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H-DBAS


NAR Molecular Biology Database Collection entry number 970
Takeda J.1,2, Suzuki Y.3, Nakao M.4,5, Kuroda T.6, Sugano S.3, Gojobori T.2,7 and Imanishi T.2,8
1Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Bio-IT Research Bldg., Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan
2Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research Bldg., Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan
3Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
4Computational Biology Research Center, National Institute of Advanced Science and Technology, AIST Bio-IT Research Bldg., Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan
5Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
6Maze Corporation, TS Bldg. 101, 3-20-2 Hatagaya, Shibuya-ku, Tokyo 151-0072, Japan
7Center for Information Biology and DDBJ, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
8Graduate School of Information Science and Technology, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, Hokkaido 060-0814, Japan

Database Description

The Human-transcriptome DataBase for Alternative Splicing (H-DBAS) is a specialized database of alternatively spliced human transcripts. In this database, each of the alternative splicing variants corresponds to a completely sequenced and carefully annotated human full-length cDNA, one of those collected for the H-Invitational human transcriptome annotation meeting. H-DBAS contains 38 664 representative alternative splicing variants in 11 744 loci, in total. The data is retrievable by various features of alternative splicing, which were annotated according to manual annotations, such as by patterns of alternative splicings, consequently invoked alternations in the encoded amino acids and affected protein motifs, GO terms, predicted subcellular localization signals and transmembrane domains. The database also records recently identified very complex patterns of alternative splicing, in which two distinct genes seemed to be bridged, nested or degenerated (multiple CDS): in all three cases, completely unrelated proteins are encoded by a single locus. By using AS Viewer, each alternative splicing event can be analyzed in the context of full-length cDNAs, enabling the user’s empirical understanding of the relation between alternative splicing event and the consequent alternations in the encoded amino acid sequences together with various kinds of affected protein motifs. H-DBAS is accessible at http://jbirc.jbic.or.jp/h-dbas/.

Acknowledgements

H-DBAS was financially supported by the Ministry of Economy, Trade and Industry of Japan (METI), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Biological Informatics Consortium (JBIC). Funding to pay the Open Access publication charges for this article was provided by JBIC.

References

1. Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan, C., Fukuchi, S., Koyanagi, K.O., Barrero, R.A., Tamura, T., Yamaguchi-Kabata, Y., Tanino, M. et al. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol, 2, e162.
2. Takeda, J., Suzuki, Y., Nakao, M., Barrero, R.A., Koyanagi, K.O., Jin, L., Motono, C., Hata, H., Isogai, T., Nagai, K. et al. (2006) Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Res, 34, 3917-3928.


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