Gene databases

Enzyme and Gene Databases, Bioinformatics and the Search for New Enzymes... 

Akagi K., Suzuki T., Stephens R.M., Jenkins N.A. and Gopeland N.G. (2004) RTGGD retroviral tagged cancer gene database. Nucleic Acids Research 32, D523 527. 

Additional dysbindin-1 isoforms are likely to exist. As discussed in Section 2.2.6.1.2, there are many known and proposed transcripts of the DTNBP1 gene in humans. In addition to those encoding dysbindin-lA, -IB, and -1C, there are five for which we know the complete exon coding sequence that would encode both a CCD and a DD. They are transcripts b, c, f, g, and h in the nomenclature of the NCBI gene database Ace View. The proteins encoded by these transcripts are predicted to be 338, 334, 219, 212, and 208 aa in length. In our nomenclature, they would be dysbindin-1 isoforms D, E, F, G, and H, respectively. In the human dorsolateral prefrontal cortex, mRNA for dysbindin-lA, -IB, -1C, and -IE has been found (i.e., Ace View human DTNBP1 transcripts a, d, e, and c, respectively R. Straub, personal communication). 

Apart from SNP analyses, there is still a paucity of published information on the gene encoding dysbindin-1 and on its transcripts. Much of the information below derives instead from bioinformatic sources, especially the NCBI gene database Ace View (http //www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html) and to a lesser extent ECgene (http //genome.ewha.ac.kr/ECgene). 

Other putative CKX genes and gene fragments have been found in gene databases of phytopathogenic bacteria, such as Streptomyces spp. [99] causing potato scab, Legionella pneumophila and cyanobacterium Anahaena variabilis (Frebortova, unpublished). 

Beroud C, Soussi T. APC gene database of germline and somatic mutations in human tumors and cell lines. Nucleic Acids Res 1996 24 121-4. 

Together with primary gene databases, the study of gene functions needs the integration of sequence data with expression data. There are multiple resources that provide this type of combined data. We mention and describe here two useful resources GATExplorer and ProteinAtlas. GATExplorer... 

Liu B, Pop M. ARDB-antibiotie resistance genes database. Nucl Acids Res. 2009 37 D443 7. doi 10.1093/nar/gkn656. 

Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project improved data processing and web-based tools. Nucl Acids Res. 2013 41 D590-6. doi 10.1093/nar/ gksl219. 

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