NOV2la, AGCGGGGGGCGCTGCCTCGAGCCTCATGGCTGCCCCTGCTTCCGTCATGGGCCCACTC

DNA Se uenCeCAGCATTGGTCCACAGACAGCCAGAGAACCAGGGAATCTCCCTAACTGGCAGCGTGGC
q CTGTGGTCGGCCCAGCATGGAGGGGAAAATCCTGGGCGGCGTCCCTGCGCCCGAGAGG

AAGTGGCCGTGGCAGGTCAGCGTGCACTACGCAGGCCTCCACGTCTGCGGCGGCTCCA

TCCTCAATGAGTACTGGGTGCTGTCAGCTGCGCACTGCTTTCACAGGGACAAGAATAT

CAAAATCTATGACATGTACGTAGGCCTCGTAAACCTCAGGGTGGCCGGCAACCACACC

CAGTGGTATGAGGTGAACAGGGTGATCCTGCACCCCACATATGAGATGTACCACCCCA

TCGGAGGTGACGTGGCCCTGGTGCAGCTGAAGACCCGCATTGTGTTTTCTGAGTCCGT

GCTCCCGGTTTGCCTTGCAACTCCAGAAGTGAACCTTACCAGTGCCAATTGCTGGGCT

ACGGGATGGGGACTAGTCTCAAAACAAGGTGAGACCTCAGACGAGCTGCAGGAGGTGC

AGCTCCCGCTGATCCTGGAGCCCTGGTGCCACCTGCTCTACGGACACATGTCCTACAT

CATGCCCGACATGCTGTGTGCTGGGGACATCCTGAATGCTAAGACCGTGTGTGAGGGC

GACTCCGGGGGCCCACTTGTCTGTGAATTCAACCGCAGCTGGTTGCAGATTGGAATTG

TGAGCTGGGGCCGAGGCTGCTCCAACCCTCTGTACCCTGGAGTGTATGCCAGTGTTTC

CTATTTCTCAAAATGGATATGTGATAACATAGAAATCACGCCCACTCCTGCTCAGCCA

GCCCCTGCTCTCTCTCCAGCTCTGGGGCCCACTCTCAGCGTCCTAATGGCCATGCTGG

CTGGCTGGTCAGTGCTGTGAGGTCAGGATACCCACTCTAGGATTCTCATGGCTGCACA

CCCTGCCCCAGCCCAGCTGCCTCCAGACCCCTAAGCATCTCCTGTCCTGGCCTCTCTG

AAGCAGACAAGGGCCACCTATCCCGGGGGTGGATGCTGAGTCCAGGAGGTGATGAGCA

AGTGTACAAAAGAAAAAAGGGAAGGGGGAGAGGGGCTGGTCAGGGAGAACCCAGCTTG

GGCAGAGTGCACCTGAGATTTGATAAGATCATTAAATATTTACAAAGCAAA

ORF Start: ATG at 26 ORF Stop: TGA at 1004 SEQ ID NO: 58 326 as MW at 35323.8kD

NOV2la, MAAPASVMGPLGPSALGLLLLLLVVAPPRVAALVHRQPENQGISLTGSVACGRPSMEG

Protein SequenceI'~RVAGNHTQWYEVNRVILHPTYEMYHPIGGDVALVQLKTRIVFSESVLPVCLATP

EVNLTSANCWATGWGLVSKQGETSDELQEVQLPLILEPWCHLLYGHMSYIMPDMLCAG

DILNAKTVCEGDSGGPLVCEFNRSWLQIGIVSWGRGCSNPLYPGVYASVSYFSKWICD

NIEITPTPAQPAPALSPALGPTLSVLMAMLAGWSVL

Further analysis of the NOV21 a protein yielded the following properties shown in Table 21B.
Table 215. Protein SequenceyProperties NOV2la PSort 0.7900 probability located in plasma membrane; 0.3000 probability located in analysis: Golgi body; 0.2000 probability located in endoplasmic reticulum (membrane);
0.1007 probability located in microbody (peroxisome) SignalP ~ Cleavage site between residues 33 and 34 analysis:
.. .. ... . Y. ", .. .... . .. . .... ... . . .. . . ... ...... . . . .. . ..
.....
A search of the NOV21 a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 21 C.

Table 21C. Geneseq Results for NOV2la -~,-NOV2la Identities/

Geneseq Protein/Organism/Length Residues/Similarities ~ Expect [Patent ~ for Identifier#, Date] Match the Matched Value ResiduesRegion AAU82747 Amino acid sequence of 1..326 3261326 (100%)0.0 novel ~

human protease #46 - Homo 1..326 326/326 (100%) Sapiens, 326 aa. [W0200200860-, A2, 03-JAN-2002]

AAB73945 Human protease T - Homo 13..288 115/286 (40%)6e-53 Sapiens, ~

290 aa. [W0200116293-A2, 4..272 152/286 (S2%) AAE03821 Human gene 4 encoded secreted13..288 115/286 (40%)6e-53 protein HWHIH 10, SEQ ID 4..272 152/286 (52%) NO: 67 ~

Homo Sapiens, 290 aa.

[W0200136440-A1, 25-MAY-AAU12282 Human PRO4327 polypeptide 13..288 1151286 (40%)6e-53 sequence - Homo Sapiens, 4..272 152/286 (52%) 290 aa.

[W0200140466-A2, 07-JUN-2001]
a AAY73388 HTRM clone 3376404 protein13..288 115/286 (40%)~6e-53 ~

sequence - Homo Sapiens, 4..272 152/286 (52%) 290 aa.

[W09957144-A2, 11-NOV-1999 In a BLAST search of public sequence databases, the NOV21 a protein was found to have homology to the proteins shown in the BLASTP data in Table 21 D.

Table 21D. Public BLASTP Results for NOV2la Protein NOV2la Identities/
Accession ~ Protein/Organism/Length Residues/ Similarities for Expect Number ' Match the Matched Value Residues Portion Q9BQR3 ' Marapsin precursor (EC 3.4.21.-) - 13..288 1151286 (40%) 1e-52 Homo Sapiens (Human), 290 aa. 4..272 152/286 (52%) Q9PVX7 ~ EPIDERMIS SPECIFIC SERINE ~ 50..314 98/275 (35%) Se-52 PROTEASE - Xenopus laevis 16..287 159/275 (57%) (African clawed frog), 389 aa.
AAH24903 . RIKEN CDNA 2010001P08 51..326 114/288 (39%) 2e-51 GENE - Mus musculus (Mouse), 45..329 158/288 (54%) 331 aa.
Q91XC4 SIMILAR TO DISTAL ~ 51..288 106/247 (42%) 6e-51 INTESTINAL SERINE 28..272 138/247 (54%) PROTEASE - Mus musculus (Mouse), 310 aa.
Q9Q'YZ9 DISTAL INTESTINAL SERINE ~ 51..288 105/247 (42%) 7e-50 PROTEASE - Mus musculus 28..272 137/247 (54%) (Mouse), 310 aa.
PFam analysis predicts that the NOV21 a protein contains the domains shown in the Table 21E.
Table 21E. Domain Analysis of NOV2la Identities/
Pfam Domain NOV2la Match Region Similarities Expect Value for the Matched Region ..
trypsin 60..288 87/265 (33%) 5.3e-72 .. ~~.. _ 172/265 (65%) ' ..~~M-' . a Examine 22.
The NOV22 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 22A.
Table 22A. NOV22 Sequence Analysis SEQ ID NO: 59 4131 by NOV22a, GTGCCGAGGATGGCCAGGCAGCCACCGCCGCCCTGGATCCATGCAGCCTTCCTCCTCT
CG105954-Ol GCCTCCTCAGTCTTGGCGGAGCCATCGAA.ATTCCTATGGTTCCAAGCATTCAGAATGA
'GCTGACGCAGCCGCCAACCATCACCAAGCAGTCAGCGAAGGATCACATCGTGGACCCC

DNA SeClLleriCe CGTGATAACATCCTGATTGAGTGTGAAGCAAAAGGGAACCCTGCCCCCAGCTTCCACT
~GGACACGAAACAGCAGATTCTTCAACATCGCCAAGGACCCCCGGGTGTCCATGAGGAG
~GAGGTCTGGGACCCTGGTGATTGACTTCCGCAGTGGCGGGCGGCCGGAGGAATATGAG
GGGG.AATATCAGTGCTTCGCCCGCAACAAATTTGGCACGGCCCTGTCCAATAGGATCC
GCCTGCAGGTGTCTAAATCTCCTCTGTGGCCCAAGGAAAACCTAGACCCTGTCGTGGT
CCAAGAGGGCGCTCCTTTGACGCTCCAGTGCAACCCCCCGCCTGGACTTCCATCCCCG
GTCATCTTCTGGATGAGCAGCGCCATGGAGCCCATCACCCAAGACAAACGTGTCTCTC
AGGGCCATAACGGAGACCTATACTTCTCCAACGTGATGCTGCAGGACATGCAGACCGA
CTACAGTTGTAACGCCCGCTTCCACTTCACCCACACCATCCAGCAGAAGAACCCTTTC
ACCCTCAAGGTCCTCACCAGTAAGCCTTATAATGACTCGTCCTTAAGAAACCACCCTG
ACATGTACAGTGCCCGAGGAGTTGCAGAAAGAACACCAAGCTTCATGTATCCCCAGGG
CACCGCGAGCAGCCAGATGGTGCTTCGTGGCATGGACCTCCTGCTGGAATGCATCGCC
TCCGGGGTCCCAACACCAGACATCGCATGGTACAAGAAAGGTGGGGACCTCCCATCTG
ATAAGGCCAAGTTTGAGAACTTTAATAAGGCCCTGCGTATCACAAATGTCTCTGAGGA
AGACTCCGGGGAGTATTTCTGCCTGGCCTCCAACAAGATGGGCAGCATCCGGCACACG
ATCTCGGTGAGAGTAAAGGCTGCTCCCTACTGGCTGGACGAACCCAAGAACCTTATTC
TGGCTCCTGGCGAGGATGGGAGACTGGTGTGTCGAGCCAATGGAAACCCCAAACCCAC
TGTCCAGTGGATGGTGAATGGGGAACCTTTGCAAGCGGCACCACCTAACCCAAACCGT
GAGGTGGCCGGAGACACCATCATCTTCCGGGACACCCAGATCAGCAGCAGGGCTGTGT
ACCAGTGCAACACCTCCAACGAGCATGGCTACCTGCTGGCCAACGCCTTTGTCAGTGT
GCTGGATGTGCCGCCTCGGATGCTGTCGCCCCGGAACCAGCTCATTCGAGTGATTCTT
~TACAACCGGACGCGGCTGGACTGCCCTTTCTTTGGGTCTCCCATCCCCACACTGCGAT
iGGTTTAAGAATGGGCAAGGAAGCAACCTGGATGGTGGCAACTACCATGTTTATGAGAA
CGGCAGTCTGGAAATTAAGATGATCCGCAAAGAGGACCAGGGCATCTACACCTGTGTC
~GCCACCAACATCCTGGGCAAAGCTGAAAACCAAGTCCGCCTGGAGGTAAAAGACCCCA
CCAGGATCTACCGGATGCCCGAGGACCAGGTGGCCAGAAGGGGCACCACGGTGCAACT
~GGAGTGTCGGGTGAAGCACGACCCCTCCCTGAAACTCACCGTCTACTGGCTGAAGGAT
IGACGAGCCGCTCTATATTGGAAACAGGATGAAGAAGGAAGACGACTCCCTGACCATCT
~TTGGGGTGGCAGAGCGGGACCAGGGCAGTTACACGTGTGTCGCCAGCACCGAGCTAGA
iCCAAGACCTGGCCAAGGCCTACCTCACCGTGCTAGGACGGCCAGACCGGCCCCGGGAC
ICTGGAGCTGACCGACCTGGCCGAGAGGAGCGTGCGGCTGACCTGGATCCCCGGGGATG
CTAACAACAGCCCCATCACAGACTACGTCGTCCAGTTTGAAGAAGACCAGTTCCAACC
TGGGGTCTGGCATGACCATTCCAAGTACCCCGGCAGCGTTAACTCAGCCGTCCTCCGG' 'CTGTCCCCGTATGTCAACTACCAGTTCCGTGTCATTGCCATCAACGAGGTTGGGAGCA
GCCACCCCAGCCTCCCATCCGAGCGCTACCGAACCAGTGGAGCACCCCCCGAGTCCAA' TCCTGGTGACGTGAAGGGAGAGGGGACCAGAAAGAACAACATGGAGATCACGTGGACG':
CCCATGAATGCCACCTCGGCCTTTGGCCCCAACCTGCGCTACATTGTCAAGTGGAGGC' GGAGAGAGACTCGAGAGGCCTGGAACAACGTCACAGTGTGGGGCTCTCGCTACGTGGTi GGGGCAGACCCCAGTCTACGTGCCCTATGAGATCCGAGTCCAGGCTGAAAATGACTTC
GGGAAGGGCCCTGAGCCAGAGTCCGTCATCGGTTACTCCGGAGAAGATTATCCCAGGG~':
CTGCGCCCACTGAAGTTAAAGTCCGAGTCATGAACAGCACAGCCATCAGCCTTCAGTG) GAACCGCGTCTACTCCGACACGGTCCAGGGCCAGCTCAGAGAGTACCGAGCCTACTAC' TGGAGGGAGAGCAGCTTGCTGAAGAACCTGTGGGTGTCTCAGAAGAGACAGCAAGCCA
GCTTCCCTGGTGACCGCCTCCGTGGCGTGGTGTCCCGCCTCTTCCCCTACAGTAACTA
CAAGCTGGAGATGGTTGTGGTCAATGGGAGAGGTGATGGGCCTCGCAGTGAGACCAAG
GAGTTCACCACCCCGGAAGGAGTACCCAGTGCCCCTAGGCGTTTCCGAGTCCGGCAGC
CCAACCTGGAGACAATCAACCTGGAATGGGATCATCCTGAGCATCCAAATGGGATCAT
GATTGGATACACTCTCAAATATGTGGCCTGTACGTTCTCCCCAGTTAACGGGACCAAA
GTAGGAAAGCAGATAGTGGAAAACTTCTCTCCCAATCAGACCAAGTTCACGGTGCAAA
GAACGGACCCCGTGTCACGCTACCGCTTTACCCTCAGCGCCAGGACGCAGGTGGGCTC
TGGGGAAGCCGTCACAGAGGAGTCACCAGCACCCCCGAATGAAGGTAGGTGCATGGCA
GCAGCCCCTGGGGTAAAACCCCCGACTACCGTGGGTGCGACGGGCGCTGTGAGCAGTA
CCGATGCTACTGCCATTGCTGCCACCACCGAAGCCACAACAGTCCCCATCATCCCAAC
TGTCGCACCTACCACCATGGCCACCACCACCACCGTCGCCACAACTACTACAACCACT
GCTGCCGCCACCACCACCACGGAGAGTCCTCCCACCACCACCTCCGGGACTAAGATAC
ACGAATCCGGTACTGCGCATCGCCCATGCTCCCCAGCCCCTGATGAGCAGTCCATATG
GAACGTCACGGTGCTCCCCAACAGTAAATGGGCCAACATCACCTGGAAGCACAATTTC
GGGCCCGGAACTGACTTTGTGGTTGAGTACATCGACAGTAACCATACGAAAAAAACTG
TCCCAGTTAAGGCCCAGGCTCAGCCTATACAGCTGACAGACCTCTATCCCGGGATGAC
ATACACGTTGCGGGTTTATTCCCGGGACAACGAGGGCATCAGCAATCATTCACGGGTT
TGCTTCCGGCCCTCCCCGCCAGCTTACACCAACAACCAAGCGGACATCGCCACCCAGG

GCTGGTTCATTGGGCTTATGTGCGCCATCGCCCTCCTGGTGCTGATCCTGCTCATCGT
CTGTTTCATCAAGAGGAGTCGCGGCGGCAAGTACCCAGTACGAGAAAAGAAGGATGTT
CCCCTTGGCCCTGAAGACCCCAAGGAAGAGGATGGCTCATTTGACTATAGGTCTTTGG
CCAGTGATGAGGACAACAAGCCCCTGCAGGGCAGTCAGACATCTCTGGACGGCACCAT
CAAGCAGCAGGAGAGTGACGACAGCCTGGTGGACTATGGCGAGGGTGGCGAGGGTCAG
TTCAATGAAGACGGCTCCTTCATCGGCCAGTACACGGTCAAAAAGGACAAGGAGGAAA
CAGAGGGCAACGAAAGCTCAGAGGCCACGTCACCTGTCAATGCTATCTACTCTCTGGC
CTAACGGAGCCCA
ORF Start: ATG at 10 ORF Stop TAA at 41_20 SEQ ID NO: 60 ~~~1370 Yaa MW at 152752.SkD
NOV22a, ~QPPPPWIHAAFLLCLLSLGGAIEIPMVPSIQNELTQPPTITKQSAKDHIVDPRDN

CG105954-Ol ILIECEAKGNPAPSFHWTRNSRFFNIAKDPRVSMRRRSGTLVIDFRSGGRPEEYEGEY

PrOteln SequenceQCFARNKFGTALSNRIRLQVSKSPLWPKENLDPVWQEGAPLTLQCNPPPGLPSPVIF

WMSSAMEPITQDKRVSQGHNGDLYFSNVMLQDMQTDYSCNARFHFTHTIQQKNPFTLK

VLTSKPYNDSSLRNHPDMYSARGVAERTPSFMYPQGTASSQMVLRGMDLLLECIASGV

PTPDIAWYKKGGDLPSDKAKFENFNKALRITNVSEEDSGEYFCLASNKMGSIRHTISV

RVKAAPYWLDEPKNLTLAPGEDGRLVCRANGNPKPTVQWMVNGEPLQAAPPNPNREVA

GDTIIFRDTQISSRAVYQCNTSNEHGYLLANAFVSVLDVPPRMLSPRNQLIRVILYNR

TRLDCPFFGSPIPTLRWFKNGQGSNLDGGNYHVYENGSLEIKMIRKEDQGIYTCVATN

ILGKAENQVRLEVKDPTRTYRMPEDQVARRGTTVQLECRVKHDPSLKLTVYWLKDDEP

LYIGNRMKKEDDSLTIFGVAERDQGSYTCVASTELDQDLAKAYLTVLGRPDRPRDLEL

TDLAERSVRLTWIPGDANNSPITDYVVQFEEDQFQPGVWHDHSKYPGSVNSAVLRLSP

YVNYQFRVIAINEVGSSHPSLPSERYRTSGAPPESNPGDVKGEGTRKNNMEITWTPMN

ATSAFGPNLRYIVKWRRRETREAWNNVTVWGSRYVVGQTPVYVPYEIRVQAENDFGKG

PEPESVIGYSGEDYPRAAPTEVKVRVMNSTAISLQWNRVYSDTVQGQLREYRAYYWRE

SSLLKNLWVSQKRQQASFPGDRLRGWSRLFPYSNYKLEMWVNGRGDGPRSETKEFT

TPEGVPSAPRRFRVRQPNLETINLEWDHPEHPNGIMIGYTLKYVACTFSPVNGTKVGK

QIVENFSPNQTKFTVQRTDPVSRYRFTLSARTQVGSGEAVTEESPAPPNEGRCMAAAP

GVKPPTTVGATGAVSSTDATAIAATTEATTVPIIPTVAPTTMATTTTVATTTTTTAAA

TTTTESPPTTTSGTKIHESGTAHRPCSPAPDEQSTWNVTVLPNSKWANITWKHNFGPG

TDFVVEYIDSNHTKKTVPVKAQAQPIQLTDLYPGMTYTLRVYSRDNEGISNHSRVCFR

PSPPAYTNNQADIATQGWFIGLMCAIALLVLILLIVCFIKRSRGGKYPVREKKDVPLG

PEDPKEEDGSFDYRSLASDEDNKPLQGSQTSLDGTIKQQESDDSLVDYGEGGEGQFNE

DGSFIGQYTVKKDKEETEGNESSEATSPVNAIYSLA

Further analysis of the NOV22a protein yielded the following properties shown in Table 22B.
"~.w.,..,..,~..~....,,...~.~..~~..~~..~,.".
~- ,~",y,~,~YTable 22B~qProtein SequencelProperties NOV22a PSort ~~ 0.4600 probability located in plasma membrane; 0.1000 probability located in analysis: endoplasmic reticulum (membrane); 0.1000 probability located in endoplasmic reticulum (lumen); 0.1000 probability located in outside SignaIP ~ Cleavage site between residues 25 and 26 analysis:
A search of the NOV22a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 22C.

Table 22C. Geneseq Results for NOV22a __ _.__ ___. _ NOV22a Identities/

Geneseq Protein/Organism/Length Residues/SimilaritiesExpect for Identifier[Patent #, Date] Match the Matched Value Residues Region AAM78714 Human protein SEQ ID NO 92..1050 928/959 (96%)0.0 Homo sapiens, 937 aa. 1..937 933/959 (96%) [W0200157190-A2, 09-AUG-2001]

AAM787I ' Human protein SEQ ID 92..1050 928/974 (95%)0.0 NO I 377 - ' Homo Sapiens, 952 aa. 1..952 933/974 (95%) [WO200157190-A2, 09-AUG-2001]

AAW59994 Human neural cell adhesion15..1072 517/1075 0.0 (48%) molecule splice variant 20..1082 708/1075 NrCAMvar (65%) - Homo Sapiens, 1304 aa.

[WO9836062-Al, 20-AUG-1998]

AAU10650 ~ Chicken Nr-CAM protein 12..1054 508/1055 ' 0.0 sequence (48%) '' - Gallus sp, 1268 aa. 12..1042 696/1055 [US6313265- (65%) B1, 06-NOV-2001]

AAB90717 Human C0722_1 protein 15..1060 509/1058 ~ 0.0 sequence (48%) SEQ ID 130 - Homo Sapiens,20..1047 701/1058 1192 (66%) aa. [WO200119988-A1, 22-MAR-In a BLAST search of public sequence databases, the NOV22a protein was found to have homology to the proteins shown in the BLASTP data in Table 22D.

Table 22D. Public BLASTP Results for NOV22a Protein NOV22a Identities/

Residues/ Expect AccessionProtein/Organism/Length Similarities for the Number Matched PortionValue Residues 042414 NEUROFASCIN PRECURSOR 13..13701026/1372 (74%)0.0 - Gallus gallus (Chicken),14..13691148/1372 (82%) 1369 ' aa.

Q91Z60 NEUROFASCIN 155 KDA I..I042 985/1042 (94%) 0.0 ISOFORM - Rattus norvegicus1..1031 1008/1042 (96%) (Rat), 1174 aa.

Q9QVN5 NEUROFASCIN ISOFORM - 25..104296511019 (94%) 0.0 Rattus sp, 1151 aa. 1..1008 987/1019 (96%) Q90924 i NEUROFASCIN PRECURSOR 13..1114844/1114 (75%) 0.0 - Gallus gallus (Chicken),14..1120949/1 114 (84%) aa.

094856 KIAA0756 PROTEIN - Homo 193..1050830/858 (96%) 0.0 Sapiens (Human), 836 1..836 833/858 (96%) as (fragment).

PFam analysis predicts that the NOV22a protein contains the domains shown in the Table 22E.

Table 22E. Domain Analysis of NOV22a Identities/

Pfam omain NOV22a Match RegionSimilarities Expect Value D ~

for the Matched Region ig 56..120 11/68 (16%) 0.032 43/68 (63%) ig 155..215 13/62 (21 %) 0.01 39/62 (63%) ig 278..335 18/61 (30%) 4.3e-11 44/61 (72%) ig 368..427 13/63 (21 %) 2.1 e-OS

~ 44163 (70%) ig 462..520 I 8162 (29%) 1.1 e-07 ~ 45/62 (73%) ig 553..611 19/60 (32%) ~ 5.9e-09 40/60 (67%) fn3 630..716 28/88 (32%) 6.6e-14 64/88 (73%) fn3 729..815 27/92 (29%) 5.9e-07--...

62/92 (67%) fn3 827..922 24/97 (25%) 3.7e-07 66/97 (68%) fn3 934..1026 20/97 (21 %) 2.1 e-08 66/97 (68%) fn3 1134..1213 22/85 (26%) 1.5e-08 56/85 (66%) Example 23.
The NOV23 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 23A.
Table 23A. NOV23 Sequence Analysis SEQ ID NO: 61 X2497 by NOV23a, GCCCCGATGGACGCCGCGTTCCTCCTCGTCCTCGGGCTGTTGGCCCAGAGCCTCTGCC

DNA SequeriCeGCCTGCCCTGAGCCGCGTGCGGAGGGCCTGGGTCATCCCCCCGATCAGCGTATCCGAG

AACCACAAGCGTCTCCCCTACCCCCTGGTTCAGGTGAGCAGGTGGAAGCACCAGTTGG

CCAGCGTCATCTCCAGCATCCAGGGCCCCGGCGTGGATGAGGAGCCCCGGGGCGTCTT

CTCTATCGCCCAGTTCACAGGGAAGGTCTTCCTCAATGCCATGCTGGACCGCGAGAAG

ACTGATCGCTTCAGGCTAAGAGGGTTTGCCCTGGACCTGGGAGGATCCACCCTGGAGG
ACCCCACGGACCTGGAGATTGTAGTTGTGGATCAGAATGACAACCGGCCAGCCTTCCT
GCAGGAGGCGTTCACTGGCCGCGTGCTGGAGGGTGCAGTCCCAGGTACCTATGTGACC
AGGGCAGAGGCCACAGATGCCGACGACCCCGAGACGGACAACGCAGCGCTGCGGTTCT
CCATCCTGCAGCAGGGCAGCCCCGAGCTCTTCAGCATCGACGAGCTCACAGGAGAGAT
CCGCACAGTGCAAGTGGGGCTGGACCGCGAGGTGGTCGCGGTGTACAATCTGACCCTG
CAGGTGGCGGACATGTCTGGAGACGGCCTCACAGCCACTGCTTCAGCCATCATCACCT
TTGATGACATCAATGACAATGCCCCCGAGTTCACCAGGGATGAGTTCTTCATGGAGGC
CATAGAGGCCGTCAGCGGAGTGGATGTGGGACGCCTGGAAGTGGAGGACAGGGACCTG
CCAGGCTCCCCAAACTGGGTGGCCAGGTTCACCATCCTGGAAGGCGACCCCGATGGGC
AGTTCACCATCCGCACGGACCCCAAGACCAACGAGGGTGTTCTGTCCATTGTGAAGGC
CCTGGACTATGAAAGCTGTGAACACTACGAAACTAAAACACACGGGCAGGATAAGACA
GAGAACGCACGGGCAGGGCTGAGGGCTGAGCGGGGCCAGGCCAAGGTCCGCGTGCATG
TGCAGGACACCAACGAGCCCCCCGTGTTCCAGGAGAACCCACTTCGGACCAGCCTAGC
AGAGGGGGCACCCCCAGGCACTCTGGTGGCCACCTTCTCTGCCCGGGACCCTGACACA
GAGCAGCTGCAGAGGCTCAGCTACTCCAAGGACTACGACCCGGAAGACTGGCTGCAAG
TGGACGCAGCCACTGGCCGGATCCAGACCCAGCACGTGCTCAGCCCGGCGTCCCCTTT
CCTCAAGGGCGGCTGGTACAGAGCCATCGTCTTGGCCCAGGATGCCTCCCAGCCCCGC
ACCGCCACCGGCACCCTGTCCATCGAGATCCTGGAGGTGAACGACCATGCACCTGTGC
TGGCCCCGCCGCCGCCGGGCAGCCTGTGCAGCGAGCCACACCAAGGCCCAGGCCTCCT
CCTGGGCGCCACGGATGAGGACCTGCCCCCCCACGGGGCCCCCTTCCACTTCCAGCTG
AGCCCCAGGCTCCCAGAGCTCGGCCGGAACTGGAGCCTCAGCCAGGTCAACCCTCTCT
CCCATCACCGTCTCCACCCAGACCCCCACCTGCCCCATGGCCCCCATTTCATGTCTGT
GGCTCACCAGCTTTTCCCCAGACCCAGCTCCGGAGCCCACAGGCGTGGCCGATGCAGA
AACCTCAGGAAGGTGTGTTGTGAATGTGGGAGGGAGGGTGTGGCGGTCGTGGGCTGTG
CGGGAGTTCTGACTAGGGGAAGTGGGCTCAGCCTGGGCGCACTGGTCATCGTGCTGGC
CAGCGCCCTCCTGCTGCTGGTGCTGGTCCTGCTCGTGGCACTCCGGGCGCGGTTCTGG
AAGCAGTCTCGGGGCAAGGGGCTGCTGCACGGCCCCCAGGACGACCTTCGAGACAATG
~TCCTCAACTACGATGAGCAAGGAGGCGGGGAGGAGGACCAGGACGCCTACGACATCAG
GATGCCCCGCAGGGCCGCCTGCACCCCCAGCCACCCCGAGTGCTGCCCACCAGCCCCC
TGGACATCGCCGACTTCATCAATGATGGCTTGGAGGCTGCAGATAGTGACCCCAGTGT
GCCGCCTTACGACACAGCCCTCATCTATGACTACGAGGGTGACGGCTCGGTGGCGGGG
GAGACTGGGGGCCCCGCTTCGCCCGGCTGGCAGACATGTATGGGCACCCGTGCGGGTT
GGAGTACGGGGCCAGATGGGACCACCAGGCCAGGGAGGGTCTTTCTCCTGGGGCACTG
CTACCCAGACACAGAGGCCGGACAGCCTGACCCTGGGGCGCAACTGGACATGCCACTC
CCC
ORF Start: ATG at 7 ~ ORF Stop: TGA at 2464 SEQ ID NO: 62 819 as MW at 89687.6kD
NOV23a, MDAAFLLVLGLLAQSLCLSLGVPGWRRPTTLYPWRRAPALSRVRRAWVIPPISVSENH
CG105963-Ol KRLPYPLVQVSRWKHQLASVISSIQGPGVDEEPRGVFSIAQFTGKVFLNAMLDREKTD
PTOtelri Se llenCe RFRLRGFALDLGGSTLEDPTDLEIVWDQNDNRPAFLQEAFTGRVLEGAVPGTWTRA
EATDADDPETDNAALRFSILQQGSPELFSIDELTGEIRTVQVGLDREWAVYNLTLQV
ADMSGDGLTATASAIITFDDINDNAPEFTRDEFFMEAIEAVSGVDVGRLEVEDRDLPG
SPNWVARFTILEGDPDGQFTIRTDPKTNEGVLSIVKALDYESCEHYETKTHGQDKTEN
ARAGLRAERGQAKVRVHVQDTNEPPVFQENPLRTSLAEGAPPGTLVATFSARDPDTEQ
LQRLSYSKDYDPEDWLQVDAATGRIQTQHVLSPASPFLKGGWRAIVLAQDASQPRTA
TGTLSIEILEVNDHAPVLAPPPPGSLCSEPHQGPGLLLGATDEDLPPHGAPFHFQLSP
RLPELGRNWSLSQVNPLSHHRLHPDPHLPHGPHFMSVAHQLFPRPSSGAHRRGRCRNL
RKVCCECGREGVAVVGCAGVLTRGSGLSLGALVIVLASALLLLVLVLLVALRARFWKQ
SRGKGLLHGPQDDLRDNVLNYDEQGGGEEDQDAYDISQLRHPTALSLPLGPPPLRRDA
PQGRLHPQPPRVLPTSPLDIADFINDGLEAADSDPSVPPYDTALIYDYEGDGSVAGTL
SSILSSQGDEDQDYDYLRDWGPRFARLADMYGHPCGLEYGARWDHQAREGLSPGALLP
RHRGRTA
Further analysis of the NOV23a protein yielded the following properties shown in Table 23B.

Table 23B. Protein Sequence Properties NOV23au '.~.~~
PSort 0.6850 probability located in endoplasmic reticulum (membrane); 0.6400 analysis: probability located in plasma membrane; 0.4600 probability located in Golgi body; 0.1000 probability located in endoplasmic reticulum (lumen) SignalP Cleavage site between residues 22 and 23 analysis:
A search of the NOV23a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 23C.
Table 23C. Geneseq Results for NOV23a NOV23a Identities!

Geneseq Protein/Organism/Length Residues!Similarities Expect [Patent for Identifier#, Date] Match the Matched Value ResiduesRegion ABG30224 Novel human diagnostic 1..819 750/820 (91%)0.0 protein #30215 - Homo Sapiens, 1..814 766/820 (92%) 814 aa.

[W0200175067-A2, 11-OCT-2001]

ABG30224 Novel human diagnostic 1..819 750/820 (91%)0.0 protein #30215 - Homo Sapiens, I ..814 766/820 (92%) 814 aa.

[W0200175067-A2, 11-OCT-2001]

AAB24089 Human PRO2198 protein sequence1..819 750/820 (91 0.0 %) SEQ ID N0:79 - Homo Sapiens,1..814 766/820 (92%) aa. [WO200053755-A2, 14-SEP-2000]

ABB57233 Mouse ischaemic condition 35..786 313/767 (40%)e-I52 related protein sequence SEQ ID 149..902436/767 (56%) NO:606 -Mus musculus, 906 aa.

[W0200188188-A2, 22-NOV-2001]

AAY70741 Human N-cadherin - Homo 40..786 311/762 (40%)e-151 Sapiens, 906 aa. [W0200021555-A1, 154..902435/762 (56%) APR-2000]
_ .. . _ _ _.. ~ . _... ._..
. .

In a BLAST search of public sequence databases, the NOV23a protein was found to have homology to the proteins shown in the BLASTP data in Table 23D.

Table 23D. Public BLASTP
Results for NOV23a P
t NOV23a Identities/
in ro rrotein/Organism/Length Residues!Similarities Expect e for Accession Number Match the Matched Value Residues Portion P55291 Muscle-cadherin precursor1..819 750/820 (91%)0.0 (M-cadherin) (Cadherin-15) 1..814 766/820 (92%) (Cadherin-14) - Homo Sapiens (Human), aa.

P33146 Muscle-cadherin precursor1..787 616/791 (77%)0.0 (M-cadherin) (Cadherin-15) 1..783 662/791 (82%) (Cadherin-14) - Mus musculus (Mouse), aa.

~~~ M-cadherin - mouse, 730 56..787 576/736 (78%)0.0 IJMSCM as I
(fragment). 1..729 620/736 (83%) ~

Q8UVQ7 N-CADHERIN - Brachydanio 39..786 316/762 (41%)e-157 rerio (Zebrafish) (Zebra danio),~ 140..8894431762 (57%) 893 aa. ~

Q90275 NEURAL-CADHERIN 39..786 315/763 (41%)e-154 PRECURSOR (N-CADHERIN) 29..779 4421763 (57%) -Brachydanio rerio (Zebrafish) I ..~, _~Zebra danio),..783 aa._..
. .

PFam analysis predicts that the NOV23a protein contains the domains shown in the Table 23E.
Table 23E. Domain Analysis of NOV23a Identities/

Pfam Domain NOV23a Match RegionSimilarities Expect Value for the Matched Region cadherin 50..143 23/111 (21%) 0.011 61/I11 (55%) cadherin 157..251 38/108 (35%) 8.7e-25 74/108 (69%) cadherin 265..367 34/107 (32%) 6.2e-18 ~ 74/107 (69%) cadherin 380..473 34/109 (31%) 7.7e-20 ~ 71/109 (65%) Cadherin_C_term634..788 83/158 (53%) 5.3e-90 146/158 (92%) Example 24.
The NOV24 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 24A.
Table 24A. NOV24 Sequence Analysis SEQ ID NO: 63 X3617 by NOV24a, GAGATGGGACTGCAATAGAAATCCGGGCAGCCCGAAGAGGCACCCAGCGCTCCAGCCA

DNA S AGAGCTGGTCCCTGCCCGCGGCCGGAGGAGGGCTAGAGCCCCTGGGCCAGCCCCCCGA

eCluenCe GCCGGCTGGGCGGGCGGGCGGGTGGGAGCAGACGCCGGGCACTGTCACCACGGGTGCG

CCGAGCGCACCGACCCGGGACACGGGCAGCTGGGGACCGCCAGATTCCACCAGCCCCC

CTTGCCCCGCAGGGGTCCTCGGCTCGCGCTCCTGGGTAGCAGCCACCCACCGGGGCGG

AGGGAGATGTCGCCCGGGGCCAGCCGCGGTCCCCGGGGAAGCCAGGCGCCGCTGATCG
i.._......_...~.....~....._____~__~________~____-___._____._.___.___._.
_._.__.

GGCGTTCAACCTGGACGTGGAAAAGCTCACAGTGTACAGCGGCCCCAAGGGCAGCTAC
TTCGGCTACGCCGTGGACTTCCACATACCCGACGCCCGCACAGCGAGTGTCTTGGTGG
GGGCGCCCAAAGCCAACACCAGCCAGCCCGATATCGTGGAAGGGGGAGCCGTCTATTA
CTGTCCTTGGCCCGCGGAGGGGTCTGCGCAGTGCAGGCAGATACCGTTTGACACCACC
AACAACAGAAAGATCAGAGTTAATGGAACCAAAGAACCTATCGAGTTCAAATCCAATC
AGTGGTTTGGAGCAACAGTGAAAGCTCACAAAGGAA.AAGTTGTGGCCTGTGCTCCTTT
ATATCACTGGAGAACTCTTAAACCGACACCAGAA.AAGGACCCAGTTGGCACCTGCTAT
GTAGCAATTCAGAACTTCAGCGCCTATGCCGAGTTCTCTCCTTGCCGGAACAGCAATG
CTGATCCGGAAGGCCAGGGTTACTGCCAAGCAGGATT'TAGTCTGGATTTTTATAAGAA
TGGAGACCTTATTGTGGGAGGACCTGGGAGTTTCTACTGGCAAGGACAAGTGATCACT
GCCAGTGTTGCAGATATCATTGCAAATTACTCATTCAAGGATATCCTCAGGAAACTGG
CAGGAGAAAAGCAGACGGAAGTGGCTCCAGCTTCCTATGATGACAGTTACCTTGGATA
CTCAGTTGCTGCTGGGGAGTTTACTGGGGATTCTCAGCAAGAATTGGTTGCTGGAATT
CCAAGAGGAGCACAGAATTTTGGATATGTTTCCATCATTAACTCTACGGATATGACGT
TTATTCAGAATTTCACGGGAGAACAGATGGCATCTTATTTTGGATATACCGTTGTCGT
ATCAGATGTTAACAGTGATGGACTGGATGATGTCCTGGTTGGGGCACCTCTCTTTATG
GAACGTGAATTTGAGAGCAACCCCAGAGAAGTAGGGCAAATCTACCTGTATTTGCAAG
TGAGCTCTCTCCTCTTCAGAGACCCCCAGATCCTCACTGGCACCGAGACGTTTGGGAG
ATTCGGTAGTGCTATGGCACACTTAGGAGACCTGAACCAAGATGGATACAATGACATT
GCCATCGGAGTGCCTTTTGCAGGCAAGGATCAAAGAGGCAAAGTGCTCATTTATAATG
GGAACAAAGATGGCTTAAACACCAAGCCTTCCCAAGTTCTGCAAGGAGTGTGGGCCTC
ACATGCTGTCCCTTCCGGATTTGGCTTTACTTTAAGAGGAGATTCAGACATAGACAAG
AATGATTACCCAGATTTGATTGT~GGTGCATTTGGAACAGGAAAAGTCGCTGTTTACA
GAGCAAGACCGGTTGTGACTGTAGATGCCCAGCTTCTGCTGCACCCAATGATTATCAA
TCTTGAAAATAAAACTTGCCAGGTTCCAGACTCTATGACATCTGCTGCCTGCTTTTCT
TTAAGAGTATGTGCATCTGTCACAGGCCAGAGCATTGCAAACACAATAGTCTTGATGG
CAGAGGTGCAATTAGATTCCCTGAAACAGAAAGGAGCTATTAAACGGACGCTCTTCCT
TGATAACCATCAGGCTCATCGCGTCTTCCCTCTTGTGATAAAA.AGGCAGAAATCCCAC
CAGTGCCAGGATTTCATCGTTTACCTTCGAGATGAAACTGAATTCCGAGATAAATTAT
CTCCAATCAACATTAGTTTGAATTACAGTTTGGACGAATCCACCTTTAAAGAAGGCCT' GGAAGTGAAACCAATATTGAACTACTACAGAGAAAACATTGTTAGTGAACAGGCTCAC' GACCAGATAAGCATCAGGTAATCATTGGAGATGAA.AATCACCTTATGCTCATAATAAA
TGCAAGAAATGAAGGGGAAGGAGCATATGAAGCTGAACTCTTTGTAATGATACCAGAA
GAGGCAGATTATGTTGGAATCGAACGCAACAACAAGGGATTTCGACCACTGAGCTGTG
AGTACAAGATGGAA.AATGTAACCAGGATGGTGGTGTGTGACCTTGGGAACCCTATGGT
GTCTGGAACAAATTATTCCCTGGGCCTCCGATTTGCAGTTCCACGTCTTGAGAAAACA
AACATGAGCATTAACTTCGATCTCCAAATCAGAAGTTCCAACAAGGACAATCCAGACA
GCAATTTTGTGAGCCTGCAAATCAACATCACTGCTGTAGCGCAGGTGGAAATAAGAGG
AGTGTCACACCCTCCGCAGATTGTTCTGCCCATTCATAACTGGGAACCAGAAGAGGAG
CCCCACAAAGAGGAGGAGGTTGGACCATTGGTGGAACATATTTATGAGCTGCACAATA

TTGGACCAAGTACCATCAGTGACACCATCCTGGAGGTGGGCTGGCCTTTCTCTGCCCFG

GGATGAATTTCTTCTCTATATTTTCCATATTCAAACTCTGGGACCTCTGCAGTGCCAA

CCAAATCCTAATATCAATCCACAGGATATAAAGCCTGCTGCCTCCCCAGAGGACACCC

CTGAGCTCAGCGCCTTTTTGCGAAACTCTACTATTCCTCATCTTGTCAGGAAGAGGGA

TGTACATGTGGTCGAATTCCACAGACAGAGCCCTGCAAAA.ATACTGAATTGTACAAAT

ATCGAGTGTTTACAAATCTCCTGTGCAGTGGGACGACTCGAAGGAGGAGAAAGCGCAG

TCCTGAAAGTCAGGTCACGATTATGGGCCCACACCTTCCTCCAGAGAAAAA.ATGATCC

CTATGCTCTTGCATCCCTGGTGTCCTTTGAAGTTAAGAAGATGCCTTATACAGATCAG

CCAGCAAAACTCCCAGAAGGAAGCATAGTAATTAAGACATCAGTTATTTGGGCAACTC

CGAATGTTTCCTTCTCAATCCCATTATGGGTAATAATACTAGCAATACTTCTTGGATT

GTTGGTTCTCGCCATTTTAACCTTAGCTTTATGGAAGTGTGGATTCTTTGACAGAGCC

AGACCTCCTCAGGAGGACATGACCGACAGGGAACAGCTGACAAATGACAAGACCCCTG

AGGCATGACAAGF,~~AAAAAAAGAAGACCAAAGACCTCAAACACTGGTCCTGTTCAAAG

AAAAAGAAAGAACATGAGGCC

ORF Start: ATG at 355 ORF Stop: TGA at 3544 SEQ ID NO: 64 1063 as MW at 117472.3kD

NOV24a, MSPGASRGPRGSQAPLIAPLCCAAAALGMLLWSPACQAFNLDVEKLTVYSGPKGSYFG

PPOtelri SeCllleriCeRKIRVNGTKEPIEFKSNQWFGATVKAHKGKVVACAPLYHWRTLKPTPEKDPVGTCYVA

IQNFSAYAEFSPCRNSNADPEGQGYCQAGFSLDFYKNGDLIVGGPGSFYWQGQVITAS

VADIIANYSFKDILRKLAGEKQTEVAPASYDDSYLGYSVAAGEFTGDSQQELVAGIPR

GAQNFGYVSIINSTDMTFIQNFTGEQMASYFGYTVVVSDVNSDGLDDVLVGAPLFMER

EFESNPREVGQIYLYLQVSSLLFRDPQILTGTETFGRFGSAMAHLGDLNQDGYNDIAI

GVPFAGKDQRGKVLIYNGNKDGLNTKPSQVLQGVWASHAVPSGFGFTLRGDSDIDKND

YPDLIVGAFGTGKVAVYRARPVVTVDAQLLLHPMIINLENKTCQVPDSMTSAACFSLR

VCASVTGQSIANTIVLMAEVQLDSLKQKGAIKRTLFLDNHQAHRVFPLVIKRQKSHQC

QDFIVYLRDETEFRDKLSPINISLNYSLDESTFKEGLEVKPILNYYRENIVSEQAHIL

VDCGEDNLCVPDLKLSARPDKHQVIIGDENHLMLIINARNEGEGAYEAELFVMIPEEA

DYVGIERNNKGFRPLSCEYKMENVTRMVVCDLGNPMVSGTNYSLGLRFAVPRLEKTNM

SINFDLQIRSSNKDNPDSNFVSLQINITAVAQVEIRGVSHPPQIVLPIHNWEPEEEPH

KEEEVGPLVEHIYELHNIGPSTISDTILEVGWPFSARDEFLLYIFHIQTLGPLQCQPN

PNINPQDIKPAASPEDTPELSAFLRNSTIPHLVRKRDVHWEFHRQSPAKILNCTNIE

CLQISCAVGRLEGGESAVLKVRSRLWAHTFLQRKNDPYALASLVSFEVKKMPYTDQPA

KLPEGSIVIKTSVIWATPNVSFSIPLWVIILAILLGLLVLAILTLALWKCGFFDRARP

PQEDMTDREQLTNDKTPEA

SEQ ID NO: 65 .3617 by ~

NOV24b, GAGATGGGACTGCAATAGAAATCCGGGCAGCCCGAAGAGGCACCCAGCGCTCCAGCCA

CG105973-02 CCAGCTGGGCCGCCCGGGAGTCCCTGGCTCTAGACCAGCCGCGAGGAGGCGCCGCGAG' DNA S AGAGCTGGTCCCTGCCCGCGGCCGGAGGAGGGCTAGAGCCCCTGGGCCAGCCCCCCGA' 8Ch1eriC8 GCCG
CT
' G
GGGCGGGCGGGCGGGTGGGAGCAGACGCCGGGCACTGTCACCACGGGTGCG

CCGAGCGCACCGACCCGGGACACGGGCAGCTGGGGACCGCCAGATTCCACCAGCCCCCi ' CTTGCCCCGCAGGGGTCCTCGGCTCGCGCTCCTGGGTAGCAGCCACCCACCGGGGCGG

AGGGAGATGTCGCCCGGGGCCAGCCGCGGTCCCCGGGGAAGCCAGGCGCCGCTGATCG

CGCCCCTCTGCTGCGCCGCGGCCGCGCTGGGGATGTTGCTGTGGTCCCCCGCCTGTCA

GGCGTTCAACCTGGACGTGGAAAAGCTCACAGTGTACAGCGGCCCCAAGGGCAGCTAC

TTCGGCTACGCCGTGGACTTCCACATACCCGACGCCCGCACAGCGAGTGTCTTGGTGG

GGGCGCCCAAAGCCAACACCAGCCAGCCCGATATCGTGGAAGGGGGAGCCGTCTATTA

CTGTCCTTGGCCCGCGGAGGGGTCCGCGCAGTGCAGGCAGATACCGTTTGACACCACC

AACAACAGAAAGATCAGAGTTAATGGAACCAAAGAACCTATCGAGTTCAAATCCAATC

AGTGGTTTGGAGCAACAGTGAAAGCTCACAAAGGAAAAGTTGTGGCCTGTGCTCCTTT

ATATCACTGGAGAACTCTTAAACCGACACCAGAAAAGGACCCAGTTGGCACCTGCTAT

GTAGCAATTCAGAACTTCAGCGCCTATGCCGAGTTCTCTCCTTGCCGGAACAGCAATG

CTGATCCGGAAGGCCAGGGTTACTGCCAAGCAGGATTTAGTCTGGATTTTTATAAGAA

TGGAGACCTTATTGTGGGAGGACCTGGGAGTTTCTACTGGCAAGGACAAGTGATCACT

GCCAGTGTTGCAGATATCATTGCAAATTACTCATTCAAGGATATCCTCAGGAAACTGG

CAGGAGAAAAGCAGACGGAAGTGGCTCCAGCTTCCTATGATGACAGTTACCTTGGATA

CTCAGTTGCTGCTGGGGAGTTTACTGGGGATTCTCAGCAAGAATTGGTTGCTGGAATT

CCAAGAGGAGCACAGAATTTTGGATATGTTTCCATCATTAACTCTACGGATATGACGT

TTATTCAGAATTTCACGGGAGAACAGATGGCATCTTATTTTGGATATACCGTTGTCGT
ATCAGATGTTAACAGTGATGGACTGGATGATGTCCTGGTTGGGGCACCTCTCTTTATG
GAACGTGAATTTGAGAGCAACCCCAGAGAAGTAGGGCAAATCTACCTGTATTTGCAAG
TGAGCTCTCTCCTCTTCAGAGACCCCCAGATCCTCACTGGCACCGAGACGTTTGGGAG
ATTCGGTAGTGCTATGGCACACTTAGGAGACCTGAACCAAGATGGATACAATGACATT
GCCATCGGAGTGCCTTTTGCAGGCAAGGATCAAAGAGGCAAAGTGCTCATTTATAATG
GGAACAAAGATGGCTTAAACACCAAGCCTTCCCAAGTTCTGCAAGGAGTGTGGGCCTC
ACATGCTGTCCCTTCCGGATTTGGCTTTACTTTAAGAGGAGATTCAGACATAGACAAG
AATGATTACCCAGATTTGATTGTGGGTGCATTTGGAACAGGAAAAGTCGCTGTTTACA
GAGCAAGACCGGTTGTGACTGTAGATGCCCAGCTTCTGCTGCACCCAATGATTATCAA
TCTTGAAAATAAAACTTGCCAGGTTCCAGACTCTATGACATCTGCTGCCTGCTTTTCT
TTAAGAGTATGTGCATCTGTCACAGGCCAGAGCATTGCAAACACAATAGTCTTGATGG
CAGAGGTGCAATTAGATTCCCTGAAACAGAAAGGAGCTATTAAACGGACGCTCTTCCT
TGATAACCATCAGGCTCATCGCGTCTTCCCTCTTGTGATAAAAAGGCAGAAATCCCAC
CAGTGCCAGGATTTCATCGTTTACCTTCGAGATGAAACTGAATTCCGAGATAAATTAT
CTCCAATCAACATTAG'T'TTGAATTACAGTTTGGACGAATCCACCTTTAAAGAAGGCCT
GGAAGTGAAACCAATATTGAACTACTACAGAGAAAACATTGTTAGTGAACAGGCTCAC
ATTCTGGTGGACTGTGGAGAAGACAATCTGTGTGTTCCTGACTTGAAGCTGTCGGCTA
GACCAGATAAGCATCAGGTAATCATTGGAGATGAAAATCACCTTATGCTCATAATAAA
TGCAAGAAATGAAGGGGAGGGAGCATATGAAGCTGAACTCTTTGTAATGATACCAGAA
GAGGCAGATTATGTTGGAATCGAACGCAACAACAAGGGATTTCGACCACTGAGCTGTG
AG'T'ACAAGATGGAAAATGTAACCAGGATGGTGGTGTGTGACCTTGGGAACCCTATGGT
GTCTGGAACAAATTATTCCCTGGGCCTCCGATTTGCAGTTCCACGTCTTGAGAAAACA
AACATGAGCATTAACTTCGATCTCCAAATCAGAAGTTCCAACAAGGACAATCCAGACA
GCAATTTTGTGAGCCTGCAAATCAACATCACTGCTGTAGCGCAGGTGGAAATAAGAGG
AGTGTCACACCCTCCGCAGATTGTTCTGCCCATTCATAACTGGGAACCAGAAGAGGAG
CCCCACAAAGAGGAGGAGGTTGGACCATTGGTGGAACATATTTATGAGCTGCACAATA
TTGGACCAAGTACCATCAGTGACACCATCCTGGAGGTGGGCTGGCCTTTCTCTGCCCG' GGATGAATTTCTTCTCTATATTTTCCATATTCAAACTCTGGGACCTCTGCAGTGCCAA
CCAAATCCTAATATCAATCCACAGGATATAAAGCCTGCTGCCTCCCCAGAGGACACCC' CTGAGCTCAGCGCCTTTTTGCGAAACTCTACTATTCCTCATCTTGTCAGGAAGAGGGA
TGTACATGTGGTCGAATTCCACAGACAGAGCCCTGCAAAAATACTGAATTGTACAAAT' TCCTGAAAGTCAGGTCACGATTATGGGCCCACACCTTCCTCCAGAGAAAAAATGATCC
CTATGCTCTTGCATCCCTGGTGTCCTTTGAAGTTAAGAAGATGCCTTATACAGATCAG
CCAGCAAAACTCCCAGAAGGAAGCATAGCAATTAAGACATCAGTTATTTGGGCAACTC
CGAATGTTTCCTTCTCAATCCCATTATGGGTAATAATACTAGCAATACTTCTTGGATT
GTTGGTTCTCGCCATTTTAACCTTAGCTTTATGGAAGTGTGGATTCTTTGACAGAGCC
AGGCATGACAAGF~3AAAAAAAGAAGACCAAAGACCTCAAACACTGGTCCTGTTCAAAG
AAAAAGAAAGAACATGAGGCC
ORF Start: ATG at 355 ORF Sto : TGA at 3544 ~EQ ID NO: 66~~~1063 as p yM~W at 117444.2kD
NOV24b, MSPGASRGPRGSQAPLIAPLCCAAAALGMLLWSPACQAFNLDVEKLTVYSGPKGSYFG

PTOtelri SeCllleriCe RKIRVNGTKEPIEFKSNQWFGATVKAHKGKWACAPLYHWRTLKPTPEKDPVGTCYVA
IQNFSAYAEFSPCRNSNADPEGQGYCQAGFSLDFYKNGDLIVGGPGSFYWQGQVITAS
VADIIANYSFKDILRKLAGEKQTEVAPASYDDSYLGYSVAAGEFTGDSQQELVAGIPR
GAQNFGYVSIINSTDMTFIQNFTGEQMASYFGYTVWSDVNSDGLDDVLVGAPLFMER
EFESNPREVGQIYLYLQVSSLLFRDPQILTGTETFGRFGSAMAHLGDLNQDGYNDIAI
GVPFAGKDQRGKVLIYNGNKDGLNTKPSQVLQGVWASHAVPSGFGFTLRGDSDTDKND
YPDLIVGAFGTGKVAVYRARPVVTVDAQLLLHPMIINLENKTCQVPDSMTSAACFSLR
VCASVTGQSIANTTVLMAEVQLDSLKQKGAIKRTLFLDNHQAHRVFPLVIKRQKSHQC
QDFIVYLRDETEFRDKLSPINISLNYSLDESTFKEGLEVKPILNYYRENIVSEQAHIL
VDCGEDNLCVPDLKLSARPDKHQVIIGDENHLMLIINARNEGEGAYEAELFVMIPEEA
DYVGIERNNKGFRPLSCEYKMENVTRMWCDLGNPMVSGTNYSLGLRFAVPRLEKTNM
SINFDLQIRSSNKDNPDSNFVSLQINITAVAQVEIRGVSHPPQIVLPIHNWEPEEEPH
KEEEVGPLVEHIYELHNIGPSTISDTILEVGWPFSARDEFLLYIFHTQTLGPLQCQPN' PNINPQDIKPAASPEDTPELSAFLRNSTIPHLVRKRDVHWEFHRQSPAKIT.~NCTNIE;

CLQISCAVGRLEGGESAVLKVRSRLWAHTFLQRKNDPYALASLVSFEVKKMPYTDQPA
KLPEGSIAIKTSVIWATPNVSFSIPLWVIILAILLGLLVLAILTLALWKCGFFDRARP
PQEDMTDREQLTNDKTPEA
Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 24B.
Table 24B. Comparison of NOV24a against NOV24b.
Protein Sequence NOV24a Residues/ Identities/
Match Residues ~ Similarities for the Matched Region NOV24b 1..1063 1010/1063 (95%) 1..1063 1010/1063 (95%) Further analysis of the NOV24a protein yielded the following properties shown in Table 24C.
Table 24C. Protein Sequence Properties NOV24a PSort 0.4600 probability located in plasma membrane; 0.1125 probability located in analysis: microbody (peroxisome); 0.1000 probability located in endoplasmic reticulum (membrane); 0.1000 probability located in endoplasmic reticulum (lumen) SignalP Cleavage site between residues 39 and 40 analysis:
A search of the NOV24a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 24D.

_... ... . ~ - Table 24D. Geneseq . __ Results for NOV24a ._.. .~.
.. . _. ~. ... . .._ .~.
. _ .

NOV24a Identities/

Geneseq Protein/Organism/Length ' Residues/Similarities Expect for Identifier(Patent #, Date] Match the Matched Value Residues Region AAM39241 Human polypeptide SEQ 29..1063 1031/1035 (99%)0.0 ID NO , 2386 - Homo Sapiens, 10351..1035 1031/1035 (99%) aa.

[W0200153312-A1, 26-JUL-2001 ]

AAM41027 Human polypeptide SEQ 24..1063 1024/1046 (97%)0.0 ID NO

5958 - Homo Sapiens, 1044~ 1..10441027/1046 (97%) aa.

[W0200153312-Al, 26-JUL-2001]

.xxr 3 ABG18895 Novel human diagnostic 8..1055 0.0 protein 500/1052 (47%) ' #18886 - Homo sapiens, 25..1049 692/1052 (65%) 1061 aa.

[W0200175067-A2, 11-OCT-2001 ]
I

ABG18895 Novel human diagnostic 8..1055 500/1052 (47%)0.0 protein #18886 - Homo sapiens, 25..1049 692/1052 (65%) 1061 aa.

_ [W0200175067-A2, 11-OCT-2001~

AAB70508 Tissue remodeling protein34..1063 474/1036 (45%)0.0 alpha 5 beta 1 integrin (VLA-5) 37..1049 667/1036 (63%) protein -Mammalian, 1049 aa.

[W0200111086-A2, 15-FEB-2001 ]

In a BLAST search of public sequence databases, the NOV24a protein was found to have homology to the proteins shown in the BLASTP data in Table 24E.

Table 24E. Public BLASTP
Results for NOV24a NOV24a Identities/

Protein AccessionProtein/Organism/Length Residues/Similarities Expect for Number Match the Matched Value ResiduesPortion P53708 Integrin alpha-8 -Homo 39..10631020/1025 (99%)0.0 Sapiens (Human), 1025 aa. 1..1025 1020/1025 (99%) 070304 INTEGRIN ALPHA8 - Mus 46..1057910/1012 (89%)0.0 musculus (Mouse), 1012 1..1012 972/1012 (95%) as (fragment).

P26009 Integrin alpha-8 precursor27..1063797/1037 (76%)0.0 - Gallus ~

gallus (Chicken), 1044 13..1044907/1037 (86%) aa.

P26008 Integrin alpha-V precursor35..1055493/1024 (48%)0.0 (Vitronectin receptor 16..1022678/1024 (66%) alpha subunit) (CD51) - Gallus gallus (Chicken), 1034 aa.

Q9MZD6 INTEGRIN ALPHA V SUBUNIT 8..1055 508/1057 (48%)0.0 PRECURSOR - Bos taurus 12..1035692/1057 (65%) (Bovine), 1047 aa.

PFam analysis predicts that the NOV24a protein contains the domains shown in the Table 24F.
Table 24F. Domain Analysis of NOV24a Identities/

Pfam DomainNOV24a Match RegionSimilarities Expect . Value for the Matched Region FG-GAP 54..117 22/67 (33%) 1.4e-15 a .
53/67 (79%) FG-GAP 264..317 19/63 (30%) 2.1e-06 42/63 (67%) FG-GAP 318..383 23/66 (35%) 1.7e-15 _49/66.(74%) .. . .

FG-GAP 384..443 29/67 (43%) 2e-16 53/67 (79%) FG-GAP 447..501 22/66 (33%) 7.8e-10 41/66 (62%) integrin_A 1035..1049 10/15 (67%) 0.00011 14/15 (93%) Example 25.
The NOV2S clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 2SA.
Table 25A. NOV2S Sequence Analysis SEQ ID N067 ~~ , ,1 S24 by NOV2Sa, TTTGCCATCATGTTGCGGTTGGTGGCAGCTTGCCCTGAGTCATGTGTGGTGTGCACCA

CG106915-O1 ~GATGTAACCCTCTGTCACCAGCTAACCTATATAGTAGCAGCCCCTATGACCACGAG

DNA SequenceGGTTTTAATCATCACCGATGGATATCTCTCCTCTATTGAGAGCACAAACCTGTCTCTC

TTGTTTAATCTTGCCCTGCTCTCCCTAAGCAGAAATGGTATCGAGGATGTTCAGGAAG

ATGCCCTGCATGGGCTTACGATGTTGCGGACCTTGTTGCTGGAGCACAACCAAATATC

CAGCTCTTCGCTCACTGATCACACCTTCAGCAAGCTTCACAGCCTGCAGGTACTGGTG

CTGAGCAATAATGCTCTCCGCACCCTACGAGGGTCTTGGTTCCGAAACACAAGCGGCC

TGACCCGGCTCCAGCTGGATGGGAATCAGATTACTAATCTCACAGACAGT~CTTTCGG

AGGCACGAATCTCCACAGTCTCAGGTATCTGGATTTATCCAACAATTTTATTTCCTAC

ATTGGGAAAGATGCCTTCCGGCCCCTGCCTCAACTACAGGAAGTGGACCTTTCCCGAA

ATAGGTTAGCCCACATGCCGGATGTGTTTACTCCACTGAAGCAGTTAATCCTTCTGAG

CTTAGATAAGAACCAGTGGAGCTGCACTTGTGATCTCCATCCCCTTGCTCGGTTTTTA

AGAAACTACATTAAGTCTTCTGCTCACACGCTCAGGAATGCCAAGGACCTAAATTGCC

AGCCATCTACCGCAGCTGTGGCAGCTGCACAGAGTGTGCTGAGGCTGTCTGAGACCAA

CTGTGATTCCAAAGCTCCCAACTTCACTCTGGTTCTAAAGGACAGAAGTCCCCTCCTC

CCAGGACCAGATGTGGCCCTGCTGACTGTCCTTGGCTTCGCAGGTGCTGTTGGTCTCA

CTTGCCTAGGTTTAGTTGTATTTAACTGGAAACTCCACCAAGGCAAAGCAAATGAACA

CACATCAGAAAACCTTTGTTGCAGAACCTTCGATGAACCCCTGTGTGCTCATGAGGCA

AGAAATTACCACACTAAGGGATACTGCAACTGCCACTTAACTCAGGAAAACGAGATAA

AGGTCATGTCCATTGTGGGGTCCAGAAAAGAAATGCCACTTTTACAGGAAAATAGCCA

TCAAGCAACATCGGCCTCTGAGTCTGCAACCCTTGACAGATCATTTAGAAACCTGAAA

AAGAAAGACCGTGGGGTAGGCAGCACTTTATTTTGCCAGGATGGTAGATTGCTGCATT

CGGAATGTTCAGAGCCTCCTGGAAATATGAGAGCTTTTAATGAAGCAGGCTTACTTAC

AACATATAATCCAAGGAAAGTTCAAAAGCTATGGAATCTTGAGCCTGGAGAAGTCCAG

CCTCAAACTCTGCAACACCATATAATAAGAACAGAAGATATCAGCAGTGACATATTTA

GAAGAAGATATGCAACACCCGCTTCAGCCTTGGCAGGAGAAAGTCTTGAGAAGCGTTT

AACAAATGAATCATGA

ORF Start: ATG at 10 ORF Stop: TGA at 1 S22 SEQ ID NO: 68 S04 as MW at 56079.2kD

NOV2Sa, MLRLVAACPESCVVCTKDVTLCHQLTYIVAAPMTTRVLIITDGYLSSIESTNLSLLFN

CG106915-Ol L~'LSLSRNGIEDVQEDALHGLTMLRTLLLEHNQISSSSLTDHTFSKLHSLQVLVLSN

P1'Oteln N~'RTLRGSWFRNTSGLTRLQLDGNQITNLTDSSFGGTNLHSLRYLDLSNNFISYIGK
Sequence DAFRPLPQLQEVDLSRNRLAHMPDVFTPLKQLILLSLDKNQG~TSCTCDLHPLARFLRNY

IKSSAHTLRNAKDLNCQPSTAAVAAAQSVLRLSETNCDSKAPNFTLVLKDRSPLLPGP

DVALLTVLGFAGAVGLTCLGLVVFNWKLHQGKANEHTSENLCCRTFDEPLCAHEARNY

HTKGYCNCHLTQENEIKVMSIVGSRKEMPLLQENSHQATSASESATLDRSFRNLKKKD

RGVGSTLFCQDGRLLHSECSEPPGNMRAFNEAGLLTTYNPRKVQKLWNLEPGEVQPQT

LQHHTIRTEDISSDIFRRRYATPASALAGESLEKRLTNES

S Further analysis of the NOV2Sa protein yielded the following properties shown in Table 2SB.
Table 2513. Protein Sequence Properties NOV25a analysis: probability located in plasma membrane; 0.3000 probability located in microbody (peroxisome); 0.2622 probability located in mitochondria) matrix space SignalP No Known Signal Sequence Predicted analysis:
A search of the NOV25a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 25C.
Table 25C. Geneseq Results for NOV25a NOV25a Identities/
~

Geneseq ProteinlOrganismlLength Residues/SimilaritiesExpect ' ~ for Identifier[Patent #, Date] Match the Matched Value Residues Region AAU83655 Human PRO protein, Seq 3..237 79/264 (29%)1 Se-19 ID No 128 - Homo sapiens, 473 22..283 1211264 (44%) aa.

[W0200208288-A2, 31-JAN-2002]

AAB49891 Human PR0526 protein sequence3..237 79/264 (29%)~ Se-19 -Homo Sapiens, 473 aa. 22..283 121/264 (44%) [W0200070050-Al, 23-NOV-2000]

AAB50908 Human PR0526 protein - 3..237 79/264 (29%)Se-19 Homo Sapiens, 473 aa. [W0200073452-22..283 121/264 (44%) A2, 07-DEC-2000]

AAU04589 Human Nogo receptor - 3..237 79/264 (29%)Se-19 Homo ~ ~

Sapiens, 473 aa. [W0200151520-22..283 121/264 (44%) A2, 19-JUL-2001 ]

AAU12362 Human PRO526 polypeptide 3..237 79/264 (29%)~ Se-19 sequence - Homo Sapiens, 22..283 121/264 (44%) 473 aa.

[WO200140466-A2, 07-JUN-2001 ]

In a BLAST search of public sequence databases, the NOV25a protein was found to have homology to the proteins shown in the BLASTP data in Table 25D.

Table 25D. Public BLASTP Results for NOVZSa Protein NOV25a Identities/

AccessionProtein/Or anism/Len th Residues/Similarities; Expect g g for Match the Matched Value Number ResiduesPortion __ ___ ___ ~
~

Q9BGY6 HYPOTHETICAL 56.5 I~DA 1..504 478/504 (94%)0.0 PROTEIN - Maraca fascicularis1..504 481/504 (94%) (Crab eating macaque) (Cynomolgus monkey), 510 aa.

Q961X3 GH01279P - Drosophila ~ 45..233 68/212 (32%)~ 3e-21 melanOgaster (Fruit fly), 313..522103/212 (48%) 615 aa.

Q9NOE3 ~ UNNAMED PROTEIN PRODUCT 3..237 82/264 (31%)~ 1e-19 - Maraca fascicularis (Crab22..283 125/264 (47%) eating macaque) (Cynomolgus monkey), 473 aa.

Q9VZ84 CG7509 PROTEIN - Drosophila45..233 69/230 (30%)6e-19 ~ melanogaster (Fruit fly),313..540103/230 (44%) 633 aa.

Q9BZR6 NOGO RECEPTOR - Homo 3..237 79/264 (29%)~ 1 e-I

sapiens (Human), 473 aa. 22..283 121/264 (44%)f PFam analysis predicts that the NOV25a protein contains the domains shown in the Table 25E.
Table 25E. Domain Analysis of NOV25a Identities/

Pfam Domain NOV25a Match RegionSimilarities Expect Value for the Matched Region LRR 58..81 7/25 (28%) 0.3 19/25 (76%) LRR 108..131 10/25 (40%) 0.11 19/25 (76%) LRR 132..155 8/25 (32%) 0.7 18/25 (72%) LRR 158..181 11/25 (44%) 0.00021 19/25 (76%) LRR 182..204 10/25 (40%) 0.093 18/25 (72%) LRRCT 214..270 15/63 (24%) 0.046 42/63 (67%) Examule 26.
The NOV26 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 26A.
Table 26A. NOV26 Sequence Analysis SEQ ID NO: 69 X3757 by NOV26a, ~CTCTTTGCCATCATGTTGCGGTTGGTGGCAGCTTGCCCTGAGTCATGTGTGGTGTGCA
CG106924-Ol CCAAAGATGTAACCCTCTGTCACCAGCTAACCTATATAGTAGCAGCCCCTATGACCAC
DNA Sequence GAGGGTTTTAATCATCACCGATGGATATCTCTCCTCTATTGAGAGCACAAACCTGTCT
CTCTTGTTTAATCTTGCCCTGCTCTCCCTAAGCAGAAATGGTATCGAGGATGTTCAGG
AAGATGCCCTGCATGGGCTTACGATGTTGCGGACCTTGTTGCTGGAGCACAACCAAAT
ATCCAGCTCTTCGCTCACTGATCACACCTTCAGCAAGCTTCACAGCCTGCAGGTACTG
GTGCTGAGCAATAATGCTCTCCGCACCCTACGAGGGTCTTGGTTCCGAAACACAAGCG
GCCTGACCCGGCTCCAGCTGGATGGGAATCAGATTACTAATCTCACAGACAGTTCTTT
CGGAGGCACGAATCTCCACAGTCTCAGGTATCTGGATTTATCCAACAATTTTATTTCC
TACATTGGGAAAGATGCCTTCCGGCCCCTGCCTCAACTACAGGAAGTGGACCTTTCCC
GAAATAGGTTAGCCCACATGCCGGATGTGTTTACTCCACTGAAGCAGTTAATCCTTCT
GAGCTTAGATAAGAACCAGTGGAGCTGCACTTGTGATCTCCATCCCCTTGCTCGGTTT
TTAAGAAACTACATTAAGTCTTCTGCTCACACGCTCAGGAATGCCAAGGACCTAAATT
GCCAGCCATCTACCGCAGCTGTGGCAGCTGCACAGAGTGTGCTGAGGCTGTCTGAGAC
CAACTGTGATTCCAAAGCTCCCAACTTCACTCTGGTTCTAAAGGACAGAAGTCCCCTC
CTCCCAGGACCAGATGTGGCCCTGCTGACTGTCCTTGGCTTCGCAGGTGCTGTTGGTC
TCACTTGCCTAGGTTTAGTTGTATTTAACTGGAAACTCCACCAAGGCAAAGCAAATGA
T ..T ~r ~.,T..,nr ~r m a T ....~,..,..,~...,..,e-.,.r ~T T
..~..,..,~.,.._..,~_ T ..,.,......,..,...~.,...~...w_ ...~._ GCAAGAAATTACCACACTAAGGGATACTGCAACTGCCACTTAACTCAGGAAAACGAGA
TAAAGGTCATGTCCATTGTGGGGTCCAGAAAAGAAATGCCACTTTTACAGGAAAATAG
CCATCAAGCAACATCGGCCTCTGAGTCTGCAACCCTTGACAGATCATTTAGAAACCTG
AA.AAAGAAAGACCGTGGGGTAGGCAGCACTTTATTTTGCCAGGATGGTAGATTGCTGC
ATTCGGAATGTTCAGAGCCTCCTGGAAATATGAGAGCTTTTAATGAAGCAGGCTTACT
TACAACATATAATCCAAGGAAAGTTCAAAAGCTATGGAATCTTGAGCCTGGAGAAGTC
CAGCCTCAA.ACTCTGCAACACCATATAATAAGAACAGAAGATATCAGCAGTGACATAT
TTAGAAGAAGATATGCAACACCCGCTTCAGCCTTGGCAGGAGAAAGTCTTGAGAAGCG
TTTAACAAATGAATCATGGCAGCCTCCAATAGAAAAAGAAGACAATGGCTTACACCCT
CACAGGCAAAGACATTTTATTACAAGCTCATCATCCAAGCCTTGTGAGCCTGAGGAAC
ACTATGTACAAAATATCGTACAAAAAAATAGATCAAAATATGATGATCCTTGTGGACT
GTTAAAACAGAGCAAACCTAGGTATTTTCAGCCAAACAATTCTCTTATCTGTAAATAT
GTGCCCTGTGAGCAATTTGAAGATTACATGAAAGAAAAGAAGCCAAATCGTAGACAAC
ACTCAAAGCCTGAGAAAGAGCAAATCCAAATTAACAGTGCAATAGAAAAATTTCTTAT
GAGTGAGGACAACATAGATTTATCAGGATTATCAACAAAAACCAAGAAAGCATATTCC
CCAAAGAGGGTTATCTTCCATGATCCTGATTTAGTAGAAATAAATAGGTCGATGATGT
CACCCAAAATATCAACCCCTTGGAAACGACAGAAAAATCAAAGTAACCAACTGACTAA
GTTGGATGTTAAAAAATTTAGCAACACTGGGGAGAGAAACAAAGGAGAA.AAATGGTTT
ACTAATTCATGGGTTCTGAAAAGGAAGAGAACCCCTCAGTCTGACCTCAAAGGGAAAA
TTAAAGGACAAAACTTAAAATTAAATTTACATCCTTTTAGAAAAGTCAGAGTCCATCC
AGAAAAATCCTTGTCAAGTCTCCCAAAGCAATGCAAGCAGGTATTGTTGCCTCCTAAG
AAATTATCCAAAACTTCTGAGACAGAAGCCAA.AATAAATACTGTGTGTTCTGCAGATT
TTCTTCAACAGTCAGAGAGTAGCAACTATGTTAGACTCACTTCAAAGAGGCTGCCTCT' GAAACATGACTCAAAGCAGACCCCATATTATCAACGAAACACTAAACGTGCCCCCCTG
CTCAGTGCTAACAACTTGCGTGTAGTCAACCAGAGCTCTATAGAAAGCAGCTGTTACT
CAGCTGGCCACATTCCTGATGGAAACACATCAAAATTGCCCCAACCTACACCCACTGA' TGCTGAGCACAGGCACTCACATTCTCAATTCTCAACTGAGCAAATGGAAGATGCAACT';
CAGCTTGAATCAAAAGTGCTTAGTTATTTAGCAACTACTTGGGAAAT1TACAGGAAGTG~, ATGTTTTACCATTCCAACATTCCAGGAGGGCTACTGACCAAGGGACAACGGAGTCCACj TGAGCACATGGGACAGAATGTATCAAAGACCAGTGAGTTAAATCAGTTTTCTTTGTCC' CCGAGGAATCAAACACAACTTTTAGATGCTCACAAGACTGACAGCTACAACAAGGAAT

~ACACTTTAGACCAAAATGAAGGCTTACAACACAGAGAGCAAAATTCAAGTCATGCACA

GCTTGAAAATAAAGAAAA.AACATTAATGACAAAACCCCAAATACCACATCAAATTGTG

GAAAATTGTATTATGGATAAGGAAGAAAATGATGTAGAAAAAAAACTTTCAAA.AACAG

AAACTTATGATTCCTCTCTCATTCCCCAAACACAATCCAAGAACAACCTATCATTTAT

GAAGACAAATTCAATTCCATACCAAAATAGAATAGAACTTCCCAAGGATATCAGTACT

TCTCCTGTTAGTAGTCAAGCCGTTTGGCACCTAACCAATAGTAGCGAAAAAGGAATTG

ACAGCACAAATGCATTGCCCAGAAATGACGGCACTGAAGCACTAGAGATAAAAATAGT

AGGGAAAGAAGAGAAAAATATGCTTGATGAAAGCAAGACAGATTCTAGTATGTTAACT

CAGATCTCACAAATGACCTTAAAAGGCATCACAAAAGAAAGGCAGCAAACTTGGGAAA

ATGGAACAAGTGAAAAATATATATTACATGATGCAAGCTCTGCCGAGGAGACCATTAC

AGCTAAAGATTTAAGTATCACAAGTTCCCATGAAACCCAAAATAGAATACTTTGCAGT

GAAGTAGATCCTGAAGTTAACAGTAATGTACATAATTTTAGAGAAGTTCAAAATATTC

AACCAGATAAAGATAGGGCACATAAAGAAGGCGCAATGACAGTGGAGACACATGAAGC

GCTTTCCTTCTTACCAGGGTTAAAAGACAGTTTTGAGGCAGAAAATGAGGTGTTTTTA

GTTCCTAGCAGAATAAATGAAGCTGAAAACTCTGCTCCAAAACCTGTACTGTATCCAC

CATCTGCTGAATATGCTACTACATCACCTTTAGAAACAGAATAAA

ORF Start: ATG at 13 ORF Stop: TAA at 3754 SEQ ID NO: 70 1247 as MW at 140902.2kD
y NOV26a, MLRLVAACPESCWCTKDVTLCHQLTYIVAAPMTTRVLIITDGYLSSIESTNLSLLFN

CG106924-Ol I'~'LSLSRNGIEDVQEDALHGLTMLRTLLLEHNQISSSSLTDHTFSKLHSLQVLVLSN

Protein SequenceN~'RTLRGSWFRNTSGLTRLQLDGNQITNLTDSSFGGTNLHSLRYLDLSNNFISYIGK

DAFRPLPQLQEVDLSRNRLAHMPDVFTPLKQLILLSLDKNQWSCTCDLHPLARFLRNY

IKSSAHTLRNAKDLNCQPSTAAVAAAQSVLRLSETNCDSKAPNFTLVLKDRSPLLPGP

DVALLTVLGFAGAVGLTCLGLWFNWKLHQGKANEHTSENLCCRTFDEPLCAHEARNY

HTKGYCNCHLTQENEIKVMSIVGSRKEMPLLQENSHQATSASESATLDRSFRNLKKKD

RGVGSTLFCQDGRLLHSECSEPPGNMRAFNEAGLLTTYNPRKVQKLWNLEPGEVQPQT

LQHHIIRTEDISSDIFRRRYATPASALAGESLEKRLTNESWQPPIEKEDNGLHPHRQR

HFITSSSSKPCEPEEHYVQNIVQKNRSKYDI?PCGLLKQSKPRYFQPNNSLICKYVPCE

QFEDYMKEKKPNRRQHSKPEKEQIQINSAIEKFLMSEDNIDLSGLSTKTKKAYSPKRV

IFHDPDLVEINRSMMSPKISTPWKRQKNQSNQLTKLDVKKFSNTGERNKGEKWFTNSW

VLKRKRTPQSDLKGKIKGQNLKLNLHPFRKVRVHPEKSLSSLPKQCKQVLLPPKKLSK

TSETEAKINTVCSADFLQQSESSNYVRLTSKRLPLKHDSKQTPWQRNTKRAPLLSAN

NLRVVNQSSIESSCYSAGHIPDGNTSKLPQPTPTDAEHRHSHSQFSTEQMEDATQLES

KVLSYLATTWENTGSDVLPFQHSRRATDQGTTESTEHMGQNVSKTSELNQFSLSPRNQ

TQLLDAHKTDSYNKEYTLDQNEGLQHREQNSSHAQLENKEKTLMTKPQIPHQIVENCI

MDKEENDVEKKLSKTETYDSSLIPQTQSKNNLSFMKTNSIPYQNRIELPKDISTSPVS

SQAVWHLTNSSEKGIDSTNALPRNDGTEALEIKIVGKEEKNMLDESKTDSSMLTQISQ

EVNSNVHNFREVQNIQPDKDRAHKEGAMTVETHEALSFLPGLKDSFEAENEVFLVPSR

INEAENSAPKPVLYPPSAEYATTSPLETE

SEQ ID NO: 71 645 by NOV26b, GGATCCGCCCTGCTCTCCCTAAGCAGAAATGGTATCGAGGATGTTCAGGAAGATGCCC

2IOO62I44 Z'GCATGGGCTTACGATGTTGCGGACCTTGTTGCTGGAGCACAACCAAATATCCAGCTC
DNA

TTCGCTCACTGATCACACCTTCAGCAAGCTTCACAGCCTGCAGGTACTGGTGCTGAGC
Sequence p~T~TGCTCTCCGCACCCTACGAGGGTCTTGGTTCCGAAACACAAGCGGCCTGACCC

GGCTCCAGCTGGATGGGAATCAGATTACTAATCTCACAGACAGTTCTTTCGGAGGCAC

GAATCTCCACAGTCTCAGGTATCTGGATTTATCCAACAATTTTATTTCCTACATTGGG

AAAGATGCCTTCCGGCCCCTGCCTCAACTACAGGAAGTGGACCTTTCCCGAAATAGGT

TAGCCCACATGCCGGATGTGTTTACTCCACTGAAGCAGTTAATCCTTCTGAGCTTAGA

TAAGAACCAGTGGAGCTGCACTTGTGATCTCCATCCCCTTGCTCGGTTTTTAAGAAAC

TACATTAAGTCTTCTGCTCACACGCTCAGGAATGCCAAGGACCTAAATTGCCAGCCAT

CTACCGCAGCTGTGGCAGCTGCACAGAGTGTGCTGAGGCTGTCTGAGACCAACTGTGA

~
iTCTCGAG

ORF Start: at I ORF Stop: end o~ sequence w SEQ ID NO: 72 2IS.aa .~MW at 23982.8kD -..
NOV26b, GSALLSLSRNGIEDVQEDALHGLTMLRTLLLEHNQISSSSLTDHTFSKLHSLQVLVLS

210062144 ~NI'TALRTLRGSWFRNTSGLTRLQLDGNQITNLTDSSFGGTNLHSLRYLDLSNNFISYIG
PrOteln Sequence ~AFRPLPQLQEVDLSRNRLAHMPDVFTPLKQLILLSLDKNQWSCTCDLHPLARFLRN
((YIKSSAHTLRNAKDLNCQPSTAAVAAAQSVLRLSETNCDLE
Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 268.
Table 26B. Comparison of NOV26a against NOV26b.
Protein Sequence ~ NOV26a Residues/ Identities/
Match Residues Similarities for the Matched Region NOV26b 60..270 199/211 (94%) 3..213 , 199/211 (94%) Further analysis of the NOV26a protein yielded the following properties shown in Table 26C.
Table 26C. Protein Sequence Properties NOV26a PSort 0.8524 probability located in mitochondria) inner membrane; 0.6000 analysis. probability located in endoplasmic reticulum (membrane); 0.3000 probability located in microbody (peroxisome); 0.2622 probability located in mitochondria) matrix space SignalP No Known Signal Sequence Predicted analysis.. . .~..... ~ . . .. . ... .. . .
S A search of the NOV26a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 26D.

Table 26D. Geneseq Results for NOV26a NOV26a Identities/

Geneseq Protein/Organism/Length Residues/ SimilaritiesExpect ~ for Identifier[Patent #, Date] Match the MatchedValue Residues Region AAU83655 Human PRO protein, Seq 3..237 79/264 (29%)1e-18 ID No 128 - Homo sapiens, 473 22..283 121/264 aa. (44%) [W0200208288-A2, 31-JAN-AAB49891 Human PR0526 protein sequence3..237 79/264 (29%)~1e-18 -Homo Sapiens, 473 aa. 22..283 I Z 11264 ' (44%) [WO200070050-A1, 23-NOV-2000) .

AAB50908 Human PR0526 protein - 3..237 79/264 (29%)1e-18 Homo sapiens, 473 aa. [W0200073452-22..283 121/264 (44%) A2, 07-DEC-2000]

AAU04589 Human Nogo receptor - 3..237 79/264 (29%)1e-18 Homo ~

Sapiens, 473 aa. [WO200151520-22..283 121/264 ~ (44%) A2, 19-JUL-2001]

AAU12362 Human PR0526 polypeptide 3..237 79/264 (29%)1e-18 sequence - Homo sapiens, 22..283 121/264 473 aa. (44%) [W0200140466-A2, 07-JUN-2001 ..

In a BLAST search of public sequence databases, the NOV26a protein was found to have homology to the proteins shown in the BLASTP data in Table 26E.

Table 26E. Public BLASTP Results for NOV26a .-.~....~. .w.....:, Protein ' NOV26a Identities/
Accession Protein/Organism/Length Residues/ : Similarities for ~ Expect Number Match the Matched Value Residues Portion Q9BGY6 HYPOTHETICAL 56.5 I~DA 1..504 478/504 (94%) . 0.0 PROTEIN - Maraca fascicularis 1..504 481/504 (94%) (Crab eating macaque) (Cynomolgus monkey), 510 aa. .
Q961X3 GH01279P - Drosophila 45..233 68/212 (32%) ~ 9e-21 melanogaster (Fruit fly), 615 aa. 313..522 103/212 (48%) Q9NOE3 UNNAMED PROTEIN PRODUCT ~ 3..237 82/264 (31%) ~ 3e-19 - Maraca fascicularis (Crab eating 22..283 125/264 (47%) macaque) (Cynomolgus monkey), 473 aa.
Q9VZ84 CG7509 PROTEIN - Drosophila 45..233 69/230 (30%) ~ l e-18 melanogaster (Fruit fly), 633 aa. 313..540 103/230 (44%) Q9BZR6 ~ NOGO RECEPTOR - Homo ~ 3..237 79/264 (29%) j 3e-18 sapiens (Human), 473 aa. 22..283 121/264 (44%) PFam analysis predicts that the NOV26a protein contains the domains shown in the Table 26F.
Table 26F. Domain Analysis of NOV26a Identities/

Pfam DomainNOV26a Match RegionSimilarities Expect Value for the Matched Region LRR 58..81 7/25 (28%) 0.3 19/25 (76%) LRR 108..131 10/25 (40%) 0.11 ~ . 19/25 (76%) LRR 132..155 8/25 (32%) 0.7 18/25 (72%) LRR 15 8..181 11 /25 (44%) 0.00021 19/25 (76%) ~

_ LRR 182..204 10/25 (40%) ~ 0.093 18/25 (72%) LRRCT 214..270 15/63 (24%) 0.046 42/63 (67%) Example 27.
The NOV27 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 27A.
_Table 27A. NOV27 Sequence Analysis __.__.__ __. _SEQ_~D NO: 73 ~~ . 358 bp.
NOV27a, ~GACTTCCTGGCTCGCCAGCCCCTTCCTTCCGGAGCCTGACCCGGGCCCGGGCGACCTC
CG106942-Ol CCCGCGCGCTTCCCGGCCGCTGCCCAGGGGGTAGAGCGGGCGCAGCCGATCACTACCT
DNA Sequence G'~CGGCCTTTTTGGCGGCCTGGCCGGGCTGTGCAGGGTGGTAGGGCAAGACGCGCGGC
TCCCAATTCTCCCCGGCGCCTTCGCCGGCCCCGGGCTTCTCGCGCTCCGCTCCGGGCT
GCACCGAGTTGGGCCGGCGCGCCGCGTTGGTGTTGCCGCGCGGCGGCAGCTCAGAGTC
TCCAGGTTGGGGCGGGCCTGGGCCGCACGGCTCCTCCACCCAGGTGACGCTGAGCAGG
CTCAGGGTGAAGCCCAGGGAGATGCCCACGGCCACGGGCCCTGCGGGCCGCAGCACCG
ACAGCAGCAGCGATGCCCGCATGGCGCCCGGACCGCGGGTCCCCGGCCCCGGCGAACC
CCCAGAGCAGCCAGAGGAGTCTCCGAGGGGGCGGGACCGGGGAGGGGGCGGATCCGGA
GGGCTCGGGCCCCGCGGGCGGGCCCGCTCCCTCCCCGCAGAGCAGAGCCAGCGGCCCG
AGCCGAATCCCCGGAGCCGCGCCTCGATTCCCCTCCAGCAGCTGCTCTGGGCTGCGCA
GGGTTCTTGCGCTCGGCACTGGAGCCTCAGCCGCGGCCGCAGCTGTCCGACGTGTCAC
TGCAAGGGCCCCGCCCCCGGGGTGGGGTCTCGGGCTCTCGCTACCGGAGAGGGAGGAG
AAGGGGGAGGTTAAAGGGGAAGGACCCCCGGAAGTGCCCCCTCCTCAGTGCGGGAGAG
GGAGACGCCGGGGGCGGAGTCCCCTGCCTCCCGCGGCGTGGTTGGTGCGTCCCATGTG
ACGTCAGAAGCAGCCCGCCCCTGCCTGGATGGTGCGCCCTGAGTGACGTCAGGAGCAG
AGGCCGGAGCTGTCCATCAGCACCAAAGGCCGCGGGCGGGCTCAGGGCATGGGGCCGC
GGTTCTGGGGCGGCCCGAGCCCCGGCTCCTGCGCCTTCCCCTTCCTCAGGCCCAGCCC
GAGTTCCCGGACGCCGCGGGACTGGAGTGCCAGCCGGTGTTGGACGTGGAGCGGCGCC
GCCACCGCGCCGACACCATTCTCTCCGGCCCAGCAGCCCCCTTCCTCGCACGACGGAC
TTTCCCTGGACCCCAGCACTATGCCGGGGACTGTGGCAACACTGCGGTTCCAGCTGCT
GCCCCCTGAGCCAGATGATGCCTTCTGGGGTGCACCTTGTGAACAGCCCCTGGAGCGC
AGGTACCAGGCACTGCCGGCCCTCGTCTGCATCATGTGCTGTTTGTTTGGAGTCGTCT
ACTGCTTCTTCGGTTACCGCTGCTTCAAGGCAGTGCTCTTTCTCACTGGGTTGCTGTT
TGGCTCGGTGGTCATCTTCCTCCTCTGCTACCGAGAGCGGGTGCTAGAGACACAGCTG
AGTGCTGGGGCGAGCGCGGGCATCGCTCTGGGCATCGGGCTGCTCTGCGGGCTGGTGG
CCATGCTAGTGCGCAGCGTGGGCCTCTTCCTGGTGGGGCTGCTGCTCGGCCTGCTGCT
CGCAGCTGCTGCCCTGCTGGGCTCCGCACCCTACTACCAGCCAGGCTCCGTGTGGGGT
CCACTGGGGCTGTTGCTGGGGGGCGGCCTGCTCTGTGCCCTGCTCACTCTGCGCTGGC
CCCGCCCACTCACCACCCTGGCCACCGCCGTGACTGGTGCTGCGCTGATCGCCACTGC
CGCTGACTACTTCGCCGAGCTGCTACTGCTGGGGCGCTACGTGGTGGAGCGACTCCGG
GCTGCTCCTGTGCCCCCACTCTGCTGGCGAAGCTGGGCCCTGCTGGCACTCTGGCCCC
TGCTCAGCCTGATGGGCGTTCTGGTGCAGTGGAGGGTGACAGCTGAGGGGGACTCCCA
CACGGAAGTGGTCATCAGCCGGCAGCGCCGACGCGTGCAACTGATGCGGATTCGGCAG
CAGGAAGATCGCAAGGAGAAAAGGCGGAAAAAGAGACCTCCTCGGGCTCCCCTCAGAG
GTCCCCGGGCTCCTCCCAGGCCTGGGCCACCAGATCCTGCTTATCGGCGCAGGCCAGT
GCCCATCAAACGCTTCAATGGAGACGTCCTCTCCCCGAGCTATATCCAGAGCTTCCGA
GACCGGCAGACCGGGAGCTCCCTGAGCTCCTTCATGGCCTCACCCACAGATGCGGACT
ATGAGTATGGGTCCCGGGGACCTCTGACAGCCTGCTCAGGCCCCCCAGTGCGGGTATA
GCCATATCTGTCTGTCTAGACTCTGCAGTCACCAGCTCTGACAGCTCGAGGAGGCCGG
TAGGCTGCAATCAGCTTCCGGTTTGGTGGTCCTTCCCA
ORF Start: ATG at 977 ORF Stop: TAG at 2261 SEQ ID NO: 74 428 as MW at 46672.91:D
NOV27a, MGPRFWGGPSPGSCAFPFLRPSPSSRTPRDWSASRCWTWSGAATAPTPFSPAQQPPSS
CG106942-Ol HDGLSLDPSTMPGTVATLRFQLLPPEPDDAFWGAPCEQPLERRYQALPALVCIMCCLF
Protein Sequence G~CFFGYRCFKAVLFLTGLLFGSVVIFLLCYRERVLETQLSAGASAGIALGIGLLC
GLVAMLVRSVGLFLVGLLLGLLLAAAALLGSAPYYQPGSVWGPLGLLLGGGLLCALLT

LRWPRPLTTLATAVTGAALIA
LWPLLSLMGVLVQWRVTAEGDSHTEWISRQRRRVQLMRIRQQEDRKEKRRKKRPPRA
PLRGPRAPPRPGPPDPAXRRRPVPIKRFNGDVLSPSYIQSFRDRQTGSSLSSFMASPT
DADYEYGSRGPLTACSGPPVRV
Further analysis of the NOV27a protein yielded the following properties shown in Table 278.
Table 275. Protein Sequence Properties NOV27a PSort 0.6000 probability located in plasma membrane; 0.4000 probability located in analysis: Golgi body; 0.3000 probability located in endoplasmic reticulum (membrane);
0.2400 probability located in nucleus SignaIP ': No Known Signal Sequence Predicted analysis:
A search of the NOV27a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 27C.
Table 27C. Geneseq Results for NOV27a ~ NOV27a Identities/
~

Geneseq Protein/Organism/Length Residues/SimilaritiesExpect [Patent ~ ~

i ~ for the Identifier#, Date) Match Value ~ Matched Residues [ Re ion g AAM34044 Peptide #8081 encoded by 79..188 60/11 l 2e-25 probe for ~ (54%) measuring placental gene I9..124 76/111 expression ~ (68%) ~
- Homo sapiens, 124 aa.

[W0200157272-A2, 09-AUG-2001]

AAM20130 Peptide #6564 encoded by 79..188 60/1 I ~ 2e-25 probe for 1 (54%) measuring cervical gene 19..124 76/I 11 expression - 1 ~ (68%) Homo Sapiens, 124 aa.

[WO200157278-A2, 09-AUG-2001]

AAM73861 Human bone marrow expressed79..188 60/111 _ 2e-25 ~ (54%) probe encoded protein SEQ 19..124 76/111 ID NO: (68%) 34167 - Homo sapiens, 124 aa.

[W0200157276-A2, 09-AUG-2001]

AAM61147 Human brain expressed single79..188 60/111 2e-25 exon (54%) probe encoded protein SEQ 19..124 76/111 ID NO: ~ (68%) 33252 - Homo Sapiens, 124 aa.

[W0200157275-A2, 09-AUG-2001]1 . ~ ~

___ _ _ . _ .
ABB24734 . 79..188 60/111 2e-25 Protein #6733 encoded by ~ (54%) probe for .

measuring heart cell gene 19..124 76/I 11 expression (68%) - Homo Sapiens, 124 aa.

[W0200157274-A2, 09-AUG-2001]
_ __ _ . _ _ _ __ _.._ _ _ _ .
_. _..
.

In a BLAST search of public sequence databases, the NOV27a protein was found to have homology to the proteins shown in the BLASTP data in Table 27D.
Table 27D. Public BLASTP Results for NOV27a Protein ~ NOV27a Identities/

AccessionProtein/Organism/Length Residues/Similarities' Expect for Number ~ Match the Matched Value Residues Portion Q9~WD2 : CG14234 PROTEIN - Drosophila103..392 82/299 (27%)3e-20 melanogaster (Fruit fly),43..329 143/299 (47%) 381 aa.

Q9CRGI 2010003B14RIK PROTEIN I 12..305531208 (2S%)~ 6e-07 - Mus musculus (Mouse), SS6 286..490 95/208 (4S%) as (fragment).

Q9NS93 SEVEN TRANSMEMBRANE . 115..305SO/20S (24%)~ 4e-OS

PROTEIN TM7SF3 - Homo 303..504 88/205 (42%) sapiens (Human), 570 aa. ~

Q9NUS4 ~ CDNA FLJl 1169 FIS, 115..305 SO/20S (24%)4e-OS
CLONE

PLACE1007282 - Homo sapiens303..504 88/205 (42%) (Human), 570 aa. j 028838 ~ Hypothetical protein 107..304 S 1/201 (2S%)~ 7e-04 Archaeoglobus fulgidus, 14..188 821201 (40%) 199 aa.

Example 28.
S The NOV28 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 28A.
Table 28A. NOV28 Sequence SEQ ID NO: 7S 2177 by NOV28a, ~ATTCCCCTTGCCGACCCACATACACCATGAAGAGGTGCAGATCGGACGAGCTGCAGCA
CG107S13-Ol ~ACAACAGGGCGAGGAGGATGGAGCTGGGCTGGAAGATGCCGCTTCCCACCTGCCGGGC
DNA Sequence GCGGACCTCCGGCCTGGGGAGACCACGGGTGCTAACTCTGCTGGCGGGCCAACTTCAG
ACGCCGGCGCTGCCGCGGCGCCCAACCCAGGTCCCCGAAGCAAGCCTCCTGATTTAAA
GAAAATCCAGCAGCTGTCAGAGGGCTCCATGTTTGGCCACGGTCTGAAGCACCTGTTC
CACAGCCGCCGTCGGTCTCGGGAAAGGGAGCACCAGACGTCTCAGGATTCCCAGCAGC
ATCAGCAGCAGCAGGGTATGTCCGACCATGACTCCCCAGATGAGAAGGAGCGCTCTCC
GGAGATGCATCGCGTCTCCTACGCCATGTCCCTGCACGACCTGCCCGCCCGGCCCACC
GCCTTCAACCGCGTGCTGCAGCAGATCCGCTCCCGGCCCTCCATCAAGCGGGGCGCCA
GCCTGCACAGCAGCAGTGGGGGCGGCAGCAGCGGGAGCAGCAGCCGGCGCACCAAGAG
TAGCTCCCTGGAGCCCCAGCGTGGCAGCCCTCACCTGCTGCGCAAGGCCCCCCAGGAC
AGCAGCCTGGCCGCCATCCTGCACCAGCACCAGTGCCGTCCCCGCTCTTCCTCCACCA
CCGACACTGCTCTGCTGCTGGCCGACGGCAGCAACGTGTACCTCCTGGCTGAGGAGGC
CGAAGGCATCGGGGACAAGGTGGATAAGGGAGACCTGGTGGCCCTGAGCCTCCCCGCC
GGCCATGGTGACACCGACGGCCCCATCAGCCTGGACGTGCCCGATGGGGCACCGGACC
CCCAGCGGACCAAGGCCGCCATTGACCACCTGCACCAGAAGATCCTGAAGATCACCGA
GCAGATCAAGATTGAGCAGGAGGCTCGCGACGACAATGTGGCAGAGTATCTGAAACTG
GCCAACAACGCGGACAAGCAGCAGGTGTCACGCATCAAGCAAGTGTTCGAGAAGAAGA

~ACCAGAAGTCAGCCCAGACCATCGCCCAGCTGCACAAGAAGCTGGAGCACTACCGCCG

GCGCCTGAAGGAGATTGAGCAGAACGGGCCCTCGCGGCAGCCCAAGGACGTGCTGCGG

GACATGCAGCAGGGGCTGAAGGACGTGGGCGCCAACGTGCGCGCAGGCATCAGCGGCT

TTGGGGGCGGCGTGGTGGAGGGCGTCAAGGGCAGCCTCTCTGGCCTCTCACAGGCCAC

CCACACCGCCGTGGTGTCCAAGCCCCGGGAGTTTGCCAGCCTCATCCGCAACAAGTTT

GGCAGTGCTGACAACATCGCCCACCTGAAGGACCCCCTGGAAGATGGGCCCCCTGAGG

AGGCAGCCCGGGCACTGAGCGGCAGTGCCACACTCGTCTCCAGCCCCAAGTATGGCAG

CGATGATGAGTGCTCCAGCGCCACGCTCAGCTCAGCCGGGGCAGGCAGCAACTCTGGG

GCTGGGCCTGGTGGGGCGCTGGGGAGCCCTAAGTCCAATGCACTGTATGGTGCTCCTG

GAAACCTGGATGCTCTGCTGGAAGAGCTACGGGAGATCAAGGAGGGACAGTCTCACCT

GGAGGACTCCATGGAAGACCTGAAGACTCAGCTGCAGAGGGACTACACCTACATGACC

CAGTGCCTGCAGGAGGAGCGCTACAGGTACGAGCGGCTGGAGGAGCAGCTCAACGACC

TGACTGAGCTTCATCAGAACGAGATGACGAACCTGAAGCAGGAGCTGGCCAGCATGGA

GGAGAAGGTGGCCTACCAGTCCTATGAGAGGGCACGGGACATCCAGGAGGCCGTGGAG

TCCTGCCTGACCCGGGTCACCAAGCTGGAGCTGCAGCAGCAACAGCAGCAGGTGGTAC

AGCTGGAGGGCGTGGAGAATGCCAACGCGCGGGCGCTGCTGGGCAAGTTCATCAACGT

GATCCTGGCGCTCATGGCCGTGCTGCTGGTGTTCGTGTCCACCATCGCCAACTTCATC

ACGCCCCTCATGAAGACACGCCTGCGCATCACCAGCACCACCCTCCTGGTCCTCGTCC

TGTTCCTCCTCTGGAAGCACTGGGACTCCCTCACCTACCTCCTGGAGCACGTGTTGCT

GCCCAGCTGAGTGGCCAGCCACACCAACCCT

ORF Start: ATG at 27 ORF Stop: TGA at 2154 SEQ ID NO: 76 709 as MW at 77503.9kD

NOV28a, MKRCRSDELQQQQGEEDGAGLEDAASFILPGADLRPGETTGANSAGGPTSDAGAAAAPN

Protein SeCluenCeHDSPDEKERSPEMHRVSYAMSLHDLPARPTAFNRVLQQIRSRPSIKRGASLHSSSGGG

SSGSSSRRTKSSSLEPQRGSPHLLRKAPQDSSLAAILHQHQCRPRSSSTTDTALLLAD

GSNVYLLAEEAEGIGDKVDKGDLVALSLPAGHGDTDGPISLDVPDGAPDPQRTKAAID

HLHQKILKITEQIKIEQEARDDNVAEYLKLANNADKQQVSRIKQVFEKKNQKSAQTIA

QLHKKLEHYRRRLKEIEQNGPSRQPKDVLRDMQQGLKDVGANVRAGISGFGGGVVEGV

KGSLSGLSQATHTAVVSKPREFASLIRNKFGSADNIAHLKDPLEDGPPEEAARALSGS

ATLVSSPKYGSDDECSSATLSSAGAGSNSGAGPGGALGSPKSNALYGAPGNLDALLEE

LREIKEGQSHLEDSMEDLKTQLQRDYTYMTQCLQEERYRYERLEEQLNDLTELHQNEM

TNLKQELASMEEKVAYQSYERARDIQEAVESCLTRVTKLELQQQQQQVVQLEGVENAN

ARALLGKFINVILALMAVLLVFVSTIANFITPLMKTRLRITSTTLLVLVLFLLWKHWD

SLTYLLEHVLLPS

Further analysis of the NOV28a protein yielded the following properties shown in Table 28B.
Table 28B. Protein Sequence Properties NOV28a PSort 0.6000 probability located in plasma membrane; 0.4000 probability located in analysis: Golgi body; 0.3000 probability located in endoplasmic reticulum (membrane);
0.3000 probability located in microbody (peroxisome) SignalP No Known Signal Sequence Predicted analysis: ~ .
A search of the NOV28a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 28C.

Table 28C. Geneseq Results for NOV28a NOV28a Identities/

Geneseq Protein/Organism/Length Residues/SimilaritiesExpect [Patent for Identifier#~, Date] Match the Matched Value Residues Region AAY94907 Human secreted protein 57..703 359/672 (53%)e-178 clone ca106_19x protein sequence13..646 438/672 (64%) SEQ

ID N0:20 - Homo Sapiens, 653 aa.

[W0200009552-Al, 24-FEB-2000]

AAM78708 Human protein SEQ ID NO 249..708 258/466 (55%)e-134 Homo Sapiens, 477 aa. 26..476 3261466 (69%) [W0200157190-A2, 09-AUG-2001]

AAU28090 Novel human secretory protein,258..708 254/457 (55%)e-132 Seq ID No 259 - Homo Sapiens, 4..445 320/457 (69%) 446 aa.

[W0200166689-A2, 13-SEP-2001]

AAM40705 Human polypeptide SEQ ID 352..703 224/355 (63%)e-117 5636 - Homo Sapiens, 369 13..362 267/355 (75%) aa. ' [W0200153312-Al, 26-JUL-2001]

AAM38919 Human polypeptide SEQ ID 379..703 209/328 (63%)e-108 NO

2064 - Homo Sapiens, 331 2..324 248/328 (74%) aa.

[W0200153312-Al, 26-JUL-2001]

In a BLAST search of public sequence databases, the NOV28a protein was found to have homology to the proteins shown in the BLASTP data in Table 28D.

_.... . _.-Table 28Dy.._. ub.ic_B _...
_ ... . _ . p ...es _.. .....
_ ..... . _._. ... 2. _ ..... P I LAST R ults for NOV
Sa ~ NOV28a ~ Identities!

Protein AccessionProtein/Organism/Length ~ Residues/Similarities Expect for Number Match the Matched Value Residues Portion 075069 Hypothetical protein I~IAA0481~ 69..709638/641 (99%)0.0 (Cerebral protein-11) 10..650 640!641 (99%) (hucep-11) Homo sapiens (Human), 650 as (fragment).

Q9ULS5 Hypothetical protein KIAAl250..708 258/465 (55%)e-134 Homo Sapiens (Human), ~ 17..466325/465 (69%) 467 as (fragment).

AAH26867 . SIMILAR TO KIAA1145 258..708 249/457 (54%)e-129 PROTEIN - Mus musculus 4..445 316/457 (68%) (Mouse), 446 aa.
~~

094876 Hypothetical protein KIAA0779393..703 202/314 (64%)e-105 - ' Homo Sapiens (Human), 1..313 241/314 (76%) 320 as (fragment).

Q9VI21 CG1021 PROTEIN - Drosophila88..675 1881409 (45%)~le-84 melan0gaster (Fruit fly),~ 252..638248/409 (59%) 638 aa. ' .
~.__.._ _~....~,'~","~". ~ ~, ......
. ..__ ._... . .

Example 29.
The NOV29 clone was analyzed, and the nucleotide and encoded polypeptide sequences axe shown in Table 29A.
Table 29A. NOV29 Sequence Analysis SEQ ID NO: 77 664 by NOV29a, ATCGCCCCTCCTGCGCTAGCGGAGGTGATCGCCGCGGCGATGCCGGAGGAGGGTTCGG

DNA Sequence GGTCGCGGGCTTGGTGATCTGCCTCGTGGTGTGCATCCAGCGCTTCGCACAGGCTCAG
CAGCAGCTGCCGCTCGAGTCACTTGGGGACCTCAGCAGGACCCCAGGCTATACTGGCA
GGGGGGCCCAGCACTGGGCCGCTCCTTCCTGCATGGACCAGAGCTGGACAAGGGGCAG
CTACGTATCCATCGTGATGGCATCTACATGGTACACATCCAGGTGACGCTGGCCATCT
GCTCCTCCACGACGGCCTCCAGGCACCACCCCACCACCCTGGCCGTGGGAATCTGCTC
TCCCGCCTCCCGTAGCATCAGCCTGCTGCGTCTCAGCTTCCACCAAGGTTGTACCATT
GCCTCCCAGCGCCTGACGCCCCTGGCCCGAGGGGACACACTCTGCACCAACCTCACTG
GGACACTTTTGCCTTCCCGAAACACTGATGAGACCTTCTTTGGAGTGCAGTGGGTGCG
CCCCTGACCACTGCTGCTGATTAGGGTTTTTTAAATTTTATTTTATTTTATTTAAGTT
CAAGAGAAAAAGTGTACACACAGGGG
ORF Start: ATG at 40 ORF Stop: TGA at 334 SEQ ID NO: 78 ~98 as MW at 10705.2kD
NOV29a, MPEEGSGCSVRRRPYGCVLRAALVPLVAGLVICLVVCIQRFAQAQQQLPLESLGDLSR
TPGYTGRGAQHWAAPSCMDQSWTRGSYVSIVMASTWYTSR

Protein Sequence Further analysis of the NOV29a protein yielded the following properties shown in Table 29B.
Table 29B. Protein Sequence Properties NOV29a PSort 0.7900 probability located in plasma membrane; 0.3000 probability located in analysis: Golgi body; 0.2000 probability located in endoplasmic reticulum (membrane);
0.1000 probability located in rnitochondrial inner membrane _ . _____ _ SignalP ~ Cleavage site between residues 45 and 46 analysis:
A search of the NOV29a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 29C.
Table 29C. Geneseq Results for NOV29a NOV29a Identities/
~

Geneseq Protein/Organism/Length Residues/SimilaritiesExpect [Patent for Identifier#, Date] Match the Matched Value ResiduesRegion AARSOI21 ~ CD27L - Homo sapiens, 1..54 54/54 (100%)7e-25 193 aa.

[WO9405691-A, 17-MAR-1994) 1..54 54/54 (100%) AAW41180 CD27 ligand - Homo Sapiens,39..54 16116 (100%)0.16 216 ~

aa. [US5716805-A, 10-FEB-1998]62..77 16/16 (100%) i AAR50122 sCD27L-3 - Homo Sapiens, 39..54 16/16 (I00%)0.16 216 aa.

[WO9405691-A, 17-MAR-1994) 62..77 16/16 (100%) AAR5397I ~ CD27-L type II transmembrane39..54 I6/I~6 (100%)0.16 ~

protein - Mammalia, 216 62..77 16/I6 (100%) aa. -[W09410308-A, 11-MAY-1994) .
_ ~."_ AAG26041 Zea mays protein fragment 24..72 19/55 (34%) 2.4 SEQ ID

NO: 30347 - Zea mays subsp.6..59 26155 (46%) mays, 172 aa. [EP1033405-A2, 06-SEP-2oooJ

In a BLAST search of public sequence databases, the NOV29a protein was found to have homology to the proteins shown in the BLASTP data in Table 29D.

Table 29D. Public BLASTP Results for NOV29a NOV29a Identities/

Protein Residues!SimilaritiesExpect for AccessionProtein/Organism/Length Match the Matched Value Number Residues ~ Portion Q96JS7 ~ TUMOR NECROSIS FACTOR 1..54 ~54/S4 (100%)2e-24 (LIGAND) SUPERFAMILY, 1..54 S4/S4 (100%) MEMBER 7 - Homo Sapiens (Human), 193 aa.

P32970 CD27 ligand (CD27-L) (CD701..54 S4/S4 (100%)2e-24 antigen) - Homo Sapiens 1..54 54/S4 (100%) (Human), 193 aa.

Q9KFY7 HYPOTHETICAL PROTEIN 39..98 18/61 (29%) 7.4 BH0329 - Bacillus halodurans,240..300 28/61 (4S%) aa.

Q9RC64 UNKNOWN - Bacillus halodurans,39..98 18/61 (29%) 7.4 262 aa. 79..139 28161 (4S%) 0342SS PURL PROTEIN - Wolinella 70..93 11/24 (4S%) 9.7 succinogenes, 331 as (fragment).8..31 1S/24 (61%) Examt~le 30.
The NOV30 clone was analyzed, and the nucleotide and encoded polypeptide sequences S are shown in Table 30A.
Table 30A. NOV30 Sequence Analysis SEQ ID N0: 79 X2840 by NOV3Oa, CGGCAGTGGCAGGAGCCGCCTTTCCGATTCCCTACGATGCGGGTGCTGAGCTATGGCA

CG107S62-O1~GGGCAGCGAAGTGACGAGCGAGACCCGCGTACGACTGTGAAAGCCACCTGGAGCCA

D CCTTGCCGGGATTGTACCTGCAGGCAGAAAGTCTTCCTACGACCGTCTTTTCCCTTAG

NA Se ltenCe q AGGCACCAGAATCCCTGTAACCATTCATCCAGGTGTTGAGAAGATATGTAGCAGCCGA

GCACCCATCTTTTGACACCGTCCTCTGAAATCAGCTTTGGAGATGCTTTCACTCTGTC

CGTCTTCTGCAGCAGCCAGGCAGAGTGCCGACTCCTTCACAGCCGTGAGGAACTCTTC

AGGCTCCAGAAGCTCTTAAACCTGATCTACAATGGAAAAAATTCTTTTTTATCTGTTT

CTCATTGGCATAGCAGTGAAAGCTCAGATCTGTCCAAAGCGTTGTGTCTGTCAGATTT
TGTCTCCTAATCTTGCAACCCTTTGTGCCAAGAAAGGGCTTTTATTTGTTCCACCAAA
CATTGACAGAAGAACTGTGGAACTGCGGTTGGCAGACAATTTTGTTACAAATATTAAA
AGGAAAGATTTTGCCAATATGACCAGCTTGGTGGACCTGACTCTATCCAGGAATACAA
TAAGTTTTATTACACCTCATGCTTTCGCTGACCTACGAAATTTGAGGGCTTTGCATTT
GAATAGCAACAGATTGACTAAAATTACAAATGATATGTTCAGTGGTCTTTCCAATCTT
CATCATTTGATACTGAACAACAATCAGCTGACTTTAATTTCCTCTACAGCGTTTGATG
ATGTCTTCGCCCTTGAGGAGCTGGATCTGTCCTATAATAATCTAGAAACCATTCCTTG
GGATGCTGTTGAGAAGATGGTTAGCTTGCATACCCTTAGTTTGGATCACAATATGATT
GATAACATTCCTAAGGGGACCTTCTCCCATTTGCACAAGATGACTCGGTTAGATGTGA
CATCAAATAAATTGCAGAAGCTACCACCTGACCCTCTCTTTCAGCGAGCTCAGGTACT

'Su::~ ~npt~ ~sut- u::w. c° A(a-.V... ~~ .
~AGCAACCTCAGGAATCATAAGCCCATCTACTTTTGCATTAAGTTTTGGTGGAAAC~CCC
TTGCATTGCAATTGTGAATTGTTGTGGTTGAGGCGTCTGTCCAGAGAAGATGACTTAG

AGACCTGTGCTTCTCCTCCACTTTTAACTGGCCGCTACTTTTGGTCAATTCCTGAAGA

AGAGTTTTTGTGTGAGCCTCCTCTCATTACTCGTCATACACATGAGATGAGAGTCCTG

GAGGGACAAAGGGCAACACTGAGGTGCAAAGCCAGGGGAGACCCTGAGCCTGCAATTC

ACTGGATTTCTCCTGAAGGGAAGCTTATTTCAAATGCAACAAGATCTCTGGTGTATGA

TAACGGAACACTTGACATTCTTATCACAACTGTAAAGGATACAGGTGCTTTTACCTGC

ATTGCTTCCAATCCTGCTGGGGAAGCAACACAAATAGTGGATCTTCATATAATTAAGC

TCCCTCACTTACTAAATAGTACAAACCATATCCATGAGCCTGATCCTGGTTCTTCAGA

TATCTCAACTTCTACCAAGTCAGGTTCTAATACAAGCAGTAGTAATGGTGATACTAAA

TTGAGTCAAGATAAAATTGTGGTGGCAGAAGCTACATCATCAACGGCACTACTTAAAT

TTAATTTTCAAAGAAATATCCCTGGAATACGTATGTTTCAAATCCAGTACAATGGTAC

TTATGATGACACCCTTGTTTACAGGATGATACCTCCTACGAGCAAAACTTTTCTGGTC

AATAATCTGGCTGCTGGAACTATGTATGACTTGTGTGTCTTGGCCATATATGATGATG

GCATCACTTCCCTCACTGCCACAAGAGTCGTGGGTTGCATCCAGTTTACTACGGAACA

GGATTATGTGCGTTGCCATTTCATGCAGTCCCAGTTTTTGGGAGGCACCATGATTATT

ATTATTGGTGGAATCATTGTAGCATCTGTGCTGGTATTCATCATTATTCTGATGATCC

GGTATAAGGTTTGCAACAATAATGGGCAACACAAGGTCACCAAGGTTAGCAATGTTTA

TTCCCAAACTAACGGGGCTCAAATACAAGGCTGTAGTGTAACGCTGCCCCAGTCCGTG

TCCAAACAAGCTGTGGGACACGAAGAGAATGCCCAGTGTTGTAAAGCTACCAGTGACA

ATGTGATTCAATCTTCAGAAACTTGTTCGAGTCAAGACTCCTCTACCACTACCTCTGC

TTTGCCTCCTTCCTGGACTTCAAGCACTTCTGTGTCCCAAAAGCAGAAAAGAAAGACT

GGCACAAAGCCAAGTACAGAACCACAGAATGAAGCCGTCACAAATGTTGAATCCCAAA

ACACTAACAGGAACAACTCAACTGCCTTGCAGTTAGCTAGCCGTCCTCCCGATTCTGT

CACAGAGGGGCCCACGTCTAAAAGAGCACATATAAAGCCAAGTAAGTTTATCACTTTG

CCTGCTGAGAGATCCGGAGCAAGGCACAAGTACTCCCTCAATGGAGAATTAAAGGAAT

ACTATTGTTATATTAACTCGCCGAACACATGTGGACTGTTTCCTAAAAGAAGCATGTC

TATGAATGTGATGTTTATTCAGTCTGACTGTTCTGATGGTCATAGTGGAAAGGCAACT

CTCAAATTCTGAGGGACTACTGGAAAGCTCTGTGTAATTTATAATTTCTTTTTCATGA

AAAATCATTTTGAGAACTCACATAGAAGATTGGAATTTGCAATTCCAATGCTGTGTAT

AAATCAACCTTCTCAGATGCTTTGCTGACTAATGTTGACCAGATTGTCCAGGAAAC

ORF Start: ATG at 380 ORF Stop: TGA at 2678 SEQ ID NO: 80 766 as MW at 84690.6kD

NOV3Oa, MEKILFYLFLIGIAVKAQICPKRCVCQILSPNLATLCAKKGLLFVPPNIDRRTVELRL

CG107S6Z-Ol ~NFVTNIKRKDFANMTSLVDLTLSRNTISFITPHAFADLRNLRALHLNSNRLTKITN

PrOtelri DMFSGLSNLHHLILNNNQLTLISSTAFDDVFALEELDLSYNNLETIPWDAVEKMVSLH
SeCItlBriCe TLSLDHNMIDNIPKGTFSHLHKMTRLDVTSNKLQKLPPDPLFQRAQVLATSGIISPST

FALSFGGNPLHCNCELLWLRRLSREDDLETCASPPLLTGRYFWSIPEEEFLCEPPLIT

RFiTHEMRVLEGQRATLRCKARGDPEPAIHWISPEGKLISNATRSLVYDNGTLDILITT

VKDTGAFTCIASNPAGEATQIVDLHIIKLPHLLNSTNHIHEPDPGSSDISTSTKSGSN

TSSSNGDTKLSQDKIWAEATSSTALLKFNFQRNIPGIRMFQIQYNGTYDDTLVYRMI

PPTSKTFLVNNLAAGTMYDLCVLAIYDDGITSLTATRVVGCIQFTTEQDYVRCHFMQS

QFLGGTMIIIIGGIIVASVLVFIIILMIRYKVCNNNGQHKVTKVSNVYSQTNGAQIQG

CSVTLPQSVSKQAVGHEENAQCCKATSDNVIQSSETCSSQDSSTTTSALPPSWTSSTS

VSQKQKRKTGTKPSTEPQNEAVTNVESQNTNRNNSTALQLASRPPDSVTEGPTSKRAH

IKPSKFITLPAERSGARHKYSLNGELKEYYCYINSPNTCGLFPKRSMSMNVMFIQSDC

SDGHSGKATLKF

SEQ ID NO: 81 238_8 by NOV3Ob, GCTCTTAAACCTGATCTACAATGGAAAAA.ATTCTTTTTTATCTGTTTCTCATTGGCAT

DNA Se LleriCeCTTGCAACCCTTTGTGCCAAGAAAGGGCTTTTATTTGTTCCACCAAACATTGACAGAA

GAACTGTGGAACTGCGGTTGGCAGACAATTTTGTTACAAATATTAAAAGGAAAGATTT

TGCCAATATGACCAGCTTGGTGGACCTGACTCTATCCAGGAATACAATAAGTTTTATT

ACACCTCATGCTTTCGCTGACCTACGAAATTTGAGGGCTTTGCATTTGAATAGCAACA

GATTGACTAAAATTACAAATGATATGTTCAGTGGTCTTTCCAATCTTCATCATTTGAT

ACTGAACAACAATCAGCTGACTTTAATTTCCTCTACAGCGTTTGATGATGTCTTCGCC

CTTGAGGAGCTGGATCTGTCCTATAATAATCTAGAAACCATTCCTTGGGATGCTGTTG

AGAAGATGGTTAGCTTGCATACCCTTAGTTTGGATCACAATATGATTGATAACATTCC

'tie , . f~~ .:nff ~ llux:i-~'-~lia'!
TAAGGGGACCTTCTCCCATTTGCACAAGATGACTCGGTTAGATGTGACATCAAATAAA

TTGCAGAAGCTACCACCTGACCCTCTCTTTCAGCGAGCTCAGGTACTAGCAACCTCAG

GAATCATAAGCCCATCTACTTTTGCATTAAGTTTTGGTGGAAACCCCTTGCATTGCAA

TTGTGAATTGTTGTGGTTGAGGCGTCTGTCCAGAGAAGATGACTTAGAGACCTGTGCT

TCTCCTCCACTTTTAACTGGCCGCTACTTTTGGTCAATTCCTGAAGAAGAGTTTTTGT

GTGAGCCTCCTCTCATTACTCGTCATACACATGAGATGAGAGTCCTGGAGGGACAAAG

GGCAACACTGAGGTGCAAAGCCAGGGGAGACCCTGAGCCTGCAATTCACTGGATTTCT

CCTGAAGGGAAGCTTATTTCAAATGCAACAAGATCTCTGGTGTATGATAACGGAACAC

TTGACATTCTTATCACAACTGTAAAGGATACAGGTGCTTTTACCTGCATTGCTTCCAA

TCCTGCTGGGGAAGCAACACAAATAGTGGATCTTCATATAATTAAGCTCCCTCACTTA

CTAAATAGTACAAACCATATCCATGAGCCTGATCCTGGTTCTTCAGATATCTCAACTT

CTACCAAGTCAGGTTCTAATACAAGCAGTAGTAATGGTGATACTAAATTGAGTCAAGA

TAAAATTGTGGTGGCAGAAGCTACATCATCAACGGCACTACTTAACTTTACTTTTCAA

AGAACTATCCCTGGAATACGTATGTTTCAAATCCAGTACAATGGTACTTATGATGACA

CCCTTGTTTACAGGATGATACCTCCTACGAGCAAAACTTTTCTGGTCAATAATCTGGC

TGCTGGAACTATGTATGACTTGTGTGTCTTGGCCATATATGATGATGGCATCACTTCC

CTCACTGCCACAAGAGTCGTGGGTTGCATCCAGTTTACTACGGAACAGGATTATGTGC

GTTGCCATTTCATGCAGTCCCAGTTTTTGGGAGGCACCATGATTATTATTATTGGTGG

AATCATTGTAGCATCTGTGCTGGTATTCATCATTATTCTGATGATCCGGTATAAGGTT

TGCAACAATAATGGGCAACACAAGGTCACCAAGGTTAGCAATGTTTATTCCCAAACTA

ACGGGGCTCAAATACAAGGCTGTAGTGTAACGCTGCCCCAGTCCGTGTCCAAACAAGC

TGTGGGACACGAAGAGATTGCCCAGTGTTGTAAAGCTACCAGTGACAATGTGATTCAA

TCTTCAGAAACTTGTTCGAGTCAGGACTCCTCTACCACTACCTCTGCTTTGCCTCCTT

CCTGGACTTCAAGCACTTCTGTGTCCCAAAAGCAGAAAAGAAAGACTGGCACAAAGCC

AAGTACAGAACCACAGAATGAAGCCGTCACAAATGTTGAATCCCAAAACACTAACAGG

AACAACTCAACTGCCTTGCAGTTAGCTAGCCGTCCTCCCGATTCTGTCACAGAGGGGC

CCACGTCTAAAAGAGCACATATAAAGCCAAATGCTTTGCTGACTAATGTTGACCAGAT

TGTCCAGGAAACACAGAGGCTGGAGTTAATCTGAAGAGCACCACTTCTCCTCTCTCTC

CTGAAAAAATTTGCCACTGATATTTTTACTGGATAAAATTCAAAAATGTTTCAATTCA

CAAAGGCTAA'T'TGTTGAACTGGTGTCGTAGAAGAAATTGTCTACAGGAGCCAAGGTGA

AAGTCTCTGATGACGGCGGAACTGGCTCCATTAGACCATGGTTCATCCTCTTTTAAAA

ACAAATTTTT

ORF Start: ATG at 21 ORF Stop: TGA at 2178 SEQ ID NO: 82 719 as MW at 79402.7kD

NOV3Ob, MEKILFYLFLIGIAVKAQICPKRCVCQILSPNLATLCAKKGLLFVPPNIDRRTVELRL

CG107562-02 ~N~TNIKRKDFANMTSLVDLTLSRNTISFITPHAFADLRNLRALHLNSNRLTKITN

Protein S8C1l1eriCeDMFSGLSNLHHLILNNNQLTLISSTAFDDVFALEELDLSYNNLETIPWDAVEKMVSLH

TLSLDHNMIDNIPKGTFSHLHKMTRLDVTSNKLQKLPPDPLFQRAQVLATSGIISPST

FALSFGGNPLHCNCELLWLRRLSREDDLETCASPPLLTGRYFWSIPEEEFLCEPPLIT

RHTHEMRVLEGQRATLRCKARGDPEPAIHWISPEGKLISNATRSLVYDNGTLDILITT

VKDTGAFTCIASNPAGEATQIVDLHIIKLPHLLNSTNHIHEPDPGSSDISTSTKSGSN

TSSSNGDTKLSQDKIWAEATSSTALLNFTFQRTIPGIRMFQIQYNGTYDDTLVYRMI

PPTSKTFLVNNLAAGTMYDLCVLAIYDDGITSLTATRVVGCIQFTTEQDYVRCHFMQS

QFLGGTMIIIIGGIIVASVLVFIIILMIRYKVCNNNGQHKVTKVSNVYSQTNGAQIQG

CSVTLPQSVSKQAVGHEEIAQCCKATSDNVIQSSETCSSQDSSTTTSALPPSWTSSTS

VSQKQKRKTGTKPSTEPQNEAVTNVESQNTNRNNSTALQLASRPPDSVTEGPTSKRAH

IKPNALLTNVDQIVQETQRLELI

SEQ ID NO: 83 1545 by NOV3OC, GGATCCCAGATCTGTCCAAAGCGTTGTGTCTGTCAGATTTTGTCTCCTAATCTTGCAA

DNA

GGAACTGCGGTTGGCAGACAATTTTGTTACAAATATTAAAAGGAAAGATTTTGCCAAT
S2qtleriCe ATGACCAGCTTGGTGGACCTGACTCTATCCAGGAATACAATAAGTTTTATTACACCTC

ATGCTTTCGCTGACCTACGAAATTTGAGGGCTTTGCATTTGAATAGCAACAGATTGAC

TAA.AATTACAAATGATATGTTCAGTGGTCTTTCCAATCTTCATCATTTGATACTGAAC

AACAATCAGCTGACTTTAATTTCCTCTACAGCGTTTGATGATGTCTTCGCCCTTGAGG

AGCTGGATCTGTCCTATAATAATCTAGAAACCATTCCTTGGGATGCTGTTGAGAAGAT

GGTTAGCTTGCATACCCTTAGTTTGGATCACAATATGATTGATAACATTCCTAAGGGG

ACCTTCTCCCATTTGCACAAGATGACTCGGTTAGATGTGACATCAAATAAATTGCAGA

AGCTACCACCTGACCCTCTCTTTCAGCGAGCTCAGGTACTAGCAACCTCAGGAATCAT

AAGCCCATCTACTTTTGCATTAAGTTTTGGTGGAAACCCCTTGCATTGCAATTGTGAA

TTGTTGTGGTTGAGGCGTCTGTCCAGAGAAGATGACTTAGAGACCTGTGCTTCTCCTC

CACTTTTAACTGGCCGCTACTTTTGGTCAATTCCTGAAGAAGAGTTTTTGTGTGAGCC

TCCTCTCATTACTCGTCATACACATGAGATGAGAGTCCTGGAGGGACAAAGGGCAACA

CTGAGGTGCAAAGCCAGGGGAGACCCTGAGCCTGCAATTCACTGGATTTCTCCTGAAG

GGAAGCTTATTTCAAATGCAACAAGATCTCTGGTGTATGATAACGGAACACTTGACAT

TCTTATCACAACTGTAAAGGATACAGGTGCTTTTACCTGCATTGCTTCCAATCCTGCT

GGGGAAGCAACACAAATAGTGGATCTTCATATAATTAAGCTCCCTCACTTACTAAATA

GTACAAACCATATCCATGAGCCTGATCCTGGTTCTTCAGATATCTCAACTTCTACCAA

GTCAGGTTCTAATACAAGCAGTAGTAATGGTGATACTAAATTGAGTCAAGATAAAATT

GTGGTGGCAGAAGCTACATCATCAACGGCACTACTTAAATTTAATTTTCGAAGAAATA

TCCCTGGAATACGTATGTTTCAAATCCAGTACAATGGTACTTATGATGACACCCTTGT

TTACAGAATGATACCTCCTACGAGCAAAACTTTTCTGGTCAATAATCTGGCTGCTGGA

ACTATGTATGACTTGTGTGTCTTGGCCATATATGATGATGGCATCACTTCCCTCACTG

CCACAAGAGTCGTGGGTTGCATCCAGTTTACTACGGAACAGGATTATGTGCGTTGCCA

TTTCATGCAGTCCCAGTTTTTGGGAGGCACCCTCGAG

ORF Start: at 1 ORF Stop: end of sequence SEQ ID NO: 84 515 as MW at 57372.8kD

NOV3OC, GSQICPKRCVCQILSPNLATLCAKKGLLFVPPNIDRRTVELRLADNFVTNIKRKDFAN

Protein Sequence~QZ'TLISSTAFDDVFALEELDLSYNNLETIPWDAVEKWSLHTLSLDHNMIDNIPKG

TFSHLHKMTRLDVTSNKLQKLPPDPLFQRAQVLATSGIISPSTFALSFGGNPLHCNCE

LLWLRRLSREDDLETCASPPLLTGRYFWSIPEEEFLCEPPLITRHTHEMRVLEGQRAT

LRCKARGDPEPAIHWISPEGKLISNATRSLVYDNGTLDILITTVKDTGAFTCIASNPA

GEATQIVDLHIIKLPHLLNSTNHTHEPDPGSSDISTSTKSGSNTSSSNGDTKLSQDKI

WAEATSSTALLKFNFRRNIPGIRMFQIQYNGTYDDTLVYRMIPPTSKTFLVNNLAAG

TMYDLCVLAIYDDGITSLTATRWGCIQFTTEQDYVRCHFMQSQFLGGTLE

SEQ ID NO: 85 1545 by NOV3Od, GGATCCCAGATCTGTCCAAAGCGTTGTGTCTGTCAGATTTTGTCTCCTAATCTTGCAA

DNA

GGAACTGCGGTTGGCAGACAATTTTGTTACAAATATTAAAAGGAAAGATTTTGCCAAT
SeqLlenCe ATGACCAGCTTGGTGGACCTGACTCTATCCAGGAATACAATAAGTTTTATTACACCTC

ATGCTTTCGCTGACCTACGAAATTTGAGGGCTTTGCATTTGAATAGCAACAGATTGAC

TAAAATTACAAATGATATGTTCAGTGGTCTTTCCAATCTTCATCATTTGATACTGAAC

AACAATCAGCTGACTTTAATTTCCTCTACAGCGTTTGATGATGTCTTCACCCTTGAGG

AGCTGGATCTGTCCTATAATAATCTAGAAACCATTCCTTGGGATGCTGTTGAGAAGAT

GGTTAGCTTGCATACCCTTAGTTTGGATCACAATATGATTGATAACA'I'TCCTAAGGGG

ACCTTCTCCCATTTGCACAAGATGACTCGGTTAGATGTGACATCAAATAAATTGCAGA

AGCTACCACCTGACCCTCTCTTTCAGCGAGCTCAGGTACTAGCAACCTCAGGAATCAT

AAGCCCATCTACTTTTGCATTAAGTTTTGGTGGAAACCCCTTGCATTGCAATTGTGAA

TTGTTGTGGTTGAGGCGTCTGTCCAGAGAAGATGACTTAGAGACCTGTGCTTCTCCTC

CACTTTTAACTGGCCGCTACTTTTGGTCAATTCCTGAAGAAGAGTTTTTGTGTGAGCC

TCCTCTCATTACTCGTCATACACATGAGATGAGAGTCCTGGAGGGACAAAGGGCAACA

CTGAGGTGCAAAGCCAGGGGAGACCCTGAGCCTGCAATTCACTGGATTTCTCCTGAAG

GGAAGCTTATTTCAAATGCAACAAGATCTCTGGTGTATGATAACGGAACACTTGACAT

TCTTATCACAACTGTAAAGGATACAGGTGCTTTTACCTGCATTGCTTCCAATCCTGCT

GGGGAAGCAACACAAATAGTGGATCTTCATATAATTAAGCTCCCTCACTTACTAAATA

GTACAAACCATATCCATGAGCCTGATCCTGGTTCTTCAGATATCTCAACTTCTACCAA

GTCAGGTTCTAATACAAGCAGTAGTAATGGTGATACTAAATTGAGTCAAGATAAAATT

GTGGTGGCAGAAGCTACATCATCAACGGCACTACTTAA.ATTTAATTTTCAAAGAAATA

TCCCTGGAATACGTATGTTTCAAATCCAGTACAATGGTACTTATGATGACACCCTTGT

TTACAGAATGATACCTCCTACGAGCAAAACTTTTCTGGTCAATAATCTGGCTGCTGGA

ACTATGTATGACTTGTGTGTCTTGGCCATATATGATGATGGCATCACTTCCCTCACTG

CCACAAGAGTCGTGGGTTGCATCCAGTTTACTACGGAACAGGATTATGTGCGTTGCCA

TTTCATGCAGTCCCAGTTTTTGGGAGGCACCCTCGAG

ORF Start: at I ~ ORF Stop: end of sequence DEMANDE OU BREVET VOLUMINEUX
LA PRESENTE PARTIE DE CETTE DEMANDE OU CE BREVET COMPREND
PLUS D'UN TOME.

NOTE : Pour les tomes additionels, veuillez contacter 1e Bureau canadien des brevets JUMBO APPLICATIONS/PATENTS
THIS SECTION OF THE APPLICATION/PATENT CONTAINS MORE THAN ONE
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Claims (50)

What is claimed is:

1. An isolated polypeptide comprising the mature form of an amino acid sequence selected from the group consisting of SEQ ID NO:2n, wherein n is an integer between 1 and 73.

2. An isolated polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:2n, wherein n is an integer between 1 and 73.

3. An isolated polypeptide comprising an amino acid sequence which is at least 95%
identical to an amino acid sequence selected from the group consisting of SEQ
ID
NO:2n, wherein n is an integer between 1 and 73.

4. An isolated polypeptide, wherein the polypeptide comprises an amino acid sequence comprising one or more conservative substitutions in the amino acid sequence selected from the group consisting of SEQ ID NO:2n, wherein n is an integer between 1 and 73.

5. The polypeptide of claim 1 wherein said polypeptide is naturally occurring.

6. A composition comprising the polypeptide of claim 1 and a carrier.

7. A kit comprising, in one or more containers, the composition of claim 6.

8. The use of a therapeutic in the manufacture of a medicament for treating a syndrome associated with a human disease, the disease selected from a pathology associated with the polypeptide of claim 1, wherein the therapeutic comprises the polypeptide of claim 1.

9. A method for determining the presence or amount of the polypeptide of claim 1 in a sample, the method comprising:

(a) providing said sample;

(b) introducing said sample to an antibody that binds immunospecifically t.
polypeptide; and (c) determining the presence or amount of antibody bound to said polypeptide, thereby determining the presence or amount of polypeptide in said sample.

10. A method for determining the presence of or predisposition to a disease associated with altered levels of expression of the polypeptide of claim 1 in a first mammalian subject, the method comprising:

a) measuring the level of expression of the polypeptide in a sample from the first mammalian subject; and b) comparing the expression of said polypeptide in the sample of step (a) to the expression of the polypeptide present in a control sample from a second mammalian subject known not to have, or not to be predisposed to, said disease, wherein an alteration in the level of expression of the polypeptide in the first subject as compared to the control sample indicates the presence of or predisposition to said disease.

11. A method of identifying an agent that binds to the polypeptide of claim 1, the method comprising:
(a) introducing said polypeptide to said agent; and (b) determining whether said agent binds to said polypeptide.

12. The method of claim 11 wherein the agent is a cellular receptor or a downstream effector.

13. A method for identifying a potential therapeutic agent for use in treatment of a pathology, wherein the pathology is related to aberrant expression or aberrant physiological interactions of the polypeptide of claim 1, the method comprising:

(a) providing a cell expressing the polypeptide of claim 1 and having a property or function ascribable to the polypeptide;

(b) contacting the cell with a composition comprising a candidate substance;
and (c) determining whether the substance alters the property or function ascribable to the polypeptide;

whereby, if an alteration observed in the presence of the substance is not observed when the cell is contacted with a composition in the absence of the substance, the substance is identified as a potential therapeutic agent.

14. A method for screening for a modulator of activity of or of latency or predisposition to a pathology associated with the polypeptide of claim 1, said method comprising:

(a) administering a test compound to a test animal at increased risk for a pathology associated with the polypeptide of claim 1, wherein said test animal recombinantly expresses the polypeptide of claim 1;

(b) measuring the activity of said polypeptide in said test animal after administering the compound of step (a); and (c) comparing the activity of said polypeptide in said test animal with the activity of said polypeptide in a control animal not administered said polypeptide, wherein a change in the activity of said polypeptide in said test animal relative to said control animal indicates the test compound is a modulator activity of or latency or predisposition to, a pathology associated with the polypeptide of claim 1.

15. The method of claim 14, wherein said test animal is a recombinant test animal that expresses a test protein transgene or expresses said transgene under the control of a promoter at an increased level relative to a wild-type test animal, and wherein said promoter is not the native gene promoter of said transgene.

16. A method for modulating the activity of the polypeptide of claim 1, the method comprising contacting a cell sample expressing the polypeptide of claim 1 with a compound that binds to said polypeptide in an amount sufficient to modulate the activity of the polypeptide.

17. A method of treating or preventing a pathology associated with the polypeptide of claim 1, the method comprising administering the polypeptide of claim 1 to a subject in which such treatment or prevention is desired in an amount sufficient to treat or prevent the pathology in the subject.

18. The method of claim 17, wherein the subject is a human.

19. A method of treating a pathological state in a mammal, the method comprising administering to the mammal a polypeptide in an amount that is sufficient to alleviate the pathological state, wherein the polypeptide is a polypeptide having an amino acid sequence at least 95% identical to a polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO:2n, wherein n is an integer between 1 and 73 or a biologically active fragment thereof.

20. An isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO:2n-1, wherein n is an integer between 1 and 73.

21. The nucleic acid molecule of claim 20, wherein the nucleic acid molecule is naturally occurring.

22. A nucleic acid molecule, wherein the nucleic acid molecule differs by a single nucleotide from a nucleic acid sequence selected from the group consisting of SEQ
ID NO: 2n-1, wherein n is an integer between 1 and 73.

23. An isolated nucleic acid molecule encoding the mature form of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID
NO:2n, wherein n is an integer between 1 and 73.

24. An isolated nucleic acid molecule comprising a nucleic acid selected from the group consisting of 2n-1, wherein n is an integer between 1 and 73.

25. The nucleic acid molecule of claim 20, wherein said nucleic acid molecule hybridizes under stringent conditions to the nucleotide sequence selected from the group consisting of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 73, or a complement of said nucleotide sequence.

26. A vector comprising the nucleic acid molecule of claim 20.

27. The vector of claim 26, further comprising a promoter operably linked to said nucleic acid molecule.

28. A cell comprising the vector of claim 26.

29. An antibody that immunospecifically binds to the polypeptide of claim 1.

30. The antibody of claim 29, wherein the antibody is a monoclonal antibody.

31. The antibody of claim 29, wherein the antibody is a humanized antibody.

32. The antibody of claim 29, wherein the antibody is a fully human antibody.

33. The antibody of claim 29, wherein the dissociation constant for the binding of the polypeptide to the antibody is less than 1 x 10-9 M.

34. The antibody of claim 29, wherein the antibody neutralizes an activity of the polypeptide.

35. A method of treating or preventing a NOVA-associated disorder, the method comprising administering to a subject in which such treatment or prevention is desired the antibody of claim 29 in an amount sufficient to treat or prevent the pathology in the subject.

36. The method of claim 35, wherein the subject is human.

37. A method for determining the presence or amount of the nucleic acid molecule of claim 20 in a sample, the method comprising:

(a) providing said sample;

(b) introducing said sample to a probe that binds to said nucleic acid molecule;
and (c) determining the presence or amount of said probe bound to said nucleic acid molecule, thereby determining the presence or amount of the nucleic acid molecule in said sample.

38. The method of claim 37 wherein presence or amount of the nucleic acid molec~
used as a marker for cell or tissue type.

39. The method of claim 38 wherein the cell or tissue type is cancerous.

40. A method for determining the presence of or predisposition to a disease associated with altered levels of expression of the nucleic acid molecule of claim 20 in a first mammalian subject, the method comprising:

a) measuring the level of expression of the nucleic acid in a sample from the first mammalian subject; and b) comparing the level of expression of said nucleic acid in the sample of step (a) to the level of expression of the nucleic acid present in a control sample from a second mammalian subject known not to have or not be predisposed to, the disease;
wherein, an alteration in the level of expression of the nucleic acid in the first subject as compared to the control sample indicates the presence of or predisposition to the disease.

41. A method of producing the polypeptide of claim 1, the method comprising culturing a cell under conditions that lead to expression of the polypeptide, wherein said cell comprises a vector comprising an isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID N0:2n-l, wherein n is an integer between 1 and 73.

42. The method of claim 41 wherein the cell is a bacterial cell.

43. The method of claim 41 wherein the cell is an insect cell.

44. The method of claim 41 wherein the cell is a yeast cell.

45. The method of claim 41 wherein the cell is a mammalian cell.

46. A method of producing the polypeptide of claim 2, the method comprising culturing a cell under conditions that lead to expression of the polypeptide, wherein said cell comprises a vector comprising an isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO:2n-1, wherein n is an integer between 1 and 73.

47. The method of claim 46 wherein the cell is a bacterial cell.

48. The method of claim 46 wherein the cell is an insect cell.

49. The method of claim 46 wherein the cell is a yeast cell.

50. The method of claim 46 wherein the cell is a mammalian cell.