Nucleic Acids Research Advance Access originally published online on November 27, 2006
Nucleic Acids Research 2007 35(Database issue):D104-D109; doi:10.1093/nar/gkl854
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Nucleic Acids Research, 2007, Vol. 35, Database issue D104-D109
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational
1 Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Bio-IT Research Building Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan 2 Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research Building Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan 3 Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan 4 Computational Biology Research Center, National Institute of Advanced Science and Technology, AIST Bio-IT Research Building Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan 5 Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari Kisarazu, Chiba 292-0818, Japan 6 Maze Corporation, TS Building 101 3-20-2 Hatagaya, Shibuya-ku, Tokyo 151-0072, Japan 7 Center for Information Biology and DDBJ, National Institute of Genetics 1111 Yata, Mishima, Shizuoka 411-8540, Japan 8 Graduate School of Information Science and Technology, Hokkaido University North 14, West 9, Kita-ku, Sapporo, Hokkaido 060-0814, Japan
*To whom correspondence should be addressed. Tel: +81 3 3599 8800; Fax: +81 3 3599 8801; Email: imanishi{at}jbirc.aist.go.jp
Received August 15, 2006. Revised October 9, 2006. Accepted October 10, 2006.
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 (AS) 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 (RASVs) in 11 744 loci, in total. The data is retrievable by various features of AS, which were annotated according to manual annotations, such as by patterns of ASs, 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 AS, 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 AS event can be analyzed in the context of full-length cDNAs, enabling the user's empirical understanding of the relation between AS 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/.
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