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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Databases, Nucleic Acid

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Disease relevance of Databases, Nucleic Acid

  • We analyzed the structure of antigen receptors of a comprehensive panel of mature B non-Hodgkin's lymphomas (B-NHLs) by comparing, at the amino acid level, their immunoglobulin (Ig)V(H)-CDR3s with CDR3 sequences present in GenBank [1].
  • A GenBank search found that it is identical to a recently cloned gene, differentiation-related gene-1 (Drg-1), isolated from differentiated HT-29 colon cancer cells [2].
  • Human and mouse cDNAs showing homology to the Clostridium perfringens enterotoxin (CPE) receptor gene (CPE-R) from Vero cells (DDBJ/EMBL/GenBankTM accession no. D88492) (Katahira, J., Inoue, N., Horiguchi, Y., Matsuda, M., and Sugimoto, N. (1997) J. Cell Biol. 136, 1239-1247) were cloned [3].
  • We have compiled the DNA sequence data for Escherichia coli K12 available from the GenBank and EMBL data libraries and independently from the literature [4].
  • Both known and novel AEGs, not reported in current DNA databases, are described that display early or late expression kinetics following HIV-1 infection or treatment with recombinant HIV-1 envelope glycoprotein (gp120) [5].

High impact information on Databases, Nucleic Acid

  • The two cloned FA genes, FAA and FAC, encode proteins that are unrelated to each other or to other proteins in GenBank [6].
  • We have now determined the complete coding sequence and exonic structure of BRCA2 (GenBank accession #U43746), and examined its pattern of expression [7].
  • This patient expresses a "compound heterozygous" genotype, with a point mutation (C877T in cDNA) and a two-nucleotide, AC deletion (620-621del in cDNA) encoded by distinct alleles of the IRAK-4 gene (GenBank/EMBL/DDBJ accession nos. AF445802 and AY186092) [8].
  • Recently, a novel CC chemokine known as MIP-3alpha or liver and activation-regulated chemokine has been identified from the EMBL/GenBank/DDBJ expressed sequence tag database [9].
  • ICA69 shows no nucleotide or amino acid sequence relation to any known sequence in GenBank, except for two short regions of similarity with BSA [10].

Chemical compound and disease context of Databases, Nucleic Acid

  • The term low-temperature-specific (LTS) is used because tacr7 is not induced by ABA or stresses such as salt, dehydration, and heat. pTACR7 was isolated by RT-PCR with mRNA from wheat crown tissue, the oligonucleotide primers derived from the barley cognate pHVCR8 (GenBank accession number L28091) [11].
  • A novel gene, designated ohb1, which encodes the oxygen-sensitive and biotin-, ATP-, thiamin-, pyridoxal phosphate-, and metal-ion-independent, reversible 4-hydroxybenzoate decarboxylase (4-HOB-DC) from the obligate anaerobe Clostridium hydroxybenzoicum JW/Z-1(T) was sequenced (GenBank accession no. AF128880) and expressed [12].
  • This report describes the mutational analysis of the amino acids involved in both the ATP and L-methionine binding sites of Leishmania donovani MAT (GenBank accession number AF179714) the aetiological agent of visceral leishmaniasis [13].
  • The 16S rRNA sequences of 128 valid and invalid Pseudomonas species, which included almost valid species of the genus Pseudomonas listed in the Approved Lists of Bacterial Names, were obtained: sequences of 59 species were determined and those of 69 species were obtained from the GenBank/EMBL/DDBJ databases [14].
  • It is a selection of 3976 entries from the Prokaryotes section of the EMBL Nucleotide Sequence Database, Release 66, and 375 entries from the Pseudomonas Community Annotation Project (PseudoCAP) [15].

Biological context of Databases, Nucleic Acid


Anatomical context of Databases, Nucleic Acid

  • We report the isolation of a cDNA, FrzA (frizzled in aorta; GenBank accession No. U85945), from bovine aortic endothelium [21].
  • We have cloned human brain and testis Sec31B protein (also known as secretory pathway component Sec31B-1 or SEC31-like 2; GenBank accession number AF274863) [22].
  • To explore the functional properties of the two alleles, a full-length cDNA encoding the beta subunit, a key functional component of the GABA receptor, was isolated from Caenorhabditis elegans (gab-1, corresponding to the GenBank locus ZC482.1) and coexpressed in Xenopus oocytes with the HG1 alleles [23].
  • Four splice forms of Kirrel2 were observed, including two that we cloned from pancreas mRNA as well as two GenBank entries, one from the brain and one from a retinoblastoma cell line [24].
  • This gene is expressed predominantly in thymocytes and encodes a newly identified intracytoplasmic protein specific for T cells, since neither the nucleotide sequence of the cDNA clone nor the deduced amino acid sequence has significant homology to sequences in the GenBank or NBRF databases [25].

Associations of Databases, Nucleic Acid with chemical compounds

  • Search of the GenBank data base with the deduced translation product revealed 42% identity and 65% similarity with 5-epi-aristolochene synthase from tobacco and 31% identity and 53% similarity with limonene synthase from spearmint [26].
  • We have identified a cytosine to thymidine transition at nucleotide 862 (GenBank accession no. S79895) of the cathepsin K coding sequence in the DNA of an affected individual from a large, consanguinous Mexican family [27].
  • The cDNA [2,395 bp plus additional poly(A) residues] contained an open reading frame from an initiator methionine at nucleotide 240 to an opal stop codon at nucleotide 1,286 (GenBank accession number UO7559), encoding a predicted protein of 349 amino acids (39 kDa) [28].
  • Probing of the GenBank expressed sequence tag (EST) data base with varied human tryptase cDNAs identified two truncated ESTs that subsequently were found to encode overlapping portions of a novel human serine protease (designated tryptase epsilon or protease, serine S1 family member 22 (PRSS22)) [29].
  • The sequence of the first 16 NH2-terminal amino acids and a GenBank search revealed that ABP is a novel protein [30].

Gene context of Databases, Nucleic Acid

  • Using these PAC clones in a cDNA selection experiment, we have isolated a Sau3A fragment homologous to the WWOX transcript (GenBank accession no. ) from normal human ovarian surface epithelial (HOSE) cells [31].
  • Surprisingly, comparison with sequences in the GenBank data base showed that the product of MAP2 has even greater homology (55% identity) with rat p67, which was characterized as an initiation factor 2-associated protein but not yet shown to have Met-AP activity [32].
  • By using the SOCS box amino acid sequence consensus, we have searched DNA databases and have identified a further 16 proteins that contain this motif [33].
  • Nucleotide sequencing of ROM7 revealed that it is identical to the BEM4 gene (GenBank accession number L27816), although its physiological function has not yet been reported [34].
  • No sequences related to REC102 have been found in the GenBank or EMBL collections [35].

Analytical, diagnostic and therapeutic context of Databases, Nucleic Acid

  • Sequence analysis of the modA gene (GenBank L34009) predicts that it encodes a periplasmic binding protein based on the presence of a leader-like sequence at its N terminus [36].
  • Sequence alignments of CPTI with the acyltransferase family of enzymes in the GenBank led to the identification of a putative catalytic triad in CPTI consisting of residues Cys-305, Asp-454, and His-473 [37].
  • Long PCR revealed a complex mutation, g.12977 ins10 del1039 (based on GenBank L78833), comprising an inverted duplication and deletion in BRCA1 that removes portions of exon 3 and intron 3, including the 5' splice site for intron 3 [38].
  • We developed a rat line showing small eye from transgenic rats that were obtained by microinjection of a DNA segment containing the human (h)tau cDNA (GenBank: BC000558: 31-677,774-1180) expressed under control of CAG promoter, which is related to Alzheimer disease, into the pronuclei rat embryos [39].
  • By Northern blot hybridization, cathepsin B and clone #7 (GenBank accession #AF106623) genes were confirmed to be overexpressed in the SHR thymus [40].


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  6. The Fanconi anaemia proteins, FAA and FAC, interact to form a nuclear complex. Kupfer, G.M., Näf, D., Suliman, A., Pulsipher, M., D'Andrea, A.D. Nat. Genet. (1997) [Pubmed]
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  12. Cloning, characterization, and expression of a novel gene encoding a reversible 4-hydroxybenzoate decarboxylase from Clostridium hydroxybenzoicum. Huang, J., He, Z., Wiegel, J. J. Bacteriol. (1999) [Pubmed]
  13. Mutational analysis of methionine adenosyltransferase from Leishmania donovani. Pérez-Pertejo, Y., Reguera, R.M., García-Estrada, C., Balaña-Fouce, R., Ordóñez, D. Eur. J. Biochem. (2004) [Pubmed]
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  16. Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Seki, M., Narusaka, M., Abe, H., Kasuga, M., Yamaguchi-Shinozaki, K., Carninci, P., Hayashizaki, Y., Shinozaki, K. Plant Cell (2001) [Pubmed]
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  19. Identification of drm, a novel gene whose expression is suppressed in transformed cells and which can inhibit growth of normal but not transformed cells in culture. Topol, L.Z., Marx, M., Laugier, D., Bogdanova, N.N., Boubnov, N.V., Clausen, P.A., Calothy, G., Blair, D.G. Mol. Cell. Biol. (1997) [Pubmed]
  20. Mutations in PEX10 is the cause of Zellweger peroxisome deficiency syndrome of complementation group B. Okumoto, K., Itoh, R., Shimozawa, N., Suzuki, Y., Tamura, S., Kondo, N., Fujiki, Y. Hum. Mol. Genet. (1998) [Pubmed]
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  22. Human Sec31B: a family of new mammalian orthologues of yeast Sec31p that associate with the COPII coat. Stankewich, M.C., Stabach, P.R., Morrow, J.S. J. Cell. Sci. (2006) [Pubmed]
  23. Study of the nematode putative GABA type-A receptor subunits: evidence for modulation by ivermectin. Feng, X.P., Hayashi, J., Beech, R.N., Prichard, R.K. J. Neurochem. (2002) [Pubmed]
  24. Kirrel2, a novel immunoglobulin superfamily gene expressed primarily in beta cells of the pancreatic islets. Sun, C., Kilburn, D., Lukashin, A., Crowell, T., Gardner, H., Brundiers, R., Diefenbach, B., Carulli, J.P. Genomics (2003) [Pubmed]
  25. Isolation of a T cell specific cDNA clone possibly involved in the T cell activation pathway. Takihara, Y., Caccia, N., Yangai, Y., Mak, T.W. Int. Immunol. (1989) [Pubmed]
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  30. Isolation, purification, and characterization of an Amadori product binding protein from a Pseudomonas sp. soil strain. Gerhardinger, C., Taneda, S., Marion, M.S., Monnier, V.M. J. Biol. Chem. (1994) [Pubmed]
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  33. Twenty proteins containing a C-terminal SOCS box form five structural classes. Hilton, D.J., Richardson, R.T., Alexander, W.S., Viney, E.M., Willson, T.A., Sprigg, N.S., Starr, R., Nicholson, S.E., Metcalf, D., Nicola, N.A. Proc. Natl. Acad. Sci. U.S.A. (1998) [Pubmed]
  34. ROM7/BEM4 encodes a novel protein that interacts with the Rho1p small GTP-binding protein in Saccharomyces cerevisiae. Hirano, H., Tanaka, K., Ozaki, K., Imamura, H., Kohno, H., Hihara, T., Kameyama, T., Hotta, K., Arisawa, M., Watanabe, T., Qadota, H., Ohya, Y., Takai, Y. Mol. Cell. Biol. (1996) [Pubmed]
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  39. Small eye phenotypes observed in a human tau gene transgenic rat. Goto, K., Yasuda, M., Sugawara, A., Kuramochi, T., Itoh, T., Azuma, N., Ito, M. Curr. Eye Res. (2006) [Pubmed]
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