CA2420983A1 - Molecules for disease detection and treatment - Google Patents

Abstract

The present invention provides purified disease detection and treatment molecule polynucleotides (mddt). Also encompassed are the polypeptides (MDDT ) encoded by mddt. The invention also provides for the use of mddt, or complements, oligonucleotides, or fragments thereof in diagnostic assays. Th e invention further provides for vectors and host cells containing mddt for th e expression of MDDT. The invention additionally provides for the use of isolated and purified MDDT to induce antibodies and to screen libraries of compounds and the use of anti-MDDT antibodies in diagnostic assays. Also provided are microarrays containing mddt and methods of use.

Description

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MOLECULES FOR DISEASE DETECTION AND TREATMENT
TECHNICAL FIELD
The present invention relates to molecules for disease detection and treatment and to the use of these sequences in the diagnosis, study, prevention, and treatment of diseases associated with, as well as effects of exogenous compounds on, the expression of molecules for disease detection and treatment.
BACKGROUND OF THE INVENTION
The human genome is comprised of thousands of genes, many encoding gene products that function in the maintenance and growth of the various cells and tissues in the body. Aberrant expression or mutations in these genes and their products is the cause of, or is associated with, a variety of human diseases such as cancer and other cell proliferative disorders. The identification of these genes and their products is the basis of an ever-expanding effort to find markers for early detection of diseases, and targets for their prevention and treatment.
For example, cancer represents a type of cell proliferative disorder that affects nearly every tissue in the body. A wide variety of molecules, either aberrantly expressed or mutated, can be the cause of, or involved with, various cancers because tissue growth involves complex and~ordered patterns of cell proliferation, cell differentiation, and apoptosis. Cell proliferation must be regulated to maintain both the number of cells and their spatial organization. This regulation depends upon the appropriate expression of proteins which control cell cycle progression in response to extracellular signals such as growth factors and other mitogens, and intracellular cues such as DNA damage or nutrient starvation. Molecules which directly or indirectly modulate cell cycle progression fall into several categories, including growth factors and their receptors, second messenger and signal transduction proteins, oncogene products, tumor-suppressor proteins, and mitosis-promoting factors.
Aberrant expression or mutations in any of these gene products can result in cell proliferative disorders such as cancer. Oncogenes are genes generally derived from normal genes that, through abnormal expression or mutation, can effect the transformation of a normal cell to a malignant one (oncogenesis). Oncoproteins, encoded by oncogenes, can affect cell proliferation in a variety of ways and include growth factors, growth factor receptors, intracellular signal transducers, nuclear transcription factors, and cell-cycle control proteins. In contrast, tumor-suppressor genes are involved in inhibiting cell proliferation. Mutations which cause reduced or loss of function in tumor-suppressor genes result in aberrant cell proliferation and cancer. Thus a wide variety of genes and their products have been found that are associated with cell proliferative disorders such as cancer, but many more may exist that are yet to be discovered.
DNA-based arrays can provide a simple way to explore the expression of a single polymorphic gene or a large number of genes. When the expression of a single gene is explored, DNA-based arrays are employed to detect the expression of specific gene variants. For example, a p53 tumor suppressor gene array is used to determine whether individuals are carrying mutations that predispose them to cancer. A cytochrome p450 gene array is useful to determine whether individuals have one of a number of specific mutations that could result in increased drug metabolism, drug resistance or drug toxicity.
DNA-based array technology is especially relevant for the rapid screening of expression of a large number of genes. There is a growing awareness that gene expression is affected in a global fashion. A genetic predisposition, disease or therapeutic treatment may affect, directly or indirectly, the expression of a large number of genes. In some cases the interactions may be expected, such as when the genes are part of the same signaling pathway. In other cases, such as when the genes participate in separate signaling pathways, the interactions may be totally unexpected. Therefore, DNA-based arrays can be used to investigate how genetic predisposition, disease, or therapeutic treatment affects the expression of a large number of genes.
The discovery of new molecules for disease detection and treatment satisfies a need in the art by providing new compositions which are useful in the diagnosis, study, prevention, and treatment of diseases associated with, as well as effects of exogenous compounds on, the expression of molecules for disease detection and treatment.
SUMMARY OF THE INVENTION
The present invention relates to human disease detection and treatment molecule polynucleotides (mddt) as presented in the Sequence Listing. The mddt uniquely identify genes encoding structural, functional, and regulatory disease detection and treatment molecules.
The invention provides an isolated polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID
NO:1-252; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90%
identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d). In one alternative, the polynucleotide comprises a polynucleotide sequence selected from the group consisting of SEQ
ID NO:1-252. In another alternative, the polynucleotide comprises at least 30 contiguous nucleotides of a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252; b) a polynucleotide comprising a naturally occurring polynucleotide comprising a polynucleotide sequence at least 90%
identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252;
c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d). In another alternative, the polynucleotide comprises at least 60 contiguous nucleotides of a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID
NO:1-252; b) a polynucleotide comprising a naturally occurring polynucleotide comprising a polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA
equivalent of a) through d).
The invention further provides a composition for the detection of expression of disease detection and treatment molecule polynucleotides comprising at least one isolated polynucleotide comprising a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA
equivalent of a) through d); and a detectable label.
The invention also provides a method for detecting a target polynucleotide in a sample, said target polynucleotide having a polynucleotide sequence of a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence of a polynucleotide selected from the group consisting of SEQ ID NO:1-252; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA
equivalent of a) through d).
The method comprises a) amplifying said target polynucleotide or fragment thereof using polymerase chain reaction amplification, and b) detecting the presence or absence of said amplified target polynucleotide or fragment thereof, and, optionally, if present, the amount thereof.
The invention also provides a method for detecting a target polynucleotide in a sample, said target polynucleotide having a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ
ID NO:1-252; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252;
c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d). The method comprises a) hybridizing the sample with a probe comprising at least 20 contiguous, nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide, and b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof. In one alternative, the invention provides a composition comprising a target polynucleotide of the method, wherein said probe comprises at least 30 contiguous nucleotides. In one alternative, the invention provides a composition comprising a target polynucleotide of the method, wherein said probe comprises at least 60 contiguous nucleotides.
The invention further provides a recombinant polynucleotide comprising a promoter sequence operably linked to an isolated polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ
ID NO:1-252; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252;
c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d). In one alternative, the invention provides a cell transformed with the recombinant polynucleotide. In another alternative, the invention provides a transgenic organism comprising the recombinant polynucleotide.
The invention also provides a method for producing a disease detection and treatment polypeptide, the method comprising a) culturing a cell under conditions suitable for expression of the disease detection and treatment polypeptide, wherein said cell is transformed with a recombinant polynucleotide, said recombinant polynucleotide comprising an isolated polynucleotide selected from the group consisting of i) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252; ii) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252; iii) a polynucleotide complementary to the polynucleotide of i); iv) a polynucleotide complementary to the polynucleotide of ii); and v) an RNA
equivalent of i) through iv), and b) recovering the disease detection and treatment polypeptide so expressed. The invention additionally provides a method wherein the polypeptide has an amino acid sequence selected from the group consisting of SEQ ID N0:253-506.
The invention also provides an isolated disease detection and treatment polypeptide (MDDT) encoded by at least one polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:I-252. The invention further provides a method of screening for a test compound that specifically binds to the polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506. The method comprises a) combining the polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506 with at least one test compound under suitable conditions, and b) detecting binding of the polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506 to the test compound, thereby identifying a compound that specifically binds to the polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506.
The invention further provides a microarray wherein at least one element of the microarray is an isolated polynucleotide comprising at least 30 contiguous nucleotides of a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA
equivalent of a) through d).
The invention also provides a method for generating a transcript image of a sample which contains polynucleotides. The method comprises a) labeling the polynucleotides of the sample, b) contacting the elements of the microarray with the labeled polynucleotides of the sample under conditions suitable for the formation of a hybridization complex, and c) quantifying the expression of the polynucleotides in the sample.
Additionally, the invention provides a method for screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA
equivalent of a) through d). The method comprises a) exposing a sample comprising the target polynucleotide to a compound, b) detecting altered expression of the target polynucleotide, and c) comparing the expression of the target polynucleotide in the presence of varying amounts of the compound and in the absence of the compound.
The invention further provides a method for assessing toxicity of a test compound, said method comprising a) treating a biological sample containing nucleic acids with the test compound; b) hybridizing the nucleic acids of the treated biological sample with a probe comprising at least 20 contiguous nucleotides of a polynucleotide selected from the group consisting of i) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ
ID NO:I-252; ii) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252;
iii) a polynucleotide complementary to the polynucleotide of i); iv) a polynucleotide complementary to the polynucleotide of ii); and v) an RNA equivalent of i) through iv). Hybridization occurs under conditions whereby a specific hybridization complex is formed between said probe and a target polynucleotide in the biological sample, said target polynucleotide comprising a polynucleotide sequence of a polynucleotide selected from the group consisting of i) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252; ii) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:I-252; iii) a polynucleotide complementary to the polynucleotide of i); iv) a polynucleotide complementary to the polynucleotide of ii); and v) an RNA equivalent of i) through iv), and alternatively, the target polynucleotide comprises a polynucleotide sequence of a fragment of a polynucleotide selected from the group consisting of i-v above;
c) quantifying the amount of hybridization complex; and d) comparing the amount of hybridization complex in the treated biological sample with the amount of hybridization complex in an untreated biological sample, wherein a difference in the amount of hybridization complex in the treated biological sample is indicative of toxicity of the test compound.
The invention further provides an isolated polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID
N0:253-506, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90%
identical to an amino acid sequence selected from the group consisting of SEQ
ID N0:253-506, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506. In one alternative, the invention provides an isolated polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID N0:253-506.
The invention further provides an isolated polynucleotide encoding a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ
ID N0:253-506, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506. In one alternative, the polynucleotide encodes a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID N0:253-506. In another alternative, the polynucleotide comprises a polynucleotide sequence selected from the group consisting of SEQ
ID NO:1-252. , Additionally, the invention provides an isolated antibody which specifically binds to a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506.
The invention further provides a composition comprising a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, and a pharmaceutically acceptable excipient. In one embodiment, the composition comprises a polypeptide ' having an amino acid sequence selected from the group consisting of SEQ ID
N0:253-506. The invention additionally provides a method of treating a disease or condition associated with decreased expression of functional MDDT, comprising administering to a patient in need of such treatment the composition.
The invention also provides a method for screening a compound for effectiveness as an agonist of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID
N0:253-506, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506. The method comprises a) exposing a sample comprising the polypeptide to a compound, and b) detecting agonist activity in the sample. In one alternative, the invention provides a composition comprising an agonist compound identified by the method and a pharmaceutically acceptable excipient. In another alternative, the invention provides a method of treating a disease or condition associated with decreased expression of functional MDDT, comprising administering to a patient in need of such treatment the composition.
Additionally, the invention provides a method for screening a compound for effectiveness as an antagonist of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID
N0:253-506, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506. The method comprises a) exposing a S sample comprising the polypeptide to a compound, and b) detecting antagonist activity in the sample.
In one alternative, the invention provides, a composition comprising an antagonist compound identified by the method and a pharmaceutically acceptable excipient. In another alternative, the invention provides a method of treating a disease or condition associated with overexpression of functional MDDT, comprising administering to a patient in need of such treatment the composition.
The invention further provides a method of screening for a compound that modulates the activity of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group 'consisting of SEQ ID N0:253-506, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID N0:253-506, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID
N0:253-506, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID N0:253-506. The method comprises a) combining the polypeptide with at least one test compound under conditions permissive for the activity of the polypeptide, b) assessing the activity of the polypeptide in the presence of the test compound, and c) comparing the activity of the polypeptide in the presence of the test compound with the activity of the polypeptide in the absence of the test compound, wherein a change in the activity of the polypeptide in the presence of the test compound is indicative of a compound that modulates the activity of the polypeptide.
DESCRIPTION OF THE TABLES
Table 1 shows the sequence identification numbers (SEQ ID NOa) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with the sequence identification numbers (SEQ ID NOa) and open reading frame identification numbers (ORF
IDs) corresponding to polypeptides encoded by the template ID.
Table 2 shows the sequence identification numbers (SEQ ID NOa) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with their GenBank hits (GI Numbers), probability scores, and functional annotations corresponding to the GenBank hits.
Table 3 shows the sequence identification numbers (SEQ ID NOa) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with polynucleotide segments of each template sequence as defined by the indicated "start" and "stop"

nucleotide positions. The reading frames of the polynucleotide segments and the Pfam hits, Pfam descriptions, and E-values corresponding to the polypeptide domains encoded by the polynucleotide segments are indicated.
Table 4 shows the sequence identification numbers (SEQ ID NOa) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with polynucleotide segments of each template sequence as defined by the indicated "start" and "stop"
nucleotide positions. The reading frames of the polynucleotide segments are shown, and the polypeptides encoded by the polynucleotide segments constitute either signal peptide (SP) or transmembrane (TM) domains, as indicated. The membrane topology of the encoded polypeptide sequence is indicated, the N-terminus (N) listed as being oriented to either the cytosolic (N in) or non-cytosolic (N out) side of the cell membrane or organelle.
Table 5 shows the sequence identification numbers (SEQ ID NOa) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with component sequence identification numbers (component IDs) corresponding to each template. The 1~ component sequences, which were used to assemble the template sequences, are defined by the indicated "start" and "stop" nucleotide positions along each template.
Table 6 shows the tissue distribution profiles for the templates of the invention.
Table 7 shows the sequence identification numbers (SEQ ID NOa) corresponding to the polypeptides of the present invention, along with the reading frames used to obtain the polypeptide segments, the lengths of the polypeptide segments, the "start" and "stop"
nucleotide positions of the polynucleotide sequences used to define the encoded polypeptide segments, the GenBank hits (GI
Numbers), probability scores, and functional annotations corresponding to the GenBank hits.
Table 8 summarizes the bioinformatics tools which are useful for analysis of the polynucleotides of the present invention. The first column of Table 8 lists analytical tools, programs, and algorithms, the second column provides brief descriptions thereof, the third column presents appropriate references, all of which are incorporated by reference herein in their entirety, and the fourth column presents, where applicable, the scores, probability values, and other parameters used to evaluate the strength of a match between two sequences (the higher the score, the greater the homology between two sequences).
DETAILED DESCRIPTION OF THE INVENTION
Before the nucleic acid sequences and methods are presented, it is to be understood that this invention is not limited to the particular machines, methods, and materials described. Although particular embodiments are described, machines, methods, and materials similar or equivalent to these embodiments may be used to practice the invention. The preferred machines, methods, and materials set forth are not intended to limit the scope of the invention which is limited only by the appended claims.
The singular forms "a", "an", and "the" include plural reference unless the context clearly dictates otherwise. All technical and scientific terms have the meanings commonly understood by one of ordinary skill in the art. All publications are incorporated by reference for the purpose of describing and disclosing the cell lines, vectors, and methodologies which are presented and which might be used in connection with the invention. Nothing in the specification is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.
Definitions As used herein, the lower case "mddt" refers to a nucleic acid sequence, while the upper case "MDDT" refers to an amino acid sequence encoded by mddt. A "full-length" mddt refers to a nucleic acid sequence containing the entire coding region of a gene endogenously expressed in human tissue.
"Adjuvants" are materials such as Freund's adjuvant, mineral gels (aluminum hydroxide), and surface active substances (lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol) which may be administered to increase a host's immunological response.
"Allele" refers to an alternative form of a nucleic acid sequence. Alleles result from a "mutation," a change or an alternative reading of the genetic code. Any given gene may have none, one, or many allelic forms. Mutations which give rise to alleles include deletions, additions, or substitutions of nucleotides. Each of these changes may occur alone, or in combination with the others, one or more times in a given nucleic acid sequence. The present invention encompasses allelic mddt.
"Amino acid sequence" refers to a peptide, a polypeptide, or a protein of either natural or synthetic origin. The amino acid sequence is not limited to the complete, endogenous amino acid sequence and may be a fragment, epitope, variant, or derivative of a protein expressed by a nucleic acid sequence.
"Amplification" refers to the production of additional copies of a sequence and is carried out using polymerase chain reaction (PCR) technologies well known in the art.
"Antibody" refers to intact molecules as well as to fragments thereof, such as Fab, F(ab')z, and Fv fragments, which are capable of binding the epitopic determinant.
Antibodies that bind MDDT
polypeptides can be prepared using intact polypeptides or using fragments containing small peptides of interest as the immunizing antigen. The polypeptide or peptide used to immunize an animal (e.g., a mouse, a rat, or a rabbit) can be derived from the translation of RNA, or synthesized chemically, and io can be conjugated to a carrier protein if desired. Commonly used carriers that are chemically coupled to peptides include bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin (KLH). The coupled peptide is then used to immunize the animal.
"Antisense sequence" refers to a sequence capable of specifically hybridizing to a target sequence. The antisense sequence may include DNA, RNA, or any nucleic acid mimic or analog such as peptide nucleic acid (PNA); oligonucleotides having modified backbone linkages such as phosphorothioates, methylphosphonates, or benzylphosphonates; oligonucleotides having modified sugar groups such as 2'-methoxyethyl sugars or 2'-methoxyethoxy sugars; or oligonucleotides having modified bases such as 5-methyl cytosine, 2'-deoxyuracil, or 7-deaza-2'-deoxyguanosine.
"Antisense sequence" refers to a sequence capable of specifically hybridizing to a target sequence. The antisense sequence can be DNA, RNA, or any nucleic acid mimic or analog.
"Antisense technology" refers to any technology which relies on the specific hybridization of an antisense sequence to a target sequence.
A "bin" is a portion of computer memory space used by a computer program for storage of data, and bounded in such a manner that data stored in a bin may be retrieved by the program.
"Biologically active" refers to an amino acid sequence having a structural, regulatory, or biochemical function of a naturally occurring amino acid sequence.
"Clone joining" is a process for combining gene bins based upon the bins' containing sequence information from the same clone. The sequences may assemble into a primary gene transcript as well as one or more splice variants.
"Complementary" describes the relationship between two single-stranded nucleic acid sequences that anneal by base-pairing (5'-A-G-T-3' pairs with its complement 3'-T-C-A-5').
A "component sequence" is a nucleic acid sequence selected by a computer program such as PHRED and used to assemble a consensus or template sequence from one or more component sequences.
A "consensus sequence" or "template sequence" is a nucleic acid sequence which has been assembled from overlapping sequences, using a computer program for fragment assembly such as the GELVIEW fragment assembly system (Genetics Computer Group (GCG), Madison WI) or using a relational database management system (RDMS).
"Conservative amino acid substitutions" are those substitutions that, when made, least interfere with the properties of the original protein, i.e., the structure and especially the function of the protein is conserved and not significantly changed by such substitutions. The table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative substitutions.

Original Residue Conservative Substitution Ala Gly, Ser Arg His, Lys Asn Asp, Gln, His Asp Asn, Glu Cys Ala, Ser Gln Asn, Glu, His Glu Asp, Gln, His Gly Ala His Asn, Arg, Gln, Glu Ile Leu, Val Leu Ile, Val Lys Arg, Gln, Glu Met Leu, Ile Phe His, Met, Leu, Trp, Tyr Ser Cys, Thr Thr Ser, Val Trp Phe, Tyr Tyr His, Phe, Trp Val Ile, Leu, Thr Conservative substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a beta sheet or alpha helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.
"Deletion" refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or amino acid residue, respectively, is absent.
"Derivative" refers to the chemical modification of a nucleic acid sequence, such as by replacement of hydrogen by an alkyl, acyl, amino, hydroxyl, or other group.
"Differential expression" refers to increased or upregulated; or decreased, downregulated, or absent gene or protein expression, determined by comparing at least two different samples. Such comparisons may be carried out between, for example, a treated and an untreated sample, or a diseased and a normal sample.
The terms "element" and "array element" refer to a polynucleotide, polypeptide, or other chemical compound having a unique and defined position on a microarray.
"E-value" refers to the statistical probability that a match between two sequences occurred by chance.
"Exon shuffling" refers to the recombination of different coding regions (exons). Since an exon may represent a structural or functional domain of the encoded protein, new proteins may be assembled through the novel reassortment of stable substructures, thus allowing acceleration of the evolution of new protein functions.

A "fragment" is a unique portion of mddt or MDDT which is identical in sequence to but shorter in length than the parent sequence. A fragment may comprise up to the entire length of the defined sequence, minus one nucleotide/amino acid residue. For example, a fragment may comprise from 10 to 1000 contiguous amino acid residues or nucleotides. A fragment used as a probe, primer, antigen, therapeutic molecule, or for other purposes, may be at least 5, 10, 15, 16, 20, 25, 30, 40, 50, 60, 75, 100, 150, 250 or at least 500 contiguous amino acid residues or nucleotides in length. Fragments may be preferentially selected from certain regions of a molecule. For example, a polypeptide fragment may comprise a certain length of contiguous amino acids selected from the first 250 or 500 amino acids (or first 25% or SO%) of a polypeptide as shown in a certain defined sequence. Clearly these lengths are exemplary, and any length that is supported by the specification, including the Sequence Listing and the figures, may be encompassed by the present embodiments.
A fragment of mddt comprises a region of unique polynucleotide sequence that specifically identifies mddt, for example, as distinct from any other sequence in the same genome. A fragment of mddt is useful, for example, in hybridization and amplification technologies and in analogous methods that distinguish mddt from related polynucleotide sequences. The precise length of a fragment of mddt and the region of mddt to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.
A fragment of MDDT is encoded by a fragment of mddt. A fragment of MDDT
comprises a region of unique amino acid sequence that specifically identifies MDDT. For example, a fragment of MDDT is useful as an immunogenic peptide for the development of antibodies that specifically recognize MDDT. The precise length of a fragment of MDDT and the region of MDDT to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.
A "full length" nucleotide sequence is one containing at least a start site for translation to a protein sequence, followed by an open reading frame and a stop site, and encoding a "full length"
polypeptide.
"Hit" refers to a sequence whose annotation will be used to describe a given template.
Criteria for selecting the top hit are as follows: if the template has one or more exact nucleic acid matches, the top hit is the exact match with highest percent identity. If the template has no exact matches but has significant protein hits, the top hit is the protein hit with the lowest E-value. If the template has no significant protein hits, but does have significant non-exact nucleotide hits, the top hit is the nucleotide hit with the lowest E-value.
"Homology" refers to sequence similarity either between a reference nucleic acid sequence and at least a fragment of an mddt or between a reference amino acid sequence and a fragment of an MDDT.

"Hybridization" refers to the process by which a strand of nucleotides anneals with a complementary strand through base pairing. Specific hybridization is an indication that two nucleic acid sequences share a high degree of identity. Specific hybridization complexes form under defined annealing conditions, and remain hybridized after the "washing" step. The defined hybridization conditions include the annealing conditions and the washing step(s), the latter of which is particularly important in determining the stringency of the hybridization process, with more stringent conditions allowing less non-specific binding, i.e., binding between pairs of nucleic acid probes that are not perfectly matched. Permissive conditions for annealing of nucleic acid sequences are routinely determinable and may be consistent among hybridization experiments, whereas wash conditions may be varied among experiments to achieve the desired stringency.
Generally, stringency of hybridization is expressed with reference to the temperature under which the wash step is carried out. Generally, such wash temperatures are selected to be about 5°C
to 20°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 and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. An equation for calculating Tm and conditions for nucleic acid hybridization is well known and can be found in Sambrook et al., 1989, Molecular Cloning:
A Laboratory Manual, 2"° ed., vol. 1-3, Cold Spring Harbor Press, Plainview NY; specifically see volume 2, chapter 9.
High stringency conditions for hybridization between polynucleotides of the present invention include wash conditions of 68°C in the presence of about 0.2 x SSC and about 0.1 % SDS, for 1 hour.
Alternatively, temperatures of about 65°C, 60°C, or 55°C
may be used. SSC concentration may be varied from about 0.2 to 2 x SSC, with SDS being present at about 0.1 %.
Typically, blocking reagents are used to block non-specific hybridization. Such blocking reagents include, for instance, denatured salmon sperm DNA at about 100-200 pg/ml. Useful variations on these conditions will be readily apparent to those skilled in the art. Hybridization, particularly under high stringency conditions, may be suggestive of evolutionary similarity between the nucleotides. Such similarity is strongly indicative of a similar role for the nucleotides and their resultant proteins.
Other parameters, such as temperature, salt concentration, and detergent concentration may be varied to achieve the desired stringency. Denaturants, such as formamide at a concentration of about 35-50% v/v, may also be used under particular circumstances, such as RNA:DNA
hybridizations. Appropriate hybridization conditions are routinely determinable by one of ordinary skill in the art.
"Immunologically active" or "immunogenic" describes the potential for a natural, recombinant, or synthetic peptide, epitope, polypeptide, or protein to induce antibody production in appropriate animals, cells, or cell lines.

"Insertion" or "addition" refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or residue, respectively, is added to the sequence.
"Labeling" refers to the covalent or noncovalent joining of a polynucleotide, polypeptide, or antibody with a reporter molecule capable of producing a detectable or measurable signal.
"Microarray" is any arrangement of nucleic acids, amino acids, antibodies, etc., on a substrate. The substrate may be a solid support such as beads, glass, paper, nitrocellulose, nylon, or an appropriate membrane.
"Linkers" are short stretches of nucleotide sequence which may be added to a vector or an mddt to create restriction endonuclease sites to facilitate cloning.
"Polylinkers" are engineered to incorporate multiple restriction enzyme sites and to provide for the use of enzymes which leave 5' or 3' overhangs (e.g., BamHI, EcoRI, and HindIII) and those which provide blunt ends (e.g., EcoRV, SnaBI, and StuI).
"Naturally occurring" refers to an endogenous polynucleotide or polypeptide that may be isolated from viruses or prokaryotic or eukaryotic cells.
"Nucleic acid sequence" refers to the specific order of nucleotides joined by phosphodiester bonds in a linear, polymeric arrangement. Depending on the number of nucleotides, the nucleic acid sequence can be considered an oligomer, oligonucleotide, or polynucleotide.
The nucleic acid can be DNA, RNA, or any nucleic acid analog, such as PNA, may be of genomic or synthetic origin, may be either double-stranded or single-stranded, and can represent either the sense or antisense (complementary) strand.
"Oligomer" refers to a nucleic acid sequence of at least about 6 nucleotides and as many as about 60 nucleotides, preferably about 15 to 40 nucleotides, and most preferably between about 20 and nucleotides, that may be used in hybridization or amplification technologies.
Oligomers may be -used as, e.g., primers for PCR, and are usually chemically synthesized.
25 "Operably linked" refers to the situation in which a first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences may be in close proximity or contiguous and, where necessary to join two protein coding regions, in the same reading frame.
30 "Peptide nucleic acid" (PNA) refers to a DNA mimic in which nucleotide bases are attached to a pseudopeptide backbone to increase stability. PNAs, also designated antigene agents, can prevent gene expression by targeting complementary messenger RNA.
The phrases "percent identity" and "% identity", as applied to polynucleotide sequences, refer to the percentage of residue matches between at least two polynucleotide sequences aligned using a standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in is the sequences being compared in order to optimize alignment between two sequences, and therefore achieve a more meaningful comparison of the two sequences.
Percent identity between polynucleotide sequences may be determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN
version 3.12e sequence alignment program. This program is part of the LASERGENE software package, a suite of molecular biological analysis programs (DNASTAR, Madison WI). CLUSTAL V is described in Higgins, D.G. and Sharp, P.M. (1989) CABIOS 5:151-153 and in Higgins, D.G. et al. (1992) CABIOS
8:189-191. For pairwise alignments of polynucleotide sequences, the default parameters are set as follows: Ktuple=2, gap penalty=5, window=4, and "diagonals saved"=4. The "weighted" residue weight table is selected as the default. Percent identity is reported by CLUSTAL V as the "percent similarity" between aligned polynucleotide sequence pairs.
Alternatively, a suite of commonly used and freely available sequence comparison algorithms is provided by the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) (Altschul, S.F. et al. (1990) J. Mol. Biol. 215:403-410), which is available from several sources, including the NCBI, Bethesda, MD, and on the Internet at http://www.ncbi.nlm.nih.gov/BLAST/. The BLAST software suite includes various sequence analysis programs including "blastn," that is used to determine alignment between a known polynucleotide sequence and other sequences on a variety of databases. Also available is a tool called "BLAST 2 Sequences" that is used for direct pairwise comparison of two nucleotide sequences. "BLAST 2 Sequences" can be accessed and used interactively at http://www.ncbi.nlm.nih.gov/gorf/b12/. The "BLAST 2 Sequences" tool can be used for both blastn and blastp (discussed below). BLAST
programs are commonly used with gap and other parameters set to default settings. For example, to compare two nucleotide sequences, one may use blastn with the "BLAST 2 Sequences" tool Version 2Ø9 (May-07-1999) set at default parameters. Such default parameters may be, for example:
Matrix: BLOSUM62 Reward for match: I
Penalty for mismatch: -2 Open Gap: 5 and Extension Gap: 2 penalties Gap x drop-off:' S0 Expect: l0 Word Size: 11 Filter: on Percent identity may be measured over the length of an entire defined sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined sequence, for instance, a fragment of at least 20, at least 30, at least 40, at least 50, at least 70, at least 100, or at least 200 contiguous nucleotides. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in figures or Sequence Listings, may be used to describe a length over which percentage identity may be measured.
Nucleic acid sequences that do not show a high degree of identity may nevertheless encode similar amino acid sequences due to the degeneracy of the genetic code. It is understood that changes in nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid sequences that all encode substantially the same protein.
The phrases "percent identity" and "% identity", as applied to polypeptide sequences, refer to the percentage of residue matches between at least two polypeptide sequences aligned using a standardized algorithm. Methods of polypeptide sequence alignment are well-known. Some alignment methods take into account conservative amino acid substitutions. Such conservative substitutions, explained in more detail above, generally preserve the hydrophobicity and acidity of the substituted residue, thus preserving the structure (and therefore function) of the folded polypeptide.
Percent identity between polypeptide sequences may be determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN
version 3.12e sequence alignment program (described and referenced above). For pairwise alignments of polypeptide sequences using CLUSTAL V, the default parameters are set as follows: Ktuple=1, gap penalty=3, window=5, and "diagonals saved"=5. The PAM250 matrix is selected as the default residue weight table. As with polynucleotide alignments, the percent identity is reported by CLUSTAL V as the "percent similarity" between aligned polypeptide sequence pairs.
Alternatively the NCBI BLAST software suite may be used. For example, for a pairwise comparison of two polypeptide sequences, one may use the "BLAST 2 Sequences"
tool V''ersion 2Ø9 (May-07-1999) with blastp set at default parameters. Such default parameters may be, for example:
Matrix: BLOSUM62 Open Gap: 71 and Extension Gap: 1 penalty Gap x drop-off: 50 Expect: l0 Word Size: 3 Filter: on Percent identity may be measured over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, a fragment of at least 15, at least 20, at least 30, at least 40, at least 50, at least 70 or at least I50 contiguous residues. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in figures or Sequence Listings, may be used to describe a length over which percentage identity may be measured.
"Post-translational modification" of an MDDT may involve lipidation, glycosylation, phosphorylation, acetylation,-racemization, proteolytic cleavage, and other modifications known in the art. These processes may occur synthetically or biochemically. Biochemical modifications will vary by cell type depending on the enzymatic milieu and the MDDT.
"Probe" refers to mddt or fragments thereof, which are used to detect identical, allelic or related nucleic acid sequences. Probes are isolated oligonucleotides or polynucleotides attached to a detectable label or reporter molecule. Typical labels include radioactive isotopes, ligands, chemiluminescent agents, and enzymes. "Primers" are short nucleic acids, usually DNA
oligonucleotides, which may be annealed to a target polynucleotide by complementary base-pairing.
The primer may then be extended along the target DNA strand by a DNA
polymerase enzyme.
Primer pairs can be used for amplification (and identification) of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR).
Probes and primers as used in the present invention typically comprise at least 15 contiguous nucleotides of a known sequence. In order to enhance specificity, longer probes and primers may also be employed, such as probes and primers that comprise at least 20, 30, 40, 50, 60, 70, 80, 90, 100, or at least 150 consecutive nucleotides of the disclosed nucleic acid sequences.
Probes and primers may be considerably longer than these examples, and it is understood that any length supported by the specification, including the figures and Sequence Listing; may be used.
Methods for preparing and using probes and primers are described in the references, for example Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2"d ed., vol. 1-3, Cold Spring Harbor Press, Plainview NY; Ausubel et a1.,1987, Current Protocols in Molecular Biology, Greene Publ. Assoc. & Wiley-Intersciences, New York NY; Innis et al., 1990, PCR Protocols, A
Guide to Methods and Applications, Academic Press, San Diego CA. PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5, 1991, Whitehead Institute for Biomedical Research, Cambridge MA).
Oligonucleotides for use as primers are selected using software known in the art for such purpose. For example, OLIGO 4.06 software is useful for the selection of PCR
primer pairs of up to 100 nucleotides each, and for the analysis of oligonucleotides and larger polynucleotides of up to 5,000 nucleotides from an input polynucleotide sequence of up to 32 kilobases.
Similar primer selection programs have incorporated additional features for expanded capabilities. For example, the PrimOU
primer selection program (available to the public from the Genome Center at University of Texas South West Medical Center, Dallas TX) is capable of choosing specific primers from megabase sequences and is thus useful for designing primers on a genome-wide scope. The Primer3 primer selection program (available to the public from the Whitehead Institute/MIT
Center for Genome Research, Cambridge MA) allows the user to input a "mispriming library," in which sequences to avoid as primer binding sites are user-specified. Primer3 is useful, in particular, for the selection of oligonucleotides for microarrays. (The source code for the latter two primer selection programs may also be obtained from their respective sources and modified to meet the user's specific needs.) The PrimeGen program (available to the public from the UK Human Genome Mapping Project Resource Centre, Cambridge UK) designs primers based on multiple sequence alignments, thereby allowing selection of primers that hybridize to either the most conserved or least conserved regions of aligned nucleic acid sequences. Hence, this program is useful for identification of both unique and conserved oligonucleotides and polynucleotide fragments. The oligonucleotides and polynucleotide fragments identified by any of the above selection methods are useful in hybridization technologies, for example, as PCR or sequencing primers, microarray elements, or specific probes to identify fully or partially complementary polynucleotides in a sample of nucleic acids. Methods of oligonucleotide selection are not limited to those described above.
"Purified" refers to molecules, either polynucleotides or polypeptides that are isolated or separated from their natural environment and are at least 60% free, preferably at least 75% free, and most preferably at least 90% free from other compounds with which they are naturally associated.
A "recombinant nucleic acid" is a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two or more otherwise separated segments of sequence.
This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques such as those described in Sambrook, su ra. The term recombinant includes nucleic acids that have been altered solely by addition, substitution, or deletion of a portion of the nucleic acid. Frequently, a recombinant nucleic acid may include a nucleic acid sequence operably linked to a promoter sequence.
Such a recombinant nucleic acid may be part of a vector that is used, for example, to transform a cell.
Alternatively, such recombinant nucleic acids may be part of a viral vector, e.g., based on a vaccinia virus, that could be use to vaccinate a mammal wherein the recombinant nucleic acid is expressed, inducing a protective immunological response in the mammal.
"Regulatory element" refers to a nucleic acid sequence from nontranslated regions of a gene, and includes enhancers, promoters, introns, and 3' untranslated regions, which interact with host proteins to cant' out or regulate transcription or translation.
"Reporter" molecules are chemical or biochemical moieties used for labeling a nucleic acid, an amino acid, or an antibody. They include radionuclides; enzymes; fluorescent, chemiluminescent, or chromogenic agents; substrates; cofactors; inhibitors; magnetic particles; and other moieties known in the art.

An "RNA equivalent," in reference to a DNA sequence, is composed of the same linear sequence of nucleotides as the reference DNA sequence with the exception that all occurrences of the nitrogenous base thymine are replaced with uracil, and the sugar backbone is composed of ribose instead of deoxyribose.
"Sample" is used in its broadest sense. Samples may contain nucleic or amino acids, antibodies, or other materials, and may be derived from any source (e.g., bodily fluids including, but not limited to, saliva, blood, and urine; chromosome(s), organelles, or membranes isolated from a cell;
genomic DNA, RNA, or cDNA in solution or bound to a substrate; and cleared cells or tissues or blots or imprints from such cells or tissues).
"Specific binding" or "specifically binding" refers to the interaction between a protein or peptide and its agonist, antibody, antagonist, or other binding partner. The interaction is dependent upon the presence of a particular structure of the protein, e.g., the antigenic determinant or epitope, recognized by the binding molecule. For example, if an antibody is specific for epitope "A," the presence of a polypeptide containing epitope A, or the presence of free unlabeled A, in a reaction containing free labeled A and the antibody will reduce the amount of labeled A
that binds to the antibody.
"Substitution" refers to the replacement of at least one nucleotide or amino acid by a different nucleotide or amino acid.
"Substrate" refers to any suitable rigid or semi-rigid support including, e.g., membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, tubing, plates, polymers, microparticles or capillaries. The substrate can have a variety of surface forms, such as wells, trenches, pins, channels and pores, to which polynucleotides or polypeptides are bound.
A "transcript image" refers to the collective pattern of gene expression by a particular tissue' or cell type under given conditions at a given time.
"Transformation" refers to a process by which exogenous DNA enters a recipient cell.
Transformation may occur under natural or artificial conditions using various methods well known in the art. Transformation may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method is selected based on the host cell being transformed.
"Transformants" include stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as cells which transiently express inserted DNA or RNA.
A "transgenic organism," as used herein, is any organism, including but not limited to animals and plants, in which one or more of the cells of the organism contains heterologous nucleic acid introduced by way of human intervention, such as by transgenic techniques well known in the art. The 2o nucleic acid is introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by microinjection or by infection with a recombinant virus. The term genetic manipulation does not include classical cross-breeding, or in vitro fertilization, but rather is directed to the introduction of a recombinant DNA
molecule. The transgenic organisms contemplated in accordance with the present invention include bacteria, cyanobacteria, fungi, and plants and animals. The isolated DNA of the present invention can be introduced into the host by methods known in the art, for example infection, transfection, transformation or transconjugation. Techniques for transferring the DNA of the present invention into such organisms are widely known and provided in references such as Sambrook et al. (1989), suura.
A "variant" of a particular nucleic acid sequence is defined as a nucleic acid sequence having at least 25% sequence identity to the particular nucleic acid sequence over a certain length of one of the nucleic acid sequences using blastn with the "BLAST 2 Sequences" tool Version 2Ø9 (May-07-1999) set at default parameters. Such a pair of nucleic acids may show, for example, at least 30%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater sequence identity over a certain defined length. The variant may result in "conservative" amino acid changes which do not affect structural and/or chemical properties. A variant may be described as, for example, an "allelic" (as defined above), "splice," "species," or "polymorphic" variant. A splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate splicing of exons during mRNA processing. The corresponding polypeptide may possess additional functional domains or lack domains that are present in the reference molecule. Species variants are polynucleotide sequences that vary from one species to another. The resulting polypeptides generally will have significant amino acid identity relative to each other. A polymorphic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species.
Polymorphic variants also may encompass "single nucleotide polymorphisms" (SNPs) in which the polynucleotide sequence varies by one base. The presence of SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.
In an alternative, variants of the polynucleotides of the present invention may be generated through recombinant methods. One possible method is a DNA shuffling technique such as MOLECULARBREEDING (Maxygen Inc., Santa Clara CA; described in U.S. Patent Number 5,837,458; Chang, C.-C. et al. (1999) Nat. Biotechnol. 17:793-797; Christians, F.C. et al. (1999) Nat.
Biotechnol. 17:259-264; and Crameri, A. et al. (1996) Nat. Biotechnol. 14:315-319) to alter or improve the biological properties of MDDT, such as its biological or enzymatic activity or its ability to bind to other molecules or compounds. DNA shuffling is a process by which a library of gene variants is produced using PCR-mediated recombination of gene fragments. The library is then subjected to selection or screening procedures that identify those gene variants with the desired properties. These preferred variants may then be pooled and further subjected to recursive rounds of DNA shuffling and selection/screening. Thus, genetic diversity is created through "artificial"
breeding and rapid molecular evolution. For example, fragments of a single gene containing random point mutations may be recombined, screened, and then reshuffled until the desired properties are optimized. Alternatively, fragments of a given gene may be recombined with fragments of homologous genes in the same gene family, either from the same or different species, thereby maximizing the genetic diversity of multiple naturally occurring genes in a directed and controllable manner.
A "variant" of a particular polypeptide sequence is defined as a polypeptide sequence having at least 40% sequence identity to the particular polypeptide sequence over a certain length of one of the polypeptide sequences using blastp with the "BLAST 2 Sequences" tool Version 2Ø9 (May-07-1999) set at default parameters. Such a pair of polypeptides may show, for example, at least 50%; at least 60%, at least 70%, at least 80%~, at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%
or greater sequence identity over a certain defined length of one of the polypeptides.
THE INVENTION
In a particular embodiment, cDNA sequences derived from human tissues and cell lines were aligned based on nucleotide sequence identity and assembled into "consensus"
or "template"
sequences which are designated by the template identification numbers (template IDs) in column 2 of Table 2. The sequence identification numbers (SEQ ID NOa) corresponding to the template IDs are shown in column 1. The template sequences have similarity to GenBank sequences, or "hits," as designated by the GI Numbers in column 3. The statistical probability of each GenBank hit is indicated by a probability score in column 4, and the functional annotation corresponding to each GenBank hit is listed in column 5.
The invention incorporates the nucleic acid sequences of these templates as disclosed in the Sequence Listing and the use of these sequences in the diagnosis and treatment of disease states characterized by defects in disease detection and treatment molecules. The invention further utilizes these sequences in hybridization and amplification technologies, and in particular, in technologies which assess gene expression patterns correlated with specific cells or tissues and their responses in vivo or in vitro to pharmaceutical agents, toxins, and other treatments. In this manner, the sequences of the present invention are used to develop a transcript image for a particular cell or tissue.
Derivation of Nucleic Acid Sequences eDNA was isolated from libraries constructed using RNA derived from normal and diseased human tissues and cell lines. The human tissues and cell lines used for cDNA
library construction were selected from a broad range of sources to provide a diverse population of cDNAs representative of gene transcription throughout the human body. Descriptions of the human tissues and cell lines used for cDNA library construction are provided in the LIFESEQ database (Incyte Genomics, Inc.
(Incyte), Palo Alto CA). Human tissues were broadly selected from, for example, cardiovascular, dermatologic, endocrine, gastrointestinal, hematopoieticlimmune system, musculoskeletal, neural, reproductive, and urologic sources.
Cell lines used for eDNA library construction were derived from, for example, leukemic cells, teratocarcinomas, neuroepitheliomas, cervical carcinoma, lung fibroblasts, and endothelial cells. Such cell lines include, for example, THP-1, Jurkat, HUVEC, hNT2, WI38, HeLa, and other cell lines commonly used and available from public depositories (American Type Culture Collection, Manassas VA). Prior to mRNA isolation, cell lines were untreated, treated with a pharmaceutical agent such as 5'-aza-2'-deoxycytidine, treated with. an activating agent such as lipopolysaccharide in the case of leukocytic cell lines, or, in the case of endothelial cell lines, subjected to shear stress.
Sequencing of the cDNAs Methods for DNA sequencing are well known in the art. Conventional enzymatic methods employ the Klenow fragment of DNA polymerase I, SEQUENASE DNA polymerase (U.S.
Biochemical Corporation, Cleveland OH), Taq polymerase (Applied Biosystems, Foster City CA), thermostable T7 polymerase (Amersham Pharmacia Biotech, Inc. (Amersham Pharmacia Biotech), Piscataway NJ), or combinations of polymerases and proofreading exonucleases such as those found in the ELONGASE amplification system (Life Technologies Inc. (Life Technologies), Gaithersburg MD), to extend the nucleic acid sequence from an oligonucleotide primer annealed to the DNA
template of interest. Methods have been developed for the use of both single-stranded and double-stranded templates. Chain termination reaction products may be electrophoresed on urea-polyacrylamide gels and detected either by autoradiography (for radioisotope-labeled nucleotides) or by fluorescence (for fluorophore-labeled nucleotides). Automated methods for mechanized reaction preparation, sequencing, and analysis using fluorescence detection methods have been developed.
Machines used to prepare cDNAs for sequencing can include the MICROLAB 2200 liquid transfer system (Hamilton Company (Hamilton), Reno NV), Peltier thermal cycler (PTC200;
MJ Research, Inc. (MJ Research), Watertown MA), and ABI CATALYST 800 thermal cycler (Applied Biosystems). Sequencing can be carried out using, for example, the ABI 373 or 377 (Applied Biosystems) or MEGABACE 1000 (Molecular Dynamics, Inc. (Molecular Dynamics), Sunnyvale CA) DNA sequencing systems, or other automated and manual sequencing systems well known in the art.
The nucleotide sequences of the Sequence Listing have been prepared by current, state-of-the-art, automated methods and, as such, may contain occasional sequencing errors or unidentified nucleotides. Such unidentified nucleotides are designated by an N. These infrequent unidentified bases do not represent a hindrance to practicing the invention for those skilled in the art. Several methods employing standard recombinant techniques may be used to correct errors and complete the missing sequence information. (See, e.g., those described in Ausubel, F.M. et al. (1997) Short Protocols in Molecular BioloQV, John Wiley & Sons, New York NY; and Sambrook, 1. et al. (1989) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, Plainview NY.) Assembly of cDNA Seouences Human polynucleotide sequences may be assembled using programs or algorithms well known in the art. Sequences to be assembled are related, wholly or in part, and may be derived from a single or many different transcripts. Assembly of the sequences can be performed using such programs as IS PHRAP (Phils Revised Assembly Program) and the GELVIEW fragment assembly system (GCG), or other methods known in the art.
Alternatively, cDNA sequences are used as "component" sequences that are assembled into "template" or "consensus" sequences as follows. Sequence chromatograms are processed, verified, and quality scores are obtained using PHRED. Raw sequences are edited using an editing pathway known as Block 1 (See, e.g., the LIFESEQ Assembled User Guide, Incyte Genomics, Palo Alto, CA).
A series of BLAST comparisons is performed and low-information segments and repetitive elements (e.g., dinucleotide repeats, Alu repeats, etc.) are replaced by "n's", or masked, to prevent spurious matches. Mitochondria) and ribosomal RNA sequences are also removed. The processed' sequences are then loaded into a relational database management system (RDMS) which assigns edited sequences to existing templates, if available. When additional sequences are added into the RDMS, a process is initiated which modifies existing templates or creates new templates from works in progress (i.e., nonfinal assembled sequences) containing queued sequences or the sequences themselves. After the new sequences have been assigned to templates, the templates can be merged into bins. If multiple templates exist in one bin, the bin can be split and the templates reannotated.
Once gene bins have been generated based upon sequence alignments, bins are "clone joined"
based upon clone information. Clone joining occurs when the 5' sequence of one clone is present in one bin and the 3' sequence from the same clone is present in a different bin, indicating that the two bins should be merged into a single bin. Only bins which share at least two different clones are merged.
A resultant template sequence may contain either a partial or a full length open reading frame, or all or part of a genetic regulatory element. This variation is due in pan to the fact that the full length cDNAs of many genes are several hundred, and sometimes several thousand, bases in length.
With current technology, cDNAs comprising the coding regions of large genes cannot be cloned because of vector limitations, incomplete reverse transcription of the mRNA, or incomplete "second strand" synthesis. Template sequences may be extended to include additional contiguous sequences derived from the parent RNA transcript using a variety of methods known to those of skill in the art.
Extension may thus be used to achieve the full length coding sequence of a gene.
Ana>ysis of the cDNA Sequences The cDNA sequences are analyzed using a variety of programs and algorithms which are well known in the art. (See, e.g., Ausubel, 1997, supra, Chapter 7.7; Meyers, R.A. (Ed.) ( 1995) Molecular Biology and Biotechnoloay, Wiley VCH, New York NY, pp. 856-853; and Table 8.) These analyses comprise both reading frame determinations, e.g., based on triplet codon periodicityfor particular organisms (Fickett, J.W. (1982) Nucleic Acids Res. 10:5303-5318);
analyses of potential 1 S start and stop codons; and homology searches.
Computer programs known to those of skill in the art for performing computer-assisted searches for amino acid and nucleic acid sequence similarity, include, for example, Basic Local Alignment Search Tool (BLAST; Altschul, S.F. (1993) J. Mol. Evol. 36:290-300;
Altschul, S.F. et al.
(1990) 1. Mol. Biol. 215:403-410). BLAST is especially useful in determining exact matches and comparing two sequence fragments of arbitrary but equal lengths, whose alignment is locally maximal and for which the alignment score meets or exceeds a threshold or cutoff score set by the user (Karlin, S. et al. (1988) Proc. Nat!. Acad. Sci. USA 85:841-845). Using an appropriate search tool (e.g., BLAST or HMM), GenBank, SwissProt, BLOCKS, PFAM and other databases may be searched for sequences containing regions of homology to a query mddt or MDDT
of the present invention.
Other approaches to the identification, assembly, storage, and display of nucleotide and polypeptide sequences are provided in "Relational Database for Storing Biomolecule Information,"
U.S.S.N. 08/947,845, filed October 9, 1997; "Project-Based Full-Length Biomolecular Sequence Database," U.S.S.N. 08/811,758, filed March 6, 1997; and "Relational Database and System for Storing Information Relating to Biomolecular Sequences," U.S.S.N. 09/034,807, filed March 4, 1998, all of which are incorporated by reference herein in their entirety.
Protein hierarchies can be assigned to the putative encoded polypeptide based on, e.g., motif, BLAST, or biological analysis. Methods for assigning these hierarchies are described, for example, in "Database System Employing Protein Function Hierarchies for Viewing Biomolecular Sequence Data," U.S.S.N. 08/812;290, filed March 6, 1997, incorporated herein by reference.

Human Disease Detection and Treatment Molecule Sequences The mddt of the present invention may be used for a variety of diagnostic and therapeutic purposes. For example, an mddt may be used to diagnose a particular condition, disease, or disorder associated with disease detection and treatment molecules. Such conditions, diseases, and disorders include, but are not limited to, a cell proliferative disorder, such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, a cancer of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus;
and an autoimmune/inflammatory disorder, such as actinic keratosis, acquired immunodeficiency syndrome (AIDS), Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, arteriosclerosis, asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis, bronchitis, bursitis, cholecystitis, cirrhosis, contact dermatitis, Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus, emphysema, erythroblastosis fetalis, erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves' disease, Hashimoto's thyroiditis, paroxysmal nocturnal hemoglobinuria, hepatitis, hypereosinophilia, irritable bowel syndrome, episodic lymphopenia with lymphocytotoxins, mixed connective tissue disease (MCTD), multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, myelofibrosis, osteoarthritis, osteoporosis, pancreatitis, polycythemia vera, polymyositis, psoriasis, Reiter's syndrome, rheumatoid arthritis, scleroderma, Sjogren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, primary thrombocythemia, thrombocytopenic purpura, ulcerative colitis, uveitis, Wemer syndrome, complications of cancer, hemodialysis, and extracorporeal circulation, trauma, and hematopoietic cancer including lymphoma, leukemia, and myeloma. The mddt can be used to detect the presence of, or to quantify the amount of, an mddt-related polynucleotide in a sample. This information is then compared to information obtained from appropriate reference samples, and a diagnosis is established. Alternatively, a polynucleotide complementary to a given mddt can inhibit or inactivate a therapeutically relevant gene related to the mddt.
Analysis of mddt Expression Patterns The expression of mddt may be routinely assessed by hybridization-based methods to determine, for example, the tissue-specificity, disease-specificity, or developmental stage-specificity of mddt expression. For example, the level of expression of mddt may be compared among different cell types or tissues, among diseased and normal cell types or tissues, among cell types or tissues at different developmental stages, or among cell types or tissues undergoing various treatments. This type of analysis is useful, for example, to assess the relative levels of mddt expression in fully or partially differentiated cells or tissues, to determine if changes in mddt expression levels are correlated with the development or progression of specific disease states, and to assess the response of a cell or tissue to a specific therapy, for example, in pharmacological or toxicological studies. Methods for the analysis of mddt expression are based on hybridization and amplification technologies and include membrane-based procedures such as northern blot analysis, high-throughput procedures that utilize, for example, microarrays, and PCR-based procedures.
Hybridization and Genetic Analysis The mddt, their fragments, or complementary sequences, may be used to identify the presence of and/or to determine the degree of similarity between two (or more) nucleic acid sequences. The mddt may be hybridized to naturally occurring or recombinant nucleic acid sequences under appropriately selected temperatures and salt concentrations. Hybridization with a probe based on the nucleic acid sequence of at least one of the mddt allows for the detection of nucleic acid sequences, including genomic sequences, which are identical or related to the mddt of the Sequence Listing.
Probes may be selected from non-conserved or unique regions of at least one of the polynucleotides of SEQ ID NO:1-252 and tested for their ability to identify or amplify the target nucleic acid sequence using standard protocols.
Polynucleotide sequences that are capable of hybridizing, in particular, to those shown in SEQ
ID NO: I-252 and fragments thereof, can be identified using various conditions of stringency. (See, e.g., Wahl, G.M. and S.L. Berger (1987) Methods Enzymol. 152:399-407; Kimmel, A.R. ( 1987) ' Methods Enzymol. 152:507-51 I.) Hybridization conditions are discussed in "Definitions."
A probe for use in Southern or northern hybridization may be derived from a fragment of an mddt sequence, or its complement, that is up to several hundred nucleotides in length and is either single-stranded or double-stranded. Such probes may be hybridized in solution to biological materials such as plasmids, bacterial, yeast, or human artificial chromosomes, cleared or sectioned tissues, or to artificial substrates containing mddt. Microarrays are particularly suitable for identifying the presence of and detecting the level of expression for multiple genes of interest by examining gene expression correlated with, e.g., various stages of development, treatment with a drug or compound, or disease progression. An array analogous to a dot or slot blot may be used to arrange and link polynucleotides to the surface of a substrate using one or more of the following: mechanical (vacuum), chemical, thermal, or UV bonding procedures. Such an array may contain any number of mddt and may be produced by hand or by using available devices, materials, and machines.
Microarrays may be prepared, used, and analyzed using methods known in the art. (See, e.g., Brennan, T.M. et al. (1995) U.S. Patent No. 5,474,796; Schena, M. et al.
(1996) Proc. Natl. Acad.
Sci. USA 93:10614-10619; Baldeschweiler et al. (1995) PCT application W095/251116; Shalom D. et al. (1995) PCT application W095/35505; Heller, R.A. et al. (1997) Proc. Natl.
Acad. Sci. USA
94:2150-2155; and Heller, M.J. et al. (1997) U.S. Patent No. 5,605,662.) Probes may be labeled by either PCR or enzymatic techniques using a variety of commercially available reporter molecules. For example, commercial kits are available for radioactive and chemiluminescent labeling (Amersham Pharmacia Biotech) and for alkaline phosphatase labeling (Life Technologies). Alternatively, mddt may be cloned into commercially available vectors for the production of RNA probes. Such probes may be transcribed in the presence of at least one labeled nucleotide (e.g., ~ZP-ATP, Amersham Pharmacia Biotech).
Additionally the polynucleotides of SEQ ID NO:1-252 or suitable fragments thereof can be used to isolate full length cDNA sequences utilizing hybridization and/or amplification procedures well known in the art, e.g., cDNA library screening, PCR amplification, etc. The molecular cloning of such full length cDNA sequences may employ the method of cDNA library screening with probes using the hybridization, stringency, washing, and probing strategies described above and in Ausubel, su ra, Chapters 3, 5, and 6. These procedures may also be employed with genomic libraries to isolate genomic sequences of mddt in order to analyze, e.g., regulatory elements.
Genetic Mapping Gene identification and mapping are important in the investigation and treatment of almost all conditions, diseases, and disorders. Cancer, cardiovascular disease, Alzheimer's disease, arthritis, diabetes, and mental illnesses are of particular interest. Each of these conditions is more complex than the single gene defects of sickle cell anemia or cystic fibrosis, with select groups of genes being predictive of predisposition for a particular condition, disease, or disorder.
For example, cardiovascular disease may result from malfunctioning receptor molecules that fail to clear cholesterol from the bloodstream, and diabetes may result when a particular individual's immune system is activated by an infection and attacks the insulin-producing cells of the pancreas. In some studies, Alzheimer's disease has been linked to a gene on chromosome 21; other studies predict a different gene and location. Mapping of disease genes is a complex and reiterative process and generally proceeds from genetic linkage analysis to physical mapping.
As a condition is noted among members of a family, a genetic linkage map traces parts of chromosomes that are inherited in the same pattern as the condition.
Statistics link the inheritance of particular conditions to particular regions of chromosomes, as defined by RFLP
or other markers.
2s (See, for example, Lander, E. S. and Botstein, D. ( 1986) Proc. Natl. Acad.
Sci. USA 83:7353-7357.) Occasionally, genetic markers and their locations are known from previous studies. More often, however, the markers are simply stretches of DNA that differ among individuals. Examples of genetic linkage maps can be found in various scientific journals or at the Online Mendelian Inheritance in Man (OMIM) World Wide Web site.
In another embodiment of the invention, mddt sequences may be used to generate hybridization probes useful in chromosomal mapping of naturally occurring genomic sequences. Either coding or noncoding sequences of mddt may be used, and in some instances, noncoding sequences may be preferable over coding sequences. For example, conservation of an mddt coding sequence among members of a multi-gene family may potentially cause undesired cross hybridization during chromosomal mapping. The sequences may be mapped to a particular chromosome, to a specific region of a chromosome, or to artificial chromosome constructions, e.g., human artificial chromosomes (HACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial P1 constructions, or single chromosome cDNA libraries. (See, e.g., Harrington, J.J. et al. ( 1997) Nat.
Genet. 15:345-355; Price, C.M. (1993) Blood Rev. 7:127-134; and Trask, B.J.
(1991) Trends Genet.
7:149-154.) Fluorescent in situ hybridization (FISH) may be correlated with other physical chromosome mapping techniques and genetic map data. (See, e.g., Meyers, supra, pp. 965-968.) Correlation between the location of mddt on a physical chromosomal map and a specific disorder, or a predisposition to a specific disorder, may help define the region of DNA
associated with that disorder.
The mddt sequences may also be used to detect polymorphisms that are genetically linked to the inheritance of a particular condition, disease, or disorder.
In situ hybridization of chromosomal preparations and genetic mapping techniques, such as linkage analysis using established chromosomal markers, may be used for extending existing genetic maps. Often the placement of a gene on the chromosome of another mammalian species, such as mouse, may reveal associated markers even if the number or arm of the corresponding human chromosome is not known. These new marker sequences can be mapped to human chromosomes and may provide valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once a disease or syndrome has been crudely correlated by genetic linkage with a particular genomic region, e.g., ataxia-telangiectasia to Hq22-23, any sequences mapping to that area may represent associated or regulatory genes for further investigation.
(See, e.g., Gatti, R.A. et al. (1988) Nature 336:577-580.) The nucleotide sequences of the subject invention may also be used to detect differences in chromosomal architecture due to translocation, inversion, etc., among normal, carrier, or affected individuals.
Once a disease-associated gene is mapped to a chromosomal region, the gene must be cloned in order to identify mutations or other alterations (e.g., translocations or inversions) that may be correlated with disease. This process requires a physical map of the chromosomal region containing the disease-gene of interest along with associated markers. A physical map is necessary for determining the nucleotide sequence of and order of marker genes on a particular chromosomal region. Physical mapping techniques are well known in the art and require the generation of overlapping sets of cloned DNA fragments from a particular organelle, chromosome, or genome.
These clones are analyzed to reconstruct and catalog their order. Once the position of a marker is determined, the DNA from that region is obtained by consulting the catalog and selecting clones from that region. The gene of interest is located through positional cloning techniques using hybridization or similar methods.
Diagnostic Uses The mddt of the present invention may be used to design probes useful in diagnostic assays.
Such assays, well known to those skilled in the art, may be used to detect or confirm conditions, 1 S disorders, or diseases associated with abnormal levels of mddt expression.
Labeled probes developed from mddt sequences are added to a sample under hybridizing conditions of desired stringency. In some instances, mddt, or fragments or oligonucleotides derived from mddt, may be used as primers in amplification steps prior to hybridization. The amount of hybridization complex formed is quantified and compared with standards for that cell or tissue. If mddt expression varies significantly from the standard, the assay indicates the presence of the condition, disorder, or disease. Qualitative or quantitative diagnostic methods may include northern, dot blot, or other membrane or dip-stick based technologies or multiple-sample format technologies such as PCR, enzyme-linked immunosorbent assay (ELISA)-like, pin, or chip-based assays.
The probes described above may also be used to monitor the progress of conditions, disorders, or diseases associated with abnormal levels of mddt expression, or to evaluate the efficacy of a particular therapeutic treatment. The candidate probe may be identified from the mddt that are specific to a given human tissue and have not been observed in GenBank or other genome databases.
Such a probe may be used in animal studies, preclinical tests, clinical trials, or in monitoring the treatment of an individual patient. In a typical process, standard expression is established by methods well known in the art for use as a basis of comparison, samples from patients affected by the disorder or disease are combined with the probe to evaluate any deviation from the standard profile, and a therapeutic agent is administered and effects are monitored to generate a treatment profile. Efficacy is evaluated by determining whether the expression progresses toward or returns to the standard normal pattern. Treatment profiles may be generated over a period of several days or several months.
Statistical methods well known to those skilled in the art may be use to determine the significance of such therapeutic agents.
The polynucleotides are also useful for identifying individuals from minute biological samples, for example, by matching the RFLP pattern of a sample's DNA to that of an individual's DNA. The polynucleotides of the present invention can also be used to determine the actual base-by-base DNA
sequence of selected portions of an individual's genome. These sequences can be used to prepare PCR primers for amplifying and isolating such selected DNA, which can then be sequenced. Using this technique, an individual can be identified through a unique set of DNA
sequences. Once a unique ID database is established for an individual, positive identification of that individual can be made from extremely small tissue samples.
In a particular aspect, oligonucleotide primers derived from the mddt of the invention may be used to detect single nucleotide polymorphisms (SNPs). SNPs are substitutions, insertions and deletions that are a frequent cause of inherited or acquired genetic disease in humans. Methods of SNP detection include, but are not limited to, single-stranded conformation polymorphism (SSCP) and fluorescent SSCP (fSSCP) methods. In SSCP, oligonucleotide primers derived from mddt are used to amplify DNA using the polymerase chain reaction (PCR). The DNA may be derived, for example, from diseased or normal tissue, biopsy samples, bodily fluids, and the like.
SNPs in the DNA cause differences in the secondary and tertiary structures of PCR products in single-stranded form, and these differences are detectable using gel electrophoresis in non-denaturing gels. In fSCCP, the oligonucleotide primers are fluorescently labeled', which allows detection of the amplimers in high-throughput equipment such as DIVA sequencing machines. Additionally, sequence database analysis methods, termed in silico SNP (isSNP), are capable of identifying polymorphisms by comparing the sequences of individual overlapping DNA fragments which assemble into a common consensus sequence. These computer-based methods filter out sequence variations due to laboratory preparation of DNA and sequencing errors using statistical models and automated analyses of DNA sequence chromatograms. In the alternative, SNPs may be detected and characterized by mass spectrometry using, for example, the high throughput MASSARRAY system (Sequenom, Inc., San Diego CA).
DNA-based identification techniques are critical in forensic technology. DNA
sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids, e.g., blood, saliva, semen, etc., can be amplified using, e.g., PCR, to identify individuals. (See, e.g., Erlich, H.
(1992) PCR TechnoloQV, Freeman and Co., New York, NY). Similarly, polynucleotides of the present invention can be used as polymorphic markers.
There is also a need for reagents capable of identifying the source of a particular tissue.
Appropriate reagents can comprise, for example, DNA probes or primers prepared from the sequences of the present invention that are specific for particular tissues.
Panels of such reagents can identify tissue by species and/or by organ type. In a similar fashion, these reagents can be used to screen tissue cultures for contamination.
The polynucleotides of the present invention can also be used as molecular weight markers on nucleic acid gels or Southern blots, as diagnostic probes for the presence of a specific mRNA in a particular cell type, in the creation of subtracted cDNA libraries which aid in the discovery of novel polynucleotides, in selection and synthesis of oligomers for attachment to an array or other support, and as an antigen to elicit an immune response.
Disease Model Systems Usine mddt The mddt of the invention or their mammalian homologs may be "knocked out" in an animal model system using homologous recombination in embryonic stem (ES) cells. Such techniques are well known in the art and are useful for the generation of animal models of human disease. (See, e.g., U.S. Patent Number 5,175,383 and U.S. Patent Number 5,767,337.) For example, mouse ES cells, such as the mouse 129/SvJ cell line, are derived from the early mouse embryo and grown in culture.
The ES cells are transformed with a vector containing the gene of interest disrupted by a marker gene, e.g., the neomycin phosphotransferase gene (neo; Capecchi, M.R. (1989) Science 244:1288-1292).
The vector integrates into the corresponding region of the host genome by homologous recombination.
Alternatively, homologous recombination takes place using the Cre-loxP system to knockout a gene of interest in a tissue- or developmental stage-specific manner (Marth, J.D.
(1996) Clin. Invest. 97:1999-2002; Wagner, K.U. et al. (1997) Nucleic Acids Res. 25:4323-4330). Transformed ES cells are identified and microinjected into mouse cell blastocysts such as those from the C57BL/6 mouse strain.
The blastocysts are surgically transferred to pseudopregnant dams, and the resulting chimeric progeny are genotyped and bred to produce heterozygous or homozygous strains.
Transgenic animals thus generated may be tested with potential therapeutic or toxic agents.
The mddt of the invention may also be manipulated in vitro in ES cells derived from human blastocysts. Human ES cells have the potential to differentiate into at least eight separate cell lineages including endoderm, mesoderm, and ectodermal cell types. These cell lineages differentiate into, for example, neural cells, hematopoietic lineages, and cardiomyocytes (Thomson, J.A. et al. (1998) Science 282:1145-1147).
The mddt of the invention can also be used to create "knockin" humanized animals (pigs) or transgenic animals (mice or rats) to model human disease. With knockin technology, a region of mddt is injected into animal ES cells, and the injected sequence integrates into the animal cell genome.
Transformed cells are injected into blastulae, and the blastulae are implanted as described above.
Transgenic progeny or inbred lines are studied and treated with potential pharmaceutical agents to obtain information on treatment of a human disease. Alternatively, a mammal inbred to overexpress mddt, resulting, e.g., in the secretion of MDDT in its milk, may also serve as a convenient source of that protein (Janne, J. et al. (1998) Biotechnol. Annu. Rev. 4:55-74).

Screening Assays MDDT encoded by polynucleotides of the present invention may be used to screen for molecules that bind to or are bound by the encoded polypeptides. The binding of the polypeptide and the molecule may activate (agonist), increase, inhibit (antagonist), or decrease activity of the polypeptide or the bound molecule. Examples of such molecules include antibodies, oligonucleotides, proteins (e.g., receptors), or small molecules.
Preferably, the molecule is closely related to the natural ligand of the polypeptide, e.g., a ligand or fragment thereof, a natural substrate, or a structural or functional mimetic. (See, Coligan et al., (1991 ) Current Protocols in ImmunoloQV 1 (2): Chapter 5.) Similarly, the molecule can be closely related to the natural receptor to which the polypeptide binds, or to at least a fragment of the receptor, e.g., the active site. In either case, the molecule can be rationally designed using known techniques.
Preferably, the screening for these molecules involves producing appropriate cells which express the polypeptide, either as a secreted protein or on the cell membrane. Preferred cells include cells from mammals, yeast, Droso~hila, or E. coli. Cells expressing the polypeptide or cell membrane fractions which contain the expressed polypeptide are then contacted with a test compound and binding, stimulation, or inhibition of activity of either the polypeptide or the molecule is analyzed.
An assay may simply test binding of a candidate compound to the polypeptide, wherein binding is detected by a fluorophore, radioisotope, enzyme conjugate, or other detectable label. Alternatively, the assay may assess binding in the presence of a labeled competitor.
Additionally, the assay can be carried out using cell-free preparations, polypeptide/molecule affixed to a solid support, chemical libraries, or natural product mixtures.
The assay may also simply comprise the steps of mixing a candidate compound with a solution containing a polypeptide, measuring polypeptide/molecule activity or binding, and comparing the polypeptide/molecule activity or binding to a standard.
Preferably, an ELISA assay using, e.g., a monoclonal or polyclonal antibody, can measure polypeptide level in a sample. The antibody can measure polypeptide level by either binding, directly or indirectly, to the polypeptide or by competing with the polypeptide for a substrate.
All of the above assays can be used in a diagnostic or prognostic context. The molecules discovered using these assays can be used to treat disease or to bring about a particular result in a patient (e.g., blood vessel growth) by activating or inhibiting the polypeptide/molecule. Moreover, the assays can discover agents which may inhibit or enhance the production of the polypeptide from suitably manipulated cells or tissues.

Transcript ImaQinQ and Toxicological Testing Another embodiment relates to the use of mddt to develop a transcript image of a tissue or cell type. A transcript image represents the global pattern of gene expression by a particular tissue or cell type. Global gene expression patterns are analyzed by quantifying the number of expressed genes and their relative abundance under given conditions and at a given time. (See Seilhamer et al., "Comparative Gene Transcript Analysis," U.S. Patent Number 5,840,484, expressly incorporated by reference herein.) Thus a transcript image may be generated by hybridizing the polynucleotides of the present invention or their complements to the totality of transcripts or reverse transcripts of a particular tissue or cell type. In one embodiment, the hybridization takes place in high-throughput format, wherein the polynucleotides of the present invention or their complements comprise a subset of a plurality of elements on a microarray. The resultant transcript image would provide a profile of gene activity pertaining to disease detection and treatment molecules.
Transcript images which profile mddt expression may be generated using transcripts isolated from tissues, cell lines, biopsies, or other biological samples. The transcript image may thus reflect mddt expression in vivo, as in the case of a tissue or biopsy sample, or in vitro, as in the case of a cell line.
Transcript images which profile mddt expression may also be used in conjunction with in vitro model systems and preclinical evaluation of pharmaceuticals, as well as toxicological testing of industrial and naturally-occun-ing environmental compounds. All compounds induce characteristic gene expression patterns, frequently termed molecular fingerprints or toxicant signatures, which are indicative of mechanisms of action and toxicity (Nuwaysir, E. F. et al. (1999) Mol. Carcinog. 24:153-159; Steiner, S. and Anderson, N. L. (2000) Toxicol. Lett. 112-113:467-71, expressly incorporated by reference herein). If a test compound has a signature similar to that of a compound with known toxicity, it is likely to share those toxic properties. These fingerprints or signatures are most useful and refined when they contain expression information from a large number of genes and gene families.
Ideally, a genome-wide measurement of expression provides the highest quality signature. Even genes whose expression is not altered by any tested compounds are important as well, as the levels of expression of these genes are used to normalize the rest of the expression data. The normalization procedure is useful for comparison of expression data after treatment with different compounds.
While the assignment of gene function to elements of a toxicant signature aids in interpretation of toxicity mechanisms, knowledge of gene function is not necessary for the statistical matching of signatures which leads to prediction of toxicity. (See, for example, Press Release 00-02 from the National Institute of Environmental Health Sciences, released February 29, 2000, available at http://www.niehs.nih.govloc/news/toxchip.htm.) Therefore, it is important and desirable in toxicological screening using toxicant signatures to include all expressed gene sequences.

In one embodiment, the toxicity of a test compound is assessed by treating a biological sample containing nucleic acids with the test compound. Nucleic acids that are expressed in the treated biological sample are hybridized with one or more probes specific to the polynucleotides of the present invention, so that transcript levels corresponding to the polynucleotides of the present invention may be quantified. The transcript levels in the treated biological sample are compared with levels in an untreated biological sample. Differences in the transcript levels between the two samples are indicative of a toxic response caused by the test compound in the treated sample.
Another particular embodiment relates to the use of MDDT encoded by polynucleotides of the present invention to analyze the proteome of a tissue or cell type. The term proteome refers to the global pattern of protein expression in a particular tissue or cell type. Each protein component of a proteome can be subjected individually to further analysis. Proteome expression patterns, or profiles, are analyzed by quantifying the number of expressed proteins and their relative abundance under given conditions and at a given time. A profile of a cell's proteome may thus be generated by separating and analyzing the polypeptides of a particular tissue or cell type.
In one embodiment, the separation is achieved using two-dimensional gel electrophoresis, in which proteins from a sample are separated by isoelectric focusing in the first dimension, and then according to molecular weight by sodium dodecyl sulfate slab gel electrophoresis in the second dimension (Steiner and Anderson, supra). The proteins are visualized in the gel as discrete and uniquely positioned spots, typically by staining the gel with an agent such as Coomassie Blue or silver or fluorescent stains. The optical density of each protein spot is generally proportional to the level of the protein in the sample. The optical densities of equivalently positioned protein spots from different samples, for example, from biological samples either treated or untreated with a test compound or therapeutic agent, are compared to identify any changes in protein spot density related to the treatment. The proteins in the spots are partially sequenced using, for example, standard methods employing chemical or enzymatic cleavage followed by mass spectrometry. The identity of the protein in a spot may be determined by comparing its partial sequence, preferably of at least 5 contiguous amino acid residues, to the polypeptide sequences of the present invention. In some cases, further sequence data may be obtained for definitive protein identification.
A proteomic profile may also be generated using antibodies specific for MDDT
to quantify the levels of MDDT expression. In one embodiment, the antibodies are used as elements on a microarray, and protein expression levels are quantified by exposing the microarray to the sample and detecting the levels of protein bound to each array element (Lueking, A. et al. (1999) Anal. Biochem.
270:103-1 I ; Mendoze, L. G. et al. (1999) Biotechniques 27:778-88). Detection may be performed by a variety of methods known in the art, for example, by reacting the proteins in the sample with a thiol-or amino-reactive fluorescent compound and detecting the amount of fluorescence bound at each array element.
Toxicant signatures at the proteome level are also useful for toxicological screening, and should be analyzed in parallel with toxicant signatures at the transcript level. There is a poor correlation between transcript and protein abundances for some proteins in some tissues (Anderson, N. L. and Seilhamer, J. (1997) Electrophoresis 18:533-537), so proteome toxicant signatures may be useful in the analysis of compounds which do not significantly affect the transcript image, but which alter the proteomic profile. In addition, the analysis of transcripts in body fluids is difficult, due to rapid degradation of mRNA, so proteomic profiling may be more reliable and informative in such cases.
In another embodiment, the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins that are expressed in the treated biological sample are separated so that the amount of each protein can be quantified. The amount of each protein is compared to the amount of the corresponding protein in an untreated biological sample.
A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample. Individual proteins are identified by sequencing the amino acid residues of the individual proteins and comparing these partial sequences to the MDDT encoded by polynucleotides of the present invention.
In another embodiment, the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins from the biological sample are incubated with antibodies specific to the MDDT encoded by polynucleotides of the present invention. The amount of protein recognized by the antibodies is quantified. The amount of protein in the treated biological sample is compared with the amount in an untreated biological sample. A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample.
Transcript images may be used to profile mddt expression in distinct tissue types. This process can be used to determine disease detection and treatment molecule activity in a particular tissue type relative to this activity in a different tissue type. Transcript images may be used to generate a profile of mddt expression characteristic of diseased tissue.
Transcript images of tissues before and after treatment may be used for diagnostic purposes, to monitor the progression of disease, and to monitor the efficacy of drug treatments for diseases which affect the activity of disease detection and treatment molecules.
Transcript images of cell lines can be used to assess disease detection and treatment molecule activity and/or to identify cell lines that lack or misregulate this activity.
Such cell lines may then be treated with pharmaceutical agents, and a transcript image following treatment may indicate the efficacy of these agents in restoring desired levels of this activity. A
similar approach may be used to assess the toxicity of pharmaceutical agents as reflected by undesirable changes in disease detection and treatment molecule activity. Candidate pharmaceutical agents may be evaluated by comparing their associated transcript images with those of pharmaceutical agents of known effectiveness.
Antisense Molecules The polynucleotides of the present invention are useful in antisense technology. Antisense technology or therapy relies on the modulation of expression of a target protein through the specific binding of an antisense sequence to a target sequence encoding the target protein or directing its expression. (See, e.g., Agrawal, S., ed. (1996) Antisense Therapeutics, Humana Press Inc., Totawa NJ; Alama, A. et al. (1997) Pharmacol. Res. 36(3):171-178; Crooke, S.T. (1997) Adv. Pharmacol.
40:1-49; Sharma, H.W. and R. Narayanan (1995) Bioessays 17(12):1055-1063; and Lavrosky, Y. et al. (1997) Biochem. Mol. Med. 62(1):11-22.) An antisense sequence is a polynucleotide sequence capable of specifically hybridizing to at least a portion of the target sequence. Antisense sequences bind to cellular mRNA and/or genomic DNA, affecting translation andlor transcription. Antisense sequences can be DNA, RNA, or nucleic acid mimics and analogs. (See, e.g., Rossi, J.J. et al. ( 1991 ) Antisense Res. Dev. 1(3):285-288; Lee, R. et al. (1998) Biochemistry 37(3):900-1010; Pardridge, W.M. et al. (1995) Proc. Natl. Acad. Sci. USA 92(12):5592-5596; and Nielsen, P. E. and Haaima, G.
(1997) Chem. Soc. Rev. 96:73-78.) Typically, the binding which results in modulation of expression occurs through hybridization or binding of complementary base pairs. Antisense sequences can also bind to DNA duplexes through specific interactions in the major groove of the double helix.
The polynucleotides of the present invention and fragments thereof can be used as antisense sequences to modify the expression of the polypeptide encoded by mddt. The antisense sequences can be produced ex vivo, such as by using any of the ABI nucleic acid synthesizer series (Applied Biosystems) or other automated systems known in the art. Antisense sequences can also be produced biologically, such as by transforming an appropriate host cell with an expression vector containing the sequence of interest. (See, e.g., Agrawal, supra.) In therapeutic use, any gene delivery system suitable for introduction of the antisense sequences into appropriate target cells can be used. Antisense sequences can be delivered intracellularly in the form of an expression plasmid which, upon transcription, produces a sequence complementary to at least. a portion of the cellular sequence encoding the target protein. (See, e.g., Slater, J.E., et al. (1998) J. Allergy Clin. Immunol. 102(3):469-475; and Scanlon, K.J., et al. (1995) 9(13):1288-1296.) Antisense sequences can also be introduced intracellularly through the use of viral vectors, such as retrovirus and adeno-associated virus vectors. (See, e.g., Miller, A.D. (1990) Blood 76:271; Ausubel, F.M. et al. (1995) Current Protocols in Molecular BioloQV, John Wiley & Sons, New York NY; Uckert, W. and W. Walther (1994) Pharmacol. Ther. 63(3):323-347.) Other gene delivery mechanisms include liposome-derived systems, artificial viral envelopes, and other systems known in the art. (See, e.g., Rossi, J.J. (1995) Br. Med. Bull. 51(1):217-225; Boado, R.J. et al. (1998) J. Pharm.
Sci. 87(I 1 ):1308-1315; and Morris, M.C. et al. (1997) Nucleic Acids Res.
25(14):2730-2736.) Expression In order to express a biologically active MDDT, the nucleotide sequences encoding MDDT or fragments thereof may be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host. Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding MDDT and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA
techniques, synthetic techniques, and in vivo genetic recombination. (See, e.g., Sambrook, supra, Chapters 4, 8, 16, and 17;
and Ausubel, supra, Chapters 9, 10, 13, and 16.) A variety of expression vector/host systems may be utilized to contain and express sequences encoding MDDT. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors;
yeast transformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculovirus);
plant cell systems transformed with viral expression vectors (e.g., cauliflower mosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal (mammalian) cell systems. (See, e.g., Sambrook, supra; Ausubel, 1995, supra, Van Heeke, G.
and S.M. Schuster (1989) J. Biol. Chem. 264:5503-5509; Bitter, G.A. et al.
(1987) Methods Enzymol.
153:516-544; Scorer, C.A. et al. (1994) Bio/Technology 12:181-184; Engelhard, E.K. et al. (1994) Proc. Natl. Acad. Sci. USA 91:3224-3227; Sandig, V. et al. (1996) Hum. Gene Ther. ?:1937-1945;
Takamatsu, N. (1987) EMBO J. 6:307-311; Coruzzi, G. et al. (1984) EMBO J.
3:1671-1680; Broglie, R. et al. (1984) Science 224:838-843; Winter, J. et al. ( 1991 ) Results Probl. Cell Differ. 17:85-105;
The McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York NY, pp.
191-196; Logan, J. and T. Shenk (1984) Proc. Natl. Acad. Sci. USA 81:3655-3659; and Harrington, J.J. et al. (1997) Nat. Genet. 15:345-355.) Expression vectors derived from retroviruses, adenoviruses, or herpes or vaccinia viruses, or from various bacterial plasmids, may be used for delivery of nucleotide sequences to the targeted organ, tissue, or cell population. (See, e.g., Di Nicola, M: et al. ( 1998) Cancer Gen. Ther. 5(6):350-356; Yu, M. et al., ( 1993) Proc.
Natl. Acad. Sci. USA
90(13):6340-6344; Buller, R.M. et al. (1985) Nature 317(6040):813-815;
McGregor, D.P. et al. (1994) Mol. Immunol. 31(3):219-226; and Verma, LM. and N. Somia (1997) Nature 389:239-242.) The invention is not limited by the host cell employed.
For long term production of recombinant proteins in mammalian systems, stable expression of MDDT in cell lines is preferred. For example, sequences encoding MDDT can be transformed into cell lines using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Any number of selection systems may be used to recover transformed cell lines. (See, e.g., Wigler, M. et al.
(1977) Cell 11:223-232; Lowy, I. et al. (1980) Cell 22:817-823.; Wigler, M. et al. (1980) Proc. Natl.
Acad. Sci. USA 77:3567-3570; Colbere-Garapin, F. et al. (1981) J. Mol. Biol.
150:1-14; Hartman, S.C.
and R.C.Mulligan (1988) Proc. Natl. Acad. Sci. USA 85:8047-8051; Rhodes, C.A.
(1995) Methods Mol. Biol. 55:121-131.) Therapeutic Uses of mddt The mddt of the invention may be used for somatic or germline gene therapy.
Gene therapy may be performed to (i) correct a genetic deficiency (e.g., in the cases of severe combined immunodeficiency (SCID)-X1 disease characterized by X-linked inheritance (Cavazzana-Calvo, M. et al. (2000) Science 288:669-672), severe combined immunodeficiency syndrome associated with an inherited adenosine deaminase (ADA) deficiency (Blaese, R.M. et al. ( 1995) Science 270:475-480;
Bordignon, C. et al. (1995) Science 270:470-475), cystic fibrosis (Zabner, J.
et al. (1993) Cell 75:207-216; Crystal, R.G. et al. ( 1995) Hum. Gene Therapy 6:643-666; Crystal, R.G.
et al. ( 1995) Hum. Gene Therapy 6:667-703), thalassemias, familial hypercholesterolemia, and hemophilia resulting from Factor VIII or Factor IX deficiencies (Crystal, R.G. (1995) Science 270:404-410;
Verma, LM. and Somia, N.
(1997) Nature 389:239-242)), (ii) express a conditionally lethal gene product (e.g., in the case of cancers which result from unregulated cell proliferation), or (iii) express a protein which affords protection against intracellular parasites (e.g., against human retroviruses, such as human immunodeficiency virus (HIV) (Baltimore, D. (1988) Nature 335:395-396;
Poeschla, E. et al. (1996) Proc. Natl. Acad. Sci. USA. 93:11395-11399), hepatitis B or C virus (HBV, HCV); fungal parasites, such as Candida albicans and Paracoccidioides brasiliensis; and protozoan parasites such as Plasmodium falciparum and Trvoanosoma cruzi). In the case where a genetic deficiency in mddt expression or regulation causes disease, the expression of mddt from an appropriate population of transduced cells may alleviate the clinical manifestations caused by the genetic deficiency.
In a further embodiment of the invention, diseases or disorders caused by deficiencies in mddt are treated by constructing mammalian expression vectors comprising mddt and introducing these vectors by mechanical means into mddt-deficient cells. Mechanical transfer technologies for use with cells in vivo or ex vitro include (i) direct DNA microinjection into individual cells, (ii) ballistic gold particle delivery, (iii) liposome-mediated transfection, (iv) receptor-mediated gene transfer, and (v) the use of DNA transposons (Morgan, R.A. and Anderson, W.F. (1993) Annu. Rev.
Biochem. 62:191-217; Ivics, Z. (1997) Cell 91:501-510; Boulay, J-L. and Recipon, H. (1998) Curr. Opin. Biotechnol.
9:445-450).

Expression vectors that may be effective for the expression of mddt include, but are not limited to, the PCDNA 3.1, EPITAG, PRCCMV2, PREP, PVAX vectors (Invitrogen, Carlsbad CA), PCMV-SCRIPT, PCMV-TAG, PEGSH1PERV (Stratagene, La Jolla CA), and PTET-OFF, PTET-ON, PTRE2, PTRE2-LUC, PTK-HYG (Clontech, Palo Alto CA). The mddt of the invention may be expressed using (i) a constitutively active promoter, (e.g., from cytomegalovirus (CMV), Rous sarcoma virus (RSV), SV40 virus, thymidine kinase (TK), or (3-actin genes), (ii) an inducible promoter (e.g., the tetracycline-regulated promoter (Gossen, M. and Bujard, H. (1992) Proc. Natl. Acad. Sci.
U.S.A. 89:5547-5551; Gossen, M. et al., (1995) Science 268:1766-1769; Rossi, F.M.V. and Blau, H.M. (1998) Curr. Opin. Biotechnol. 9:451-456), commercially available in the T-REX plasmid (Invitrogen); the ecdysone-inducible promoter (available in the plasmids PVGRXR and PIND;
Invitrogen); the FK506/rapamycin inducible promoter; or the RU486/mifepristone inducible promoter (Rossi, F.M.V. and Blau, H.M. supra), or (iii) a tissue-specific promoter or the native promoter of the endogenous gene encoding MDDT from a normal individual.
Commercially available liposome transformation kits (e.g., the PERFECT LIPID
TRANSFECTION KIT, available from Invitrogen) allow one with ordinary skill in the art to deliver polynucleotides to target cells in culture and require minimal effort to optimize experimental parameters. In the alternative, transformation is performed using the calcium phosphate method (Graham, F.L. and Eb, A.J. ( 1973) Virology 52:456-467), or by electroporation (Neumann, E. et al.
(1982) EMBO J. 1:841-845). The introduction of DNA to primary cells requires modification of these standardized mammalian transfection protocols.
In another embodiment of the invention, diseases or disorders caused by genetic defects with respect to mddt expression are treated by constructing a retrovirus vector consisting of (i) mddt under the control of an independent promoter or the retrovirus long terminal repeat (LTR) promoter, (ii) appropriate RNA packaging signals, and (iii) a Rev-responsive element (RRE) along with additional retrovirus cis-acting RNA sequences and coding sequences required for efficient vector propagation.
Retrovirus vectors (e.g., PFB and PFBNEO) are commercially available (Stratagene) and are based on published data (Riviere, I. et al. (1995) Proc. Natl. Acad. Sci. U.S.A.
92:6733-6737), incorporated by reference herein. The vector is propagated in an appropriate vector producing cell line (VPCL) that expresses an envelope gene with a tropism for receptors on the target cells or a promiscuous o envelope protein such as VSVg (Armentano, D. et al. (1987) J. Virol. 61:1647-1650; Bender, M.A. et al. (1987) J. Virol. 61:1639-1646; Adam, M.A. and Miller, A.D. (1988) J.
Virol. 62:3802-3806; Dull, T.
et al. (1998) J. Virol. 72:8463-8471; Zufferey, R. et al. (1998) J. Virol.
72:9873-9880). U.S. Patent Number 5,910,434 to Rigg ("Method for obtaining retrovirus packaging cell lines producing high transducing efficiency retroviral supernatant") discloses a method for obtaining retrovirus packaging cell lines and is hereby incorporated by reference. Propagation of retrovirus vectors, transduction of a population of cells (e.g., CD4+ T-cells), and the return of transduced cells to a patient are procedures well known to persons skilled in the art of gene therapy and have been well documented (Ranga, U. et al. (1997) J. Virol. 71:7020-7029; Bauer, G. et al. (1997) Blood 89:2259-2267; Bonyhadi, M.L. (1997) J. Virol. 71:4707-4716; Ranga, U. et al. (1998) Proc. Natl. Acad.
Sci. U.S.A. 95:1201-1206; Su, L. (1997) Blood 89:2283-2290).
In the alternative, an adenovirus-based gene therapy delivery system is used to deliver mddt to cells which have one or more genetic abnormalities with respect to the expression of mddt. The construction and packaging of adenovirus-based vectors are well known to those with ordinary skill in the art. Replication defective adenovirus vectors have proven to be versatile for importing genes encoding immunoregulatory proteins into intact islets in the pancreas (Csete, M.E. et al. (1995) Transplantation 27:263-268). Potentially useful adenoviral vectors are described in U.S. Patent Number 5,707,618 to Armentano ("Adenovirus vectors for gene therapy"), hereby incorporated by reference. For adenoviral vectors, see also Antinozzi, P.A. et al. (1999) Annu. Rev. Nutr. 19:511-544 and Verma, LM. and Somia, N. (1997) Nature 18:389:239-242, both incorporated by reference herein.
In another alternative, a herpes-based, gene therapy delivery system is used to deliver mddt to target cells which have one or more genetic abnormalities with respect to the expression of mddt. The use of herpes simplex virus (HSV)-based vectors may be especially valuable for introducing mddt to cells of the central nervous system, for which HSV has a tropism. The construction and packaging of herpes-based vectors are well known to those with ordinary skill in the art. A
replication-competent herpes simplex virus (HSV) type 1-based vector has been used to deliver a reporter gene to the eyes of primates (Liu, X. et al. (1999) Exp. Eye Res.169:385-395). The construction of a HSV-1 virus vector has also been disclosed in detail in U.S. Patent Number 5,804,413 to DeLuca ("Herpes simplex virus strains for gene transfer"), which is hereby incorporated by reference.
U.S. Patent Number 5,804,413 teaches the use of recombinant HSV d92 which consists of a genome containing at least one exogenous gene to be transferred to a cell under the control of the appropriate promoter for purposes including human gene therapy. Also taught by this patent are the construction and use of recombinant HSV strains deleted for ICP4, ICP27 and ICP22. For HSV vectors, see also Goins, W.
F. et al. 1999 J. Virol. 73:519-532 and Xu, H. et al., (1994) Dev. Biol.
163:152-161, hereby incorporated by reference. The manipulation of cloned herpesvirus sequences, the generation of recombinant virus following the transfection of multiple plasmids containing different segments of the large herpesvirus genomes, the growth and propagation of herpesvirus, and the infection of cells with herpesvirus are techniques well known to those of ordinary skill in the art.
In another alternative, an alphavirus (positive, single-stranded RNA virus) vector is used to deliver mddt to target cells. The biology of the prototypic alphavirus, Semliki Forest Virus (SFV), has been studied extensively and gene transfer vectors have been based on the SFV
genome (Garoff, H.

and Li, K-J. (1998) Curr. Opin. Biotech. 9:464-469). During alphavirus RNA
replication, a subgenomic RNA is generated that normally encodes the viral capsid proteins.
This subgenomic RNA
replicates to higher levels than the full-length genomic RNA, resulting in the overproduction of capsid proteins relative to the viral proteins with enzymatic activity (e.g., protease and polymerase).
Similarly, inserting mddt into the alphavirus genome in place of the capsid-coding region results in the production of a large number of mddt RNAs and the synthesis of high levels of MDDT in vector transduced cells. While alphavirus infection is typically associated with cell lysis within a few days, the ability to establish a persistent infection in hamster normal kidney cells (BHK-21) with a variant of Sindbis virus (SIN) indicates that the lytic replication of alphaviruses can be altered to suit the needs of the gene therapy application (Dryga, S.A. et al. (1997) Virology 228:74-83).
The wide host range of alphaviruses will allow the introduction of mddt into a variety of cell types.
The specific transduction of a subset of cells in a population may require the sorting of cells prior to transduction. The methods of manipulating infectious cDNA clones of alphaviruses, performing alphavirus cDNA and RNA
transfections, and performing alphavirus infections, are well known to those with ordinary skill in the 1 ~ art.
Antibodies Anti-MDDT antibodies may be used to analyze protein expression levels. Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, and Fab fragments. For descriptions of and protocols of antibody technologies, see, e.g., Pound J.D.
(1998) Immunochemical Protocols, Humana Press, Totowa, NJ.
The amino acid sequence encoded by the mddt of the Sequence Listing may be analyzed by appropriate software (e.g., LASERGENE NAVIGATOR software, DNASTAR) to determine regions of high immunogenicity. The optimal sequences for immunization are selected from the C-terminus, the N-terminus, and those intervening, hydrophilic regions of the polypeptide which are likely to be exposed to the external environment when the polypeptide is in its natural conformation.
Analysis used to select appropriate epitopes is also described by Ausubel (1997, supra, Chapter 11.7).
Peptides used for antibody induction do not need to have biological activity;
however, they must be antigenic. Peptides used to induce specific antibodies may have an amino acid sequence consisting of at least five amino acids, preferably at least 10 amino acids, and most preferably at least I S amino acids. A peptide which mimics an antigenic fragment of the natural polypeptide may be fused with another protein such as keyhole hemolimpet cyanin (KLH; Sigma, St. Louis MO) for antibody production. A peptide encompassing an antigenic region may be expressed from an mddt, synthesized as described above, or purified from human cells.
Procedures well known in the art may be used for the production of antibodies.
Various hosts including mice, goats, and rabbits, may be immunized by injection with a peptide. Depending on the host species, various adjuvants may be used to increase immunological response.
In one procedure, peptides about 15 residues in length may be synthesized using an ABI 431 A
peptide synthesizer (Applied Biosystems) using fmoc-chemistry and coupled to KLH (Sigma) by reaction with M-maleimidobenzoyl-N-hydroxysuccinimide ester (Ausubel, 1995, su ra). Rabbits are immunized with the peptide-KLH complex in complete Freund's adjuvant. The resulting antisera are tested for antipeptide activity by binding the peptide to plastic, blocking with 1 % bovine serum albumin (BSA), reacting with rabbit antisera, washing, and reacting with radioiodinated goat anti-rabbit IgG.
Antisera with antipeptide activity are tested for anti-MDDT activity using protocols well known in the art, including ELISA, radioimmunoassay (RIA), and immunoblotting.
In another procedure, isolated and purified peptide may be used to immunize mice (about 100 pg of peptide) or rabbits (about 1 mg of peptide). Subsequently, the peptide is radioiodinated and used to screen the immunized animals' B-lymphocytes for production of antipeptide antibodies. Positive cells are then used to produce hybridomas using standard techniques. About 20 mg of peptide is sufficient for labeling and screening several thousand clones. Hybridomas of interest are detected by screening with radioiodinated peptide to identify those fusions producing peptide-specific monoclonal antibody. In a typical protocol, wells of a multi-well plate (FAST, Becton-Dickinson, Palo Alto, CA) are coated with affinity-purified, specific rabbit-anti-mouse (or suitable anti-species IgG) antibodies at 10 mglml. The coated wells are blocked with 1 % BSA and washed and exposed to supernatants from hybridomas. After incubation, the wells are exposed to radiolabeled peptide at 1 mg/ml.
Clones producing antibodies bind a quantity of labeled peptide that is detectable above background. Such clones are expanded and subjected to 2 cycles of cloning.
Cloned hybridomas are injected into pristane-treated mice to produce ascites, and monoclonal antibody is purified from the ascitic fluid by affinity chromatography on protein A (Amersham Pharmacia Biotech). Several procedures for the production of monoclonal antibodies, including in vitro production, are described in Pound (supra). Monoclonal antibodies with antipeptide activity are tested for anti-MDDT activity using protocols well known in the art, including ELISA, RIA, and immunoblotting.
Antibody fragments containing specific binding sites for an epitope may also be generated.
For example, such fragments include, but are not limited to, the F(ab')2 fragments produced by pepsin digestion of the antibody molecule, and the Fab fragments generated by reducing the disulfide bridges of the F(ab')2 fragments. Alternatively, construction of Fab expression libraries in filamentous bacteriophage allows rapid and easy identification of monoclonal fragments with desired specificity (Pound, supra, Chaps. 45-47). Antibodies generated against polypeptide encoded by mddt can be used to purify and characterize full-length MDDT protein and its activity, binding partners, etc.

Assa s~UsinQ Antibodies Anti-MDDT antibodies may be used in assays to quantify the amount of MDDT
found in a particular human cell. Such assays include methods utilizing the antibody and a label to detect expression level under normal or disease conditions. The peptides and antibodies of the invention may be used with or without modification or labeled by joining them, either covalently or noncovalently, with a reporter molecule.
c Protocols for detecting and measuring protein expression using either polyclonal or monoclonal antibodies are well known in the art. Examples include ELISA, RIA, and fluorescent activated cell sorting (FACS). Such immunoassays typically involve the formation of complexes between the MDDT and its specific antibody and the measurement of such complexes. These and other assays are described in Pound su ra).
Without further elaboration, it is believed that one skilled in the art can, using the preceding description, utilize the present invention to its fullest extent. The following preferred specific embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever.
The disclosures of all patents, applications, and publications mentioned above and below, including U.S. Serial No. 60/230,517, U.S. Serial No. 60/230,599, U.S. Serial No. 60/230,514, U.S. Serial No. 60/231,167, U.S. Serial No. 60/230,598, U.S. Serial No.
60/230,988, U.S. Serial No.
60/230,518, U.S. Serial No. 60/230,515, U.S. Serial No. 60/229,751, U.S.
Serial No. 60/230,610, U.S.
Serial No. 60/229,749, U.S. Serial No. 60/229,750, U.S. Serial No. 60/230,597, U.S. Serial No.
60/230,505, U.S. Serial No. 60/231,163, U.S. Serial No. 60/229,747, U.S.
Serial No. 60/229,748, U.S.
Serial No. 60/230,583, U.S. Serial No. 60/230,519, U.S. Serial No. 60/230,595, U.S. Serial No.
60/230,865, U.S. Serial No. 60/230,989, and U.S. Serial No. 60/230,951, are hereby expressly incorporated by reference.
EXAMPLES
I. Construction of cDNA Libraries RNA was purchased from CLONTECH Laboratories, Inc. (Palo Alto CA) or isolated from various tissues. Some tissues were homogenized and lysed in guanidinium isothiocyanate, while others were homogenized and lysed in phenol or in a suitable mixture of denaturants, such as TRIZOL (Life Technologies), a monophasic solution of phenol and guanidine isothiocyanate.
The resulting lysates were centrifuged over CsCI cushions or extracted with chloroform. RNA was precipitated with either isopropanol or sodium acetate and ethanol, or by other routine methods.
Phenol extraction and precipitation of RNA were repeated as necessary to increase RNA
purity. In most cases, RNA was treated with DNase. For most libraries, poly(A+) RNA was isolated using oligo d(T)-coupled paramagnetic particles (Promega Corporation (Promega), Madison WI), OLIGOTEX latex particles (QIAGEN, Inc. (QIAGEN), Valencia CA), or an OLIGOTEX
mRNA
purification kit (QIAGEN). Alternatively, RNA was isolated directly from tissue lysates using other RNA isolation kits, e.g., the POLY(A)PURE mRNA purification kit (Ambion, Inc., Austin TX).
In some cases, Stratagene was provided with RNA and constructed the corresponding cDNA
libraries. Otherwise, cDNA was synthesized and cDNA libraries were constructed with the UNIZAP vector system (Stratagene Cloning Systems, Inc. (Stratagene), La Jolla CA) or SUPERSCRIPT plasmid system (Life Technologies), using the recommended procedures or similar methods known in the art. (See, e.g., Ausubel, 1997, supra, Chapters 5.1 through 6.6.) Reverse transcription was initiated using oligo d(T) or random primers. Synthetic oligonucleotide adapters were ligated to double stranded cDNA, and the cDNA was digested with the appropriate restriction enzyme or enzymes. For most libraries, the cDNA was size-selected (300-1000 bp) using SEPHACRYL S1000, SEPHAROSE CL2B, or SEPHAROSE CL4B column chromatography (Amersham Pharmacia Biotech) or preparative agarose gel electrophoresis. cDNAs were ligated into compatible restriction enzyme sites of the polylinker of a suitable plasmid, e.g., PBLUESCRIPT
plasmid (Stratagene), PSPORT1 plasmid (Life Technologies), PCDNA2.1 plasmid (Invitrogen, Carlsbad CA), PBK-CMV plasmid (Stratagene), or pINCY (Incyte Genomics, Palo Alto CA), or derivatives thereof. Recombinant plasmids were transformed into competent E.
coli cells including XL1-Blue, XL1-BIueMRF, or SOLR from Stratagene or DHSa, DH10B, or ElectroMAX

from Life Technologies.
II. Isolation of cDNA Clones Plasmids were recovered from host cells by in vivo excision using the UNIZAP
vector system (Stratagene) or by cell lysis. Plasmids were purified using at least one of the following: the Magic or WIZARD Minipreps DNA purification system (Promega); the AGTC Miniprep purification kit (Edge BioSystems, Gaithersburg MD); and the QIAWELL 8, QIAWELL 8 Plus, and QIAWELL 8 Ultra plasmid purification systems or the R.E.A.L. PREP 96 plasmid purification kit (QIAGEN). Following precipitation, plasmids were resuspended in 0.1 ml of distilled water and stored, with or without lyophilization, at 4°C.
Alternatively, plasmid DNA was amplified from host cell lysates using direct link PCR in a high-throughput format. (Rap, V.B. (1994) Anal. Biochem. 216:1-14.) Host cell lysis and thermal cycling steps were carried out in a single reaction mixture. Samples were processed and stored in 384-well plates, and the concentration of amplified plasmid DNA was quantified fluorometrically using PICOGREEN dye (Molecular Probes, Inc. (Molecular Probes), Eugene OR) and a FLUOROSKAN
II fluorescence scanner (Labsystems Oy, Helsinki, Finland).

III. Sequencing and Analysis cDNA sequencing reactions were processed using standard methods or high-throughput instrumentation such as the ABI CATALYST 800 thermal cycler (Applied Biosystems) or the PTC-200 thermal cycler (MJ Research) in conjunction with the HYDRA microdispenser (Robbins Scientific Corp., Sunnyvale CA) or the MICROLAB 2200 liquid transfer system (Hamilton). cDNA
sequencing reactions were prepared using reagents provided by Amersham Pharmacia Biotech or supplied in ABI sequencing kits such as the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (Applied Biosystems). Electrophoretic separation of cDNA
sequencing reactions and detection of labeled polynucleotides were carried out using the MEGABACE

sequencing system (Molecular Dynamics); the ABI PRISM 373 or 377 sequencing system (Applied Biosystems) in conjunction with standard ABI protocols and base calling software; or other sequence analysis systems known in the art. Reading frames within the cDNA sequences were identified using standard methods (reviewed in Ausubel, 1997, supra, Chapter 7.7). Some of the cDNA sequences were selected for extension using the techniques disclosed in Example VIII.
IV. Assembly and Analysis of Sequences Component sequences from chromatograms were subject to PHRED analysis and assigned a quality score. The sequences having at least a required quality score were subject to various pre-processing editing pathways to eliminate, e.g., low quality 3' ends, vector and linker sequences, polyA
tails, Alu repeats, mitochondria) and ribosomal sequences, bacterial contamination sequences, and sequences smaller than 50 base pairs. In particular, low-information sequences and repetitive elements (e.g., dinucleotide repeats, Alu repeats, etc.) were replaced by "n's", or masked, to prevent spurious matches.
Processed sequences were then subject to assembly procedures in which the sequences were assigned to gene bins (bins). Each sequence could only belong to one bin.
Sequences in each gene bin were assembled to produce consensus sequences (templates). Subsequent new sequences were added to existing bins using BLASTn (v.1.4 WashU) and CROSSMATCH. Candidate pairs were identified as all BLAST hits having a quality score greater than or equal to 150. Alignments of at least 82% local identity were accepted into the bin. The component sequences from each bin were assembled using a version of PHRAP. Bins with several overlapping component sequences were assembled using DEEP PHRAP. The orientation (sense or antisense) of each assembled template was determined based on the number and orientation of its component sequences.
Template sequences as disclosed in the sequence listing correspond to sense strand sequences (the "forward"
reading frames), to the best determination. The complementary (antisense) strands are inherently disclosed herein. The component sequences which were used to assemble each template consensus sequence are listed in Table 5, along with their positions along the template nucleotide sequences.
Bins were compared against each other and those having local similarity of at least 82% were combined and reassembled. Reassembled bins having templates of insufficient overlap (less than 95%
local identity) were re-split. Assembled templates were also subject to analysis by STITCHER/EXON MAPPER algorithms which analyze the probabilities of the presence of splice variants, alternatively spliced exons, splice junctions, differential expression of alternative spliced genes across tissue types or disease states, etc. These resulting bins were subject to several rounds of the above assembly procedures.
Once gene bins were generated based upon sequence alignments, bins were clone joined based upon clone information. If the 5'sequence of one clone was present in one bin and the 3' sequence from the same clone was present in a different bin, it was likely that the two bins actually belonged together in a single bin. The resulting combined bins underwent assembly procedures to regenerate the consensus sequences.
The final assembled templates were subsequently annotated using the following procedure.
Template sequences were analyzed using BLASTn (v2.0, NCBI) versus gbpri (GenBank version 124). "Hits" were defined as an exact match having from 95% local identity over 200 base pairs through 100% local identity over 100 base pairs, or a homolog match having an E-value, i.e. a probability score, of <_ 1 x 10'8. The hits were subject to frameshift FASTx versus GENPEPT
(GenBank version 124). (See Table 8). In this analysis, a homolog match was defined as having an E-value of <_ 1 x l0- . The assembly method used above was described in "System and Methods for Analyzing Biomolecular Sequences," U.S.S.N. 09/276,534, filed March 25, 1999, and the LIFESEQ
Gold user manual (Incyte) both incorporated by reference herein.
Following assembly, template sequences were subjected to motif, BLAST, and functional analyses, and categorized in protein hierarchies using methods described in, e.g., "Database System Employing Protein Function Hierarchies for Viewing Biomolecular Sequence Data," U.S.S.N.
08/812,290, filed March 6, 1997; "Relational Database for Storing Biomolecule Information," U.S.S.N.
08/947,845, filed October 9> 1997; "Project-Based Full-Length Biomolecular Sequence Database,"
U.S.S.N. 08/811,758, filed March 6, 1997; and "Relational Database and System for Storing Information Relating to Biomolecular Sequences," U.S.S.N. 09/034,807, filed March 4, 1998, all of which are incorporated by reference herein.
The template sequences were further analyzed by translating each template in all three forward reading frames and searching each translation against the Pfam database of hidden Markov model-based protein families and. domains using the HMMER software package (available to the public from Washington University School of Medicine, St. Louis MO). Regions of templates which, when translated, contain similarity to Pfam consensus sequences are reported in Table 3, along with descriptions of Pfam protein domains and families. Only those Pfam hits with an E-value of c 1 x 10'' are reported. (See also World Wide Web site http://pfam.wustl.edu/ for detailed descriptions of Pfam protein domains and families.) Additionally, the template sequences were translated in all three forward reading frames, and each translation was searched against hidden Markov models for signal peptides using the HMMER
software package. Construction of hidden Markov models and their usage in sequence analysis has been described. (See, for example, Eddy, S.R. (1996) Curr. Opin. Str. Biol.
6:361-365.) Only those signal peptide hits with a cutoff score of I 1 bits or greater are reported. A
cutoff score of 1 I bits or greater corresponds to at least about 91-94% true-positives in signal peptide prediction. Template sequences were also translated in all three forward reading frames, and each translation was searched against TMAP, a program that uses weight matrices to delineate transmembrane segments on protein sequences and determine orientation, with respect to the cell cytosol (Persson, B. and P.
Argos (1994) J. Mot. Biol. 237:182-192; Persson, B. and P. Argos (1996) Protein Sci. 5:363-371.) I S Regions of templates which, when translated, contain similarity to signal peptide or transmembrane consensus sequences are reported in Table 4.
The results of HMMER analysis as reported in Tables 3 and 4 may support the results of BLAST analysis as reported in Table 2 or may suggest alternative or additional properties of template-encoded polypeptides not previously uncovered by BLAST or other analyses.
Template sequences are further analyzed using the bioinformatics tools listed in Table 8, or using sequence analysis software known in the art such as MACDNASIS PRO
software (Hitachi Software Engineering, South San Francisco CA) and LASERGENE software (DNASTAR).
Template sequences may be further queried against public databases such as the GenBank rodent;
mammalian, vertebrate, prokaryote, and eukaryote databases.
The template sequences were translated to derive the corresponding longest open reading frame as presented by the polypeptide sequences as reported in Table 2.
Alternatively, a polypeptide of the invention may begin at any of the methionine residues within the full length translated polypeptide. Polypeptide sequences were subsequently analyzed by querying against the GenBank protein database (GENPEPT, (GenBank version 124)). Full length polynucleotide sequences are also analyzed using MACDNASIS PRO software (Hitachi Software Engineering, South San Francisco CA) and LASERGENE software (DNASTAR). Polynucleotide and polypeptide sequence alignments are generated using default parameters specified by the CLUSTAL algorithm as incorporated into the MEGALIGN multisequence alignment program (DNASTAR), which also calculates the percent identity between aligned sequences. ' Table 7 shows sequences with homology to the polypeptides of the invention as identified by BLAST analysis against the GenBank protein (GENPEPT) database. Column 1 shows the polypeptide sequence identification number (SEQ ID NO:) for the polypeptide segments of the invention. Column 2 shows the reading frame used in the translation of the polynucleotide sequences encoding the polypeptide segments. Column 3 shows the length of the translated polypeptide segments. Columns 4 and 5 show the start and stop nucleotide positions of the polynucleotide sequences encoding the polypeptide segments. Column 6 shows the GenBank identification number (GI Number) of the nearest GenBank homolog. Column 7 shows the probability score for the match between each polypeptide and its GenBank homolog. Column 8 shows the annotation of the GenBank homolog.
V. Analysis of Polynucleotide Expression Northern analysis is a laboratory technique used to detect the presence of a transcript of a gene and involves the hybridization of a labeled nucleotide sequence to a membrane on which RNAs from a particular cell type or tissue have been bound. (See, e.g., Sambrook, supra, ch. 7; Ausubel, 1995, supra, ch. 4 and 16.) Analogous computer techniques applying BLAST were used to search for identical or related molecules in cDNA databases such as GenBank or LIFESEQ (Incyte Genomics). This analysis is much faster than multiple membrane-based hybridizations. In addition, the sensitivity of the computer search can be modified to determine whether any particular match is categorized as exact or similar.
The basis of the search is the product score, which is defined as:
BLAST Score x Percent Identity 5 x minimum { length(Seq. 1 ), length(Seq. 2) }
The product score takes into account both the degree of similarity between two sequences and the length of the sequence match. The product score is a normalized value between 0 and 100, and is calculated as follows: the BLAST score is multiplied by the percent nucleotide identity and the product is divided by (5 times the length of the shorter of the two sequences). The BLAST score is calculated by assigning a score of +5 for every base that matches in a high-scoring segment pair (HSP), and -4 for every mismatch. Two sequences may share more than one HSP
(separated by gaps). If there is more than one HSP, then the pair with the highest BLAST
score is used to calculate the product score. The product score represents a balance between fractional overlap and quality in a BLAST alignment. For example, a product score of 100 is produced only for 100%
identity over the entire length of the shorter of the two sequences being compared. A product score of 70 is produced either by 100% identity and 70% overlap at one end, or by 88% identity and 100% overlap at the other. A product score of 50 is produced either by 100% identity and 50%
overlap at one end, or 79%
identity and 100% overlap.
VI. Tissue Distribution Profiling A tissue distribution profile is determined for each template by compiling the cDNA library tissue classifications of its component cDNA sequences. Each component sequence, is derived from a cDNA library constructed from a human tissue. Each human tissue is classified into one of the following categories: cardiovascular system; connective tissue; digestive system; embryonic structures; endocrine system; exocrine glands; genitalia, female; genitalia, male; germ cells; hemic and immune system; liver; musculoskeletal system; nervous system; pancreas;
respiratory system; sense organs; skin; stomatognathic system; unclassified/mixed; or urinary tract.
Template sequences, component sequences, and cDNA library/tissue information are found in the LIFESEQ GOLD
database (Incyte Genomics, Palo Alto CA).
Table 6 shows the tissue distribution profile for the templates of the invention. For each template, the three most frequently observed tissue categories are shown in column 3, along with the percentage of component sequences belonging to each category. Only tissue categories with percentage values of z 10% are shown. A tissue distribution of "widely distributed" in column 3 indicates percentage values of <10% in all tissue categories.
VII. Transcript Image Analysis Transcript images are generated as described in Seilhamer et al., "Comparative Gene Transcript Analysis," U.S. Patent Number 5,840,484, incorporated herein by reference.
VIII. Extension of Polynucleotide Sequences and Isolation of a Full-length cDNA
Oligonucleotide primers designed using an mddt of the Sequence Listing are used to extend the nucleic acid sequence. One primer is synthesized to initiate 5' extension of the template, and the other primer, to initiate 3' extension of the template. The initial primers may be designed using OLIGO
4.06 software (National Biosciences, Inc. (National Biosciences), Plymouth MN), or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC
content of about 50% or more, and to anneal to the target sequence at temperatures of about 68°C to about 72°C. Any stretch of nucleotides which would result in hairpin structures and primer-primer dimerizations are avoided. Selected human cDNA libraries are used to extend the sequence. If more than one extension is necessary or desired, additional or nested sets of primers are designed.
High fidelity amplification is obtained by PCR using methods well known in the art. PCR is performed in 96-well plates using the PTC-200 thermal cycler (MJ Research).
The reaction mix contains DNA template, 200 nmol of each primer, reaction buffer containing Mg'+, (NH,~)ZSO,,, and f3-mercaptoethanol, Taq DNA polymerise (Amersham Pharmacia Biotech), ELONGASE
enzyme (Life Technologies), and Pfu DNA polymerise (Stratagene), with the following parameters for primer pair PCI A and PCI B: Step 1: 94°C, 3 min; Step 2: 94°C, IS sec; Step 3: 60°C, 1 min; Step 4: 68°C, 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68°C, 5 min;
Step 7: storage at 4°C. In the alternative, the parameters for primer pair T7 and SK+ are as follows: Step 1:
94°C, 3 min; Step 2:
94°C, 15 sec; Step 3: 57°C, 1 min; Step 4: 68°C, 2 min;
Step 5: Steps 2, 3, and 4 repeated 20 times;
Step 6: 68°C, S min; Step 7: storage at 4°C.
The concentration of DNA in each well is determined by dispensing 100 p1 PICOGREEN
quantitation reagent (0.25% (v/v); Molecular Probes) dissolved in IX Tris-EDTA
(TE) and 0.5 p1 of undiluted PCR product into each well of an opaque fluorimeter plate (Corning Incorporated (Corning), Corning NY), allowing the DNA to bind to the reagent. The plate is scanned in a FLUOROSKAN II
(Labsystems Oy) to measure the fluorescence of the sample and to quantify the concentration of DNA. A 5 p1 to 10 p1 aliquot of the reaction mixture is analyzed by electrophoresis on a 1 % agarose mini-gel to determine which reactions are successful in extending the sequence.
The extended nucleotides are desalted and concentrated, transferred to 384-well plates, digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison WI), and sonicated or sheared prior to religation into pUC 18 vector (Amersham Pharmacia Biotech). For shotgun sequencing, the digested nucleotides are separated on low concentration (0.6 to 0.8%) agarose gels, fragments are excised, and agar digested with AGAR ACE
(Promega). Extended clones are religated using T4 ligase (New England Biolabs, Inc., Beverly MA) into pUC 18 vector (Amersham Pharmacia Biotech), treated with Pfu DNA polymerise (Stratagene) to fill-in restriction site overhangs, and transfected into competent E. coli cells. Transformed cells are selected on antibiotic-containing media, individual colonies are picked and cultured overnight at 37°C in 384-well 2~ plates in LB/2x carbenicillin liquid media.
The cells are lysed, and DNA is amplified by PCR using Taq DNA polymerise (Amersham Pharmacia Biotech) and Pfu DNA polymerise (Stratagene) with the following parameters: Step 1:
94°C, 3 min; Step 2: 94°C, 15 sec; Step 3: 60°C, 1 min;
Step 4: 72°C, 2 min; Step 5: steps 2, 3, and 4 repeated 29 times; Step 6: 72°C, 5 min; Step 7: storage at 4°C.
DNA is quantified by PICOGREEN
reagent (Molecular Probes) as described above. Samples with low DNA recoveries are reamplified using the same conditions as described above. Samples are diluted with 20%
dimethysulfoxide (1:2, v/v), and sequenced using DYENAMIC energy transfer sequencing primers and the DYENAMIC
DIRECT kit (Amersham Pharmacia Biotech) or the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (Applied Biosystems)_ In like manner, the mddt is used to obtain regulatory sequences (promoters, introns, and enhancers) using the procedure above, oligonucleotides designed for such extension, and an appropriate genomic library.
IX. Labeling of Probes and Southern Hybridization Analyses Hybridization probes derived from the mddt of the Sequence Listing are employed for screening cDNAs, mRNAs, or genomic DNA. The labeling of probe nucleotides between 100 and 1000 nucleotides in length is specifically described, but essentially the same procedure may be used with larger cDNA fragments. Probe sequences are labeled at room temperature for 30 minutes using a T4 polynucleotide kinase, y32P-ATP, and O.SX One-Phor-All Plus (Amersham Pharmacia Biotech) buffer and purified using a ProbeQuant G-50 Microcolumn (Amersham Pharmacia Biotech). The probe mixture is diluted to 10' dpm/pg/ml hybridization buffer and used in a typical membrane-based hybridization analysis.
The DNA is digested with a restriction endonuclease such as Eco RV and is electrophoresed through a 0.7% agarose gel. The DNA fragments are transferred from the agarose to nylon membrane (NYTRAN Plus, Schleicher & Schuell, Inc., Keene NH) using procedures specified by the manufacturer of the membrane. Prehybridization is carried out for three or more hours at 68°C, and hybridization is earned out overnight at 68°C. To remove non-specific signals, blots are sequentially washed at room temperature under increasingly stringent conditions, up~to O.lx saline sodium citrate (SSC) and 0.5% sodium dodecyl sulfate. After the blots are placed in a PHOSPHORIMAGER
cassette (Molecular Dynamics) or are exposed to autoradiography film, hybridization patterns of standard and experimental lanes are compared. Essentially the same procedure is employed when screening RNA.
X. Chromosome Mapping of mddt The cDNA sequences which were used to assemble SEQ ID NO:1-252 are compared with sequences from the Incyte LIFESEQ database and public domain databases using BLAST and other implementations of the Smith-Waterman algorithm. Sequences from these databases that match SEQ
ID NO:1-252 are assembled into clusters of contiguous and overlapping sequences using assembly algorithms such as PHRAP (Table 8). Radiation hybrid and genetic mapping data available from public resources such as the Stanford Human Genome Center (SHGC), Whitehead Institute for Genome Research (WIGR), and Genethon are used to determine if any of the clustered sequences have been previously mapped. Inclusion of a mapped sequence in a cluster will result in the assignment of all sequences of that cluster, including its particular SEQ ID
NO:, to that map location.
The genetic map locations of SEQ ID NO:1-252 are described as ranges, or intervals, of human chromosomes. The map position of an interval, in centiMorgans, is measured relative to the terminus of the chromosome's p-arm. (The centiMorgan (cM) is a unit of measurement based on recombination frequencies between chromosomal markers. On average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA in humans, although this can vary widely due to hot and cold spots of recombination.) The cM distances are based on genetic markers mapped by Genethon which provide boundaries for radiation hybrid markers whose sequences were included in each of the clusters.
XI. Microarray Analysis Probe Preparation from Tissue or Cell Samples Total RNA is isolated from tissue samples using the guanidinium thiocyanate method and polyA+ RNA is purified using the oligo (dT) cellulose method. Each polyA+ RNA
sample is reverse transcribed using MMLV reverse-transcriptase, 0.05 pg/pl oligo-dT primer (21 mer), 1 X first strand buffer, 0.03 units/pl RNase inhibitor, 500 pM dATP, 500 pM dGTP, 500 ~tM dTTP, 40 pM dCTP, 40 pM dCTP-Cy3 (BDS) or dCTP-Cy5 (Amersham Pharmacia Biotech). The reverse transcription reaction is performed in a 25 ml volume containing 200 ng polyA+ RNA with GEMBRIGHT kits (Incyte). Specific control polyA+ RNAs are synthesized by in vitro transcription from non-coding yeast genomic DNA (W. Lei, unpublished). As quantitative controls, the control mRNAs at 0.002 ng, 0.02 ng, 0.2 ng, and 2 ng are diluted into reverse transcription reaction at ratios of 1:100,000, 1:10,000, 1:1000, I :100 (w/w) to sample mRNA respectively. The control mRNAs are diluted into reverse transcription reaction at ratios of 1:3, 3:1, 1:10, 10:1, 1:25, 25:1 (w/w) to sample mRNA differential expression patterns. After incubation at 37°C for 2 hr, each reaction sample (one with Cy3 and another with Cy5 labeling) is treated with 2.5 ml of 0.5M sodium hydroxide and incubated for 20 minutes at 85° C to the stop the reaction and degrade the RNA. Probes are purified using two successive CHROMA SPIN 30 gel filtration spin columns (CLONTECH Laboratories, Inc.
(CLONTECH), Palo Alto CA) and after combining, both reaction samples are ethanol precipitated using 1 ml of glycogen (1 mg/ml), 60 ml sodium acetate, and 300 ml of 100%
ethanol. The probe is then dried to completion using a SpeedVAC (Savant Instruments Inc., Holbrook NY) and resuspended in 14 p1 5X SSC10.2% SDS.
Microarray Preparation Sequences of the present invention are used to generate array elements. Each array element is amplified from bacterial cells containing vectors with cloned cDNA inserts.
PCR amplification uses primers complementary to the vector sequences flanking the cDNA insert. Array elements are amplified in thirty.cycles of PCR from an initial quantity of 1-2 ng to a final quantity greater than 5 pg.
Amplified array elements are then purified using SEPHACRYL-400 (Amersham Pharmacia Biotech).
Purified array elements are immobilized on polymer-coated glass slides. Glass microscope slides (Corning) are cleaned by ultrasound in 0.1 % SDS and acetone, with extensive distilled water washes between and after treatments. Glass slides are etched in 4%
hydrofluoric acid (VWR
Scientific Products Corporation (VWR), West Chester, PA), washed extensively in distilled water, and coated with 0.05% aminopropyl silane (Sigma) in 95% ethanol. Coated slides are cured in a 110°C
oven.
Array elements are applied to the coated glass substrate using a procedure described in US
Patent No. 5,807,522, incorporated herein by reference. 1 p1 of the array element DNA, at an average concentration of 100 ng/pl, is loaded into the open capillary printing element by a high-speed robotic apparatus. The apparatus then deposits about 5 n1 of array element sample per slide.
Microarrays are UV-crosslinked using a STRATALINKER UV-crosslinker (Stratagene).
Microarrays are washed at room temperature once in 0.2% SDS and three times in distilled water.
Non-specific binding sites are blocked by incubation of microarrays in 0.2%
casein in phosphate buffered saline (PBS) (Tropix, Inc., Bedford, MA) for 30 minutes at 60°C followed by washes in 0.2% SDS and distilled water as before.
Hybridization Hybridization reactions contain 9 Nl of probe mixture consisting of 0.2 pg each of Cy3 and Cy5 labeled cDNA synthesis products in 5X SSC, 0.2% SDS hybridization buffer. The probe mixture is heated to 65° C for 5 minutes and is aliquoted onto the microarray surface and covered with an 1.8 cmz coverslip. The arrays are transferred to a waterproof chamber having a cavity just slightly larger than a microscope slide. The chamber is kept at 100% humidity internally by the addition of 140 p1 of 5x SSC in a corner of the chamber. The chamber containing the arrays is incubated for about 6.5 hours at 60° C. The arrays are washed for 10 min at 45° C in a first wash buffer (1 X SSC, Ø1 %
SDS), three times for 10 minutes each at 45° C in a second wash buffer (0.1 X SSC), and dried.
Detection Reporter-labeled hybridization complexes are detected with a microscope equipped with an Innova 70 mixed gas 10 W laser (Coherent, Inc., Santa Clara CA) capable of generating spectral lines at 488 nm for excitation of Cy3 and at 632 nm for excitation of CyS. The excitation laser light is focused on the array using a 20X microscope objective (Nikon, Inc., Melville NY). The slide containing the array is placed on a computer-controlled X-Y stage on the microscope and raster-scanned past the objective. The 1.8 cm x 1.8 cm array used in the present example is scanned with a resolution of 20 micrometers.
In two separate scans, a mixed gas multiline laser excites the two fluorophores sequentially.
Emitted light is split, based on wavelength, into two photomultiplier tube detectors (PMT 81477, Hamamatsu Photonics Systems, Bridgewater NJ) corresponding to the two fluorophores. Appropriate filters positioned between the array and the photomultiplier tubes are used to filter the signals. The emission maxima of the fluorophores used are 565 nm for Cy3 and 650 nm for CyS. Each array is typically scanned twice, one scan per fluorophore using the appropriate filters at the laser source, although the apparatus is capable of recording the spectra from both fluorophores simultaneously.
The sensitivity of the scans is typically calibrated using the signal intensity generated by a cDNA control species added to the probe mix at a known concentration. A
specific location on the array contains a complementary DNA sequence, allowing the intensity of the signal at that location to be correlated with a weight ratio of hybridizing species of 1:100,000. When two probes from different sources (e.g., representing test and control cells), each labeled with a different fluorophore, are hybridized to a single array for the purpose of identifying genes that are differentially expressed, the calibration is done by labeling samples of the calibrating cDNA with the two fluorophores and adding identical amounts of each to the hybridization mixture.
The output of the photomultiplier tube is digitized using a 12-bit RTI-835H
analog-to-digital (A/D) conversion board (Analog Devices, Inc., Norwood, MA) installed in an IBM-compatible PC
computer. The digitized data are displayed as an image where the signal intensity is mapped using a linear 20-color transformation to a pseudocolor scale ranging from blue (low signal) to red (high signal). The data is also analyzed quantitatively. Where two different fluorophores are excited and measured simultaneously, the data are first corrected for optical crosstalk (due to overlapping emission spectra) between the fluorophores using each lluorophore's emission spectrum.
A grid is superimposed over the fluorescence signal image such that the signal from each spot is centered in each element of the grid. The fluorescence signal within each element is then integrated to obtain a numerical value corresponding to the average intensity of the signal. The software used for signal analysis is the GEMTOOLS gene expression analysis program (Incyte).
XII. Complementary Nucleic Acids Sequences complementary to the mddt are used to detect, decrease, or inhibit expression of the naturally occurring nucleotide. The use of oligonucleotides comprising from about 15 to 30 base pairs is typical in the art. However, smaller or larger sequence fragments can also be used..
Appropriate oligonucleotides are designed from the mddt using OLIGO 4.06 software (National Biosciences) or other appropriate programs and are synthesized using methods standard in the art or ordered from a commercial supplier. To inhibit transcription, a complementary oligonucleotide is designed from the most unique 5' sequence and used to prevent transcription factor binding to the promoter sequence. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding and processing of the transcript.

XIII. Expression of MDDT
Expression and purification of MDDT is accomplished using bacterial or virus-based expression systems.. For expression of MDDT in bacteria, cDNA is subcloned into an appropriate vector containing an antibiotic resistance gene and an inducible promoter that directs high levels of cDNA transcription. Examples of such promoters include, but are not limited to, the trp-lac (tac) hybrid promoter and the TS or T7 bacteriophage promoter in conjunction with the lac operator regulatory element. Recombinant vectors are transformed into suitable bacterial hosts, e.g., BL21(DE3). Antibiotic resistant bacteria express MDDT upon induction with isopropyl beta-D-thiogalactopyranoside (IPTG). Expression of MDDT in eukaryotic cells is achieved by infecting insect or mammalian cell lines with recombinant Autographica californica nuclear polyhedrosis virus (AcMNPV), commonly known as baculovirus. The nonessential polyhedrin gene of baculovirus is replaced with cDNA encoding MDDT by either homologous recombination or bacterial-mediated transposition involving transfer plasmid intermediates. Viral infectivity is maintained and the strong polyhedrin promoter drives high levels of cDNA transcription. Recombinant baculovirus is used to I ~ infect Spodoptera frugiperda (Sf9) insect cells in most cases, or human hepatocytes, in some cases.
Infection of the latter requires additional genetic modifications to baculovirus. (See e.g., Engelhard, supra; and Sandig, supra.) In most expression systems, MDDT is synthesized as a fusion protein with, e.g., glutathione S-transferase (GST) or a peptide epitope tag, such as FLAG or 6-His, permitting rapid, single-step, affinity-based purification of recombinant fusion protein from crude cell lysates. GST, a 26-kilodalton enzyme from Schistosoma japonicum, enables the purification of fusion proteins on immobilized glutathione under conditions that maintain protein activity and antigenicity (Amersham Pharmacia Biotech). Following purification, the GST moiety can be proteolytically cleaved from MDDT at specifically engineered sites. FLAG, an 8-amino acid peptide, enables immunoaffinity purification 2~ using commercially available monoclonal and polyclonal anti-FLAG antibodies (Eastman Kodak Company, Rochester NY). 6-His, a stretch of six consecutive histidine residues, enables purification on metal-chelate resins (QIAGEN). Methods for protein expression and purification are discussed in Ausubel (1995, supra, Chapters 10 and 16). Purified MDDT obtained by these methods can be used directly in the following activity assay.
XIV. Demonstration of MDDT Activity MDDT, or biologically active fragments thereof, are labeled with '25I Bolton-Hunter reagent.
(See, e.g., Bolton, A.E. and W.M. Hunter (1973) Biochem_ J. 133:529-539.) Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled MDDT, washed, and any wells with labeled MDDT complex are assayed. Data obtained using different concentrations of MDDT are used to calculate values for the number, affinity, and association of MDDT with the candidate molecules.
Alternatively, molecules interacting with MDDT are analyzed using the yeast two-hybrid system as described in Fields, S. and O. Song (1989) Nature 340:245-246, or using commercially available kits based on the two-hybrid system, such as the MATCHMAKER system (CLONTECH).
MDDT may also be used in the PATHCALLING process (CuraGen Corp., New Haven CT) which employs the yeast two-hybrid system in a high-throughput manner to determine all interactions between the proteins encoded by two large libraries of genes (Nandabalan, K.
et al. (2000) U.S.
Patent No. 6,057,1 O1 ).
XV. Functional Assays MDDT function is assessed by expressing mddt at physiologically elevated levels in mammalian cell culture systems. cDNA is subcloned into a mammalian expression vector containing a strong promoter that drives high levels of cDNA expression. Vectors of choice include pCMV
SPORT (Life Technologies) and pCR3.1 (Invitrogen Corporation, Carlsbad CA), both of which contain the cytomegalovirus promoter. 5-10 pg of recombinant vector are transiently transfected into a human cell line, preferably of endothelial or hematopoietic origin, using either liposome formulations or electroporation. 1-2 ltg of an additional plasmid containing sequences encoding a marker protein are co-transfected.
Expression of a marker protein provides a means to distinguish transfected cells from nontransfected cells and is a reliable predictor of cDNA expression from the recombinant vector Marker proteins of choice include, e.g., Green Fluorescent Protein (GFP;
CLONTECH), CD64, or a CD64-GFP fusion protein. Flow cytometry (FCM), an automated laser optics-based technique, is used to identify transfected cells expressing GFP or CD64-GFP and to evaluate the apoptotic state of the cells and other cellular properties.
FCM detects and quantifies the uptake of fluorescent molecules that diagnose events preceding or coincident with cell death. These events include changes in nuclear DNA content as measured by staining of DNA with propidium iodide; changes in cell size and granularity as measured by forward light scatter and 90 degree side light scatter; down-regulation of DNA synthesis as measured by decrease in bromodeoxyuridine uptake; alterations in expression of cell surface and intracellular proteins as measured by reactivity with specific antibodies; and alterations in plasma membrane composition as measured by the binding of fluorescein-conjugated Annexin V protein to the cell surface. Methods in flow cytometry are discussed in Ormerod, M. G. (1994) Flow Cytometry, Oxford, New York NY.
The influence of MDDT on gene expression can be assessed using highly purified populations of cells transfected with sequences encoding MDDT and either CD64 or CD64-GFP.
CD64 and CD64-GFP are expressed on the surface of transfected cells and bind to conserved regions of human immunoglobulin G (IgG). Transfected cells are efficiently separated from nontransfected cells using magnetic beads coated with either human IgG or antibody against CD64 (DYNAL, Inc., Lake Success NY). mRNA can be purified from the cells using methods well known by those of skill in the art. Expression of mRNA encoding MDDT and other genes of interest can be analyzed by northern analysis or microarray techniques.
XVI. Production of Antibodies MDDT substantially purified using polyacrylamide gel electrophoresis (PAGE;
see, e.g., Harrington, M.G. (1990) Methods Enzymol. 182:488-495), or other purification techniques, is used to immunize rabbits and to produce antibodies using standard protocols.
Alternatively, the MDDT amino acid sequence is analyzed using LASERGENE
software (DNASTAR) to determine regions of high immunogenicity, and a corresponding peptide is synthesized and used to raise antibodies by means known to those of skill in the art.
Methods for selection of appropriate epitopes, such as those near the C-terminus or in hydrophilic regions are well described in the art. (See, e.g., Ausubel, 1995, supra, Chapter 1 1.) Typically, peptides 15 residues in length are synthesized using an ABI 43 I A
peptide synthesizer (Applied Biosystems) using fmoc-chemistry and coupled to KLH
(Sigma) by reaction with N-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) to increase immunogenicity. (See, e.g., Ausubel, supra.) Rabbits are immunized with the peptide-KLH complex in complete Freund's adjuvant. Resulting antisera are tested for antipeptide activity by, for example, binding the peptide to plastic, blocking with 1 % BSA, reacting with rabbit antisera, washing, and reacting with radio-iodinated goat anti-rabbit IgG. Antisera with antipeptide activity are tested for anti-MDDT activity using protocols well known in the art, including ELISA, RIA, and immunoblotting.
XVII. Purification of Naturally Occurring MDDT Using Specific Antibodies Naturally occurring or recombinant MDDT is substantially purified by immunoaffinity chromatography using antibodies specific for MDDT. An immunoaffinity column is constructed by covalently coupling anti-MDDT antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech). After the coupling, the resin is blocked and washed according to the manufacturer's instructions.
Media containing MDDT are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of MDDT (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/MDDT binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and MDDT is collected.
All publications and patents mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described method and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention.
Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the above-described modes for carrying out the invention which are obvious to those skilled in the field of molecular biology or related fields are intended to be within the scope of the following claims.

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SE6Z Template ID GI NumberProbability ID Score NO: Annotation 1 LG:150318.1:2000SEP08g 116435810 Homo Sapiens PR-domain containing protein 14 (PRDM 14) mRNA, ~

2 LG:022529.1:2000SEP08g 100472720 Homo sapiens mRNA for KIAA1599 protein, partial cds.

3 LG:352559.1:2000SEP08g 13560887l .00E-11 Homo Sapiens EZFIT-related protein mRNA, complete 4 LG:175223.1:2000SEP08g 10433955l .00E-43 (fl) (Homo Sapiens) unnamed protein LG:476989.1:2000SEP088124073940 Homo sapiens tripartite motif protein TRIM7 (TRIM7) mRNA, b LG:253268.7:2000SEP088122393680 Homo Sapiens LYST-interacting protein LIP9 mRNA, partial 7 LG:401322.1:2000SEP088136236825.00E-26 Homo Sapiens, tubulin alpha 1, clone MGC:2321, 8 LG:1328436.1:2000SEP08845895872.00E-55 Homo sapiens mRNA for KIAA0972 protein, complete 9 LG:475404.1:2000SEP088104341940 Homo Sapiens cDNA FLJ 12606 fis, clone NT2RM4001483, moderately similar LG:1384132.1:2000SEP08g 140428491.00E-71 Homo sapiens cDNA FLJ 14959 fis, clone PLACE4000156, moderately similar 11 LG:410804.18:2000SEP088135433253.00E-74 Homo Sapiens, hypothetical protein MGC8407, clone MGC:1820, mRNA, complete 12 LG:1082306.1:2000SEP08g 133253360 Homo sapiens, clone MGC:10520, mRNA, complete 13 LG:233814.4:2000SEP08g 104348731.00E-1 Homo Sapiens bb cDNA FLJ 13044 fis, clone NT2RP3001355, weakly similar to TRICARBOXYLATE

TRANSPORT

SEQ Template ID GI NumberProbability ID Score NO: Annotation 14 ~ LG:977478.5:2000SEP08g 126980000 Homo sapiens mRNA for KIAA1728 protein, partial cds.

15 LG:025931.1:2000SEP08g 104363590 Homo sapiens cDNA FLJ 14011 fis, clone Y79AA 1002472, weakly similar to 16 LG:885368.1:2000SEP08g440824 9.00E-60 (fl) (Arabidopsis thaliana) ribosomal 17 LG:1054900.1:2000SEP08g 120529820 Homo Sapiens mRNA;cDNA

DKFZp43411610 (from clone DKFZp43411610);

18 LG:995186.2:2000SEP08g 120529820 Homo sapiens mRNA;cDNA

DKFZp43411610 (from clone DKFZp43411610);

19 LG:435048.23:2000SEP08g104328661.00E-177 Homo sapiens cDNA FLJ 11583 fis, clone HEMBA1003680, weakly similar to PUTATI VE

AMINOPEPTIDASE

ZK353.6 IN

20 LG:954859.1:2000SEP08g104382241.00E-176 Homo Sapiens cDNA: FLJ21990 fis, clone HEP06386.

21 LG:364370.1:2000SEP08g140431501.00E-163 Homo sapiens, ribosomal protein L13, clone MGC:15490, mRNA, 22 LG:1098789.1:2000SEP08g 14029703l .00E-137Homo Sapiens myosin regulatory light chain (MRLC2) mRNA, 23 LG:201540.2:2000SEP08g 1240738b0 Homo sapiens tripartite motif protein TRIM5 isoform delta (TRIMS) mRNA, 24 LG:1077357.1:2000SEP08g104363614.00E-66 Homo sapiens cDNA FLJ 14012 fis, clone Y79AA 1002482, moderately similar SEQ Template ID GI NumberProbability ID Score NO: Annotation 25 LG:1048846.4:2000SEP08g 104399741.00E-154 Homo Sapiens cDNA: FLJ23327 fis, clone HEP12630, highly similar to HSZNF37 Homo Sapiens ZNF37A

26 LG:336685.1:2000SEP08g 126973170 Homo Sapiens partial mRNA
for 27 LG;1076253.1:2000SEP08g79592765.00E-34 Homo sapiens mRNA for KIAA1508 protein, partial cds.

28 LG;1400b01.2:2000SEP08g 140422920 Homo sapiens cDNA FLJ 14636 fis, clone NT2RP2001233, weakly similar to 29 LG:1079092.3:2000SEP08g 120529826.00E-07 Homo sapiens mRNA;cDNA

DKFZp43411 b 10 (from clone DKFZp43411610);

30 LG:108b064.1:2000SEP08g 104363613.00E-76 Homo Sapiens cDNA FLJ 14012 fis, clone Y79AA 1002482, moderately similar 31 LG:1400608.1:2000SEP08g 120527311.00E-175 Homo sapiens mRNA;cDNA

DKFZp7b1 G

(from clone DKFZp761 G
18121 );

32 LG:399275.5:2000SEP08g 140420340 Homo sapiens cDNA FLJ 14486 fis, clone MAMMA1002650, weakly similar to 33 LG:293943.1:2000SEP08g70226032.00E-24 (fl) (Homo sapiens) unnamed protein 34 LG:345884.1:2000SEP08g135917110 Homo Sapiens immunoglobulin receptor translocation associated protein 2b (IRTA2) mRNA, 35 LG:400967.1:2000SEP08g100471821.00E-176 Homo Sapiens mRNA for KIAA1559 protein, partial cds.

36 LG:024556.b:2000SEP08g 119992760 Homo sapiens solute carrier (SLC25A18) mRNA, complete cds;

nuclear gene for SEQ Template ID GI NumberProbability ID Score NO: Annotation 37 LG:081189.3:2000SEP08g 143257680 Homo sapiens mRNA for KIAA1776 protein (fibrillin3), 38 LG:018258.1:2000SEP08g 128322883.00E-97 Q (Mus musculus) 39 LG:450399.3:2000SEP08g130975991.00E-10 Homo sapiens, Similar to ribosomal protein L23, clone IMAGE:3606198, 40 LG:451122.1:2000SEP08gb002102 2.00E-38 (fl) (Digitalis lanata) Acyl-CoA binding protein (ACBP) 41 LG:451682.1:2000SEP08g8b71496 1.00E-134 (fl) (Oryza sativa) alpha 3 subunit of 20S proteasome 42 LG:238631.4:2000SEP08g128039940 Homo sapiens, Similar to HLA class II region expressed gene KE2, clone MGC:4178, mRNA, 43 LG:236654.1:2000SEP08g1 15584872.00E-08 Homo sapiens mRNA for B-cell lymphoma/leukae mia 11 B (BCL11 B

44 LG:332655.1:2000SEP08g 128565597.00E-93 Q (Mus musculus) 45 LG:217396.2:2000SEP08g 100472940 Homo Sapiens mRNA for KIAA1610 protein, partial cds.

46 LG:090574.1:2000SEP08g 128454165.00E-37 Q (Mus musculus) 47 LG:202943.1:2000SEP08g 120608290 Homo sapiens serologically defined breast cancer antigen NY-BR-38 mRNA, 48 LG:236928.1:2000SEP08g 143885740 Macaca fascicularis brain cDNA clone:6~trA-49 LG:215169.2:2000SEP08g790349 1.00E-22 Homo Sapiens (clone NE68) gene 50 LG:410726.1:2000SEP08g99b3805 2.00E-17 Homo Sapiens zinc ftnger protein ZNF287 (ZNF287) 51 LG:234372.2:2000SEP08g 104368540 Homo sapiens cDNA: FLJ2089b fis, clone ADKA03527.

52 LG:022629.1:2000SEP08g 138794421.00E-178 (fl) (Mus musculus) Similar to RIKEN

cDNA 2310035M22 53 LG:068682.1:2000SEP08g 138986160 Homo Sapiens serine/threonine protein kinase SSTK

(SSTK) mRNA, SE9 Template ID GI NumberProbability ID Score NO: Annotation 54 LG:222335.1:2000SEP08g142501370 Homo Sapiens, Similar to RIKEN

cDNA 5730421 gene, clone 55 LG:331342.1:2000SEP08g104340810 Homo sapiens cDNA FLJ12538 fis, clone NT2RM4000356, moderately similar to RAS-RELATED

56 LG:021770.1:2000SEP08g9408105 2.00E-47 Homo sapiens dNT-2 gene for mitochondria) 5'(3'}

deoxyribonucleotid 57 LG:181607.9;2000SEP08g128342448.00E-91 Q(Mus musculus) 58 LG:1042768,1:2000SEP08g139379821.00E-180 Homosapiens, translocase of inner mitochondria) membrane 17 (yeast) homolog A, clone MGC:14756, 59 LG:282729.1;2000SEP08g123142681.00E-107 (5' incom)(Homo sapiens) dJ
14N 1,2 (novel S-100/ICaBP

type calcium binding domain 60 LG:998305.3:2000SEP08g120530986.00E-88 Homo sapiens mRNA; cDNA

DKFZp434A171 (from clone DKFZp434A171 );

61 LG:1135213.1:2000SEP08g6692607 2.00E-69 (fl) (Mus musculus) MGA protein 62 LG:267762.1;2000SEP08g128549771.00E-135 Q(Musmusculus) 63 LG:120744.1;2000SEP08g120527730 Homosaplens mRNA; cDNA

DKFZp564B052 (from clone DKFZp564B052);

64 LG:403409.1:2000SEP08g8896163 0 Homo sapiens kinesin-like protein GAKIN mRNA, 65 LG:226874.3:2000SEP08g3688393 3.00E-05 Homo sapiens mRNA for triple LIM

66 LG:1045521.4:2000SEP08g104367424.00E-58 Homo sapiens cDNA FLJ14310 fis, clone 67 LG:275876.1:2000SEP08g5912051 6.00E-30 (3' and 5' incom) (Homo sapiens) SEQ Template ID GI NumberProbabilityAnnotation ID Score NO:

68 LG:475127,7:2000SEP08872941076,00E-44 (fl) (Drosophila melanogaster) CG4638 gene 69 LG:1572b3,1:2000SEP08830474023.00E-40 (fl) (Homo Sapiens) monocarboxylate transporter 70 LG:247382.7:2000SEP08842402925.00E-25 Homo sapiens mRNA for KIAA0902 protein, complete 71 LG:197367,5:2000SEP088101726807.00E-14 (fl) (Bacillus halodurans) stage V sporulation protein C
(peptidyl-72 LG:218090.5:2000SEP08892953440 Homo sapiens HSKM-B (HSKM-B) mRNA, complete 73 LG:216612.4:2000SEP08886556770 Homo Sapiens mRNA; cDNA

DKFZp547M236 (from clone 74 LG:197614.1:2000SEP08g 133586410 Macaca fascicularis brain 75 LG:378428.1:2000SEP08872640260 (fl) (Homo Sapiens) dJ876B10.2 (novel protein (ortholog of 7b LG:286639.1:2000SEP08g 133832640 Homo Sapiens mRNA for actin related protein, 77 LG:389870.1:2000SEP08g 143883359.00E-63 Macaca fascicularis brain cDNA clone:QfIA-78 LG:1387485.b:2000SEP08g 104352090 Homo Sapiens cDNA FLJ132b1 fis, clone OVARC 1000885, weakly similar to OXIDOREDUCTASE

79 LG:230151,1:2000SEP08886556470 Homo sapiens mRNA; cDNA

DKFZp762M

(from clone 80 LG:215158,5:2000SEP088104401b20 Homo sapiens cDNA: FLJ23465 fis, clone HSI10904.

81 LG:235840.1:2000SEP088140423430 Homo sapiens cDNA FLJ 146bb fis, clone NT2RP2003000, weakly similar to TUMOR NECROSIS

FACTOR, ALPHA-?3 SEQ Template ID GI Number ID Probability NO: Score Annotation 82 LG:350272.1:2000SEP08g134772340 Homo sapiens, Similar to RIKEN

cDNA 0610037N03 gene, clone 83 LG:232190.1:2000SEP08g 104349681.00E-143Homo Sapiens cDNA FLJ 13105 fis, clone NT2RP3002351, weakly similar to Human mRNA
for NAD-dependent methylene tetra hyd rofolate 84 LG:1068127.1:2000SEP08g 104367241.00E-140Homo Sapiens cDNA FLJ 14297 fis, clone 85 LG:408751.3:2000SEP08g8886024 0 Homo sapiens collapsin response mediator protein-5 (CRMPS) mRNA, 86 LG:1078933.1:2000SEP08g140428430 Homo Sapiens cDNA FLJ 14954 fis, clone PLACE3000169, weakly similar to 87 LG:958731.1:2000SEP08g9758769 6.00E-88 (fl) (Arabidopsis thaliana) 11-beta-hydroxysteroid 88 LG:024125.5:2000SEP08g120529580 Homo Sapiens mRNA;cDNA

DKFZp566J2046 (from clone DKFZp566J2046);

89 LG:373637.3:2000SEP08g1 11187400 Homo Sapiens UGTI gene locus, complete 90 LG:1053229.1:2000SEP08g128043220 Homo Sapiens, clone MGC:4054, mRNA, complete 91 LG:248364.1:2000SEP08g 128475990 Q (Mus musculus) 92 LG:477130.1:2000SEP08g6650751 1.00E-55 (fl) (Ceratopteris richardii) ribosomal 93 LG:113786.17:2000SEP08g104405150 Homo sapiens mRNA for FLJ00106 protein, partial cds.

94 LG:347b35.1:2000SEP08g 115279960 Homo sapiens NOTCH2 protein (NOTCH2) mRNA, 95 LG:242966.4:2000SEP0889955987 0 Homo sapiens clone SEQ Template ID GI NumberProbability ID Score NO: Annotation 96 LG:217814,1:2000SEP08g 104389770 Homo Sapiens cDNA; FLJ22551 fis, clone HSI00804.

97 LG:476452.1:2000SEP08841268091.00E-121 (fl) (Oryza sativa) glyoxalase I

98 LG:1100657.1:2000SEP088340298 1.00E-107 Human vasopressin mRNA, complete 99 LG:1132418.2:2000SEP088126534722,00E-86 Homo sapiens, proteasome (prosome, macropain) subunit, beta type, 100 LG:1098570.1:2000SEP08835069 1.00E-171 H.sapiens RNA
for nm23-H2 gene.

101 LG:1097987.1:2000SEP08893688380 Homo sapiens mRNA;cDNA

DKFZp5471014 (from clone 102 LG:337818.2:2000SEP088140423950 Homo Sapiens cDNA FLJ 14699 fis, clone NT2RP200b571, moderately similar to CYTOCHROME

103 LG:1040582.1:2000SEP08g 135292771.00E-119 Homo Sapiens, aldo-keto reductase family 1, member Al (aldehyde reductase), clone 104 LG:1099122.1:2000SEP08g 130977168.00E-86 Homo sapiens, guanine nucleotide binding protein (G
protein?, gamma 5, clone 105 LG:1327449.1:2000SEP08g 140421092.00E-96 Homo Sapiens cDNA FLJ 14531 fis, clone NT2RM2000371, v~reakly similar to POLYRIBONUCLEOTI

DE

106 LG:227933.5:2000SEP08892800280 Macaca fascicularis brain 107 LG:1043709.2:2000SEP088128045884.00E-30 Homo sapiens, Similar to gene product, clone MGC:886, 108 LG:1099871.1:2000SEP08g 126526981.00E-154 Homo Sapiens, purine-rich element binding protein B, clone MGC:1947, SEQ Template ID GI NumberProbability ID Score NO: Annotation 109 LG:1399139.4:2000SEP08g104370770 Homo Sapiens cDNA: FLJ21069 fis, clone CAS01594.

110 LG:236386.1:2000SEP08g 134771316.00E-87 (fl) (Homo Sapiens) SH3 and PX

domain-containing 111 LG:1015157.1:2000SEP08g1881781 5.00E-72 glyoxalase I

(human, HeLa cells, mRNA Partial, 112 LG:1065433.1:2000SEP08g4589587 8.00E-29 Homo Sapiens mRNA for KIAA0972 protein, complete 113 LG:236992.4:2000SEP08g122483810 Homo Sapiens mRNA for SEMB, 114 LG:1071124.1:2000SEP08g135434180 Homo sapiens, Similar to zinc finger protein 304, clone MGC:4079, mRNA, 115 LG:206425.2:2000SEP08g120528832.00E-90 Homo sapiens mRNA; cDNA

DKFZp564C2478 (from clone DKFZp564C2478);

116 LG:885747.2:2000SEP08g 128045042.00E-49 Homo sapiens, ' Similar to ribosomal protein L31, clone MGC:1641, mRNA, 117 LG;1140501.1:2000SEP08g120529190 Homosapiens mRNA; cDNA

DKFZp56411782 (from clone DKFZp56411782);

118 LG:001239.1:2000SEP08g141646120 Homo sapiens sialic acid binding immunoglobulin-like lectin 119 LG:018980.1:2000SEP08g 104351490 Homo sapiens cDNA FW 13220 fis, clone NT2RP4002047, moderately similar to GTP-BINDING

120 LG:1083120.3:2000SEP08g515786 3.00E-66 H.sapiens (MAR7) chromosome DNA, 302bp.

121 LG:233258,3:2000SEP08g104331250 Homo Sapiens cDNA FLJ 11790 fis, clone 122 LG:999062.1:2000SEP08g9759463 3.00E-60 (ii) (Arabidopsis thaliana) 40S

123 LG:887776.1:2000SEP08g342294 l .00E-66 Macaca mulatta serum albumin SEQ Template ID GI NumberProbability ID Score NO: Annotation 124 LG:1400301.2:2000SEP08g12751104l .00E-23 Homo sapiens PNAS-130 mRNA, 125 LG:1329362,1:2000SEP08g140428490 Homo Sapiens cDNA FLJ 14959 fis, clone PLACE4000156, moderately similar 126 LG:109b498.1:2000SEP088130972061.00E-110 Homo Sapiens, ribosomal protein, large, P1, clone MGC:5215, mRNA, 127 LG:1096337.1:2000SEP088130972061.00E-121 Homo sapiens, ribosomal protein, large, P1, clone MGC:5215, mRNA, 128 LG:1400579.1:2000SEP088104379454.00E-61 Homo sapiens cDNA; FLJ21781 fis, clone HEP00223.

129 LG:1080091.1:2000SEP0881043b7241.00E-154 Homo Sapiens cDNA FLJ 14297 fis, clone 130 LG:1082203.1:2000SEP088104399290 Homo Sapiens cDNA: FLJ23296 fis, clone HEP10656.

131 LG:1084051.1:2000SEP08868075861.00E-104 Novel human gene mapping to chomosome 1.

132 LG:1082393.1:2000SEP088109540430 Homo sapiens KRAB zinc finger protein ZFQR

133 LG:1086183.1:2000SEP088126551646.00E-58 Homo sapiens, zinc finger protein 256, clone MGC:1413, mRNA, complete 134 LG:1090268.1:2000SEP088139384790 Homo sapiens, Similar to hypothetical protein FLJ22301, clone 135 LG:1400597.5:2000SEP088142501451.00E-156 Homo Sapiens, hypothetical protein FLJ23407, clone MGC:14819, mRNA, complete 136 LG:1080307.2:2000SEP088140438402.00E-34 Homo Sapiens, clone MGC:14429, mRNA, complete 137 LG:1400b03.2:2000SEP08845895654.00E-31 Homo sapiens mRNA for KIAA0961 protein, complete SE9 Template ID GI NumberProbability ID Score NO. Annotation 138 LG:1052984.1:2000SEP08g139379980 Homo Sapiens, Similar to DNA-binding protein, clone MGC:14780, 139 LG:1091259.1:2000SEP08g1043bb750 Homo sapiens cDNA FLJ 14260 fis, clone PLACE 1001118, weakly similar to 140 LG:1082263.2:2000SEP08g135b0887S.OOE-13 Homo sapiens EZFIT-related protein mRNA, complete 141 LG:1048604.2:2000SEP08g142498436.00E-67 Homo sapiens, Similar to hypothetical protein FLJ23233, clone MGC:14876, 142 LG:1085254.3:2000SEP08g104375590 Homo Sapiens cDNA: FLJ21457 fis, clone COL04705.

143 LG:1400606.2:2000SEP08g140425499.00E-54 Homo sapiens cDNA FLJ 14779 fis, clone NT2RP4000398, moderately similar 144 LG:1090358.2:2000SEP08g 100471826.00E-30 Homo Sapiens mRNA for KIAA1559 protein, partial cds.

145 LG:1079064.2:2000SEP08g104346490 Homo sapiens cDNA FLJ12895 fis, clone NT2RP2004187, weakly similar to 146 LG:10768bb.1:2000SEP08g104364b00 Homo sapiens cDNA FLJ14087 fis, clone MAMMA1000183, weakly similar to 147 LG:969359.1:2000SEP08g 132790041.00E-120 Homo sapiens, ferritin, light polypeptide, clone MGC:10465, mRNA, 148 LG:366783.1;2000SEP08g9651703 0 Homo Sapiens carboxypeptidase B precursor (CPAH) mRNA, complete 149 LG:332176.3:2000SEP08g 133659000 Macaca fascicularis brain cDNA clone:6~flA-SE6~ Template ID GI NumberProbability ID Score NO: Annotation 150 LG:994938.1:2000SEP0887023331 1.00E-76 Homo sapiens cDNA FLJ 10961 fis, clone PLACE 1000588, highly similar to INTERFERON-151 LG:982800.1:2000SEP08g 120532800 Homo Sapiens mRNA;cDNA

DKFZp434J037 (from clone DKFZp434J037);

152 LG:977850.7:2000SEP08g 104369595.00E-64 Homo Sapiens cDNA: FLJ20984 fis, clone CAE00871.

153 LG:234748.2:2000SEP08g 131827540 Homo sapiens HPHRP mRNA, 154 LG:306284.1:2000SEP08g 140436480 Homo Sapiens, clone MGC:14161, mRNA, complete 155 LI:333170.3:2000SEP088123140831.00E-93 (fl)(Homosapiens) dJ1007G16.5 (novel high-mobility group (nonhistone chromosomal) 156 LI:336685.2:2000SEP08812b973170 Homo sapiens partial mRNA
for 157 LI:279013.5:2000SEP08812840b733.00E-55 p(Mus musculus) 158 LI:1037075.1:2000SEP088l 13425400 Homo Sapiens mRNA for putative white family ATP-binding cassette transporter (ABCG4 159 LI:1073403.1:2000SEP08812804b809.00E-63 Homo sapiens, S100 calcium-binding protein, beta (neural), clone MGC:1323, 160 LI:107529b.1:2000SEP088128030841.00E-112 Homo sapiens, mitochondrial ribosomal protein L12, clone MGC:8610, mRNA, 161 LI:1085501.1:2000SEP088126537841.00E-140 Homo sapiens, clone IMAGE:3349601, 162 LI:108b181.1:2000SEP0883043444 1.00E-146 Homo sapiens mRNA for EDF-1 163 LI:1164493.1:2000SEP088134364390 Homo Sapiens, clone MGC:4400, mRNA, complete SE6~ Template ID GI NumberProbability ID Score NO: Annotation 164 LI:1175097.1:2000SEP08g 139379084.00E-45 Homo sapiens, Similar to protein, clone MGC:12515, mRNA, 165 LI:1092948.1:2000SEP08g 128044142.00E-49 Homo Sapiens, Similar to hypothetical protein FLJ10891, clone MGC:925, 166 LI;380378.2:2000SEP08g8655612 3.00E-79 Homo sapiens mRNA;cDNA

DKFZp762O1415 (from clone 167 LI:1029674.1:2000SEP08g9651088 4.00E-07 Macaca fascicularis brain 168 LI:2048601.3:2000SEP08g 104348801.00E-106 Homo sapiens cDNA FLJ 13048 fis, clone NT2RP3001399, weakly similar to 169 LI:1186208.1:2000SEP08g 120527311.00E-175 Homo sapiens mRNA;cDNA

DKFZp761 G

(from clone DKFZp761 G
18121 );

170 LI:1170753.1:2000SEP088142499951.00E-101 Homo Sapiens, clone MGC:12518, mRNA, complete 171 LI:1180908,1:2000SEP088140428490 Homo Sapiens cDNA FLJ 14959 fis, clone PLACE4000156, moderately similar 172 LI:1182900.2:2000SEP08g 100473040 Homo sapiens mRNA for KIAA

protein, partial cds.

173 LI:1169548.2:2000SEP08g 140178320 Homo Sapiens mRNA for KIAA1808 protein, partial cds.

174 LI:1039974.1:2000SEP088133660830 Homo saplens MARKL1 mRNA
for MAP/microtubule affinity-regulating kinase like 1, 175 LI:I 175765.2:2000SEP088137527535.00E-16 Homo sapiens zinc finger 1111 mRNA, complete cds.

176 LI:313948.1:2000SEP0889651098 0 Macaca fascicularis brain SEQ Template ID GI NumberProbability ID Score NO: Annotation 177 LI:335923.2:2000SEP088119907703.00E-73 (fl)(Homo Sapiens) bA534G20.1.1 (novel protein similar to Lysozyme C-1 (1,4-beta-N-acylmuramidase C, 178 LI:345884.1:2000SEP088135917130 Homo sapiens immunoglobulin receptor translocation associated protein 2c (IRTA2) mRNA, 179 Ll:417127.1:2000SEP08g 126527261.OOE-bb Homo Sapiens, clone I MAG E:33525bb, 180 LI:451710.1:2000SEP08g 138990571.00E-61 (fl) (Mercurialis annua) ribosomal 18'1 LI:406882.2:2000SEP0887019948 2.00E-57 Homo Sapiens cDNA FLJ20081 fis, clone COL03242.

182 LI:728223.1:2000SEP0882b24328 2.00E-44 (fl) (Oryza sativa) 183 LI:289783.19:2000SEP08g 126547140 Homo sapiens, Similar to glucose regulated protein, S8 kDa, clone 184 LI:235255.8:2000SEP088125973110 Homo sapiens clone IMAGE:72154 tRNA-guanine transglycosylase (TGT) mRNA, 185 LI:237b93.5:2000SEP08g 124067724.00E-52 (fl) (Homo Sapiens) unnamed protein 186 LI:433670.3:2000SEP08g 141332500 Homo Sapiens mRNA for KIAA1479 protein, partial cds.

187 LI:202943.4:2000SEP08g 120608290 Homo sapiens serologically defined breast cancer antigen NY-BR-38 mRNA, 188 LI:068682.1:2000SEP088135403250 Homo sapiens serine/threonine kinase FKSG82 (FKSG82) mRNA, 189 LI:203301.3:2000SEP088100471600 Homo Sapiens mRNA for KIAA1548 protein, partial cds.

190 LI:02072b.3:2000SEP08g 128340871.00E-157 Q (Mus musculus) 8l SEQ Template ID GI NumberProbability ID Score NO: Annotation 191 LI:027209.1:2000SEP08g 131594801.00E-127 (fl) (Homo sapiens) Translation may initiate at the ATG

codon at nucleotides 192 LI:108819.1:2000SEP08g 120527730 Homo Sapiens mRNA;cDNA

DKFZp564B052 (from clone DKFZp564B052);

193 LI:021759.1:2000SEP088120061030 Homo sapiens IRAI

mRNA, complete cds, alternatively 194 LI:1165967.1:2000SEP088135291031.00E-172 Homo sapiens, ribosomal protein S27a, clone MGC:12414, mRNA, 195 LI:1166315.1:2000SEP088126538001.00E-116 Homo Sapiens, peptidylprolyl isomerase A

(cyclophilin A), clone MGC:2351, 196 LI:204626.1:2000SEP088128447701.00E-138 Q(Musmusculus) 197 LI:801140.1:2000SEP088128043220 Homo sapiens, clone MGC:4054, mRNA, complete 198 LI:286639.1:2000SEP08g 139383180 Homo sapiens, clone MGC:15664, mRNA, complete 199 LI:288905.4:2000SEP08g 126980560 Homo sapiens mRNA for KIAA1756 protein, partial cds.

200 LI:332161.1:2000SEP08g 143883352.00E-62 Macaca fascicularis brain cDNA clone:QfIA-201 LI:184867.1:2000SEP0887209586 4.00E-47 (fl) (Rattus norvegicus) 202 LI:229932.4:2000SEP088104381870 Homo sapiens cDNA: FLJ21963 fis, clone HEP05583.

203 LI:1189932.1;2000SEP088124838870 Homo sapiens solute carrier mRNA, complete 204 LI:1076689.1:2000SEP08g 128047586.00E-20 Homo sapiens, ribonuclease precursor, clone MGC:3554, mRNA, 205 LI:415181.2:2000SEP08g 117621000 (fl) (Zea mat's) myo-inositol 1-SEQ Template ID GI NumberProbability ID Score NO: Annotation 206 LI:296358.1:2000SEP08g 120531480 Homo sapiens mRNA; cDNA

DKFZp434G2226 (from clone D KFZp434G2226);

207 LI:205186.3:2000SEP0885b7232 4.00E-17 (fl) (Mus musculus) proline-rich protein 208 LI:220537.2:2000SEP08g 133658960 Macaca fascicularis brain cDNA clone:QfIA-209 LI:248364.2:2000SEP08g 128475990 Q (Mus musculus) 210 LI:2048338.1:2000SEP08g 128489053.00E-78 0 (Mus musculus) 211 LI:1185203.8:2000SEP08g 112310843.00E-85 Macaca fascicularis brain 212 LI:021770.3:2000SEP0885931541 2.00E-45 Homo Sapiens genomic DNA, chromosome 22q11.2, BCRL2 213 LI:1185841.1:2000SEP088142695010 Homo Sapiens unconventional myosin 1 G
valine form (MYOI
G) mRNA, MY01 G-V

214 LI:I 181710.1:2000SEP0887959206 2.00E-49 Homo sapiens mRNA for KIAA1473 protein, partial cds.

215 LI:2048959.1:2000SEP0885817101 1.00E-16 Homo sapiens mRNA; cDNA

D KFZp434G
1 b21 (from clone 21 b LI:798494.1:2000SEP08g 100471822.00E-23 Homo sapiens mRNA for KIAA1559 protein, partial cds.

217 LI:2049223.1:2000SEP0887959206 2.00E-43 Homo sapiens mRNA for KIAA1473 protein, partial cds.

218 LI:1177833.1:2000SEP08g 120529820 Homo sapiens mRNA; cDNA

DKFZp43411610 (from clone DKFZp43411610);

219 LI:20492b7,1:2000SEP088515786 6.OOE-bl H.sapiens (MAR7) chromosome DNA, 302bp.

220 LI:1165939.1:2000SEP0887020753 9.00E-13 Homo sapiens cDNA FLJ205b2 fis, clone KAT11992.

221 LI:1170958.1:2000SEP0885262556 l .00E-14 Homo sapiens mRNA; cDNA

DKFZp569D2231 (from clone DKFZp569D2231 );

SEQ Template ID GI NumberProbability ID Score NO: Annotation 222 LI:1089827.1:2000SEP088140422920 Homo Sapiens cDNA FLJ 14636 fis, clone NT2RP2001233, weakly similar to 223 LI:792112.1:2000SEP088104379454.00E-61 Homo Sapiens cDNA: FLJ21781 fis, clone HEP00223.

224 LI:282219.2:2000SEP088126566307.00E-63 Homo Sapiens Kruppel-like zinc finger protein mRNA, complete 225 LI:1088010.2:2000SEP088136236320 Homo sapiens, clone MGC:13105, mRNA, complete 226 LI:1165276.1:2000SEP0886807586 1.00E-106 Novel human gene mapping to chomosome 1.

227 LI:1169524.2:2000SEP088100471825.00E-30 Homo sapiens mRNA for KIAA1559 protein, partial cds.

228 LI:I 180255.1:2000SEP088140178700 Homo Sapiens mRNA for KIAA1827 protein, partial cds.

229 LI: ) 091903.1:2000SEP08g 140423722.00E-49 Homo Sapiens cDNA FLJ 14686 fis, clone NT2RP2004961, moderately similar to Rattus norvegicus KRAB/zinc finger 230 LI:1169219.1:2000SEP088139379980 Homo sapiens, Similar to DNA-binding protein, clone MGC:14780, 231 LI:2050313.1:2000SEP088128623190 Homo Sapiens mRNA for WDC146, 232 LI:209351.3:2000SEP088140427940 Homo Sapiens cDNA FLJ 14923 fis, clone PLACE 1008244, weakly similar to VEGETATIBLE

233 LI:119900.1:2000SEP08g 140428212.00E-66 Homo Sapiens cDNA FLJ 14939 fis, clone PLACE 1010702, moderately similar 234 LI:2052274.1:2000SEP0888698839 4.00E-07 Homo sapiens genomic DNA, chromosome 8q23, g4 _.

SE6~ Template ID GI NumberProbability ID Score NO: Annotation 235 LI:1075502.1:2000SEP088139601411.00E-114 Homo sapiens, uridine monophosphate synthetase (orotate phosphoribosyl transferase and orotidine-5'-decarboxylase), 236 LI:813697.1:2000SEP0887020744 6.00E-59 Homo sapiens cDNA FLJ20557 fis, clone KATI
1869.

237 LI:8142b1.1:2000SEP0887023331 1.00E-76 Homo sapiens cDNA FLJ109b1 fis, clone PLACE 1000588, highly similar to INTERFERON-238 LI:775334.1:2000SEP0884589587 3.00E-23 Homo sapiens mRNA for KIAA0972 protein, complete 239 LI:1180325.1:2000SEP088104381590 Homo sapiens cDNA: FLJ21941 fis, clone HEP04524.

240 LI:I 183147.3:2000SEP088104400840 Homo sapiens cDNA: FLJ23407 fis, clone HEP19601.

241 LI:1175373.3:2000SEP0887243242 5.00E-51 Homo sapiens mRNA for KIAA1431 protein, partial cds.

242 LI:813757.1:2000SEP0884589587 1.00E-31 Homo sapiens mRNA for KIAA0972 protein, complete 243 LI:1182979.2:2000SEP088140422922.00E-87 Homo Sapiens cDNA FLJ14636 fis, clone NT2RP2001233, weakly similar to 244 LI:I 177823.2:2000SEP088120529820 Homo sapiens mRNA;cDNA

DKFZp43411610 (from clone DKFZp43411610);

245 LI:1174279.1:2000SEP088100471821.00E-27 Homo sapiens mRNA for KIAA1559 protein, partial cds.

246 LI:1178411.1:20005EP088140428430 Homo sapiens cDNA FLJ 14954 fis, clone PLACE3000169, weakly similar to SEQ Template ID GI NumberProbability ID Score NO: Annotation 247 LI:I 182739.1:2000SEP08g126551648.00E-31 Homo sapiens, zinc finger protein 256, clone MGC:1413, mRNA, complete 248 LI:234937.4:2000SEP08g128044180 Homo sapiens, clone MGC:1136, mRNA, complete 249 LI:1170660.1:2000SEP08g 143884190 Macaca fascicularis brain cDNA clone:6~moA-250 LI:1144409.1:2000SEP08g 120532800 Homo sapiens mRNA;cDNA

DKFZp434J037 (from clone DKFZp434J037);

251 LI:246290.10:2000SEP088104386950 Homo Sapiens cDNA: FLJ22347 fis, clone HRC06188.

252 LI:280034.1:2000SEP08g 128470231.00E-132 p (Mus musculus) p ~O ~O o0 O ~O O ~O N M ~ ~ O L(~ ~ 00 ~O ~O o0 1~ ~Y O~ Iw ~ m ~ M O, OO~ ~ ~ ~ NOV ~-OONOO OOO OOO ~~OOO ~ rOrrMM
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SEQ ID Template ID Start StopFrame Domain Topology NO:

34 LG:345884.1:2000SEP0856 142 forward TM N out 35 LG:400967.1:2000SEP08470 547 forward TM N out 36 LG:02455b.b:2000SEP08529 597 forward TM N in 37 LG:081189.3:2000SEP08627 686 forward TM N out 38 LG:018258.1:2000SEP08430 507 forward TM N out 38 LG:018258.1:2000SEP08444 503 forward TM N out 39 LG:450399.3:2000SEP08145 231 forward TM N out 39 LG:450399.3:2000SEP08417 503 forward TM N in 40 LG:451122.1:2000SEP08328 390 forward TM N in 41 LG:451682.1:2000SEP0893 155 forward TM

42 LG:238631.4:2000SEP08526 612 forward TM N out 42 LG:238631.4:2000SEP08477 563 forward TM

43 LG:236654.1:2000SEP08236 295 forward TM N out 44 LG:332655.1:2000SEP08541 621 forward TM N out 44 LG:332655.1:2000SEP08536 598 forward TM N out 44 LG:332655.1:2000SEP08626 688 forward TM N out 44 LG:332655.1:2000SEP08887 949 forward TM N out 44 LG:332b55.1;2000SEP08965 1027forward TM N out 44 LG:332655.1:2000SEP08912 998 forward TM N out 45 LG:217396.2:2000SEP08317 391 forward TM N out 45 LG:217396.2:2000SEP081127 1189forward TM N out 46 LG:090574.1:2000SEP0849 108 forward TM N out 47 LG:202943.1:2000SEP08590 658 forward TM N out 47 LG:202943.1:2000SEP08842 928 forward TM N out 47 LG:202943.1:2000SEP08552 638 forward TM N out 48 LG:236928.1:2000SEP08349 435 forward TM N in 48 LG:236928.1:2000SEP08448 519 forward TM N in 48 LG:236928.1:2000SEP08592 642 forward TM N in 48 LG:236928.1:2000SEP08706 768 forward TM N in 48 LG:236928.1:2000SEP08778 840 forward TM N in , 1 48 LG:23b928.1:2000SEP08967 1038forward TM N in 48 LG:23b928.1:2000SEP081318 1374forward TM N in 48 LG:236928.1:2000SEP081609 1695forward TM N in 48 LG;236928.1:2000SEP081933 2016forward TM N in 48 LG:236928.1:2000SEP082161 2247forward TM N in 48 LG:236928.1:2000SEP082419 2475forward TM N in 48 LG:23b928.1:2000SEP082818 2865forward TM N in 48 LG:236928.1:2000SEP082884 2946forward TM N in 48 LG:236928.1:2000SEP082980 3042forward TM N in 48 LG:236928.1:2000SEP083076 3138forward TM N in 48 LG:236928.1:2000SEP08335 421 forward TM N in 48 LG:236928.1:2000SEP08437 499 forward TM N in 48 LG:23b928.1:2000SEP08524 586 forward TM N in 48 LG:236928.1:2000SEP08659 718 forward TM N in 48 LG:236928.1:2000SEP081268 1351forward TM N in 48 LG:236928.1:2000SEP081400 1471forward TM N in 48 LG:236928.1:2000SEP081472 1534forward TM N in 48 LG:23b928.1:2000SEP081586 1669forward TM N in 48 LG:23b928.1:2000SEP081745 1831forward TM N in 48 LG:236928.1:2000SEP081877 1963forward TM N in SE6~ Template ID Start StopFrame Domain Topology ID NO:

48 LG;236928.1:2000SEP082015 2101forward TM N in 48 LG:236928.1:2000SEP082501 2587forward TM N in 48 LG:23b928.1:2000SEP082639 2716forward TM N in 48 LG:236928.1:2000SEP082786 2872forward TM N in 48 LG:23b928.1:2000SEP082894 2980forward TM N in 48 LG:236928.1:2000SEP08471 551 forward TM N in 48 LG:236928.1:2000SEP08738 824 forward TM N in 48 LG:236928.1:2000SEP081287 1340forward TM N in 48 LG:236928.1:2000SEP081626 1712forward TM N in 48 LG:236928.1:2000SEP081890 1976forward TM N in 48 LG:236928.1:2000SEP082034 2120forward TM N in 48 LG:236928.1:2000SEP082118 2186forward TM N in 48 LG:236928.1:2000SEP082520 2591forward TM N in 48 LG:236928.1:2000SEP082763 2846forward TM N in 48 LG:236928,1:2000SEP082916 2978forward TM N in 48 LG:236928.1:2000SEP083003 3065forward TM N in 49 LG:215169.2:2000SEP081363 1413forward TM N in 49 LG:215169.2:2000SEP08503 589 forward TM N out 49 LG:215169.2:2000SEP081727 1813forward TM N out 49 LG:215169.2:2000SEP08237 302 forward TM N out 49 LG:2151b9.2:2000SEP08837 923 forward TM N out 49 LG:2151b9.2:2000SEP081398 1460forward TM N out 49 LG:2151b9.2:2000SEP081470 1532forward TM N out 49 LG:215169.2:2000SEP081605 1b58forward TM N out 50 LG:410726.1:2000SEP0831 93 forward TM N out 50 LG:410726.1:2000SEP08115 177 forward TM N out 50 LG:410726.1:2000SEP08463 549 forward TM N out 51 LG:234372.2:2000SEP08325 411 forward TM N in 51 LG:234372.2:2000SEP082492 2578forward TM N out 51 LG:234372.2:2000SEP082669 2743forward TM N out 51 LG:234372.2:2000SEP08723 809 forward TM N in 52 LG:022629.1:2000SEP08268 354 forward TM N out 52 LG:022b29.1:2000SEP08385 459 forward TM N out 52 LG:022b29,1:2000SEP08559 645 forward TM N out 52 LG:022629,1:2000SEP08796 882 forward TM N out 52 LG:022629.1:2000SEP08281 358 forward TM N in 53 LG:068682.1:2000SEP08707 793 forward TM N out 54 LG:222335.1:2000SEP08847 933 forward TM N in 54 LG:222335.1:2000SEP08973 1023forward TM N in 54 LG:222335.1:2000SEP081030 1101forward TM N in 54 LG:222335.1:2000SEP081216 1290forward TM N in 54 LG:222335.1:2000SEP0823 109 forward TM

54 LG:222335.1:2000SEP08314 373 forward TM

54 LG:222335.1:2000SEP08428 514 forward TM

54 LG:222335.1:2000SEP08728 784 forward TM

54 LG:222335.1:2000SEP08794 868 forward TM

54 LG:222335.1:2000SEP08965 1051forward TM

54 LG:222335.1:2000SEP08603 674 forward TM N in 54 LG:222335,1:2000SEP08921 983 forward TM N in 54 LG:222335.1:2000SEP081014 1076forward TM N in SEQ ID Template ID StartStop Frame Domain Topology NO:

54 LG:222335.1:2000SEP081101 1187 forward TM N in 54 LG:222335.1:2000SEP081227 1277 forward TM N in 55 LG:331342,1:2000SEP0822 96 forward TM N out 55 LG:331342.1:2000SEP08289 339 forward TM N out 55 LG:331342,1:2000SEP08645 731 forward TM N in 56 LG:021770.1:2000SEP08286 372 forward TM N in 56 LG:021770.1:2000SEP08400 477 forward TM N in 56 LG:021770.1:2000SEP08502 579 forward TM N in 56 LG:021770.1:2000SEP08784 852 forward TM N in 56 LG:021770.1:2000SEP081237 1323 forward TM N in 56 LG:021770.1:2000SEP082416 2499 forward TM N in 56 LG:021770.1:2000SEP082611 2697 forward TM N in 56 LG:021770.1:2000SEP081115 1201 forward TM N in 56 LG:021770.1:2000SEP081262 1336 forward TM N in 56 LG:021770.1:2000SEP082426 2509 forward TM N in 56 LG:021770.1:2000SEP082726 2776 forward TM N in 56 LG:021770.1:2000SEP08534 614 forward TM N in 56 LG:021770.1:2000SEP081260 1346 forward TM N in 56 LG:021770.1:2000SEP081461 1547 forward TM N in 56 LG:021770.1:2000SEP081695 1778 forward TM N in 56 LG:021770.1:2000SEP082496 2576 forward TM N in 56 LG:021770.1:2000SEP082727 2792 forward TM N in 57 LG:181607.9:2000SEP08439 525 forward TM N out 58 LG:1042768.1:2000SEP08695 751 forward TM N out 58 LG:1042768.1:2000SEP0893 143 forward TM N in 58 LG:1042768.1:2000SEP08201 287 forward TM N in 58 LG:1042768.1:2000SEP08351 437 forward TM N in 59 LG:282729.1:2000SEP08256 309 forward TM N out 60 LG:998305.3:2000SEP08429 488 forward TM N in 60 LG:998305,3:2000SEP08705 770 forward TM N in 61 LG:1135213.1:2000SEP0841 127 forward TM N out 61 LG:1135213.1:2000SEP08215 274 forward TM N out 61 LG:1135213.1:2000SEP08293 379 forward TM N out 61 LG:1135213.1:2000SEP08389 475 forward TM N out 62 LG:2677b2.1:2000SEP08854 937 forward TM N in 62 LG:2b77b2.1:2000SEP081283 1345 forward TM N in 62 LG:2b77b2.1:2000SEP081445 1531 forward TM N in b2 LG:267762.1:2000SEP081383 1469 forward TM N out b3 LG:120744.1:2000SEP08181 249 forward TM N out b3 LG:120744,1:2000SEP08188 256 forward TM

b3 LG:120744.1:2000SEP08275 328 forward TM

b4 LG:403409.1:2000SEP08136 222 forward TM N out 64 LG:403409.1:2000SEP08973 1029 forvvardTM N out 64 LG:403409.1:2000SEP081285 1371 forward TM N out 64 LG:403409.1:2000SEP08182 268 forward TM N in 65 LG:226874.3:2000SEP08231 278 forward TM N out 66 LG:1045521,4:2000SEP081216 1266 forward TM N in 66 LG:1045521,4:2000SEP081567 1653 forward TM N in 66 LG:1045521.4:2000SEP081699 1761 forward TM N in 66 LG:1045521.4:2000SEP083091 3177 forward TM N in SE6~ Template ID StartStop Frame Domain Topology ID NO:

66 LG:1045521.4:2000SEP083508 3582 forward TM N in 66 LG:1045521.4:2000SEP081652 1714 forward TM N in 66 LG:1045521.4:2000SEP082444 2500 forward TM N in 66 LG:1045521.4:2000SEP082627 2713 forward TM N in 66 LG:1045521.4:2000SEP083017 3088 forward TM N in 66 LG:1045521.4:2000SEP083317 3385 forward TM N in 66 LG:1045521.4:2000SEP081530 1604 forward TM N in 66 LG:1045521.4:2000SEP082496 2549 forward TM N in 66 LG:1045521.4:2000SEP082931 3017 forward TM N in 66 LG:1045521.4:2000SEP083267 3341 forward TM N in 67 LG:275876.1:2000SEP08775 849 forward TM N in 67 LG:275876.1:2000SEP08949 1002 forward TM N in 67 LG:275876.1:2000SEP08842 928 forward TM N out 67 LG:275876.1:2000SEP08777 842 forward TM N in 68 LG:475127.7:2000SEP08137 223 forward TM N in 69 LG:157263.1:2000SEP08175 249 forward TM N in 69 LG:157263.1:2000SEP08295 345 forward TM N in 69 LG:157263.1:2000SEP08406 492 forward TM N in 69 LG:157263.1:2000SEP08793 867 forward TM N in 69 LG:157263.1:2000SEP08889 951 forward TM N in 69 LG:157263.1:2000SEP081081 1143 forward TM N in 69 LG:157263.1:2000SEP0811 1230 forward TM N in b8 1 69 LG:1572b3.1:2000SEP081255 1341 forward TM N in 69 LG:157263.1:2000SEP08482 544 forward TM N out 69 LG:157263.1:2000SEP08563 625 forward TM N out b9 LG:157263.1:2000SEP08180 266 forward TM N out 70 LG:247382.7:2000SEP08808 894 forward TM

70 LG:247382.7:2000SEP08650 709 forward TM N out 70 LG:247382.7:2000SEP081412 1495 forward TM N out 71 LG:197367.5:2000SEP08454 510 forward TM N out 72 LG:218090.5:2000SEP0885 156 forward TM N out 72 LG:218090.5:2000SEP08417 494 forward TM N out 73 LG:216612.4:2000SEP081615 1701 forward TM N in 73 LG:216612.4:2000SEP081942 2007 forward TM N in 73 L6:216b12.4:2000SEP082182 2268 forward TM N in 73 LG:216612.4:2000SEP082413 2487 forward TM N in 73 LG:216612.4:2000SEP081583 1660 forward TM N in 73 LG:216612.4:2000SEP082114 2176 forward TM N in 73 LG:216612.4:2000SEP082216 2278 forward TM N in 73 LG:216b12.4:2000SEP082339 2425 forward TM N in 73 LG:216612.4:2000SEP082483 2542 forward TM N in 73 LG:216612.4:2000SEP08120 206 forward TM N in 73 LG;216612.4:2000SEP08234 284 forward TM N in 73 LG:216b12.4:2000SEP08327 413 forward TM N in 73 LG:21bb12.4:2000SEP08444 530 forward TM N in 73 LG:21bb12.4:2000SEP08810 896 forward TM N in 73 LG;216b12.4:2000SEP08942 1028 forward TM ' N in 73 LG:216612.4:2000SEP081644 1730 forward TM N in 73 LG:216612.4:2000SEP081950 2012 forward TM N in 73 LG:216b12.4:2000SEP082037 2099 forward TM N in !Q?

SE6~ Template ID StartStop Frame Domain Topology ID NO:

73 LG:216612.4:2000SEP082292 2378 forward TM N in 73 LG:216612.4:2000SEP082529 2615 forward TM N in 74 LG;197b14.1:2000SEP08484 537 forward TM N in 74 LG:197614.1:2000SEP082308 2367 forward TM N in 74 LG:197614.1:2000SEP083175 3246 forward TM N in 74 LG:197b14.1:2000SEP083298 3354 forward TM N in 74 LG;197614.1:2000SEP083556 3612 forward TM N in 74 LG:197614.1:2000SEP083739 3825 forward TM N in 74 LG:197614.1:2000SEP083964 4050 forward TM N in 74 LG:197b14.1:2000SEP084063 4134 forward TM N in 74 LG:197b14.1:2000SEP084147 4215 forward TM N in 74 LG:197614.1:2000SEP08374 460 forward TM N out 74 LG:197614.1:2000SEP08800 862 forward TM N out 74 LG:197614.1:2000SEP08875 937 forward TM N out 74 LG:197614.1:2000SEP081352 1414 forward TM N out 74 LG;197614.1:2000SEP081436 1498 forward TM N out 74 LG:197614.1:2000SEP082312 2398 forward TM N out 74 LG;197614.1:2000SEP083422 3469 forward TM N out 74 LG:197b14.1:2000SEP083632 3718 forward TM N out 74 LG;197614.1:2000SEP083773 3835 forward TM N out 74 LG:197614.1:2000SEP083932 4003 forward TM N out 74 LG:197614.1:2000SEP084040 4126 forward TM N out 74 LG:197614.1:2000SEP084244 4312 forward TM N out 74 LG:197614.1:2000SEP084448 4504 forward TM N out 74 LG;197614.1:2000SEP08489 575 forward TM

74 LG;197614.1:2000SEP082967 3017 forward TM

74 LG;197614.1:2000SEP083663 3749 forward TM

74 LG:197614.1:2000SEP083912 3974 forward TM

74 LG:197614.1:2000SEP084020 4082 forward TM

74 LG:197b14.1:2000SEP084341 4427 forward TM

75 LG;378428.1:2000SEP08703 789 forward TM N in 75 LG:378428.1:2000SEP081336 1422 forward TM N in 75 LG:378428.1:2000SEP081924 2010 forward TM N in 75 LG:378428.1:2000SEP082188 2268 forward TM N in 75 LG:378428.1:2000SEP082171 2224 forward TM N in 75 LG:378428.1:2000SEP081527 1577 forward TM N out 75 LG:378428.1:2000SEP081665 1751 forward TM N out 75 LG;378428.1:2000SEP081968 2054 forward TM N out 75 LG:378428.1:2000SEP082205 2291 forward TM N out 76 LG;286639.1:2000SEP08127 213 forward TM

76 LG:286b39.1:2000SEP08970 1032 forward TM

76 LG:286639.1:2000SEP081066 1128 forward TM

76 LG:286b39.1:2000SEP081588 1662 forward TM

76 LG:28bb39.1:2000SEP081786 1872 forward TM

76 LG:286639.1:2000SEP0862 148 forward TM N in 76 LG:28bb39.1:2000SEP081772 1825 forward TM N in 76 LG:286b39.1:2000SEP08267 320 forward TM N out 76 LG:28bb39.1:2000SEP08999 1085 forward TM N out 76 LG:28bb39.1:2000SEP081902 1967 forward TM N out 77 LG:389870.1:2000SEP081066 1113 forward TM N out SE6~ Template ID StartStop Frame Domain Topology ID NO:

77 LG:389870.1:2000SEP081055 1120 forward TM N in 77 LG:389870.1:2000SEP081059 1142 forward TM N in 78 LG:1387485.b:2000SEP081213 1275 forward TM N in 78 LG:1387485.b:2000SEP08206 292 forward TM N in 78 LG:1387485.b:2000SEP08824 886 forward TM N in 78 LG:1387485,b:2000SEP08914 976 forward TM N in 78 LG:1387485.b:2000SEP081244 1321 forward TM N in 78 LG:1387485.6:2000SEP08396 473 forward TM N out 78 LG:1387485.6:2000SEP08537 602 forward TM N out 78 LG:1387485.6:2000SEP08660 746 forward TM N out 78 LG:1387485.b:2000SEP08786 872 forward TM N out 78 LG:1387485.b:2000SEP081164 1226 forward TM N out 78 LG:1387485.6:2000SEP081245 1307 forward TM N out 79 LG:230151.1:2000SEP081774 1860 forward TM N in 79 LG:230151.1:2000SEP081091 11 forward TM N out b5 2 79 LG:230151.1:2000SEP081193 1246 forward TM N out 79 LG:230151.1:2000SEP081757 1843 forward TM N out 80 LG:215158.5:2000SEP08199 267 forward TM N out 80 LG:215158.5:2000SEP08820 873 forward TM N out 80 LG:215158.5:2000SEP08892 945 forward TM N out 80 LG:215158.5:2000SEP08908 985 forward TM N out 80 LG:215158.5:2000SEP081433 1504 forward TM N out 80 LG:215158.5:2000SEP08447 533 forward TM

81 LG:235840.1:2000SEP08265 342 forward TM N out 81 LG:235840.1:2000SEP08511 579 forward TM N out 81 LG:235840.1:2000SEP08577 639 forward TM N out 81 LG:235840.1:2000SEP08730 786 forward TM N out 81 LG:235840.1:2000SEP082011 2082 forward TM N out 81 LG:235840.1:2000SEP082110 2172 forward TM N out 81 LG:235840.1:2000SEP082326 2406 forward TM N out 81 LG:235840.1:2000SEP082416 2502 forward TM N out 81 LG:235840.1:2000SEP0811 178 forward TM N out b 2 81 LG:235840.1:2000SEP08191 253 forward TM N out 81 LG:235840.1:2000SEP08500 586 forward TM N out 81 LG:235840.1:2000SEP08731 817 forward TM N out 81 LG:235840.1:2000SEP08848 91 forward TM N out b 2 81 LG:235840.1:2000SEP08956 1030 forward TM N out 81 LG:235840.1:2000SEP081973 2050 forward TM N out 81 LG:235840.1:2000SEP08192 278 forward TM N out 81 LG:235840.1:2000SEP08516 590 forward TM N out 81 LG:235840.1:2000SEP08711 797 forward TM N out 81 LG:235840.1:2000SEP08819 905 forward TM N out 81 LG:235840.1:2000SEP081446 1529 forward TM N out 81 LG:235840.1:2000SEP081893 1976 forward TM N out 81 LG:235840.1:2000SEP082298 2360 forward TM N out 82 LG:350272.1:2000SEP081675 1746 forward TM N in 82 LG:350272.1:2000SEP082374 2436 forward TM N in 82 LG:350272,1:2000SEP08104 190 forward TM N in 82 LG:350272.1:2000SEP082264 2332 forward TM N in 82 LG:350272.1:2000SEP082369 2440 forward TM N in SE6~ Template ID StartStop Frame Domain Topology ID NO:

82 LG:350272.1:2000SEP0812 95 forward TM N in 82 LG:350272.1:2000SEP08993 1052 forward TM N in 82 LG:350272.1:2000SEP082067 2138 forward TM N in 82 LG:350272.1:2000SEP082334 2399 forward TM N in 83 LG:232190.1:2000SEP08592 678 forward TM N in 83 LG:232190.1:2000SEP081423 1500 forward TM N in 83 LG:232190.1:2000SEP08158 241 forward TM N in 83 LG:232190.1:2000SEP08293 373 forward TM N in 83 LG:232190.1:2000SEP08644 730 forward TM N in 83 LG:232190.1:2000SEP08761 847 forward TM N in 83 LG:232190.1:2000SEP081466 1552 forward TM N in 83 LG:232190.1:2000SEP08279 356 forward TM N in 83 LG:232190.1:2000SEP08588 674 forward TM N in 83 LG:232190.1:2000SEP08936 1022 forward TM N in 84 LG:1068127.1:2000SEP08423 470 forward TM

85 LG:408751.3:2000SEP082194 2253 forward TM N out 85 LG:408751.3:2000SEP082320 2406 forward TM N out 85 LG:408751.3:2000SEP081907 1993 forward TM N out 85 LG:408751.3:2000SEP082378 2464 forward TM N out 85 LG:408751.3:2000SEP081866 1928 forward TM N in 85 LG:408751.3:2000SEP082328 2414 forward TM N in 86 LG:1078933.1:2000SEP08905 991 forward TM N in 86 LG:1078933.1;2000SEP08924 1010 forward TM N in 87 LG:958731.1:2000SEP0815 101 forward TM N out 88 LG:024125.5:2000SEP08474 554 forward TM

89 LG:373b37.3:2000SEP08473 559 forward TM N in 89 LG:373637.3:2000SEP08854 934 forward TM N in 90 LG:1053229.1:2000SEP08410 487 forward TM N out 91 LG:248364.1:2000SEP08439 495 forward TM N out 92 LG:477130.1:2000SEP0837 108 forward TM N in 92 LG:477130.1:2000SEP08406 489 forward TM N in 92 LG:477130.1:2000SEP08685 759 forward TM N in 92 LG:477130.1:2000SEP08641 727 forward TM N in 92 LG:477130.1:2000SEP08741 827 forward TM N in 93 LG:113786.17:2000SEP0889 139 forward TM N out 93 LG:113786.17:2000SEP0818 b8 forward TM

94 LG:347635.1:2000SEP08220 294 forward TM N out 94 LG;347635.1:2000SEP08406 456 forward TM N out 94 LG:347635.1:2000SEP08479 550 forward TM N out 94 LG:347635.1:2000SEP081283 1369 forward TM N out 94 LG:347635.1:2000SEP08615 701 forward TM N out 94 LG:347635.1:2000SEP081347 1397 forward TM N out 95 LG:242966.4:2000SEP081439 1510 forward TM N in 96 LG:217814.1:2000SEP081621 1689 forward TM N out 96 LG;217814.1:2000SEP081622 1708 forward TM N out 96 LG:217814.1:2000SEP08246 302 forward TM N in 96 LG:217814.1:2000SEP081695 1772 forward TM N in 97 LG:476452.1:2000SEP08556 624 forward TM N out 97 LG:476452.1:2000SEP08988 1074 forward TM N out 98 LG:I 100657.1:2000SEP0831 117 forward TM N out 10~

SEQ ID Template ID StartStop Frame Domain Topology NO:

99 LG:1132418.2:2000SEP0843 129 forward TM N out 99 LG:1132418.2:2000SEP08244 327 forward TM N out 100 LG:1098570.1:2000SEP08400 453 forward TM N out 100 LG:1098570.1:2000SEP0826 85 forward TM N out 101 LG:1097987.1:2000SEP08152 208 forward TM N out 101 LG:1097987.1:2000SEP08141 215 forward TM

101 LG:1097987.1:2000SEP08912 971 forward TM

102 LG:337818.2:2000SEP0840 117 forward TM N out 102 LG:337818.2:2000SEP08532 618 forward TM N out 102 LG:337818.2:2000SEP08907 993 forward TM N out 102 LG:337818.2:2000SEP081360 1425 forward TM N out 103 LG:1040582.1:2000SEP0831 117 forward TM N in 103 LG:1040582.1:2000SEP08539 595 forward TM N out 103 LG:1040582.1:2000SEP08330 416 forward TM N out 104 LG:1099122.1:2000SEP08385 456 forward TM N out 104 LG:1099122.1:2000SEP08236 292 forward TM N in 104 LG:1099122.1:2000SEP08350 436 forward TM N in 104 LG:1099122.1:2000SEP08258 308 forward TM N out 104 LG:1099122.1:2000SEP08420 470 forward TM N out 105 LG:1327449.1:2000SEP08112 198 forward TM N out 105 LG:1327449.1:2000SEP08268 318 forward TM N out 105 LG:1327449.1:2000SEP08395 481 forward TM N out 106 LG:227933.5:2000SEP081114 1200 forward TM N in 106 LG:227933.5:2000SEP081231 1290 forward TM N in 106 LG:227933.5:2000SEP08255 308 forward TM N out 107 LG:1043709.2:2000SEP08600 b50 forward TM N out 108 LG:1099871.1:2000SEP08181 243 forward TM N out 109 LG:1399139.4:2000SEP08289 3b9 forward TM N out 109 LG:1399139.4:2000SEP08616 684 forward TM N out 109 LG:1399139.4:2000SEP08185 235 forward TM

109 LG:1399139.4:2000SEP08555 641 forward TM N out 110 LG:23638b.1:2000SEP08106 171 forward TM N out 110 LG:23638b.1:2000SEP08271 357 forward TM N out 110 LG:23b38b.1:2000SEP083097 3159 forward TM N out 110 LG:236386.1:2000SEP083715 3789 forward TM N out 110 LG:23638b.1:2000SEP083093 3164 forward TM N out 110 LG:23638b.1:2000SEP083759 3812 forward TM N out 111 LG:1015157.1:2000SEP08320 406 forward TM N in 112 LG:1065433.1:2000SEP08790 876 forward TM N in 113 LG:236992.4:2000SEP08421 471 fornrardTM N out 113 LG:236992.4:2000SEP0814 100 forward TM N out 114 LG:1071124.1:2000SEP08171 257 forward TM N out 115 LG:206425.2:2000SEP08175 237 forward TM N in 115 LG:206425.2:2000SEP08424 483 forward TM N in 115 LG:206425.2:2000SEP081810 1896 forward TM N in 115 LG:206425.2:2000SEP081939 2001 forward TM N in 115 LG:206425.2:2000SEP08404 457 forward TM N in 115 LG:206425.2:2000SEP0821 2254 forward TM N in b8 2 115 LG:206425.2:2000SEP08561 620 forward TM N out 115 LG;20b425.2:2000SEP081908 1994 forward TM N out SEQ ID Template ID StartStop Frame Domain Topology NO:

116 LG:885747.2:2000SEP08125 205 forward TM N in 116 LG:885747.2:2000SEP08135 191 forward TM N out 116 LG:885747.2:2000SEP08189 239 fonrvardTM N out 117 LG:1140501.1:2000SEP08622 708 forward TM N out 117 LG:1140501.1:2000SEP08844 918 forward TM N out 117 LG:1140501.1:2000SEP081138 1206 forward TM N out 117 LG:1140501.1:2000SEP0886 169 forward TM N out 117 LG:1140501.1:2000SEP08221 301 forward TM N out 1 17 LG:1140501.1:2000SEP08617 703 forward TM N out 117 LG:I 140501.1:2000SEP08606 677 forward TM N in 118 LG:001239.1:2000SEP081048 1122 forward TM N out 118 LG:001239.1:2000SEP08669 755 forward TM N out 118 LG:001239.1:2000SEP081911 1976 forward TM N out 119 LG:018980.1:2000SEP08124 204 forward TM N out 119 LG:018980.1:2000SEP08944 997 forward TM N out 119 LG:018980.1;2000SEP08405 464 forward TM N out 119 LG:018980.1:2000SEP08900 986 forward TM N out 119 LG:018980.1:2000SEP081017 1103 forward TM N out 120 LG:1083120.3:2000SEP08214 291 forward TM N out 120 LG:1083120.3:2000SEP08233 319 forward TM N out 120 LG:1083120.3:2000SEP08252 320 forward TM N in 121 LG:233258.3:2000SEP0858 141 forward TM

121 LG:233258.3:2000SEP081783 1842 forward TM

121 LG:233258.3:2000SEP082248 2322 forward TM

121 LG:233258.3:2000SEP084522 4596 forward TM

121 LG:233258.3:2000SEP084208 4294 forward TM N out 121 LG:233258.3:2000SEP084478 4534 forward TM N out 121 LG:233258.3:2000SEP08390 476 forward TM N in 121 LG:233258.3:2000SEP082766 2852 forward TM N in 122 LG:999062.1:2000SEP08455 508 forward TM N in 122 LG:999062.1:2000SEP08510 596 forward TM N in 123 LG:887776.1:2000SEP0814 91 forward TM N out 124 LG:1400301.2:2000SEP08445 531 forward TM N out 124 LG:1400301.2:2000SEP08456 518 forward TM N out 125 LG:1329362.1:2000SEP0818 104 forward TM N out 126 LG:1096498.1:2000SEP08137 199 forward TM N out 126 LG:1096498.1:2000SEP08201 269 forward TM N out 126 LG:1096498.1:2000SEP08321 371 forward TM N out 127 LG:1096337.1:2000SEP08625 711 forward TM N out 127 LG:1096337.1:2000SEP08500 553 forward TM

128 LG:1400579.1:2000SEP08797 883 forward TM N out 128 LG:1400579.1:2000SEP089 86 forward TM N out 128 LG:1400579.1:2000SEP08669 755 forward TM N out 129 LG:1080091.1:2000SEP0867 114 forward TM N out 129 LG:1080091.1:2000SEP08435 497 forward TM N out 130 LG:1082203.1:2000SEP081438 1521 forward TM N in 130 LG:1082203.1:2000SEP08155 217 forward TM N out 130 LG:1082203.1:2000SEP08272 358 forward TM N out 131 LG:1084051.1:2000SEP08301 366 forward TM N out 131 LG:1084051.1:2000SEP08934 1017 forward TM N out SEQ ID Template ID Start StopFrame Domain Topology NO:

131 LG:1084051.1;2000SEP081072 1140forward TM N out 131 LG:1084051.1:2000SEP08875 961 forward TM N out 131 LG:1084051.1:2000SEP08882 968 forward TM N in 131 LG:1084051.1:2000SEP081071 1151forward TM N in 132 LG:1082393.1:2000SEP08505 579 forward TM N in 132 LG:1082393.1:2000SEP081710 1784forward TM N in 133 LG:108b183.1:2000SEP081093 1179forward TM N out 133 LG:1086183.1:2000SEP081166 1252forward TM N in 133 LG:1086183.1:2000SEP0815 86 forward TM

133 LG:1086183.1:2000SEP08381 437 forward TM

133 LG:1086183.1:2000SEP081194 1280forward TM

134 LG:10902b8.1:2000SEP081882 1953forward TM N out 134 LG:10902b8.1:2000SEP081969 2055forward TM N out 134 LG:1090268.1:2000SEP081670 1729forward TM N out 134 LG:1090268.1:2000SEP081853 1939forward TM N out 134 LG:1090268.1:2000SEP081997 2083forward TM N out 134 LG:1090268.1:2000SEP081485 1550forward TM N in 134 LG:1090268.1:2000SEP081869 1943forward TM N in 134 LG:10902b8.1;2000SEP081962 2048forward TM N in 135 LG:1400597.5;2000SEP08134 199 forward TM N in 136 LG:1080307.2:2000SEP08275 346 forward TM N out 136 LG:1080307.2;2000SEP08347 403 forward TM N out 136 LG:1080307.2:2000SEP08183 269 forward TM N in 136 LG:1080307.2;2000SEP08303 371 forward TM N in 137 LG:1400603.2:2000SEP08792 878 forward TM N in 137 LG:1400603.2;2000SEP08903 971 forward TM N in 137 LG:1400603.2;2000SEP081068 1151forward TM N in 138 LG:1052984.1:2000SEP08496 582 forward TM N in 138 LG:1052984.1:2000SEP08509 595 forward TM N out 138 LG:1052984.1;2000SEP08495 581 forward TM

139 LG:1091259.1:2000SEP08799 885 forward TM N in 140 LG:10822b3.2:2000SEP081390 1458forward TM N in 140 LG:1082263.2;2000SEP081558 1644forward TM N in 140 LG:10822b3.2;2000SEP0883 169 forward TM

140 LG:10822b3.2;2000SEP081526 1612fonnrardTM

140 LG:10822b3.2:2000SEP081578 1664forward TM N in 141 LG:1048604.2:2000SEP08562 618 forward TM N in 141 LG:1048604.2:2000SEP08697 768 forward TM N in 141 LG:1048604.2:2000SEP08856 930 forward TM N in 141 LG:1048604.2:2000SEP08332 418 forward TM N in 141 LG:1048604.2:2000SEP08689 775 forward TM N in 141 LG:1048604.2:2000SEP081115 1192forward TM N in 141 LG:1048604.2:2000SEP08483 557 forward TM N in 141 LG:1048604.2:2000SEP08570 638 forward TM N in 141 LG:1048604.2:2000SEP08678 743 forward TM N in 141 LG:1048604.2;2000SEP081113 1199forward TM N in 142 LG:1085254.3:2000SEP08331 378 forward TM N in 142 LG:1085254.3;2000SEP08204 290 forward TM N out 143 LG:1400606.2:2000SEP081096 1176forward TM N out 143 LG:140060b.2:2000SEP08794 880 forward TM N in los SE6Z Template ID StartStop Frame Domain Topology ID NO:

143 LG:1400606.2:2000SEP081031 1117 forward TM N in 143 LG:1400606.2:2000SEP0893 173 forward TM N in 143 LG:1400606.2:2000SEP08765 851 forward TM N in 144 LG:1090358.2:2000SEP08250 336 forward TM N in 144 LG:1090358.2:2000SEP08758 844 forward TM N out 144 LG:1090358.2:2000SEP08848 919 forward TM N out 144 LG:1090358.2:2000SEP08974 1060 forward TM N out 145 LG:1079064.2:2000SEP08862 936 forward TM N out 146 LG:1076866.1:2000SEP082113 2187 forward TM N in 146 LG:107686b.1:2000SEP082111 2170 forward TM

146 LG:107b866.1:2000SEP08501' 587 forward TM N in 146 LG:1076866.1;2000SEP082148 2234 forward TM N in 147 LG:9b9359.1:2000SEP08256 303 forward TM N out 147 LG;969359.1:2000SEP08276 350 forward TM N out 148 LG:366783.1:2000SEP081060 1143 forward TM N in 148 LG:3bb783.1:2000SEP08470 550 forward TM

148 LG:366783.1:2000SEP081050 1109 forward TM N in 149 LG:332176.3:2000SEP08442 495 forward TM N in 149 LG:332176.3:2000SEP08209 295 forward TM N in 149 LG:332176.3:2000SEP08234 299 forward TM N in 149 LG:332176.3:2000SEP08792 851 forward TM N in 149 LG:332176.3:20005EP08876 938 forward TM N in 149 LG:332176.3:2000SEP08966 1028 forward TM N in 150 LG:994938.1:2000SEP08562 618 forward TM N out 150 LG:994938.1:2000SEP08287 343 forward TM N out 150 LG:994938.1:2000SEP08512 598 forward TM N out 150 LG:994938.1:2000SEP08279 356 forward TM N out 150 LG:994938.1:2000SEP08474 557 forward TM N out 151 LG:982800.1:2000SEP0825 81 forward TM N,out 151 LG:982800.1:2000SEP081708 1782 forward TM N out 151 LG:982800.1:2000SEP082305 2391 forward TM N out 151 LG:982800.1:2000SEP081658 1744 forward TM N in 151 LG:982800.1:2000SEP081880 1927 forward TM N in 151 LG:982800.1:2000SEP082255 2341 forward TM N in 151 LG:982800.1:2000SEP081614 1697 forward TM N in 151 LG:982800.1:2000SEP082220 2306 forward TM N in 152 LG:977850.7:2000SEP0858 144 forward TM N out 152 LG:977850.7:2000SEP08187 237 forward TM N out 152 LG:977850.7:2000SEP0835 112 forward TM N out 152 LG:977850.7:2000SEP0848 116 forward TM N in 153 LG:234748.2;2000SEP0825 99 forward TM N out 153 LG:234748.2:2000SEP08601 663 forward TM N out 153 LG:234748.2:2000SEP08679 741 forward TM N out 153 LG:234748.2:2000SEP08871 957 forward TM N out 153 LG:234748.2:2000SEP081162 1230 forward TM N out 153 LG:234748.2:2000SEP081237 1302 forward TM N out 153 LG:234748.2:2000SEP081579 1641 forward TM N out 153 LG:234748.2:2000SEP081984 2070 forward TM N out 153 LG:234748.2:2000SEP082110 2196 forward TM N out 153 LG:234748.2:2000SEP082308 2355 forward TM N out SE6Z Template ID StartStop Frame Domain Topology ID NO:

153 LG:234748.2:2000SEP08359 421 forward TM

153 LG:234748.2:2000SEP08464 526 forward TM

153 LG:234748.2:2000SEP08656 742 forward TM

153 LG:234748.2:2000SEP08899 949 forward TM

153 LG:234748.2:2000SEP08995 1057 forward TM

153 LG:234748.2:2000SEP081076 1138 forward TM

153 LG:234748.2:2000SEP081412 1489 forward TM

153 LG:234748.2:2000SEP081925 1999 forward TM

153 LG:234748.2:2000SEP082012 2071 forward TM

153 LG:234748.2:2000SEP082105 2191 forward TM

153 LG:234748.2:2000SEP082204 2290 forward TM

153 LG:234748.2:2000SEP08393 455 forward TM N in 153 LG:234748.2:2000SEP08474 536 forward TM N in 153 LG:234748.2:2000SEP08645 725 forward TM N in 153 LG:234748.2:2000SEP08801 863 forward TM N in 153 LG:234748.2:2000SEP08894 956 forward TM N in 153 LG:234748.2:2000SEP081485 1535 forward TM N in 153 LG:234748.2:2000SEP082052 2114 forward TM N in 153 LG:234748.2:2000SEP082145 2207 forward TM N in 153 LG;234748.2:2000SEP082238 2300 forward TM N in 154 LG:30b284.1:2000SEP08255 305 forward TM N in 177 LI:335923.2:2000SEP08149 229 forward TM N in 178 LI:345884.1:2000SEP0861 147 forward TM N out 179 LI:417127.1:2000SEP08148 201 forward TM N in 1 .

179 LI:417127.1:2000SEP08114 200 forward TM N in 180 LI:451710.1:2000SEP08502 588 forward TM N in 180 LI:451710.1:2000SEP08453 515 forward TM N in 181 LI:40b882.2:2000SEP08109 180 forward TM N in 181 LI:406882.2:2000SEP08514 597 forward TM N in 181 LI:40b882.2;2000SEP081045 1101 forward TM N in 181 LI:40b882.2:2000SEP08293 379 forward TM N out 181 LI:40b882.2:2000SEP08653 739 forward TM N out 181 LI:406882.2:2000SEP081091 1141 forward TM N out 181 LI:40b882.2;2000SEP08675 746 forward TM N out 182 LI:728223.1:2000SEP0845 131 forward TM N out 182 LI:728223.1:2000SEP08129 179 forward TM N out 183 LI:289783.19:2000SEP0810 93 forward TM N in 183 LI:289783.19:2000SEP08151 204 forward TM N in 183 LI:289783.19:2000SEP0811 94 forward TM

183 LI:289783.19:2000SEP08140 226 forward TM

183 LI:289783.19:2000SEP08489 575 forward TM . N
3 in 184 LI:235255.8:2000SEP08985 1044 forward TM N out 185 LI:237b93.5:2000SEP08355 429 forward TM N in 186 LI:433670.3:2000SEP0879 165 forward TM

186 LI:433670.3:2000SEP08598 681 forward TM

186 LI:433b70.3:20005EP08796 8b7 forward TM

186 LI:433b70.3:2000SEP0874 1 forward TM N in b0 2 186 LI:433670.3:2000SEP08221 292 forward TM N in 186 LI:433b70.3:2000SEP08662 73b forward TM N in 186 LI:433b70.3:2000SEP08848 898 forward TM N in SEQ ID Template ID StartStop Frame Domain Topology NO:

186 LI:433b70,3:2000SEP0875 161 forward TM N in 186 LI:433670.3:2000SEP08387 449 forward TM N in 186 LI:433670,3:2000SEP08651 737 forward TM N in 187 LI:202943,4:2000SEP08535 609 forward TM N out 187 LI:202943,4:2000SEP081570 1656 forward TM N out ' 1 187 LI:202943.4:2000SEP08342 395 forward TM N out 187 LI:202943.4:2000SEP08495 557 forward TM N out 187 LI:202943,4:2000SEP08579 641 forward TM N out 187 LI:202943,4:2000SEP08759 845 forward TM N out 187 LI:202943.4:2000SEP081653 1721 forward TM N out 187 LI:202943,4:2000SEP081905 1991 forward TM N out 188 LI:Ob8b82,1:2000SEP08700 786 forward TM N out 189 LI:203301.3:2000SEP08643 729 forward TM N out 189 LI:203301,3:2000SEP081510 1572 forward TM N out 189 LI:203301,3:2000SEP081585 1647 forward TM N out 189 LI:203301,3:2000SEP081774 1842 forward TM N out 189 LI:203301.3:2000SEP082014 2100 forward TM N out 189 LI:203301,3:2000SEP082158 2220 forward TM N out 189 LI:203301,3:2000SEP082383 2469 forward TM N out 189 LI:203301,3:2000SEP082548 2634 forward TM N out 189 LI:203301,3:2000SEP082662 2724 forward TM N out 189 LI:203301,3:2000SEP082749 2835 forward TM N out 189 LI:203301.3:2000SEP081685 1771 forward TM N in 189 LI:203301.3:2000SEP0821 2233 forward TM N in b2 2 189 LI:203301.3:2000SEP082342 2428 forward TM N in 189 LI:203301.3:2000SEP082519 2572 forward TM N in 189 LI:203301.3:2000SEP082597 2674 forward TM N in 189 LI:203301.3:2000SEP08117 170 forward TM N in 189 LI:203301.3:2000SEP08387 470 forward TM N in 189 LI:203301.3:2000SEP081086 1136 forward TM N in 189 LI:203301.3:2000SEP081344 1430 forward TM N in ~ 3 189 LI:203301.3:2000SEP081626 1712 forward TM N in 189 LI:203301.3:2000SEP082364 2435 forward TM N in 189 LI:203301,3:2000SEP082604 2672 forward TM N in 190 LI:02072b.3:2000SEP081363 1449 forward TM N in 190 LI:020726.3:2000SEP081795 1863 forward TM N in 190 LI:020726.3:2000SEP081930 1992 forward TM N in 190 LI:02072b.3:2000SEP08545 631 forward TM N in 190 LI:02072b.3:2000SEP08656 742 forward TM N in 190 LI:02072b,3:2000SEP08767 829 forward TM N in 190 LI:020726.3:2000SEP08839 901 forward TM N in 190 LI:020726.3:2000SEP08938 1024 forward TM N in 190 LI:02072b.3:2000SEP081391 1477 forward TM N in 190 LI:020726.3:2000SEP081598 1672 forward TM N in 190 LI:020726.3:2000SEP081790 1852 forward TM N in 190 LI:02072b.3:2000SEP081874 1936 forward TM N in 190 LI:02072b,3:2000SEP081958 2020 forward TM N in 191 LI:027209.1:2000SEP0825 111 forward TM N out 191 LI:027209.1:2000SEP081129 1203 forward TM N out 191 LI:027209.1:2000SEP081219 1305 forward TM N out SEQ ID Template ID Start StopFrame Domain Topology NO:

191 LI:027209.1:2000SEP081447 1533forward TM N out 191 LI:027209.1:2000SEP08413 475 forward TM N out 191 LI:027209.1:2000SEP08527 601 forward TM N out 191 LI:027209.1:2000SEP08659 739 forward TM N out 191 LI:027209.1:2000SEP08785 847 forward TM N out 191 LI:027209.1:2000SEP081178 1234forward TM N out 191 LI:027209.1:2000SEP081232 1309forward TM N out 191 LI:027209.1:2000SEP081379 1465forward TM N out 191 LI:027209.1:2000SEP08510 563 forward TM N in 191 LI:027209.1:2000SEP08882 938 forward TM N in 191 LI:027209.1:2000SEP08945 1016forward TM N in 191 LI:027209.1:2000SEP081041 1112forward TM N in 191 LI:027209.1:2000SEP081146 1208forward TM N in 191 LI:027209.1:2000SEP081224 1286forward TM N in 192 LI:108819.1:2000SEP08196 264 forward TM N in 192 LI:108819.1:2000SEP08203 271 forward TM

192 LI:108819.1:2000SEP08290 343 forward TM

193 LI:021759.1:2000SEP08133 186 forward TM N out 193 LI:021759.1:2000SEP0859 115 forward TM N out 193 LI:021759.1:2000SEP08495 581 forward TM N in 193 LI:021759.1:2000SEP08981 1067forward TM N in 194 LI:1165967.1:2000SEP08323 403 forward TM N out 195 LI:1166315,1:2000SEP08693 749 forward TM N out 196 LI:204626.1:2000SEP0819 99 forward TM N out 197 LI:801140.1:2000SEP08421 498 forward TM N in 198 LI:28bb39,1:2000SEP08127 213 forward TM N out 198 LI:28bb39.1:2000SEP08982 1068forward TM N out 198 LI:28bb39.1:2000SEP081879 1944forward TM N out 198 LI:286b39.1:2000SEP0862 148 forward TM N out 198 LI:28bb39,1:2000SEP08965 1027forward TM N out 198 LI:28bb39.1:2000SEP081061 1123forward TM N out 198 LI:28bb39.1:2000SEP081589 1663forward TM N out 198 LI:28bb39.1:2000SEP081787 1873forward TM N out 198 LI:286b39.1:2000SEP08267 320 forward TM N out 198 LI:286b39.1:2000SEP081794 1847forward TM N out 199 LI:288905.4:2000SEP08868 927 forward TM N out 199 LI:288905.4:2000SEP081552 1638forward TM N out 199 LI:288905.4:2000SEP081913 1975forward TM N out 199 LI:288905.4:2000SEP082000 2062forward TM N out 199 LI:288905.4:2000SEP0899 158 forward TM N in 200 LI:3321b1.1:2000SEP081507 1587forward TM N in 200 LI:3321b1.1:2000SEP081663 1743forward TM N in 200 U:3321b1.1:2000SEP082314 2400forward TM N in 200 LI:3321b1.1:2000SEP082890 2940forward TM N in 200 LI:3321b1.1:2000SEP08776 835 forward TM

200 LI:332161.1:2000SEP081340 1393forward TM

200 LI:3321b1.1:2000SEP081493 1579forward TM

200 U:3321b1.1:2000SEP081637 1717forward TM

200 U:332161.1:2000SEP081880 1966forward TM

200 LI:3321b1.1:2000SEP082075 2161forward TM

SE6Z Template ID StartStop Frame Domain Topology ID NO:

200 LI:332161.1:2000SEP082744 2818 forward TM

200 LI:332161,1:2000SEP08258 311 forward TM N in 200 LI:332161.1:2000SEP081524 1610 forward TM N in 200 LI:332161.1:2000SEP082025 2111 forward TM N in 200 LI:332161.1:2000SEP082289-2375 forward TM N in 201 LI:1848b7.1:2000SEP081985 2041 forward TM N in 201 LI:184867.1:2000SEP08771 854 forward TM N out 202 LI:229932,4:2000SEP087b 162 forward TM N out 202 LI:229932.4:2000SEP08229 300 forward TM N out 202 LI:229932.4:2000SEP081249 1329 forward TM N out 202 LI:229932.4:2000SEP081438 1524 forward TM N out 202 LI:229932.4:2000SEP081678 1764 forward TM N out 202 LI:229932.4:2000SEP08b8 142 forward TM N out 202 LI:229932.4:2000SEP08215 271 forward TM N out 202 LI:229932.4:2000SEP08734 820 forward TM N out 202 LI:229932.4:2000SEP081220 1291 forward TM N out 202 LI:229932.4:2000SEP081565 1618 forward TM N out 202 LI:229932.4:2000SEP08b0 146 forward TM

202 LI:229932,4:2000SEP08348 425 forward TM

202 LI:229932,4:2000SEP08762 848 forward TM

202 LI:229932.4:2000SEP081239 1325 forward TM

202 LI:229932.4:2000SEP081401 1487 forward TM

202 LI:229932.4:2000SEP081629 1703 forward TM

203 LI:1189932.1:2000SEP08277 363 forward TM N out 203 LI:1189932.1:2000SEP081141 1203 forward TM N out.

203 LI:1189932.1:2000SEP081216 1278 forward TM N out 203 LI:1189932.1:2000SEP081411 1497 forward TM N out 203 LI:I 189932.1:2000SEP081642 1707 forward TM N out 203 LI:1189932.1:2000SEP081795 1881 forward TM N out 203 LI:1189932.1:2000SEP082125 2211 forward TM N out 203 LI:1189932.1:2000SEP0889 151 forward TM N in 203 LI:1189932.1:2000SEP08218 304 forward TM N in 203 LI:1189932.1:2000SEP08320 388 forward TM N in 203 LI:1189932.1:2000SEP08386 451 forward TM N in 203 LI:1189932.1:2000SEP08572 643 forward TM N in 203 LI;1189932.1:2000SEP081142 1222 forward TM N in 203 LI:1189932.1:2000SEP081412 1498 forward TM N in 203 LI:1189932.1:2000SEP081928 1990 forward TM N in 203 LI;1189932.1:2000SEP082021 2107 forward TM N in 203 LI:1189932.1:2000SEP082141 2227 forward TM N in 203 LI:1189932.1:2000SEP08522 608 forward TM N out 203 LI:1189932.1:2000SEP08858 944 forward TM N out 203 LI:1189932.1:2000SEP081161 1247 forward TM N out 203 LI:1189932.1:2000SEP081992 2066 forward TM N out 203 LI:1189932.1:2000SEP082139 2210 forward TM N out 204 LI:1076689.1:2000SEP0843 114 forward TM N in 204 LI:1076689.1:2000SEP08326 373 forward TM N in 205 LI:415181,2:2000SEP081033 1113 forward TM N in 205 LI:415181.2:2000SEP081363 1434 forward TM N in 205 LI:415181.2:2000SEP08914 1000 forward TM

SEQ ID Template ID StartStop Frame Domain Topology NO:

206 LI:29b358.1:2000SEP08760 819 forward TM N out 206 LI:29b358.1:2000SEP08997 1068 forward TM N out 206 LI:296358.1:2000SEP081147 1233 forward TM N out 206 LI;296358.1:2000SEP08197 247 forward TM N out 206 LI:296358.1:2000SEP08356 442 forward TM N out 207 LI:20518b.3:2000SEP08644 697 forward TM N in 207 LI:20518b.3:2000SEP08812 877 forward TM N in 208 LI:220537.2:20005EP08595 681 forward TM N in 208 LI:220537.2:2000SEP081429 1515 forward TM N in 208 LI:220537.2:2000SEP08245 331 forward TM N out 208 LI:220537.2:2000SEP08362 415 forward TM N out 208 LI:220537.2:2000SEP081058 1129 forward TM N out 208 LI:220537.2:2000SEP081136 1222 forward TM N out 208 LI:220537.2:2000SEP081472 1555 forward TM N out 208 LI:220537.2:2000SEP081820 1897 forward TM N out 208 LI:220537.2:2000SEP0821 299 forward TM N out b 3 208 LI:220537.2:2000SEP08447 509 forward TM N out 208 LI:220537.2:2000SEP08522 584 forward TM N out 208 LI:220537.2:2000SEP08624 686 forward TM N out 208 LI:220537.2:2000SEP08702 764 forward TM N out 208 LI:220537.2:2000SEP081467 1553 forward TM N out 208 LI:220537.2:2000SEP081806 1892 forward TM N out 209 LI:248364.2:2000SEP08439 495 forward TM N out 210 LI:2048338.1:2000SEP08268 354 forward TM N in 210 LI:2048338.1:2000SEP08385 459 forward TM N in 210 LI:2048338.1:2000SEP08541 591 forward TM N in 210 LI:2048338.1:2000SEP08281 358 forward TM N in 211 Li:l 185203.8:2000SEP0873 135 forward TM N out 211 LI:1185203.8:2000SEP08148 210 forward TM N out 211 LI:1185203.8:2000SEP08226 294 forward TM N out 212 LI:021770.3:2000SEP08593 673 forward TM N out 212 LI:021770.3;2000SEP08348 434 forward TM N in 212 LI:021770.3:2000SEP08462 539 forward TM N in 212 LI:021770.3:2000SEP08564 641 forward TM N in . 212 LI:021770.3:2000SEP08861 944 forward TM N in 213 LI:1185841.1:2000SEP081132 1182 forward TM N out 213 LI:118584'1.1:2000SEP082434 2520 forward TM N out 213 LI:1185841.1:2000SEP08965 1030 forward TM N in 213 LI:1185841.1:2000SEP082381 2437 forward TM N in 214 LI:1181710.1:2000SEP08221 307 forward TM N out 215 LI:2048959.1:2000SEP08262 318 forward TM N out 21 b LI:798494.1:2000SEP08595 657 forward TM N out 21 b LI:798494,1:2000SEP08670 732 forward TM N out 21 b LI:798494.1:2000SEP08215 268 forward TM N out 21 b LI:798494.1:2000SEP0812 62 forward TM N out 21 b LI:798494.1:2000SEP0860 113 forward TM N out 217 LI:2049223.1:2000SEP08436 507 forward TM , N
1 in 217 LI;2049223.1:2000SEP08416 484 forward TM N out 218 LI:1177833.1:2000SEP08712 798 forward TM N in 219 LI;2049267.1:2000SEP08215 289 forward TM N out 5E6~ Template ID StartStop Frame Domain Topology ID NO:

219 LI:20492b7.1:2000SEP08240 323 forward TM N out 220 LI:1165939.1:2000SEP08554 640 forward TM

221 LI:1170958.1:2000SEP08326 376 forward TM N out 222 LI:1089827.1:2000SEP081507 1584 forward TM N in 223 LI:792112.1:2000SEP08818 892 forward TM N in 223 LI:792112.1:2000SEP089 86 forward TM

223 LI:792112.1:2000SEP08669 755 forward TM

223 LI:792112.1:2000SEP08783 860 forward TM

224 LI:282219.2:2000SEP08661 732 forward TM N out 224 LI:282219.2:2000SEP08497 577 forward TM N in 224 LI:282219.2:2000SEP08659 745 forward TM N in 224 LI:282219.2:2000SEP08408 458 forward TM N in 225 LI:1088010.2:2000SEP08289 375 forward TM N in 225 LI:1088010.2;2000SEP08716 793 forward TM N in 225 LI:1088010.2:2000SEP081229 1315 forward TM N in 225 LI:1088010.2:2000SEP08903 980 forward TM N out 225 LI:1088010.2:2000SEP081002 1088 forward TM N out 225 LI:1088010.2:2000SEP081185 1247 forward TM N out 225 LI:1088010.2:2000SEP081272 1334 forward TM N out 226 LI:1165276.1:2000SEP08301 363 forward TM N in 226 LI:11b527b.1;2000SEP08882 968 forward TM N out 227 LI:11b9524.2:2000SEP08623 709 forward TM

227 LI:1169524.2:2000SEP08713 778 forward TM

227 LI:1169524.2:2000SEP08842 928 forward TM

228 LI:I 180255.1:2000SEP08731 784 forward TM N in 228 LI:1180255.1;2000SEP08872 931 forward TM N in 228 LI:1180255.1:2000SEP081199 1285 forward TM N in 229 LI:1091903.1:2000SEP08454 540 forward TM N out 230 LI :1169219.1: 496 582 fo rwa TM N i 2000SE P08 rd 1 n 230 LI:1169219.1:2000SEP08509 595 forward TM N out 230 LI:1169219.1:2000SEP08495 581 forward TM

231 LI:2050313.1:2000SEP082605 2664 forward TM N in 231 LI:2050313.1:2000SEP083229 3315 forward TM N in 231 LI:2050313.1:2000SEP083412 3498 forward TM N in 231 LI:2050313.1:2000SEP081886 1954 forward TM N in 231 LI:2050313.1:2000SEP082654 2731 forward TM N in 231 LI:2050313.1:2000SEP082924 2986 forward TM N in 231 LI:2050313.1:2000SEP083029 3091 forward TM N in 231 LI:2050313.1:2000SEP083482 3568 forward TM N in 231 LI:2050313.1:2000SEP08855 920 forward TM N out 231 LI:2050313.1:2000SEP082445 2531 forward TM N out 231 LI:2050313.1:2000SEP082646 2708 forward TM N out 231 LI:2050313.1:2000SEP082721 2783 forward TM N out 231 LI:2050313.1:2000SEP083114 3170 forward TM N out 231 L1:2050313.1:2000SEP083504 3590 forward TM N out 232 LI:209351.3:2000SEP08586 645 forward TM N in 232 LI;209351.3:2000SEP081945 2025 forward TM N in 232 LI:209351.3:2DOOSEP08353 415 forward TM

232 LI:209351.3:2000SEP08665 718 forward TM

232 LI:209351.3:2000SEP081313 1387 forward TM

SEQ ID Template ID StartStop Frame Domain Topology NO:

232 LI:209351,3:2000SEP081991 2041 forward TM

232 LI:209351.3:2000SEP082153 2230 forward TM

232 LI:209351.3:2000SEP082390 2443 forward TM

232 LI:209351,3:2000SEP08801 869 forward TM N in 232 LI:209351,3:2000SEP081926 2006 forward TM N in 232 LI:209351.3:2000SEP082382 2456 forward TM N in 233 LI:119900.1:2000SEP08667 744 forward TM N in 233 LI:119900.1:2000SEP08521 607 forward TM N out 233 LI:119900.1:2000SEP08719 799 forward TM N out 233 LI:119900.1:2000SEP0824 98 forward TM

233 LI:119900,1:2000SEP08678 764 forward TM

234 LI:2052274.1:2000SEP08332 418 forward TM N in 234 LI:2052274.1:2000SEP081526 1612 forward TM N in 234 LI:2052274.1:2000SEP08939 1025 forward TM N in 234 LI:2052274.1:2000SEP081500 1586 forward TM N in 235 LI:1075502.1:2000SEP08200 277 forward TM N in 235 LI:1075502.1:2000SEP08483 569 forward TM N in 236 LI:813697.1:2000SEP08805 867 forward TM

236 LI:813b97.1:2000SEP08224 283 forward TM

236 LI:813697,1:2000SEP081638 1715 forward TM N out 236 LI:813697.1:2000SEP081722 1808 forward TM N out 237 LI:8142b1,1:2000SEP08562 618 forward TM

237 LI:814261,1:2000SEP08287 343 forward TM N out 237 LI:814261.1:2000SEP08512 598 forward TM N out 237 LI:814261,1:2000SEP08279 356 forward TM N out 237 LI:814261.1:2000SEP08474 557 forward TM N out 238 LI:775334.1:2000SEP08898 984 forward TM N in 238 LI:775334.1:2000SEP08581 661 forward TM N out 239 LI:1180325.1:2000SEP08833 919 forward TM N in 240 LI:1183147.3:2000SEP08268 342 forward TM N in 240 LI:1183147.3:2000SEP08370 456 forward TM N in 240 LI:1183147.3:2000SEP08712 798 forward TM N in 240 LI:1183147.3:2000SEP08937 1023 forward TM N in 240 LI:I 183147.3:2000SEP08374 460 forward TM N in 240 LI:1183147.3:2000SEP08800 871 forward TM N in 240 LI:1183147,3:2000SEP08968 1045 forward TM N in 240 LI:1183147.3:2000SEP081385 1450 forward TM N in 240 LI:1183147.3:2000SEP08156 224 forward TM N out 240 LI:1183147.3:2000SEP08285 347 forward TM N out 240 LI:1183147.3:2000SEP08414 500 forward TM N out 240 LI:1183147.3:2000SEP08687 770 forward TM N out 240 LI:1183147.3:2000SEP08846 932 forward TM N out 240 LI:1183147.3:2000SEP081002 1067 forward TM N out 241 LI:1175373.3:2000SEP08283 357 forward TM N out 242 LI:813757.1:2000SEP08744 827 forward TM N in 243 LI:1182979.2:2000SEP08370 456 forward TM N in 243 LI:1182979.2:2000SEP08742 828 forward TM N in 243 U:1182979.2:2000SEP08705 767 forward TM N out 243 LI:1182979,2:2000SEP08783 845 forward TM N out 244 U:1177823.2:2000SEP08307 393 forward TM N out SEQ ID Template ID Start StopFrame Domain Topology NO:

244 LI;1177823.2:2000SEP08311 370 forward TM N in 245 LI:1174279.1:2000SEP08634 720 forward TM N out 245 LI:1174279.1:2000SEP08724 789 forward TM N out 246 LI;1178411.1:2000SEP081357 1443forward TM

246 LI;1178411.1:2000SEP081290 1376forward TM N in 246 LI:I 178411.1:2000SEP081419 1472forward TM N in 247 LI;1182739.1:2000SEP08853 939 forward TM N in 247 LI;1182739.1:2000SEP081900 1986forward TM N in 247 LI;1182739.1:2000SEP082131 2217forward TM N in 247 LI:1182739.1:2000SEP082341 2403forward TM N in 247 LI;1182739.1:2000SEP082446 2508forward TM N in 247 LI;1182739.1:2000SEP08803 859 forward TM N in 247 LI:1182739.1:2000SEP081268 1351forward TM N in 247 LI;1182739.1:2000SEP081445 1513forward TM N in 247 LI;1182739.1:2000SEP081796 1882forward TM N in 247 LI; l 182739.1:2000SEP082090 2176forward TM N in 247 LI:1182739.1:2000SEP082267 2323forward TM N in 247 LI:1182739.1:2000SEP082363 2449forward TM N in 247 LI;1182739.1:2000SEP081182 1244forward TM N out 247 LI:1182739.1:2000SEP081254 1316forward TM N out 247 LI:1182739.1:2000SEP082100 2156forward TM N out 247 LI:1182739.1:2000SEP082301 2387forward TM N out 248 LI:234937.4:2000SEP08301 387 forward TM N out 249 LI:1170660.1:2000SEP08604 690 forward TM N in 249 LI:1170bb0.1:2000SEP08757 843 forward TM N in 249 LI:1170660.1:2000SEP08937 990 forward TM N in 249 LI;1170660.1:2000SEP081111 1179forward TM N in 249 LI:1170b60.1:2000SEP08512 583 forward TM

249 LI;1170660.1:2000SEP08911 973 forward TM

249 LI;1170660.1:2000SEP08986 1048forward TM

249 LI:1170660.1:2000SEP08252 323 forward TM N out 249 LI:1170660.1:2000SEP08591 677 forward TM N out 249 LI:1170660.1:2000SEP08774 860 forward TM N out 250 LI:1144409.1:2000SEP0825 81 forward TM N out 250 LI:1144409.1:2000SEP081708 1782forward TM N out 250 LI:1144409.1:2000SEP082281 2367forward TM N out 250 LI:1144409.1:2000SEP081658 1744forward TM N in 250 LI:1144409.1:2000SEP081880 1927forward TM N in 250 LI:1144409.1:2000SEP082294 2380forward TM N in 250 LI:1144409.1:2000SEP081614 1697forward TM N in 250 LI;1144409.1:2000SEP082217 2303forward TM N in 251 LI:246290.10:2000SEP08248 304 forward TM N out 251 LI:24b290.10:2000SEP08641 727 forward TM N out 251 LI:246290.10:2000SEP083 89 forward TM N out 252 LI:280034.1:2000SEP08279 365 forward TM N out SEQ ID Template ID Component Start Stop NO: ID

1 LG:150318.1:2000SEP0848254086 1 350 1 LG:150318.1:2000SEP08482540H 1 1 238 1 LG:150318.1:2000SEP08602113478 126 531 1 LG:150318.1:2000SEP08602113488 126 537 1 LG:150318.1:2000SEP086021134H 126 629 2 LG:022529.1:2000SEP087593029H1 1 521 2 LG:022529.1:2000SEP08g 1645695 112 517 2 LG:022529.1:2000SEP082160267H1 275 514 2 LG:022529.1:2000SEP085284828H1 309 583 2 LG:022529,1:2000SEP08g 1880347 313 601 2 LG:022529,1:2000SEP087352207H1 330 707 2 LG:022529.1:2000SEP086863346H1 339 830 2 LG:022529,1:2000SEP083351341 H1 423 681 2 LG:022529,1:2000SEP08077299H 1 432 632 2 LG:022529.1:2000SEP08078146H 1 438 646 2 LG:022529.1:2000SEP083801790F6 523 1030 2 LG:022529.1:2000SEP083801790H1 523 823 2 LG:022529,1:2000SEP083769238F6 523 1043 2 LG:022529.1:2000SEP083802590H1 524 810 2 LG:022529.1:2000SEP086217218H1 549 1039 2 LG:022529-.1:2000SEP0885743872 664 1137 2 LG:022529,1:2000SEP0883051534 685 1047 2 LG:022529.1:2000SEP0884195758 789 1045 3 LG:352559.1:2000SEP086453567H1 1 503 3 LG:352559.1:2000SEP084052122H1 185 457 3 LG:352559.1:2000SEP084052122F7 185 636 3 LG:352559.1:2000SEP0883897399 255 371 4 LG:175223.1:2000SEP083081155F6 1 417 4 LG:175223.1:2000SEP083081155H 2 315 4 LG:175223.1:2000SEP08308115576 31 465 4 LG:175223.1:2000SEP08g 1648354 58 457 4 LG:175223.1:2000SEP085800009H1 99 507 LG:476989.1:2000SEP086874941 Hl 1 169 5 LG:476989.1:2000SEP086874955H1 1 204 5 LG:476989.1:2000SEP0884393499 51 432 5 LG:476989.1:2000SEP0884190810 96 432 b LG:253268,7:2000SEP086772515H1 607 1083 b LG:253268.7:2000SEP0885526194 596 941 b LG:253268.7:2000SEP0884729197 690 941 b LG:253268.7:2000SEP0885809986 501 941 b LG:253268.7:2000SEP0882540947 535 937 b LG:2532b8.7:2000SEP088922062 586 935 b LG:253268.7:2000SEP086772515) 454 961 b LG:253268,7:2000SEP082535554F6 493 929 b LG:253268.7:2000SEP0884392225 520 923 b LG:253268,7:2000SEP0883424830 561 923 b LG:253268,7:2000SEP0884533991 464 923 6 LG:253268,7:2000SEP088885146 693 914 6 LG:253268,7:2000SEP088917418 564 914 6 LG:253268.7:2000SEP088888754 605 914 1i3 SEQ ID Template ID Component Start Stop NO: ID

6 LG:253268.7:2000SEP08892219b 606 913 b LG:253268.7:2000SEP088888391 595 912 b LG:25326B.7;2000SEP0885364213 457 897 b LG:253268.7:2000SEP088990349 560 886 b LG:253268.7:2000SEP088888707 589 884 b LG:253268.7:2000SEP088885121 574 884 b LG:253268.7;2000SEP088888978 669 883 b LG:2532b8.7:2000SEP088990350 535 881 6 LG:253268.7:2000SEP086852955H 306 854 b LG:253268.7;2000SEP087236518H1 249 789 b LG:253268.7;2000SEP082535554H1 493 737 6 LG:253268.7:2000SEP088889930 353 601 b LG:253268.7:2000SEP088888417 353 587 b LG:2532b8.7;2000SEP085773584H1 b9 5b9 b LG:253268.7:2000SEP0848875781 1 536 7 LG:401322.1:2000SEP084875149Th 344 737 7 LG:401322.1:2000SEP0883202357 457 784 7 LG:401322.1;2000SEP08748032H1 574 776 7 LG:401322.1;2000SEP08750543H 1 1 183 7 LG:401322.1:2000SEP08g 1474315 42 323 7 LG:401322.1:2000SEP083722596H 61 333 7 LG:401322.1;2000SEP084875149Fb 70 195 7 LG:401322.1:2000SEP084875149H 70 257 7 LG:401322.1:2000SEP0865b1179H1 71 633 7 LG:401322.1:2000SEP0820290948b 110 485 7 LG:401322.1:2000SEP082029094H 121 372 7 LG:401322.1:2000SEP08595041 OH 125 401 7 LG:401322.1:2000SEP085950630H 125 405 7 LG:401322.1:2000SEP08g4998bb0 180 478 7 LG:401322.1:2000SEP084933727H 239 384 7 LG:401322.1:2000SEP083533254H 273 564 8 LG:1328436.1:2000SEP082505871 H 1 210 8 LG:1328436.1:2000SEP086200837H1 4 346 8 LG:1328436.1:2000SEP08620156878 26 343 8 LG:1328436.1:2000SEP086201568H1 26 629 8 LG:1328436.1:2000SEP086201568F8 26 211 8 LG:1328436.1:2000SEP0882b30885 36 432 8 LG:1328436.1:2000SEP088723429 7 191 8 LG:1328436.1:2000SEP08620083778 76 343 8 LG:1328436.1:2000SEP088725043 91 362 8 LG:1328436.1:2000SEP088725147 312 572 9 LG:475404.1:2000SEP08460544H1 20 245 9 LG:475404.1:2000SEP085998240H 1 484 9 LG:475404.1:2000SEP08599824078 1 408 9 LG:475404.1:2000SEP085998240F8 1 398 9 LG:475404.1:2000SEP0845596bH1 20 255 9 LG:475404.1:2000SEP08455162H1 20 272 9 LG:475404.1:2000SEP084551628b 20 521 9 LG:475404.1:2000SEP08458061 H 20 259 9 LG:475404.1:2000SEP084605448b 20 326 SEQ ID Template ID Component Start Stop NO: ID

9 LG:475404.1:2000SEP083206542H1 25 202 9 LG:475404.1:2000SEP084663964H1 37 289 9 LG:475404.1:2000SEP087652675J1 47 172 9 LG:475404.1:2000SEP08g 1807165 81 278 9 LG:475404.1:2000SEP0882401959 129 486 9 LG:475404.1:2000SEP083614680H1 155 272 9 LG:475404.1:2000SEP0885101146 180 486 LG:1384132.1:2000SEP085754964H1 1 453 10 LG;1384132.1:2000SEP0885366771 73 480 10 LG;1384132.1:2000SEP083246016H1 198 446 11 LG:410804.18:2000SEP083270045H1 1 252 12 LG;1082306.1:2000SEP082590822H1 60 224 12 LG;1082306.1:2000SEP082875044H1 13 269 12 LG;1082306.1:2000SEP085944268H1 12 288 12 LG:108230b.1:2000SEP08908479H1 39 241 12 LG;1082306.1:2000SEP082972368F6 1 586 12 LG;1082306.1:2000SEP082972368H1 1 292 12 LG:1082306.1:2000SEP081831460H1 393 656 12 LG:1082306.1:2000SEP0882270170 247 638 12 LG:1082306.1:2000SEP081732781 H 118 297 12 LG:108230b.1:2000SEP084136083H 590 657 12 LG:1082306.1:2000SEP085152624H1 463 723 12 LG:108230b.1:2000SEP082634451 H1 434 685 13 LG:233814.4:2000SEP086907331 J 757 1055 13 LG:233814.4:2000SEP087435089H1 1 580 13 LG:233814.4:2000SEP087579295H1 475 927 13 LG:233814.4:2000SEP082818676H1 511 729 13 LG:233814.4:2000SEP081943949H 632 863 13 LG:233814.4:2000SEP087403021 H 703 1146 14 LG:977478.5:2000SEP087087230H 1 549 14 LG:977478.5:2000SEP085525655H2 50 293 14 LG:977478.5:2000SEP087198649H 74 395 14 LG:977478.5:2000SEP083218939H 1 b4 284 14 LG:977478.5:2000SEP08213794777 182 714 14 LG:977478.5:2000SEP08- 2137242H1 274 541 14 LG:977478.5:2000SEP08297042376 312 783 14 LG:977478.5:2000SEP082970423F6 319 720 14 LG:977478.5:2000SEP082970423H2 319 633 14 LG:977478.5:2000SEP0886464000 464 821 14 LG:977478.5:2000SEP08974781 H 501 774 14 LG:977478.5:2000SEP0886044798 530 821 LG:025931.1:2000SEP086075128F6 1 524 15 LG:025931.1:2000SEP087002695H 272 846 15 LG:025931.1:2000SEP08194900286 435 707 15 LG:025931.1:2000SEP081949002H 435 692 15 LG:025931.1:2000SEP0886711855 473 929 15 LG:025931.1:2000SEP083348048H 497 748 15 LG:025931.1:2000SEP087382758H 573 962 15 LG:025931.1:2000SEP085844022H 224 474 15 LG:025931.1:2000SEP085844022F6 223 614 SEQ ID Template ID Component Start Stop NO: ID

15 LG:025931.1:2000SEP086075128H1 1 185 16 LG:885368.1:2000SEP08590978277 1 494 16 LG:885368.1:2000SEP086269652H1 1 415 16 LG:885368.1:2000SEP085909782H1 1 306 1 b LG:885368.1:2000SEP085909782F7 1 578 1 b LG:885368.1:2000SEP086269652F8 1 682 1 b LG:885368.1:2000SEP085909795H 1 305 16 LG:885368.1:2000SEP085909895H1 1 133 16 LG:885368,1:2000SEP08626965278 99 618 1 b LG:885368.1:2000SEP084982679Th 377 550 17 LG:1054900.1:2000SEP082327449H1 15 248 17 LG:1054900.1:2000SEP082327457Th 1 3b4 17 LG:1054900.1:2000SEP082327449Th 1 288 17 LG:1054900.1:2000SEP082327449Rb 13 408 17 LG:1054900.1:2000SEP082327457Rb 13 402 17 LG:1054900.1:2000SEP086537441H1 147 499 17 LG:1054900.1:2000SEP085108773H1 196 254 18 LG:995186.2:2000SEP085056145Fb 1 549 18 LG:995186.2:2000SEP086061051 F8 169 669 19 LG:435048.23:2000SEP086867561 H1 1 461 19 LG:435048.23:2000SEP083531553H1 53 327 20 LG:954859.1:2000SEP08g6196726 233 638 20 LG:954859.1:2000SEP08g2344451 154 637 20 LG:954859.1:2000SEP08381411076 148 602 20 LG:954859,1:2000SEP0838150937b 146 591 20 LG:954859.1:2000SEP08b475045H1 1 548 20 LG:954859.1:2000SEP086413028H1 1 373 21 LG:364370,1:2000SEP086798273H1 1 497 21 LG:364370,1:200QSEP086798273F8 1 574 21 LG:364370.1:2000SEP084431872H1 3 82 21 LG:364370.1:2000SEP08679240278 9 592 21 LG:364370,1:2000SEP086792402F8 9 705 21 LG:364370,1:2000SEP086792402H 9 500 21 LG:364370,1:2000SEP08679827378 362 543 22 LG:1098789.1:2000SEP0835370027b 1 461 23 LG:201540.2:2000SEP085764854H 2 545 23 LG:201540.2:2000SEP0846640b8Fb 1 31 b 23 LG:201540.2:2000SEP084664068H 2 237 23 LG:201540.2:2000SEP085968685H 26 592 23 LG:201540.2:2000SEP083160094H 98 362 23 LG:201540.2:2000SEP08652754H 1 101 353 23 LG:201540.2:2000SEP086788325H 118 489 23 LG:201540.2:2000SEP08g 1950834 690 910 23 LG:201540.2:2000SEP082739044Fb 689 1171 23 LG:201540.2:2000SEP086829490) 703 1219 23 LG:201540.2:2000SEP082739044H 690 924 23 LG:201540.2:2000SEP087328749H 733 1261 23 LG:201540.2:2000SEP086829490H 712 1219 23 LG:201540.2:2000SEP082857116H 777 1049 23 LG:201540.2:2000SEP08g7b9612 173 528 SE6~ Template ID Component Start Stop ID NO: ID

23 LG:201540.2:2000SEP086490433H1 287 779 23 LG:201540.2:2000SEP08509607476 604 1006 23 LG:201540.2:2000SEP087262169H1 642 1193 23 LG:201540.2:2000SEP086310909H1 308 887 23 LG:201540.2;2000SEP085096074H2 347 523 23 LG:201540.2:2000SEP085096074F6 347 703 23 LG:201540.2:2000SEP087701612)1 518 1093 23 LG:201540.2:2000SEP084053114H 1 100 386 23 LG:201540.2:2000SEP084319192H 1 131 397 23 LG:201540.2;2000SEP083414632H1 132 252 23 LG:201540.2:2000SEP087200283H 1 142 699 24 LG:1077357.1:2000SEP086245903F8 120 547 24 LG:1077357.1:2000SEP086245903H 1 121 532 24 LG:1077357.1:2000SEP08g3250058 1 408 24 LG:1077357.1:2000SEP08g3694145 26 408 24 LG:1077357.1:2000SEP08g4333202 140 407 24 LG:1077357.1:2000SEP086779728) 1 1 370 25 LG:1048846.4:2000SEP08543304379 1 476 25 LG:1048846.4:2000SEP083256037H1 191 435 25 LG:1048846.4:2000SEP08325603786 191 354 25 LG:1048846.4:2000SEP083207387H1 213 461 25 LG:104884b.4:2000SEP084316787H 1 247 532 25 LG:1048846.4:2000SEP08463086478 263 483 26 LG:33bb85.1;2000SEP08g 1422427 85 461 26 LG:336b85.1:2000SEP083167506H 1 1 292 26 LG:336685.1;2000SEP08g3751213 82 477 26 LG:336b85.1;2000SEPOSg3039675 93 477 26 LG:336685.1:2000SEP087612160)1 631 1172 26 LG:336685.1:2000SEP087585885H2 458 1146 26 LG:336685.1;2000SEP087330357H 1 428 965 26 LG:336b85.1;2000SEP087612160H 1 246 869 26 LG:33bb85.1;2000SEP08g3844561 389 808 26 LG:336685.1:2000SEP08g2702908 347 805 26 LG:336685.1:2000SEP08g 1422428 441 805 27 LG:1076253.1:2000SEP085677775H 1 24 273 27 LG:1076253.1:2000SEP08828479H 1 617 874 27 LG:1076253.1:2000SEP085677775F6 24 610 27 LG:107b253.1:2000SEP087392292H 1 1 584 27 LG:1076253.1:2000SEP084896201 F8 298 724 27 LG:1076253.1:2000SEP084896201 H 298 566 27 LG:1076253.1:2000SEP087933083H 1 389 898 27 LG:1076253.1:2000SEP082717909H1 429 684 27 LG:1076253.1:2000SEP0839244381 585 1112 27 LG:1076253.1:2000SEP08489620178 826 1314 27 LG:1076253.1:2000SEP084896201 T9 872 1357 27 LG:1076253.1:2000SEP08398964676 1029 1418 27 LG:1076253.1:2000SEP08277919576 1078 1411 27 LG:1076253.1:2000SEP08398964686 354 748 27 LG:1076253.1:2000SEP083989646H 1 354 512 28 LG:1400601.2:2000SEP086967393H 1 1 600 SE6~ Template ID Component Start Stop ID NO: ID

29 LG:1079092.3:2000SEP086002889F8 1 660 29 LG:1079092.3:2000SEP08600288978 104 612 30 LG:1086064.1:2000SEP0845612286 6 395 30 LG:1086064.1:2000SEP085941956H1 8 286 30 LG:1086064.1:2000SEP084727660F6 1 542 30 LG:1086064.1:2000SEP087355369H1 1 526 30 LG:1086064.1:2000SEP083730253H 9 315 30 LG:1086064.1:2000SEP081798649F6 6 361 30 LG:1086064.1:2000SEP0845612281 6 583 30 LG:1086064.1:2000SEP08787063H 1 16 134 30 LG:1086064.1:2000SEP087354016H1 19 537 30 LG:1086064.1:2000SEP08456122F1 45 518 30 LG:108bOb4.1:2000SEP083523404H1 127 467 30 LG:1086064.1:2000SEP0845612276 154 476 30 LG:1086064.1:2000SEP081698965F6 165 529 30 LG:1086064.1:2000SEP08169896576 179 500 30 LG:1086064.1:2000SEP082514834H1 16 323 30 LG.1086064.1:2000SEP08456180H 1 6 246 30 LG:1086064.1:2000SEP084549786H1 1 245 30 LG:1086064.1:2000SEP084822628H1 2 283 30 LG:1086064.1:2000SEP08457138H 1 6 149 30 LG:1086064.1:2000SEP084727660H1 1 267 30 LG:1086064.1:2000SEP08458658H 1 6 239 30 LG:1086064.1:2000SEP08461412H1 6 260 30 LG:1086064.1:2000SEP08456122H1 6 247 30 LG:1086064.1:2000SEP08460344H1 6 278 30 LG:1086064.1:2000SEP08460848H1 b 242 30 LG:1086064.1:2000SEP081698965H1 165 396 30 LG:108bOb4.1:2000SEP081322674H1 2 256 30 LG:108b064.1:2000SEP08460283H 1 6 240 30 LG:1086064.1:2000SEP083735303H1 22 340 30 LG:1086064.1:2000SEP081798649H1 6 280 30 LG:1086064.1:2000SEP081698730H1 165 359 31 LG:1400608.1:2000SEP084399221 Hl 25 234 31 LG:1400608.1:2000SEP085120882F6 1 353 31 LG:1400608.1:2000SEP08014670H 1 7 288 31 LG:1400608.1:2000SEP085378061 H1 133 391 31 LG:1400608.1:2000SEP085378061 F6 133 591 31 LG:1400608.1:2000SEP08g4265183 180 641 31 LG:1400608.1:2000SEP084881456H 274 353 31 LG:1400608.1:2000SEP082882961 H 13 272 31 LG:1400608.1:2000SEP085120882H1 1 265 31 LG:1400b08.1:2000SEP081899877H1 41 265 31 LG:1400608.1:2000SEP08g 195931 41 357 b 32 LG:399275.5:2000SEP082054642H1 354 539 32 LG:399275.5:2000SEP087688287H1 1 410 32 LG:399275.5:2000SEP081561014H 169 351 32 LG:399275.5:2000SEP087688287) 192 657 33 LG:293943.1:2000SEP08710240388 1 647 33 LG:293943.1:2000SEP08g2007300 100 453 ._~

SEQ ID Template ID Component Start Stop NO: ID

33 LG:293943.1:2000SEP086425161 T7 254 362 33 LG:293943.1:2000SEP086425161 H1 254 537 33 LG:293943,1:2000SEP086425161 F7 254 537 33 LG:293943.1:2000SEP087009531 H1 384 720 34 LG:345884.1:2000SEP08776081 1 54 260 34 LG:345884,1:2000SEP08g4991320 187 645 34 LG:345884,1:2000SEP084676488Th 209 615 34 LG:345884,1:2000SEP08g2240240 1 310 34 LG:345884.1:2000SEP084676488H1 2 258 34 LG:345884.1:2000SEP084676488F6 1 387 35 LG:400967.1:2000SEP08g2161571 1 424 35 LG:400967.1:2000SEP08184168H1 1 169 35 LG:400967,1:2000SEP085491896H 16 250 35 LG:400967.1:2000SEP085772680H1 36 528 35 LG:400967.1:2000SEP083156449H1 183 343 35 LG:400967.1:2000SEP08g3151140 215 672 35 LG:4009b7.1:2000SEP08g2656954 333 629 35 LG:400967.1:2000SEP08g5745679 375 664 35 LG:400967.1:2000SEP08g21 62512 511 664 36 LG:024556.b:2000SEP085875448H1 1 284 36 LG:024556.b:2000SEP085413554F6 4 491 36 LG:024556.b:2000SEP086329517H1 b 146 36 LG:024556.b:2000SEP087190073H2 34 527 36 LG:024556.b:2000SEP083758768H1 37 307 36 LG:024556.b:2000SEP085370118H1 54 301 36 LG:024556,b:2000SEP085370118F6 54 bib 36 LG:024556.b:2000SEP088764662 96 484 36 LG:024556,b:2000SEP088874234 96 444 36 LG:024556.b:2000SEP088571259 103 459 36 LG:024556.b:2000SEP085407536H1 239 489 36 LG:02455b.b:2000SEP087044534H1 250 451 36 LG:02455b.b:2000SEP087047004H1 250 732 36 LG:024556,6:2000SEP085423663F6 303 790 36 LG:024556.b:2000SEP085423663H1 303 560 36 LG:02455b,b:2000SEP088767562 343 633 36 LG:02455b,b:2000SEP085857590H1 401 647 36 LG:024556.b:2000SEP086447737H1 469 654 37 LG:081189,3:2000SEP0884078107 458 904 37 LG:081189.3:2000SEP0885768539 453 904 37 LG:081189,3:2000SEP0884736702 453 905 37 LG:081189.3:2000SEP086938064H 465 871 37 LG:081189.3:2000SEP086941504H1 468 853 37 LG:081189,3:2000SEP082358206H1 336 414 37 LG:081189.3:2000SEP081811707H1 225 465 37 LG:081189.3:2000SEP081811707F6 225 698 37 LG:081189,3:2000SEP087358905H1 1 478 38 LG:018258.1:2000SEP08g 1012122 1 131 38 LG:018258.1:2000SEP081443432H1 1 253 38 LG:018258.1:2000SEP081443432F6 1 268 38 LG:018258.1:2000SEP081632787H1 140 373 SEQ ID Template ID Component Start Stop NO: ID

38 LG:018258.1:2000SEP081632787F6 140 610 38 LG:018258.1:2000SEP08g 1012076 184 489 38 LG:OI 8258.1;2000SEP085944405H 374 533 39 LG:450399.3:2000SEP085910662H 1 295 39 LG:450399.3;20005EP085910662F6 1 552 39 LG:450399.3:2000SEP085910662F8 1 510 39 LG:450399.3:2000SEP08591066276 9 605 39 LG:450399.3:2000SEP08591066279 b7 576 39 LG:450399.3:2000SEP08591066278 146 593 40 LG:451122.1:2000SEP086269521 H 5 418 40 LG:451122.1:2000SEP085910718H1 1 288 40 LG:451122.1:2000SEP08591071879 280 348 40 LG:451122.1:2000SEP085910718F8 1 457 40 LG:451122.1:2000SEP085910718F6 1 448 40 LG:451122.1:2000SEP08591071876 1 422 40 LG:451122.1;2000SEP086269521 F8 5 448 40 LG:451122.1:2000SEP08591071878 1 361 41 LG:451 b82.1;2000SEP085913661 H 1 283 41 LG:451682.1;2000SEP085913661 F8 1 569 41 LG:451 b82.1;2000SEP085913661 F6 1 575 41 LG:451682.1;2000SEP085913661 T6 213 821 42 LG:238631.4:2000SEP08g 1277788 1 426 42 LG:238631.4:2000SEP085406438H 1 261 42 LG:238631.4;2000SEP085951609H1 3 368 42 LG:238631.4;2000SEP08586434H1 4 314 42 LG:238631.4:2000SEP083120923H 5 313 42 LG:238631.4;2000SEP084815047H1 10 276 42 LG:238631.4:2000SEP083743301 H 12 255 42 LG:238631.4;2000SEP083736553H1 86 318 42 LG:238631.4;2000SEP085598455H1 292 540 42 LG:238631.4;2000SEP08g5855963 384 846 42 LG:238631.4:2000SEP08g4070653 392 850 42 LG:238631.4:2000SEP08g3665831 396 847 42 LG:238631.4;2000SEP08g3246602 400 858 42 LG:238631.4:2000SEP08g2161232 410 665 42 LG:238631.4:20005EP08g4525307 437 848 42 LG:238631.4:2000SEP08g 1404313 467 847 42 LG:238631.4:2000SEP08g3253470 464 858 42 LG:238631.4:2000SEP08g3250117 469 847 42 LG:238631.4:2000SEP08g2269451 484 847 42 LG:238631.4:2000SEP08g3735117 484 845 42 LG:238631.4;2000SEP08g4223250 506 848 42 LG:238631.4;2000SEP08g5766307 542 847 42 LG:238631.4:2000SEP08g3737372 551 847 42 LG:238631.4:2000SEP08g3016184 580 858 42 LG:238631.4:2000SEP08g3734551 604 845 42 LG:238631.4:20005EP08g54471 b7 621 845 42 LG:238b31.4;20005EP08g47621 b2 621 845 42 LG:238631.4:2000SEP08g 1231962 670 848 42 LG:238631.4;2000SEP082406581 H 12 116 SEQ ID Template ID Component Start Stop NO: ID

42 LG:238631.4:2000SEP083401789H1 13 239 42 LG:238631.4:2000SEP084648809H1 13 297 42 LG:238631.4:2000SEP083634010H1 15 201 42 LG:238631.4:2000SEP084653815H1 16 316 42 LG:238631.4:2000SEP083152423H1 13 281 42 LG:238631.4:2000SEP084414637H1 12 275 42 LG:238631.4:2000SEP086121345H1 14 648 42 LG:238631.4:2000SEP083428203H 15 274 42 LG:238631.4:2000SEP083744645H 1 b 309 42 LG:238631.4:2000SEP082698861 H1 18 305 42 LG:238631.4:2000SEP084143702H1 18 299 42 LG:238631.4:2000SEP083995879H1 18 309 42 LG:238631.4:2000SEP081830216H1 18 247 42 LG:238631.4:2000SEP082998645H1 19 295 42 LG:238631.4:2000SEP085464919H 19 306 42 LG:238631.4:2000SEP081713036H 19 257 42 LG:238631.4:2000SEP086116806H1 19 314 42 LG:238631.4:2000SEP085788396H 19 305 42 LG:238631.4:2000SEP085121572H1 19 299 42 LG:238b31.4;2000SEP084715287H1 20 256 42 LG:238631.4:2000SEP086197104H1 23 561 42 LG:238631.4:2000SEP08493734H 1 28 246 42 LG:238631.4:2000SEP083988991 H1 40 341 42 LG:238631.4:2000SEP082048688H1 59 314 42 LG:238631.4:2000SEP082757550H1 59 328 42 LG:238631.4:2000SEP082755553H1 59 330 43 LG:23bb54.1:2000SEP08670448Th 802 1151 43 LG:236654.1:2000SEP0867718486 802 1154 43 LG:236654.1:2000SEP0882810503 842 1188 43 LG:236654.1:2000SEP0882336018 909 1189 43 LG:236654.1:2000SEP082892611 H1 947 1180 43 LG:236654.1:2000SEP081289991 Hl 1083 1189 43 LG:236654.1:2000SEP08g 1979821 1 187 43 LG:236654.1:2000SEP0883835204 1 325 43 LG:236654.1:2000SEP0886990824 1 298 43 LG:236654.1:2000SEP0886704413 1 299 43 LG:236b54.1:2000SEP086757618J1 8 93 43 LG:236b54.1:2000SEP087604986J1 9 544 43 LG:236654.1:2000SEP0884072180 18 469 43 LG:236654.1:2000SEP083519808H1 80 368 43 LG:236b54.1:2000SEP088843784 234 500 43 LG:236654.1:2000SEP081614746F6 288 734 43 LG:236b54.1:2000SEP081614746H1 288 506 43 LG:236654.1:2000SEP087604986H1 364 845 43 LG:236654.1:2000SEP081575232H1 366 578 43 LG:236654.1:2000SEP0882209653 404 914 43 LG:236654.1:2000SEP086322462H1 521 720 43 LG:236b54.1:2000SEP082892611Th 647 1138 43 LG:236654.1:2000SEP0885660108 723 1188 43 LG:236b54.1:2000SEP081614746Th 735 1150 SEQ ID Template ID Component Start Stop NO: ID

43 LG:23bb54.1:2000SEP08g53b5441 749 1190 43 LG:236654.1:2000SEP08g3b44249 768 1191 43 LG:236654.1:2000SEP08677184H 1 802 1073 43 LG:236654.1:2000SEP0867044886 802 1188 43 LG:236654.1:2000SEP08670448H 1 802 1057 44 LG:332655.1:2000SEP08570522H 1 606 876 44 LG:332655.1:2000SEP083872248Th 663 1142 44 LG:332655.1:2000SEP082850393Tb 700 1142 44 LG:332655.1:2000SEP08g2835010 71 b 1069 44 LG:332655.1:2000SEP08g47b3947 847 1144 44 LG:332655.1:2000SEP08g498b3b7 978 1144 44 LG:332655.1:2000SEP08g5bb1482 980 1142 44 LG:332655.1:2000SEP08516193H 1 1027 1136 44 LG:332655.1:2000SEP085070935H1 498 757 44 LG:332655.1:2000SEP08g 1959326 479 914 44 LG:332655.1:2000SEP08g 1947735 206 551 44 LG:332655.1:2000SEP083096881 H 265 401 44 LG:332655.1:2000SEP083098886H 275 541 44 LG:332655.1:2000SEP087600091 H 314 782 44 LG:332655.1:2000SEP082850393Fb 1 499 44 LG:332655.1:2000SEP082850393H1 2 289 44 LG:332655.1:2000SEP08861289H 1 3 241 44 LG;332b55.1:2000SEP08228764086 5 485 44 LG:332655.1:2000SEP082287640H1 5 255 44 LG:332655.1:2000SEP083872248Fb 11 517 44 LG:332655.1:2000SEP083872248H1 11 301 44 LG:332b55.1:2000SEP083403385H1 114 3bb 44 LG:332655.1:2000SEP081821848H1 133 370 44 LG:332655.1:2000SEP083531915H 153 445 44 LG:332655.1:2000SEP082059050H1 160 405 44 LG:332655.1:2000SEP085742858H1 164 474 44 LG:332655.1:2000SEP082733553H1 185 415 44 LG:332655.1:2000SEP085025820H1 188 470 45 LG:217396.2:2000SEP085b28336Rb 940 1483 45 LG:217396.2:2000SEP086265192H1 695 1273 45 LG:217396.2:2000SEP085868595H1 984 1252 45 LG:217396.2:2000SEP0858b8595Fb 972 1252 45 LG:217396.2:2000SEP08g 1187240 97b 1186 45 LG:21739b.2:2000SEP087676247J2 625 1182 45 LG:217396.2:2000SEP087706403H1 548 1138 45 LG:217396,2:2000SEP08g1195854 640 960 45 LG:217396.2:2000SEP087351185H1 427 957 45 LG:21739b.2:2000SEP08g4648085 606 87b 45 LG:217396.2:2000SEP0850712b1 H1 578 837 45 LG:217396.2:2000SEP085071261 F6 578 824 45 LG:217396.2:2000SEP08g 1921151 518 739 45 LG:217396.2:2000SEP086875193H1 159 671 45 LG:21739b.2:2000SEP08698940bH1 250 649 45 LG:217396.2:2000SEP08g 1921152 105 513 45 LG:21739b.2:2000SEP082996140F6 1 621 SEQ ID Template ID Component Start Stop NO: ID

45 LG:217396.2:2000SEP08g2818339 123 530 45 LG:217396.2:2000SEP083750696H 1 232 517 45 LG:21739b.2:2000SEP087676247H2 1 401 45 LG:217396.2:2000SEP085071261 T6 1 375 45 LG:217396.2:2000SEP082996140H 1 1 265 46 LG:090574.1:2000SEP082b599bbFb 1 192 46 LG:090574.1:2000SEP08265996bTb 1 194 46 LG:090574.1:2000SEP0826599bbH 1 1 247 47 LG:202943.1:2000SEP08122659086 174 583 47 LG:202943.1:2000SEP085639884H 1 136 365 47 LG:202943.1:2000SEP081226590Th 383 888 47 LG:202943.1:2000SEP085092132H 1 515 763 47 LG:202943.1:2000SEP081226590H 1 174 418 47 LG:202943.1:2000SEP08g2020858 180 420 47 LG:202943.1:2000SEP087213845H 1 242 792 47 LG:202943.1:2000SEP082579002H2 975 1177 47 LG:202943.1:2000SEP086472564H 1 942 1357 47 LG:202943.1:20005EP087151349H 1 58 561 47 LG:202943.1:2000SEP085089408H 1 1 270 47 LG:202943.1:2000SEP085091008H 1 1 269 47 LG:202943.1:2000SEP087594783H 1 818 1226 47 LG:202943.1:2000SEP0864b9878H 1 624 1185 47 LG:202943.1:2000SEP085092608H 1 1 274 48 LG:236928.1:2000SEP083227840H 1 1509 1789 48 LG:236928.1:2000SEP082487371 H 1524 1754 48 LG:236928.1:2000SEP0829088bbH 1 1579 17b8 48 LG:236928.1:2000SEP08g2538920 1584 1877 48 LG:236928.1:2000SEP08487800H1 1633 1905 48 LG:236928.1:2000SEP085404331 H 1669 1966 48 LG:236928,1:2000SEP082904955Th 1672 2110 48 LG:236928.1:2000SEP084243773H 1 1679 1938 48 LG:23b928.1:2000SEP082904b24H 1 1682 1978 48 LG:236928.1:2000SEP08g4990382 1689 2149 48 LG:236928.1:2000SEP083291485Th 1692 2110 48 LG:236928.1:2000SEP087365257H1 1694 2145 48 LG:236928.1:2000SEP08g31445b5 1717 2158 48 LG:236928.1:2000SEP08g3144841 1723 2149 48 LG:236928.1:2000SEP087761153H1 1 630 48 LG:236928.1:2000SEP082905587H1 26 296 48 LG:236928,1:2000SEP087741081 H 173 752 48 LG:236928.1:2000SEP081491957H 1 180 280 48 LG:236928.1:2000SEP084741520H1 195 447 48 LG:23b928.1:2000SEP084741520F6 195 579 48 LG:23b928.1:2000SEP086616428H1 203 717 48 LG:236928.1:2000SEP084697183H1 235 483 48 LG:236928.1:2000SEP084697183Fb 235 679 48 LG:236928.1:2000SEP084028773H1 432 694 48 LG:236928.1:2000SEP084028773F8 441 957 48 LG:236928.1:2000SEP087761153) 1 472 1051 48 LG:236928,1:2000SEP087109534H 1 524 1104 SEQ ID Template ID Component Start Stop NO: ID

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48 LG:236928.1:2000SEP086138111 H 2539 2849 48 LG:236928.1:2000SEP0883179767 2580 2982 48 LG:236928.1:2000SEP08727813H 1 2595 2826 48 LG:236928.1:2000SEP084367390H2 2598 2853 48 LG:236928.1:2000SEP08g 1190057 2621 2982 48 LG:236928.1:2000SEP0884986351 2683 2973 48 LG:236928.1:2000SEP0882526245 2756 2973 48 LG:236928.1:2000SEP081717327Th 2855 3383 48 LG:236928.1:2000SEP081717327H1 2862 3109 48 LG:236928.1:2000SEP081717327F6 2862 3351 49 LG:215169.2:2000SEP086037163H1 602 1129 49 LG:215169.2:2000SEP086207071 H 928 1536 49 LG:215169.2:2000SEP087098455H1 1246 1637 49 LG:215169.2:2000SEP086970186H1 1305 1880 49 LG:215169.2:2000SEP0885176731 1 212 49 LG:215169.2:2000SEP0885431398 1 377 49 LG:215169.2:2000SEP0884114328 1 456 49 LG:215169.2:2000SEP0886704290 1 472 49 LG:215169.2:2000SEP086477953H1 1373 1881 49 LG:215169.2:2000SEP087714805H1 1384 1978 49 LG:215169.2:2000SEP081486266H 1519 1767 49 LG:215169.2:2000SEP082843912H1 1718 1991 49 LG:215169.2:2000SEP081384143H1 1883 2133 49 LG:215169.2:2000SEP084901661 H 436 630 49 LG:215169.2:2000SEP084901 bbl 436 633 49 LG:215169:2:2000SEP087269396H1 112 652 49 LG:215169.2:2000SEP087322496H1 156 636 49 LG:215169.2:2000SEP086314811H1 311 833 49 LG:215169.2:2000SEP0885664682 18 244 50 LG:410726.1:2000SEP082071327H1 360 550 50 LG:410726.1:20005EP086912958J1 426 1019 50 LG:410726.1:2000SEP084583753H1 453 741 50 LG:410726.1:2000SEP087699696J1 724 1108 50 LG:410726.1:2000SEP082071327Th 751 1186 50 LG:410726.1:2000SEP0884176194 788 1231 50 LG:410726.1:2000SEP0883178308 806 1226 50 LG:41072b.1:2000SEP0884149782 899 1217 50 LG:410726.1:2000SEP086912958H1 912 1382 50 LG:41072b.1:2000SEP0883797002 1049 1163 50 LG:410726.1:2000SEP0883180193 1210 1289 50 LG:410726.1:2000SEP086534376H 1 277 50 LG:410726.1:2000SEP086392976H 1 276 50 LG:410726.1:2000SEP087233013H 68 590 50 LG:41072b.1:2000SEP086033171 F6 b9 623 50 LG:41072b.1:2000SEP086033171 H 74 509 50 LG:41072b.1:2000SEP08g 1648352 98 503 50 LG:410726.1:2000SEP083023715H 259 523 50 LG:41072b.1:2000SEP082071327F6 360 659 51 LG:234372.2:2000SEP081661362T6 2456 2794 51 LG:234372.2:2000SEP0882277847 2649 2848 SEQ ID Template ID Component Start Stop NO: ID

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56 LG:021770.1:2000SEP08243837H1 1071 1231 56 LG:021770.1:2000SEP081007489H 1138 1433 56 LG:021770.1:2000SEP08g6472352 1247 1618 56 LG:021770.1:2000SEP087396616H1 1261 1773 56 LG:021770.1:2000SEP08g2155826 1268 1631 56 LG:021770.1:2000SEP088311 6842 1287 1641 56 LG:021770.1:2000SEP08g709667 1293 1623 56 LG:021770.1:2000SEP08g2100629 1294 1624 56 LG:021770.1:2000SEP08g816343 1352 1619 56 LG:021770.1:2000SEP088816686 1358 1619 56 LG:021770.1:2000SEP088670313 1362 1610 56 LG:021770.1:2000SEP088682772 1366 1610 56 LG:021770.1:2000SEP087756477) 1399 1997 56 LG:021770.1:2000SEP082615849H1 1419 1605 56 LG:021770.1:2000SEP085259534H1 1463 1620 5b LG:021770.1:2000SEP0882719096 1552 1630 56 LG:021770.1:2000SEP083483806F6 1564 2025 56 LG:021770.1:2000SEP083483806H 1564 1742 56 LG:021770.1:2000SEP083187717Th 1586 1971 5b LG:021770.1:2000SEP083352115H1 1659 1749 56 LG:021770.1;2000SEP081812178H1 1713 1979 56 LG:021770.1:2000SEP087756477H1 1781 2056 5b LG:021770.1;2000SEP085851722H1 1851 2056 56 LG:021770.1:2000SEP08318771786 1876 2056 56 LG:021770.1;2000SEP081967278Th 1884 2471 56 LG:021770.1:2000SEP084187256H1 1909 2057 56 LG:021770.1:2000SEP084184364H1 1914 2132 56 LG:021770.1;2000SEP083483806Th 1931 2478 56 LG:021770.1:2000SEP087250489H1 1945 2497 56 LG:021770.1:2000SEP087250522H1 1945 2491 56 LG:021770.1;2000SEP085686262T6 1952 2470 56 LG:021770.1;2000SEP083187717H1 1983 2044 56 LG:021770.1:2000SEP082570543H1 2327 2515 56 LG:021770.1;2000SEP08257054386 2327 2515 56 LG:021770.1;2000SEP082570543T6 2327 2477 56 LG:021770.1;2000SEP085958482H1 2341 2503 56 LG:021770.1;2000SEP081618155Th 2368 2477 56 LG:021770.1;2000SEP084692935H1 2368 2420 56 LG:021770.1:2000SEP0886470601 2368 2522 56 LG:021770.1:2000SEP081732834H 2373 2450 56 LG:021770.1:2000SEP0882782960 2445 2581 56 LG:021770.1:2000SEP086100740H 2452 2643 56 LG:021770.1:2000SEP083249668Th 2561 3105 56 LG:021770.1:2000SEP083249668F6 2813 3082 56 LG:021770.1:2000SEP083249668H1 2932 3082 57 LG:181607.9:2000SEP087344412H1 37 548 57 LG:181607.9:2000SEP087616670H 40 579 57 LG:181607.9;2000SEP083382088H1 71 302 57 LG:181607.9:2000SEP083622354H1 71 323 57 LG:181607.9:2000SEP083810979H 79 382 ~36 SEQ ID Template ID Component Start Stop NO: ID

57 LG:181607.9:2000SEP086314189F8 80 762 57 LG:181607.9:2000SEP084763755H1 93 271 57 LG:181607.9:2000SEP08g 1317224 95 516 57 LG:181607.9:2000SEP082734055H 105 366 57 LG:181607.9:2000SEP082986979H 107 350 57 LG:181607.9:2000SEP08g885028 221 484 57 LG:181607.9:2000SEP08g88501 b 222 578 57 LG:181607.9:2000SEP083735039H 266 504 57 LG:181607.9:2000SEP083199148H 1 268 58 LG:1042768.1:2000SEP086798443H 1 438 58 LG:1042768.1:2000SEP086790795F8 1 602 58 LG:1042768.1:2000SEP086790795H 1 529 58 LG:1042768.1:2000SEP086798443F8 1 618 58 LG:10427b8.1:2000SEP08679079578 244 850 59 LG:282729.1:2000SEP084365538Fb 1 292 59 LG:282729.1:2000SEP084365538H 1 261 59 LG:282729.1:2000SEP086810113) 11 398 59 LG:282729,1:2000SEP086810113H 13 399 59 LG:282729.1:2000SEP085137624H 248 353 59 LG:282729.1:2000SEP08g4069212 253 704 59 LG:282729.1:2000SEP08513762476 354 664 b0 LG:998305.3:2000SEP083591650H 1 282 60 LG:998305.3:2000SEP083651255H 65 362 60 LG:998305.3:2000SEP083b51255Fb 66 617 60 LG:998305.3:2000SEP083462213H1 477 742 60 LG:998305.3:2000SEP08365125576 577 927 b0 LG:998305.3:2000SEP081853882H1 669 803 60 LG:998305.3:2000SEP081854687H1 669 962 60 LG:998305.3:2000SEP081854b87Fb 669 956 b0 LG:998305.3:2000SEP082244779H1 776 928 61 LG:1135213.1:2000SEP084145560H1 1 337 61 LG:1135213.1:2~OSEP087182979H1 1 537 61 LG:1135213.1:2000SEP08g4929b8b 1 1581 61 LG:1135213.1:2000SEP08g 1881193 113 359 61 LG:1135213.1:2000SEP08798770H 1 206 449 61 LG:1 135213.1:2000SEP08g 1198b95 214 498 61 LG:1 135213.1:2000SEP08g l b37735 380 642 61 LG:1135213.1:2000SEP08g2204b79 39 511 61 LG:1135213.1:2000SEP085540595H1 1 195 61 LG:1135213.1:2000SEP08g 19707b9 1 345 61 LG:1135213.1:2000SEP08g 1970753 1 325 61 LG:1135213.1:2000SEP08g 1971048 1 253 61 LG:1135213.1:2000SEP08g 1970777 1 223 61 LG:1135213.1:2000SEP08g815792 8 284 61 LG:1135213.1:2000SEP08g 1441646 3 303 61 LG:1135213.1:2000SEP08g4372035 14 479 61 LG:1135213.1:2000SEP08g2930515 35 487 6l LG:1135213.1:2000SEP08g4897951 44 477 61 LG:1135213.1:2~OSEP08609028H 1 27 178 61 LG:1135213.1:2000SEP08g2782816 15 417 _- -1.J /

SEQ ID Template ID Component Start Stop NO: ID

61 LG:1135213.1:2000SEP088432b525 1 141 61 LG:1135213.1:2000SEP0882525795 28 236 62 LG:267762.1:2000SEP083941090F8 1 334 b2 LG:267762.1:2000SEP081704531 H 153 292 b2 LG:267762.1:2000SEP087658244) 267 830 b2 LG:267762.1:2000SEP085674936Fb 283 888 b2 LG:267762.1:2000SEP085674936H 283 545 b2 LG:267762.1:2000SEP085785070H 482 768 b2 LG:2b77b2.1:2000SEP082831361 H 514 783 62 LG:2b77b2.1:2000SEP08g 1523057 527 994 b2 LG:267762.1:2000SEP086244881 H 600 677 62 LG:267762.1:2000SEP083731660H1 675 978 b2 LG:267762.1:2000SEP0881950270 777 1103 62 LG:267762.1:2000SEP085674936Th 782 1313 b2 LG:267762.1:2000SEP087762849)1 824 1474 62 LG:267762.1:2000SEP08g 1523013 882 1063 62 LG:267762.1:2000SEP0883b78477 895 1352 62 LG:267762.1:2000SEP082797262H1 986 1231 62 LG:267762.1:2000SEP082797262F6 986 1555 62 LG:267762,1:2000SEP083732853H1 1059 1205 62 LG:267762.1:2000SEP08g7bb9b7 1146 1503 62 LG:2677b2.1:2000SEP082797262Tb 1199 1 b45 b2 LG:2677b2.1:2000SEP086768646)1 1221 1437 62 LG:267762.1:2000SEP082561680H1 1367 1657 62 LG:267762.1:2000SEP0883750b27 1401 1 b45 62 LG:267762.1:2000SEP0882557941 1510 1645 b3 LG:120744.1:2000SEP085643301 H 1 266 63 LG:120744.1:2000SEP085643301 Fb 1 412 63 LG:120744.1:2000SEP087007819H1 12 557 63 LG:120744.1:2000SEP087161666H1 34 435 b3 LG:120744,1:2000SEP087008530H1 19 4b3 b3 LG:120744.1:2000SEP0871b16bbF8 34 651 63 LG:120744.1:2000SEP087017571 H1 42 211 b3 LG:120744,1:2000SEP087017571 F8 41 656 b3 LG:120744,1:2000SEP083277305H1 128 393 b3 LG:120744,1:2000SEP083277305Fb 138 728 b3 LG:120744.1:2000SEP083565182H1 492 782 63 LG:120744.1:2000SEP085643301 R8 940 111 b b3 LG:120744,1:2000SEP0884293857 672 947 b3 LG:120744.1:2000SEP08716166688 707 11 b9 b3 LG:120744,1:2000SEP082992317H 81 b 1098 63 LG:120744,1:2000SEP085643301 R6 823 1115 b4 LG:403409,1:2000SEP085643224H1 22 276 64 LG:403409.1:2000SEP08g 1998848 22 296 b4 LG:403409,1:2000SEP083126704H 22 298 64 LG:403409,1:2000SEP083126978Fb 22 hl 64 LG:403409,1:2000SEP083126704F6 22 600 64 LG:403409.1:2000SEP08325b088H1 24 259 64 LG:403409.1:2000SEP081728945H1 26 246 64 LG:403409.1:2000SEP086141236H1 28 370 SEQ ID Template ID Component Start Stop NO: ID

b4 LG:403409,1:2000SEP086141236F8 28 633 b4 LG:403409.1:2000SEP086328822H 47 592 64 LG:403409,1:2000SEP083388023H1 89 361 b4 LG:403409,1:2000SEP086134014H1 110 401 b4 LG:403409,1:2000SEP083323733H1 192 461 64 LG:403409.1:2000SEP083409854H1 357 618 64 LG:403409,1:2000SEP084068325F6 515 1108 b4 LG:403409,1:2000SEP084068325H1 517 804 b4 LG:403409.1:2000SEP083629455H 560 835 b4 LG:403409,1:2000SEP085499626H1 1 255 ~

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80 LG:215158.5:2000SEP081003336H1 1100 1374 80 LG:215158,5:2000SEP082569722H1 1021 1325 80 LG:215158.5:2000SEP086890146) 909 131 1 b 80 LG:215158.5:2000SEP084511922H1 1068 1310 80 LG:215158,5:2000SEP08327249376 749 1244 80 LG:215158,5:2000SEP083729041 Hl 1048 1279 80 LG:215158.5:2000SEP085965623H1 718 1285 80 LG:215158,5:2000SEP084622635H1 1064 1315 80 LG:215158.5:2000SEP084292907H1 1038 1296 80 LG:215158.5:2000SEP08476338679 850 1479 80 LG:215158.5:2000SEP087685225H1 864 1489 80 LG:215158.5:2000SEP08741942271 844 1457 80 LG:215158.5:2000SEP087060657H1 920 1499 80 ~ LG:215158.5:2000SEP084325938H1 1326 1508 80 LG:215158,5:2000SEP084322970H1 1294 1491 80 LG:215158,5:2000SEP084005972H1 1242 1487 80 LG:215158.5:2000SEP085948161 H1 1242 1521 80 LG:215158.5:2000SEP0884510841 1367 1555 80 LG:215158,5:2000SEP0884395334 1123 1554 80 LG:215158,5:2000SEP0885591405 1366 1553 80 LG:215158,5:2000SEP0882595148 1258 1553 80 LG:215158.5:2000SEP085512202H1 1303 1551 80 LG:215158,5:2000SEP0882198087 1121 1536 80 LG:215158.5:2000SEP08372904171 1049 1522 80 LG:215158.5:2000SEP087930783H1 918 1556 80 LG:215158,5:2000SEP081831292H1 1274 1523 80 LG:215158,5:2000SEP08503433876 1073 1521 80 LG:215158,5:2000SEP08218148076 1200 1521 80 LG:215158.5:2000SEP08228840476 1139 1521 80 LG:215158,5:2000SEP08256972276 1021 1517 80 LG:215158.5:2000SEP086727494H1 732 1343 80 LG:215158.5:2000SEP081423205H1 1204 1445 80 LG:215158.5:2000SEP086401017H1 1160 1405 80 LG:215158.5:2000SEP085984486H1 1192 1483 80 LG:215158,5:2000SEP0884075380 979 1353 80 LG:215158.5:2000SEP082375777H1 1216 1437 80 LG:215158,5:2000SEP083762291 H 11 b3 1433 80 LG:215158.5:2000SEP0883181429 1153 1559 80 LG:215158,5:2000SEP081896331 H1 1443 1559 80 LG:215158.5:2000SEP0884004067 1170 1556 80 LG:215158,5:2000SEP086058031 H1 721 782 80 LG:215158,5:2000SEP083097624F6 214 720 80 LG:215158,5:2000SEP085294643H1 404 570 80 LG:215158.5:2000SEP08309762476 1 438 81 LG:235840.1:2000SEP082676570F6 2277 2647 81 LG:235840.1:2000SEP08267657076 2277 2655 81 LG:235840.1:2000SEP0883744074 2254 2'704 81 LG:235840.1:2000SEP083992215H1 1800 2095 81 LG:235840.1:2000SEP087193758H2 1810 2237 81 LG:235840.1:2000SEP0882836920 2235 2701 SEQ ID Template ID Component Start Stop NO: ID

81 LG:235840.1:2000SEP085835079H1 2239 2462 81 LG:235840,1:2000SEP0882238015 2338 2683 81 LG:235840,1:2000SEP0882737235 2301 2666 81 LG:235840.1:2000SEP0882669827 2286 2666 81 LG:235840.1:2000SEP088692242 2389 2711 81 LG:235840.1:2000SEP0882575700 2357 2637 81 LG:235840.1:2000SEP081451436T6 2352 2667 81 LG:235840.1:2000SEP082549073H1 2351 2602 81 LG:235840.1:2000SEP084249979F6 1 363 81 LG:235840.1:2000SEP0894289181 2442 2707 81 LG:235840.1:2000SEP085187170H1 2459 2666 81 LG:235840.1:2000SEP0882727328 2478 2695 81 LG:235840.1:2000SEP0886197748 2554 2664 81 LG:235840.1:2000SEP08g 1391398 2413 2703 81 LG:235840.1:2000SEP08729197H1 2442 2666 81 LG:235840,1:2000SEP08942891 R6 2442 2707 81 LG:235840.1:2000SEP0882705998 2407 2701 81 LG:235840.1:2000SEP08g 1967662 1129 1516 81 LG:235840.1:2000SEP085286802H1 1076 1250 81 LG:235840.1:2000SEP083595241 H1 941 1230 81 LG:235840.1:2000SEP085914590H1 976 1212 81 LG:235840.1:2000SEP085914590F8 976 1536 81 LG:235840.1:2000SEP087633624H1 586 1140 81 LG:235840.1:2000SEP084725620H1 503 767 81 LG:235840.1:2000SEP088928335 600 888 81 LG:235840.1:2000SEP084249979H1 1 247 81 LG:235840.1:2000SEP087659126H1 21 526 81 LG:235840.1:2000SEP08424997986 89 580 81 LG:235840.1:2000SEP087633624) 394 1002 81 LG:235840.1:2000SEP08541 1412H 1297 1562 81 LG:235840.1:2000SEP085501637F6 1303 1503 81 LG:235840.1:2000SEP085501637H 1303 1538 81 LG:235840.1:2000SEP08g 1932950 1379 1864 81 LG:235840.1:2000SEP087613750) 1195 1784 81 LG:235840.1:2000SEP084243528H 1218 1465 81 LG:235840.1:2000SEP0846641 69H 1222 1414 81 LG:235840.1:2000SEP084664169F6 1222 1675 81 LG:235840.1:2000SEP085511564H 1222 1385 81 LG:235840.1:2000SEP086306648H 1230 1694 81 LG:235840.1:2000SEP081451436F1 1500 1933 81 LG:235840.1:2000SEP081451436F6 1500 2008 81 LG:235840.1:2000SEP081451436H 1500 1767 81 LG:235840.1:2000SEP086160452H 1530 1821 81 LG:235840.1:2000SEP08g 1389188 1448 1703 81 LG:235840.1:2000SEP08531327H1 1449 1692 81 LG:235840.1:2000SEP086334626H 1455 1902 81 LG:235840.1:2000SEP085204143H 1445 1709 81 LG:235840.1:2000SEP082286077H1 1694 1932 81 LG:235840.1:2000SEP085989717H1 1735 1985 81 LG:235840.1:2000SEP087065831 H 1 b 14 2104 15~

SEQ ID Template ID Component Start Stop NO: ID

81 LG:235840.1:2000SEP087613750H 1669 2267 81 LG:235840.1:2000SEP084898449H 1682 1867 81 LG:235840.1;2000SEP083464906H 1690 2022 81 LG:235840.1;2000SEP08004533H 1 1582 1874 81 LG:235840.1:2000SEP086730659H 1604 1825 81 LG:235840.1:2000SEP084196254H 2224 2519 81 LG:235840.1;2000SEP08591459088 1568 2109 81 LG:235840.1:2000SEP082960481 H2 1566 1853 81 LG:235840.1:2000SEP085056390H 1578 1850 81 LG:235840.1;2000SEP08503438276 2283 2679 81 LG:235840.1:2000SEP082676562H1 2277 2526 81 LG:235840.1:2000SEP085693701 H 2282 2543 81 LG:235840.1:2000SEP087738333H 2045 2594 81 LG:235840.1;2000SEP08466416976 2049 2595 81 LG:235840.1;2000SEP08639274H1 2058 2332 81 LG:235840.1;2000SEP08544137H1 2149 2293 81 LG:235840.1;2000SEP08g 1270286 2033 2216 81 LG:235840.1;2000SEP081285809H 1979 221 1 b 81 LG:235840.1:2000SEP086442655H 1795 2303 81 LG:235840.1:2000SEP086711829H 1755 2246 81 LG:235840.1;2000SEP084351829H 1735 2063 81 LG:235840.1;2000SEP087213696H 1946 2423 81 LG:235840.1;2000SEP08g692276 1883 2221 81 LG:235840.1:2000SEP08g692306 1883 1965 81 LG:235840.1;2000SEP086377861 H 1919 2189 82 LG:350272.1;2000SEP0896082086 1570 1941 82 LG:350272.1:2000SEP082697244H 1573 1858 82 LG:350272.1:2000SEP08960820H 1 1570 1845 82 LG:350272.1;2000SEP087326176H1 1452 1912 82 LG:350272.1:2000SEP086311958H 1468 1895 82 LG:350272.1:2000SEP086201854H 1480 1915 82 LG:350272.1;2000SEP083559406H1 1479 1582 82 LG:350272.1:2000SEP083490063H 1481 1775 82 LG:350272.1;2000SEP08502069671 1335 1784 82 LG:350272.1:2000SEP082538770H 1336 1545 82 LG:350272.1:2000SEP08g2674996 1426 1831 82 LG:350272.1:2000SEP08g 1186534 1432 1832 82 LG:350272.1:2000SEP08603382H 1 1336 1584 82 LG:350272.1;2000SEP083740987H 1339 1633 82 LG:350272.1:2000SEP08502058871 1354 1783 82 LG:350272.1:2000SEP084241989H 1420 1748 82 LG:350272.1:2000SEP0858181386 1212 1561 82 LG:350272.1:2000SEP087322258H 1251 1868 82 LG:350272.1;2000SEP082127622H1 1277 1536 82 LG:350272.1;2000SEP087082642H 857 1251 82 LG:350272.1:2000SEP08g 1152456 872 1 192 82 LG:350272.1;2000SEP08g3958809 873 1219 82 LG:350272.1:2000SEP08g3277672 873 1323 82 LG:350272.1:2000SEP08g3249855 873 1308 82 LG:350272.1:2000SEP08g 11 O 1302 901 1173 SEQ ID Template ID Component Start Stop NO: ID

82 LG:350272.1:2000SEP0882820552 903 1337 82 LG:350272.1:20005EP085020696H 907 1173 82 LG:350272.1:2000SEP085062519H 941 1210 82 LG:350272.1:2000SEP0883163179 974 1240 82 LG;350272.1:2000SEP085696180H1 1003 1267 82 LG:350272.1:2000SEP086821260J 1043 1481 82 LG:350272.1:2000SEP083224632H2 1053 1337 82 LG:350272.1:20005EP087764948H 1150 1503 82 LG:350272.1:2000SEP083721403H 1177 1425 82 LG:350272.1:2000SEP085865088H 1201 1485 82 LG:350272.1:2000SEP08581813H 1 1212 1475 82 LG:350272.1:2000SEP084010319H 2042 2252 82 LG:350272.1:2000SEP081741002T6 2042 2491 82 LG:350272.1:2000SEP082650967H1 2043 2222 82 LG:350272.1:2000SEP084013519H 2051 2256 82 LG:350272.1:2000SEP084353493H 2051 2142 82 LG:350272.1:2000SEP08211293H 1 2348 2536 82 LG:350272.1;2000SEP084353485H 2051 2140 82 LG:350272.1;2000SEP08211114H1 2052 2102 82 LG:350272.1:2000SEP083621890H 2051 2133 82 LG:350272.1;2000SEP08581813Th 2053 2491 82 LG:350272.1;2000SEP08211696H 1 2348 2529 82 LG:350272.1;2000SEP0882820887 2054 2532 82 LG:350272.1:2000SEP081684883T6 2062 2494 82 LG:350272.1:2000SEP08633648H 1 2354 2542 82 LG:350272.1:20005EP081684883F6 2062 2529 82 LG:350272.1;2000SEP086606673H 2077 2530 82 LG:350272.1;2000SEP083565543H1 2365 2487 82 LG:350272.1;2000SEP0882359505 2443 2529 82 LG:350272.1:2000SEP0884649884 2445 2523 82 LG:350272.1:2000SEP0884970896 2078 2534 82 LG:350272.1:2000SEP0884125734 2080 2518 82 LG:350272.1:2000SEP0883741618 2095 2538 82 LG:350272.1;2000SEP0886038705 2111 2529 82 LG:350272.1:2000SEP0884074869 2114 2535 82 LG:350272.1:2000SEP0885755616 2127 2535 82 LG:350272.1;2000SEP0882465965 2144 2535 82 LG:350272.1:2000SEP0882669493 2154 2531 82 LG:350272.1:2000SEP0884618967 2155 2529 82 LG:350272.1:2000SEP0882270187 2176 2532 82 LG:350272.1:2000SEP088855861 2193 2526 82 LG:350272.1:2000SEP0885397025 2183 2529 82 LG:350272.1:2000SEP0883307326 2185 2538 82 LG:350272.1:2000SEP086615126H1 2467 2529 82 LG:350272.1:2000SEP0882715505 2186 2535 82 LG:350272.1:2000SEP0884267877 2203 2523 82 LG:350272.1:2000SEP0884267523 2203 2523 82 LG:350272.1:2000SEP0884267458 2203 2523 82 LG:350272.1:2000SEP081637245H1 2205 2400 82 LG:350272.1;2000SEP0882669985 2196 2427 SEQ ID Template ID Component Start Stop NO: ID

82 LG:350272.1:2000SEP082561156H1 2221 2501 82 LG:350272.1:2000SEP0885364704 2224 2530 82 LG:350272.1:2000SEP086843381 H1 2239 2529 82 LG:350272.1:2000SEP0885755074 2262 2535 82 LG:350272.1:2000SEP086326064H 2271 2532 82 LG:350272.1:2000SEP085306551 H 2276 2400 82 LG:350272.1:2000SEP08644238Th 2276 2495 82 LG:350272.1:20005EP085306583H1 2277 2429 82 LG:350272.1:2000SEP086383176H 2285 2491 82 LG:350272.1:2000SEP0884079566 2287 2529 82 LG:350272.1:2000SEP0882577306 2288 2529 82 LG:350272.1;2000SEP0885812197 2319 2515 82 LG:350272.1:2000SEP081684883H 2327 2529 82 LG:350272.1;2000SEP083932451 Hl 2346 2529 .

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146 LG:1076866.1:2000SEP086078450H1 1574 1858 146 LG:1076866.1:2000SEP084830902F8 1600 2178 146 LG:1076866.1:2000SEP081697599H1 1610 1747 146 LG:1076866.1:2000SEP08g5439960 519 944 146 LG:1076866.1:2000SEP0862578286 1796 2053 146 LG:1076866.1:2000SEP081543396H1 1477 1682 146 LG:1076866.1:2000SEP086742253F8 1205 1744 146 LG:107b8bb.1:2000SEP084830902F9 1600 2157 146 LG:1076866.1:2000SEP08625782H1 1796 2039 146 LG:10768bb.1:2000SEP084764175H1 1755 2006 147 LG:969359.1:2000SEP086795715H1 3 510 147 LG:969359.1:2000SEP086798649F8 3 488 147 LG:969359.1:2000SEP086798649H 3 299 147 LG:969359.1:2000SEP086795715F8 3 571 147 LG:969359.1:2000SEP086793426H 10 454 147 LG:969359.1:2000SEP086790981 T8 1 b9 792 147 LG:969359.1:2000SEP086292801 H 303 449 147 LG:969359.1:2000SEP08679864978 599 773 147 LG:969359,1:2000SEP08679342678 657 779 147 LG:969359.1:2000SEP08g 1616171 710 900 147 LG:969359.1:2000SEP086790981 H1 1 486 147 LG:969359,1:2000SEP086790981 F8 1 497 148 LG:36b783.1:2000SEP08g 1068298 1080 1313 148 LG:366783.1:2000SEP08g 1068059 1069 1310 148 LG:3b6783.1:2000SEP08494840376 621 1232 148 LG:36b783.1:2000SEP084948403F6 441 948 148 LG:366783.1:2000SEP084948403H1 441 676 148 LG:366783.1:2000SEP084600759H1 286 543 148 LG:366783.1:2000SEP08576358777 1 472 149 LG:332176.3:2000SEP086623593H1 203 786 149 LG:332176.3:2000SEP087338995H1 662 1225 149 LG:332176.3:2000SEP086623593J1 731 1329 149 LG:332176.3:2000SEP08632623877 856 1019 149 LG:332176.3:2000SEP087618143J1 1 467 149 LG:332176.3:2000SEP08g 1975879 32 318 149 LG:332176.3:2000SEP08146751177 100 537 149 LG:332176.3:2000SEP086326238H1 107 405 149 LG:332176.3:2000SEP08526662H 1 124 307 149 LG:332176.3:2000SEP082856544H 133 245 149 LG:332176.3:2000SEP087247177H1 161 539 150 LG:994938.1:2000SEP08959442H 1 1 275 150 LG:994938.1:2000SEP08960385H 1 1 184 150 LG:994938.1:2000SEP0895944286 1 366 150 LG:994938,1:2000SEP08338787278 185 740 150 LG:994938.1:2000SEP08g2934522 342 630 150 LG:994938.1:2000SEP086325528H1 346 538 150 LG:994938.1:2000SEP08407022H 1 371 614 150 LG:994938.1:2000SEP0896038576 423 772 150 LG:994938.1:2000SEP08g2242138 425 810 150 LG:994938.1:2000SEP0895944276 431 761 SE6Z Template ID Component Start Stop ID NO: ID

150 LG:994938.1:2000SEP0882969314 445 541 151 LG:982800.1:2000SEP083118103H1 2147 2437 151 LG:982800.1:2000SEP086020943H1 2062 2430 151 LG:982800.1:2000SEP083219963H1 2062 2228 151 LG:982800.1:2000SEP0882540261 2063 2448 151 LG:982800.1:2000SEP086147820H1 2078 2363 151 LG:982800.1:2000SEP084445313H1 2080 2266 151 LG:982800.1:2000SEP08955100T2 2090 2570 151 LG:982800.1:2000SEP0895510081 2090 2453 151 LG:982800.1:2000SEP089551 OOH 2090 2358 151 LG:982800.1:2000SEP083814175Th 2095 2570 151 LG:982800.1:2000SEP0882011857 2103 2393 151 LG:982800.1:2000SEP082875837H1 2116 2394 151 LG:982800.1:2000SEP08g 1849425 2131 2424 151 LG:982800.1:2000SEP084337528Th 2144 2581 151 LG:982800.1:2000SEP083118103F6 2146 2582 151 LG:982800.1:2000SEP08822341 R1 2189 2449 151 LG:982800.1:2000SEP0883086258 2215 2609 151 LG:982800.1:2000SEP082101604Th 2217 2565 151 LG:982800.1:2000SEP08636591 H 2217 2470 151 LG:982800.1:2000SEP0882809907 2239 2430 151 LG:982800.1:2000SEP08496959H 1 2271 2449 151 LG:982800.1:2000SEP08g 1927355 2303 2606 151 LG:982800.1:2000SEP08406063H 1 2316 2543 151 LG:982800.1:2000SEP087335618H1 2331 2616 151 LG:982800.1:2000SEP0884329276 2347 2613 151 LG:982800,1:2000SEP08630611 H 2382 2607 151 LG:982800.1:2000SEP0890464682 2397 2601 151 LG:982800.1:2000SEP08904646H 1 2398 2608 151 LG:982800.1:2000SEP086870517H1 1296 1814 151 LG:982800.1:2000SEP083814709H1 1477 1746 151 LG:982800.1:2000SEP083814709F7 1498 1730 151 LG:982800.1:2000SEP084556204H1 1561 1642 151 LG:982800.1:2000SEP084551845F6 1561 1744 151 LG:982800.1:2000SEP084557749H1 1561 1744 151 LG:982800.1:2000SEP084556204F8 1561 2151 151 LG:982800.1:2000SEP084557749F8 1580 2139 151 LG:982800.1:2000SEP08210160486 2028 2532 151 LG:982800.1:2000SEP082101604H1 2028 2294 151 LG:982800,1:2000SEP0882016400 2051 2147 151 LG:982800.1:2000SEP08804149H 1 2058 21 b2 151 LG:982800.1:2000SEP083485587H1 2062 2165 151 LG:982800.1:2000SEP083999943H1 2062 2229 151 LG:982800.1:2000SEP084337528F6 583 991 151 LG:982800.1:2000SEP084337528H1 583 841 151 LG:982800.1:2000SEP082790452H2 853 1006 151 LG:982800.1:2000SEP082792488H1 853 1139 151 LG:982800.1:2000SEP082792488F6 853 1240 151 LG:982800.1:2000SEP087269729H1 1056 1608 151 LG:982800.1:2000SEP08g 1802842 1156 1515 SE6Z Template ID Component Start Stop ID NO: ID

151 LG:982800.1:2000SEP085734055H1 1230 1497 151 LG:982800.1:2000SEP087654174H1 356 465 151 LG:982800.1:2000SEP087697207) 399 886 151 LG:982800.1:2000SEP087697207H1 399 860 151 LG:982800.1:2000SEP087608868) 407 762 151 LG:982800.1:2000SEP084265753H1 513 695 151 LG:982800.1:2000SEP08279248876 2157 2565 151 LG:982800.1:2000SEP086321 O1 H 2161 2424 151 LG:982800.1:2000SEP083479107H1 2175 2356 151 LG:982800.1:2000SEP08822341 H 2189 2412 151 LG:982800.1:2000SEP08505559H 1 2150 2362 151 LG:982800.1:2000SEP087609838) 42 593 151 LG:982800.1:2000SEP087617315)1 307 888 151 LG:982800.1:2000SEP087617315H 1 258 151 LG:982800.1:2000SEP084841542H1 12 274 151 LG:982800.1:2000SEP08g5632630 2501 2607 151 LG:982800.1:2000SEP08g3961700 2503 2607 151 LG:982800.1:2000SEP084383061H1 2412 2583 151 LG:982800.1:2000SEP082130512H1 2412 2606 152 LG:977850.7:2000SEP086832831 H 1 270 152 LG:977850.7:2000SEP086832952H1 2 270 153 LG:234748.2:2000SEP083810352H1 1966 2273 153 LG:234748.2:2000SEP085878092H1 2081. 2258 153 LG:234748.2:2000SEP08g 1696827 1956 2256 153 LG:234748.2:2000SEP08g4901064 1794 2244 153 LG:234748.2:2000SEP085016719H1 1953 2241 153 LG:234748.2:2000SEP086752013H1 1629 2144 153 LG:234748.2:2000SEP086314130H1 1611 2120 153 LG:234748.2:2000SEP08g3173456 1782 2119 153 LG:234748.2:2000SEP08678118H 1 1823 2085 153 LG:234748.2:2000SEP082044168H1 1756 2014 153 LG:234748.2:2000SEP085267795H1 1758 1977 153 LG:234748.2:2000SEP081505116F6 1546 1947 153 LG:234748.2:2000SEP083740114H1 1651 1940 153 LG:234748.2:2000SEP082047028H1 1025 1286 153 LG:234748.2:2000SEP081413260H1 1022 1267 153 LG:234748.2:2000SEP08g3886794 890 1258 153 LG:234748.2:2000SEP082047028F6 938 1286 153 LG:234748.2:2000SEP08g 1481863 868 1308 153 LG:234748.2:2000SEP084922824H1 1032 1296 153 LG:234748.2:2000SEP082284804H1 1177 1407 153 LG:234748.2:2000SEP08228480486 1017 1407 153 LG:234748.2:2000SEP085833129H1 1126 1391 153 LG:234748.2:2000SEP083906375H1 1201 1379 153 LG:234748.2:2000SEP084440961H1 1055 1342 153 LG:234748.2:2000SEP08538715176 1030 1323 153 LG:234748.2:2000SEP08g6658351 866 1324 153 LG:234748.2:2000SEP083320618F6 503 1049 153 LG:234748,2:2000SEP083716611 Fb 520 1007 153 LG:234748.2:2000SEP084178471 H 924 998 SEQ ID Template ID Component Start Stop NO: ID

153 LG:234748.2:2000SEP083270832H1 741 990 153 LG:234748.2:2000SEP0882819681 533 959 153 LG:234748.2:2000SEP0883870024 513 956 153 LG;234748.2:2000SEP0882112072 617 954 153 LG:234748.2:2000SEP0885664450 549 950 153 LG:234748.2:2000SEP082914043H1 648 917 153 LG:234748.2:2000SEP083669215Th 531 909 153 LG:234748.2:2000SEP083093657H1 658 902 153 LG:234748.2:2000SEP084316137H1 550 823 153 LG:234748.2;2000SEP083533183H1 626 818 153 LG:234748.2:2000SEP083716611 H 521 812 153 LG:234748.2:2000SEP083792070H 508 790 153 LG:234748.2:2000SEP083705837F6 355 760 153 LG:234748.2:2000SEP086444785H 572 1112 153 LG:234748.2:2000SEP083693858H1 800 1101 153 LG:234748.2:2000SEP083463580H1 843 1101 153 LG:234748.2;2000SEP086731509H1 604 1166 153 LG:234748.2:2000SEP083716611Th 608 1129 153 LG:234748.2:2000SEP0885431286 728 1125 153 LG:234748.2:2000SEP0883058557 948 1125 153 LG:234748.2:2000SEP086444794H1 626 1112 153 LG:234748.2:2000SEP082293674H1 1250 1473 153 LG:234748.2:2000SEP083935051H1 1163 1446 153 LG:234748.2:2000SEP086044392H1 759 1251 153 LG:234748.2:2000SEP086044534H1 730 1251 153 LG:234748.2:2000SEP085087050H1 1321 1503 153 LG:234748.2:2000SEP082743371F6 2356 2826 153 LG:234748.2:2000SEP0885438479 2180 2633 153 LG:234748.2:2000SEP0886992169 2256 2632 153 LG:234748.2:2000SEP088474041 b 2388 2629 153 LG:234748.2:2000SEP0884600044 2230 2626 153 LG:234748.2:2000SEP0886992693 2346 2626 153 LG:234748.2:2000SEP08150511676 2043 2589 153 LG:234748.2:2000SEP082743371H1 2356 2580 153 LG:234748.2:2000SEP08g 1481317 21 b4 2559 153 LG:234748.2:2000SEP08g 1523156 21 b9 2560 153 LG:234748.2:2000SEP0885426194 2139 2552 153 LG:234748.2:2000SEP0885630258 2178 2549 153 LG:234748.2:2000SEP0885176173 2163 2549 153 LG:234748.2:2000SEP0883050489 2285 2503 153 LG:234748.2:2000SEP083825734H1 2211 2484 153 LG:234748.2:2000SEP084598219H1 2146 2428 153 LG:234748.2:2000SEP084520112H1 2216 2343 153 LG:234748.2;2000SEP0883174864 2007 2343 153 LG:234748.2:2000SEP084309556H1 1990 2308 153 LG:234748.2:2000SEP08332061876 1712 2301 153 LG:234748.2:2000SEP085150811 F6 24 300 153 LG:234748.2:2000SEP085150811 H1 25 297 153 LG:234748.2:2000SEP086044392) 1 474 153 LG:234748.2:2000SEP086044534)1 1 465 20~

SEQ ID Template ID Component Start Stop NO: ID

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232 LI:209351.3:2000SEP0870716459V1 1544 1914 232 LI:209351.3:2000SEP083255709H1 2086 2344 232 LI:209351.3;2000SEP085301828H1 2106 2373 232 LI:209351.3:2000SEP0870161870V1 1 218 232 LI:209351.3;2000SEP088673230 156 464 232 LI:209351.3:2000SEP087071881 OV 1176 1521 232 LI:209351.3:2000SEP086010851382 1182 1406 232 LI:209351.3:2000SEP0870715834V1 1427 1974 232 LI:209351.3:2000SEP0870911910V1 2015 2551 232 LI:209351.3;2000SEP0870914639V1 2023 2608 232 LI:209351.3;2000SEP0871271313V1 2024 2603 232 L1:209351.3;2000SEP082257709H1 2057 2316 232 LI:209351.3;2000SEP0870913790V1 2001 2514 232 LI:209351.3;2000SEP082137158F6 1980 2454 232 LI:209351.3:2000SEP082137158H1 1980 2232 232 LI:209351.3;2000SEP0870717485V1 1807 2348 232 LI:209351.3:2000SEP0882032832 1909 2262 232 LI:209351.3:2000SEP0870911075V1 1700 2271 232 LI:209351.3:2000SEP0870716432V1 1726 2302 232 LI:209351.3;2000SEP0870718263V1 1756 2199 232 LJ:209351.3:2000SEP0870715831 1756 2169 232 LI:209351.3:2000SEP0870716717V1 1791 2236 232 LI:209351.3:2000SEP087071 b 125V 1803 2348 232 LI:209351.3;2000SEP0870153905V1 1206 1436 232 LJ:209351.3;2000SEP0882563746 1225 1547 232 LJ:209351.3:2000SEP085774651 H1 1230 1826 232 LI:209351.3;2000SEP082864359F6 755 1165 232 LI:209351.3:2000SEP082864359H1 755 1059 233 LI:119900.1;2000SEP082616951 T6 428 822 233 LI:119900:1:2000SEP082831669Th 513 815 233 LI:119900.1:2000SEP083255201 H1 50 305 233 U:119900.1:2000SEP086205811H1 75 642 233 LI:119900.1:2000SEP0886710166 403 854 233 LI:119900.1:2000SEP086131670H1 37 327 233 LI:119900.1:2000SEP083255201 R6 49 278 233 LI:119900.1:2000SEP08g 1259907 1 258 233 LJ:119900.1:2000SEP0881440983 1 328 233 LI:119900.1:2000SEP086131670F8 37 470 233 LI:119900.1:2000SEP082423774H1 604 828 233 LI:119900.1:2000SEP0886639199 638 841 233 LI:119900.1:2000SEP082831669H1 520 787 233 LI:119900.1:2000SEP0882437451 571 854 233 LI: l 19900.1:2000SEP08599026H 1 644 854 233 LI:119900.1:2000SEP085077681 Hl 737 854 233 LI:119900.1:2000SEP082831669F6 520 854 234 LI;2052274.1:2000SEP0871742269V1 355 819 234 LI;2052274.1:2000SEP0871747037V1 890 1276 234 LI:2052274.1:2000SEP087318950H2 1212 1722 234 LI:2052274.1:2000SEP088766967 1227 1590 234 LI;2052274.1:2000SEP082797262T6 1282 1732 SE6~ ID Template ID Component Start Stop NO: ID

234 LI:2052274.1:2000SEP0871742947V1 1071 1509 234 LI:2052274.1:2000SEP0871744365V1 1154 1687 234 ~ LI:2052274.1:2000SEP083732853H1 1138 1288 234 LI:2052274.1:2000SEP087318884H2 1212 1732 234 LI:2052274.1:2000SEP08877185H1 341 601 234 LI:2052274.1:2000SEP085674936Th 858 1398 234 LI:2052274.1:2000SEP0871741876V 885 1417 234 LI:2052274.1:2000SEP0871742240V1 1008 1509 234 LI:2052274.1:2000SEP0871746493V1 1016 1530 234 LI:2052274.1:2000SEP0871742262V1 1052 1509 234 LI:2052274.1:2000SEP082797262F6 1065 1642 234 LI:2052274.1:2000SEP082797262H1 1065 1314 234 LI:2052274.1:2000SEP084157540H1 60 240 234 LI:2052274.1:2000SEP084157540F8 96 559 234 LI:2052274.1:2000SEP081704531 H1 160 301 234 LI:2052274.1:2000SEP087658244) 342 905 234 LI:2052274.1:2000SEP0871741928V1 576 809 234 LI:2052274.1:2000SEP082831361 H1 586 859 234 LI:2052274.1:2000SEP0871744286V1 993 1509 234 LI:2052274.1:2000SEP08g1523013 960 1142 234 LI:2052274.1:2000SEP08g3678477 973 1437 234 LI:2052274.1:2000SEP0871747321 931 1123 234 LI:2052274.1:2000SEP0871741847V1 957 1509 234 LI:2052274.1:2000SEP0871743248V1 355 807 234 LI:2052274.1:2000SEP087986547H1 830 1316 234 LI:2052274.1:2000SEP0871746536V1 753 1314 234 LI:2052274.1:2000SEP083731660H1 750 1057 234 LI:2052274.1:2000SEP0871745329V1 795 1125 234 LI:2052274.1:2000SEP0871743782V1 811 1172 234 LI:2052274.1:2000SEP0871745857V1 811 1172 234 LI:2052274,1:2000SEP0887718586 341 824 234 LI:2052274,1:2000SEP082672580F6 559 824 234 LI:2052274.1:2000SEP085674936F6 355 966 234 LI:2052274.1:2000SEP0871743956V1 355 937 234 LI:2052274.1:2000SEP0871743912V1 355 872 234 LI:2052274,1:2000SEP0871743192V1 351 981 ' 234 LI:2052274.1:2000SEP0871744831 355 1004 234 LI:2052274.1:2000SEP0871742129V1 576 808 234 LI:2052274.1:2000SEP084333137H1 356 633 234 LI:2052274.1:2000SEP087762849)1 903 1561 234 LI:2052274.1:2000SEP082561680H1 1452 1744 234 LI:2052274.1:2000SEP08g7456825 1461 1765 234 LI:2052274,1:2000SEP0871744355V 1451 1509 234 LI:2052274,1:2000SEP08g3750627 . 1488 1732 234 LI:2052274.1:2000SEP08g2557941 1597 1732 234 LI:2052274,1:2000SEP086768646)1 1304 1524 234 LI:2052274.1:2000SEP0871746594V 1336 1420 234 LI:2052274.1:2000SEP0871742519V1 599 1286 234 LI:2052274.1:2000SEP086244881 H1 673 752 234 LI:2052274.1:2000SEP0871742310V1 692 1387 SEQ ID Template ID Component Start Stop NO: ID

234 LI:2052274.1:2000SEP0871743501 748 1476 234 LI:2052274.1:2000SEP082672580H1 559 805 234 LI:2052274,1:2000SEP08g 1523057 599 1073 234 LI:2052274.1:2000SEP085674936H1 355 617 234 LI:2052274.1:2000SEP083941090F8 8 345 234 LI:2052274.1:2000SEP086700546H1 1 595 234 LI:2052274,1:2000SEP083941090H1 8 66 234 LI:2052274,1:2000SEP0871742091 355 845 234 L1:2052274.1:2000SEP0871743407V1 355 808 234 LI:2052274.1:2000SEP08g 1950270 853 1182 234 LI:2052274,1:2000SEP082294119H1 409 676 234 LI:2052274,1:2000SEP082113527H1 459 707 234 LI:2052274,1.:2000SEP0871743734V1 474 980 234 LI:2052274,1:2000SEP083014561 H 478 776 234 LI:2052274,1:2000SEP085785070H1 554 844 235 LI:1075502.1:2000SEP086797669H1 1 553 235 LI:1075502,1:2000SEP086796045F8 1 552 235 LI:1075502,1:2000SEP08679604578 320 924 235 LI:1075502.1:2000SEP08679766978 443 858 235 LI:1075502.1:2000SEP086797669F8 1 628 235 LI:1075502.1:2000SEP086796045H1 1 576 236 LI:813b97.1:2000SEP0870098909V1 962 1433 236 LI:813b97.1:2000SEP0870096440V 963 1288 236 LI:813697.1:2000SEP0870095040V1 1192 1603 236 LI:813697.1:2000SEP0870098067V1 1211 1547 236 LI:813697.1:2000SEP0862003376 1219 1766 236 LI:813b97.1:2000SEP0859818576 1219 1766 236 LI:813b97.1:2000SEP086348658F8 1244 1892 236 LI:813697.1:2000SEP086351670H1 1244 1566 236 LI:813b97.1:2000SEP08237366776 1252 1766 236 LI:813b97.1:2000SEP0870099645V1 1260 1758 236 LI:813b97.1:2000SEP08g1691544 1279 1719 236 LI:813697.1:2000SEP08g5888049 1380 1800 236 LI:813b97.1:2000SEP08g6838088 1415 1807 236 LI:813b97.1:2000SEP08g3232965 1434 1799 236 LI:813697.1:2000SEP085694708H1 - 1462 1696 236 LI:813697.1:2000SEP08g6577365 1469 1805 236 LI:813697.1:20~SEP0870097391 1483 1804 236 LI:813697.1:2000SEP086912262H 1491 1980 236 LI:813697.1:2000SEP08g3145102 1537 1802 236 LI.813697.1:2000SEP0870099964V1 1554 1804 236 LI:813697.1:2000SEP08g2695352 1676 1805 236 L1:813697.1:2000SEP0886565886 1703 1874 236 LI:813b97.1:2000SEP08865658H1 1703 1804 236 LI:813b97.1:2000SEP0870096773V1 636 1050 236 LI.813697.1:2000SEP0871204835V1 597 1202 236 LI:813697.1:2000SEP0870097075V1 892 1293 236 LI:813697.1:2000SEP0870099616V1 899 1321 236 LI:813697.1:2000SEP0870094872V1 579 967 236 LI:813b97.1:2000SEP0870097494V1 917 ~ 1341 SE6~ Template ID Component Start Stop ID NO: ID

236 LI:813697.1:2000SEP0871204896V1 598 1326 236 LI:813b97.1:2000SEP087172041 H1 1 529 236 LI:813b97.1:2000SEP087280634H1 315 878 236 LI:813b97.1:2000SEP0870099218V1 389 888 236 LI:813697.1:2000SEP0870094639V1 389 758 236 LI:813697.1:2000SEP0862003386 389 722 236 LI:813b97.1:2000SEP08620033H1 389 645 236 LI:813697.1:2000SEP0870095662V1 411 870 236 LI:813b97.1:2000SEP081897294H1 433 681 236 LI:813b97.1:2000SEP0870099939V1 445 984 236 LI:813b97.1:2000SEP0870094912V1 511 961 236 LI:813697.1:2000SEP0870099297V1 531 992 236 LI:813697.1:2000SEP0870097017V1 539 945 236 LI:813b97.1:2000SEP0870098266V1 745 1001 236 LI:813b97.1:2000SEP0870100073V1 595 1062 237 LI:814261.1:2000SEP08959442H1 1 275 237 LI:814261.1:2000SEP0895944286 1 366 237 LI:814261.1:2000SEP08960385H1 1 184 237 LI:8142b1.1:2000SEP08338787278 185 740 237 LI:814261.1:2000SEP0882934522 342 630 237 LI:814261.1:2000SEP086325528H1 346 538 237 LI:8142b1.1:2000SEP08407022H1 371 614 237 LI:814261.1:2000SEP0896038576 423 772 237 LI:8142b1.1:2000SEP0882242138 425 810 237 LI:814261.1:2000SEP0895944276 431 761 237 LI:8142b1.1:2000SEP0882969314 445 541 238 LI:775334.1:2000SEP087331759H1 1 582 238 LI:775334.1:2000SEP086551320H1 191 774 238 LI:775334.1:2000SEP086551320F8 204 726 238 LI:775334.1:2000SEP087331161 H1 240 671 238 LI:775334.1:2000SEP088573781 414 701 238 LI:775334.1:2000SEP083765106H 420 71 1 b 238 LI:775334.1:2000SEP087403132H1 646 1274 238 LI:775334.1:2000SEP0882219872 682 1070 238 LI:775334.1:2000SEP086313951 H1 789 1175 238 LI:775334.1:2000SEP088775988 858 1083 238 LI:775334.1:2000SEP0881386925 917 1332 238 LI:775334.1:2000SEP08g 1376602 954 1380 238 LI:775334.1:2000SEP08105380H1 1161 1369 238 LI:775334.1:2000SEP0810538086 1161 1486 238 LI:775334.1:20~SEP0870932886V1 102 403 238 LI:775334.1:2000SEP0870930434V1 173 394 238 LI:775334.1:2000SEP0870930903V1 102 404 238 LI:775334.1:2000SEP0871276885V1 102 404 238 LI:775334.1:2000SEP0871277249V1 173 321 238 LI:775334.1:2000SEP0870930969V1 102 420 238 LI:775334.1:2000SEP0870931830V1 102 420 238 LI:775334.1:2000SEP0870929143V1 173 401 238 LI:775334.1:2000SEP0870929226V1 102 420 238 LI:775334.1:2000SEP0870929616V1 102 420 25~

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<110> INCYTE GENOMICS, INC.
JACKSON, Stuart LINCOLN, Stephen E.
ALTUS, Christina M.
DUFOUR, Gerard E.
CHALUP, Michael S.
HILLMAN, Jennifer L.
JONES, Anissa Lee YU, Jimmy Y.
WRIGHT, Rachel J.
GIETZEN, Darryl LIU, Tommy F .
YAP, Pierre E.
DAHL, Christopher R.
MOMIYAMA, Monika G.
BRADLEY, Diana L.
ROHATGI, Sameer D.
HARRIS, Bernard ROSEBERRY, Ann M.
GERSTIN,Jr., Edward H.
PERALTA, Careyna H.
DAVID, Marie H.
PANZER, Scott R.
FLORES, Vincent DAFFO, Abel MARWAHA, Rakesh CHEN, Alice J.
CHANG, Simon C.
AU, Alan P.
INMAN, Rebekah R.
<120> MOLECULES FOR DISEASE DETECTION AND TREATMENT
<130> PT-1183 PCT
<140> To Be Assigned <141> Herewith <150> 60/230,517; 60/230,599; 60/230,514; 60/231,167; 60/230,598;
60/230,988; 60/230,518; 60/230,515; 60/229,751; 60/230,610;
60/229,749; 60/229,750; 60/230,597; 60/230,505; 60/231,163;
60/229,747; 60/229,748; 60/230,583; 60/230,519; 60/230,595;
60/230,865; 60/230,989; 60/230,951 <151> 2000-09-06; 2000-09-06; 2000-09-06; 2000-09-07; 2000-09-06;
2000-09-06; 2000-09-06; 2000-09-06; 2000-09-05; 2000-09-06;
2000-09-05; 2000-09-05; 2000-09-06; 2000-09-06; 2000-09-07;
2000-09-05; 2000-09-05; 2000-09-05; 2000-09-06; 2000-09-06;
2000-09-06; 2000-09-06; 2000-09-07 <160> 506 <170> PERL Program <210> 1 <211> 537 <212> DNA
<213> Homo Sapiens <220>
<221> misc_feature <223> Incyte ID No: LG:150318.1:2000SEP08 <400> 1 gcaccggcct cacaagtgtt ctacatgtgg gaaatgtttc tctcagtctt ccagcctaaa 60 caaacacatg cgagtccact ctggagacag accataccag tgtgtgtatt gtactaagag 120 gttcacagcc tccagcatac tccgcacaca catcaggcag cactccgggg agaagccctt 180 caaatgcaag tactgtggta aatcttttgc atcccatgct gcccatgaca gccatgtccg 240 gcgttcacac aaggaggacg atggctgctc atgcagcatc tgtgggaaaa tcttctcaga 300 tcaagaaaca ttctactccc acatgaagtt tcatgaagac tactagccct gccaggcaca 360 aagtgctggg ataacgggtg tagagccacc acacctggcc taaaatataa tgaaaaagtt 420 agatacttag agaaattaaa aagatcctga caactttacc tcattgctaa agctgtaact 480 cgtgcacaag atccagcgta catctatttt cacacactcc atatcctcct cttgtgc 537 <210> 2 <211> 1039 <212> DNA
<213> Homo Sapiens <220>
<221> misc_feature <223> Incyte ID No: LG:022529.1:2000SEP08 <400> 2 ctggtgcccc tctccacgac tccgcgtttc cctcccggtg ccctctcccc gagcccctct 60 ccccgcgccc ctctctgcct tccccgctgt gcccccgtcc ctgggctcct tgcccttccc 120 cactgggccc ctagcctcct cgcggcgtca cccgagcccc ctcctcgatc cgcggccccc 180 gctccctccg ccctcttccc tctctcactt cccacgcccc ctcttcgcgc tcctctctcc 240 tccccttgcc gcccagccca ggctctggag ttgggggaga gcccagggct ccagtcgctc 300 cggaggaggc gtgaatcgcg cagggattga ctaatttggg gtggggggtg cggtgggcga 360 tggagcagcc tgaggacatg gcgtcgctga gcgagttcga ctccttggcg ggcagcatcc 420 cggccaccaa ggtggagatc accgtgtcct gcaggaacct cctggacaaa gacatgtttt 480 ccaagtccga cccactgtgc gtcatgtata cccaagggat ggagaacaag cagtggcggg 540 agtttgggcg caccgaagtc atcgacaaca cgctcaatcc tgacttcgtg cgcaagttca 600 ttgtggatta ctttttcgag gagaagcaga acctccgttt tgatctatac gacgttgact 660 ctaagagtcc tgatttatcc aaacacgatt tcctgggcca ggccttctgc acccttggag 720 agattgtggg gtcccctggg agccgcctgg aaaagcccct cacggaaaag ctgttactct 780 gaagcgggct ctgggatgag gaatccaagg cttctcacag tggagcctga tgatgtcttc 840 agggaccagc cagggctggc cgtgtggtga gggtgacctc tcttgtccct atttctcagg 900 aagtaccagg ggcagggccc ttgcctgtat aaacgattct tacctttccc cacactgggg 960 aacactggtc accattcttt ggtgtccata tttctctgga cggccaccct cacactttgc 1020 atttaaacta actaattta 1039 <210> 3 <211> 636 <212> DNA
<213> Homo Sapiens <220>
<221> misc_feature <223> Incyte ID No: LG:352559.1:2000SEP08 <400> 3 tgtagtttcc tcaactactg cctcagctct acaatcccag agtaaagctc ttctccaaat 60 gaagagccag gaagaggtag aggtggcagg aattaaactt tgtaaagcca tgtccctggg 120 ttcactgact ttcacagatg tggccataga cttttcccaa gatgaatggg agtggctgaa 180 tcttgctcag agaagtttgt acaagaaggt gatgttagaa aactacagga acctagtttc 240 agtgggtctt-tgcatttcta aaccagatgt gatctcctta ctggagcaag agaaagaccc 300 ttgggtgata aaaggaggga tgaacagagg cctgtgccca gacttggagt gtgtgtgggt 360 gaccaaatca ttatctttaa accaggatat ttatgaagaa aaattacccc cggcaatcat 420 aatggaaaga cttaaaagct atgaccttga atgttcaaca ttagggaaaa actggaaatg 480 tgaagacttg tttgagaggg agcttgtaaa ccagaagaca cattttaggc aagagaccat 540 cactcatata gatactctta ttgaaaaaag agatcactct aacaaatctg ggacagtttt 600 tcatctgaat acattatctt atataaaaca gatttt 636 <210> 4 <211> 507 DEMANDE OU BREVET VOLUMINEUX
LA PRESENTE PARTIE DE CETTE DEMANDE OU CE BREVET COMPREND
PLUS D'UN TOME.

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Claims (60)

What is claimed is:

1. An isolated polynucleotide selected from the group consisting of:
a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-252, b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ
ID NO:1-252, c) a polynucleotide complementary to the polynucleotide of a), d) a polynucleotide complementary to the polynucleotide of b), and e) an RNA equivalent of a)-d).

2. An isolated polynucleotide of claim 1, selected from the group consisting of SEQ ID NO:1-252.

3. An isolated polynucleotide comprising at least 30 contiguous nucleotides of a polynucleotide of claim 1.

4. An isolated polynucleotide comprising at least 60 contiguous nucleotides of a polynucleotide of claim 1.

5. A composition for the detection of expression of disease detection and treatment polynucleotides comprising at least one of the polynucleotides of claim 1 and a detectable label.

6. A method for detecting a target polynucleotide in a sample, said target polynucleotide having a sequence of a polynucleotide of claim I, the method comprising:
a) amplifying said target polynucleotide or fragment thereof using polymerase chain reaction amplification, and b) detecting the presence or absence of said amplified target polynucleotide or fragment thereof, and, optionally, if present, the amount thereof.

7. A method for detecting a target polynucleotide in a sample, said target polynucleotide having a sequence of a polynucleotide of claim 1, the method comprising:

a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide or fragments thereof, and b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof.

8. A method of claim 7, wherein the probe comprises at least 30 contiguous nucleotides.

9. A method of claim 7, wherein the probe comprises at least 60 contiguous nucleotides.

10. A recombinant polynucleotide comprising a promoter sequence operably linked to a polynucleotide of claim 1.

11. A cell transformed with a recombinant polynucleotide of claim 10.

12. A transgenic organism comprising a recombinant polynucleotide of claim l0.

13. A method for producing a disease detection and treatment polypeptide encoded by a polynucleotide of claim 1, the method comprising:
a) culturing a cell under conditions suitable for expression of the disease detection and treatment polypeptide, wherein said cell is transformed with a recombinant polynucleotide comprising a promoter sequence operably linked to a polynucleotide of claim 1, and b) recovering the disease detection and treatment polypeptide so expressed.

14. A method of claim 13, wherein the polypeptide has an amino acid sequence selected from the group consisting of SEQ ID NO:253-506.

15. An isolated disease detection and treatment polypeptide (MDDT) encoded by at least one of the polynucleotides of claim 2.

16. A method of screening for a test compound that specifically binds to the polypeptide of claim 15, the method comprising:

a) combining the polypeptide of claim 15 with at least one test compound under suitable conditions, and b) detecting binding of the polypeptide of claim 15 to the test compound, thereby identifying a compound that specifically binds to the polypeptide of claim 15.

17. A microarray wherein at least one element of the microarray is a polynucleotide of claim 3.

18. A method for generating a transcript image of a sample which contains polynucleotides, the method comprising:
a) labeling the polynucleotides of the sample, b contacting the elements of the microarray of claim 17 with the labeled polynucleotides of the sample under conditions suitable for the formation of a hybridization complex, and c) quantifying the expression of the polynucleotides in the sample.

19. A method for screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide sequence of a polynucleotide of claim 1, the method comprising:
a) exposing a sample comprising the target polynucleotide to a compound, under conditions suitable for the expression of the target polynucleotide, b) detecting altered expression of the target polynucleotide, and c) comparing the expression of the target polynucleotide in the presence of varying amounts of the compound and in the absence of the compound.

20. A method for assessing toxicity of a test compound, said method comprising:
a) treating a biological sample containing nucleic acids with the test compound, b) hybridizing the nucleic acids of the treated biological sample with a probe comprising at least 20 contiguous nucleotides of a polynucleotide of claim 1 under conditions whereby a specific hybridization complex is formed between said probe and a target polynucleotide in the biological sample, said target polynucleotide comprising a polynucleotide sequence of a polynucleotide of claim 1 or fragment thereof, c) quantifying the amount of hybridization complex, and d) comparing the amount of hybridization complex in the treated biological sample with the amount of hybridization complex in an untreated biological sample, wherein a difference in the amount of hybridization complex in the treated biological sample is indicative of toxicity of the test compound.

21. An array comprising different nucleotide molecules affixed in distinct physical locations on a solid substrate, wherein at least one of said nucleotide molecules comprises a first oligonucleotide or polynucleotide sequence specifically hybridizable with at least 30 contiguous nucleotides of a target polynucleotide, and wherein said target polynucleotide is a polynucleotide of claim 1.

22. An array of claim 21, wherein said first oligonucleotide or polynucleotide sequence is completely complementary to at least 30 contiguous nucleotides of said target polynucleotide.

23. An array of claim 21, wherein said first oligonucleotide or polynucleotide sequence is completely complementary to at least 60 contiguous nucleotides of said target polynucleotide

24. An array of claim 21, wherein said first oligonucleotide or polynucleotide sequence is completely complementary to said target polynucleotide.

25. An array of claim 21, which is a microarray.

26. An array of claim 21, further comprising said target polynucleotide hybridized to a nucleotide molecule comprising said first oligonucleotide or polynucleotide sequence.

27. An array of claim 21, wherein a linker joins at least one of said nucleotide molecules to said solid substrate.

28. An array of claim 21, wherein each distinct physical location on the substrate contains multiple nucleotide molecules, and the multiple nucleotide molecules at any single distinct physical location have the same sequence, and each distinct physical location on the substrate contains nucleotide molecules having a sequence which differs from the sequence of nucleotide molecules at another distinct physical location on the substrate.

29. An isolated polypeptide selected from the group consisting of:
a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:253-506, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90%

identical to an amino acid sequence selected from the group consisting of SEQ
ID
NO:253-506, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:253-506, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:253-506.

30. An isolated polypeptide of claim 29, having a sequence selected from the group consisting of SEQ ID NO:253-506.

31. An isolated polynucleotide encoding a polypeptide of claim 29.

32. An isolated polynucleotide encoding a polypeptide of claim 30.

33. An isolated polynucleotide of claim 32, having a sequence selected from the group consisting of SEQ ID NO:1-252.

34. An isolated antibody which specifically binds to a disease detection and treatment polypeptide of claim 29.

35. A diagnostic test for a condition or disease associated with the expression of MDDT in a biological sample, the method comprising:
a) combining the biological sample with an antibody of claim 34, under conditions suitable for the antibody to bind the polypeptide and form an antibody:polypeptide complex, and b) detecting the complex, wherein the presence of the complex correlates with the presence of the polypeptide in the biological sample.

36. The antibody of claim 34, wherein the antibody is:
a) a chimeric antibody, b) a single chain antibody, c) a Fab fragment, d) a F(ab')2 fragment, or e) a humanized antibody.

37. A composition comprising an antibody of claim 34 and an acceptable excipient.

38. A method of diagnosing a condition or disease associated with the expression of MDDT
in a subject, comprising administering to said subject an effective amount of the composition of claim 37.

39. A composition of claim 37, wherein the antibody is labeled.

40. A method of diagnosing a condition or disease associated with the expression of MDDT
in a subject, comprising administering to said subject an effective amount of the composition of claim 39.

41. A method of preparing a polyclonal antibody with the specificity of the antibody of claim 34, the method comprising:
a) immunizing an animal with a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:253-506, or an immunogenic fragment thereof, under conditions to elicit an antibody response, b) isolating antibodies from said animal, and c) screening the isolated antibodies with the polypeptide, thereby identifying a polyclonal antibody which binds specifically to a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:253-506.

42. An antibody produced by a method of claim 41.

43. A composition comprising the antibody of claim 42 and a suitable carrier.

44. A method of making a monoclonal antibody with the specificity of the antibody of claim 34, the method comprising:
a) immunizing an animal with a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:253-506, or an immunogenic fragment thereof, under conditions to elicit an antibody response, b) isolating antibody producing cells from the animal, c) fusing the antibody producing cells with immortalized cells to form monoclonal antibody-producing hybridoma cells, d) culturing the hybridoma cells, and e) isolating from the culture monoclonal antibody which binds specifically to a polypeptide having an amino acid sequence selected from the group consisting of SEQ
ID NO:253-506.

45. A monoclonal antibody produced by a method of claim 44.

46. A composition comprising the antibody of claim 45 and a suitable carrier.

47. The antibody of claim 34, wherein the antibody is produced by screening a Fab expression library.

48. The antibody of claim 34, wherein the antibody is produced by screening a recombinant immunoglobulin library.

49. A method of detecting a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:253-506 in a sample, the method comprising:
a) incubating the antibody of claim 34 with a sample under conditions to allow specific binding of the antibody and the polypeptide, and b) detecting specific binding, wherein specific binding indicates the presence of a polypeptide having an amino acid sequence selected from the group consisting of SEQ
ID NO:253-506 in the sample.

50. A method of purifying a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:253-506 from a sample, the method comprising:
a) incubating the antibody of claim 34 with a sample under conditions to allow specific binding of the antibody and the polypeptide, and b) separating the antibody from the sample and obtaining the purified polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:253-506.

51. A composition comprising a polypeptide of claim 29 and a pharmaceutically acceptable excipient.

52. A composition of claim 51, wherein the polypeptide has an amino acid sequence of SEQ
ID NO:253-506.

53. A method for treating a disease or condition associated with decreased expression of functional MDDT, comprising administering to a patient in need of such treatment the composition of claim 51.

54. A method for screening a compound for effectiveness as an agonist of a polypeptide of claim 29, the method comprising:
a) exposing a sample comprising a polypeptide of claim 29 to a compound, and~
b) detecting agonist activity in the sample.

55. A composition comprising an agonist compound identified by a method of claim 54 and a pharmaceutically acceptable excipient.

56. A method for treating a disease or condition associated with decreased expression of functional MDDT, comprising administering to a patient in need of such treatment a composition of claim 55.

57. A method for screening a compound for effectiveness as an antagonist of a polypeptide of claim 29, the method comprising:
a) exposing a sample comprising a polypeptide of claim 29 to a compound, and b) detecting antagonist activity in the sample.

58. A composition comprising an antagonist compound identified by a method of claim 57 and a pharmaceutically acceptable excipient.

59. A method for treating a disease or condition associated with overexpression of functional MDDT, comprising administering to a patient in need of such treatment a composition of claim 58.

60. A method of screening for a compound that modulates the activity of the polypeptide of claim 29, said method comprising:
a) combining the polypeptide of claim 29 with at least one test compound under conditions permissive for the activity of the polypeptide of claim 29;
b) assessing the activity of the polypeptide of claim 29 in the presence of the test compound, and c) comparing the activity of the polypeptide of claim 29 in the presence of the test compound with the activity of the polypeptide of claim 29 in the absence of the test compound, wherein a change in the activity of the polypeptide of claim 29 in the presence of the test compound is indicative of a compound that modulates the activity of the polypeptide of claim 29.