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    Nucleic Acids Res. 2010 Jan;38(Database issue):D86-90. Epub 2009 Dec 7.

    H-DBAS: human-transcriptome database for alternative splicing: update 2010.

    Takeda J, Suzuki Y, Sakate R, Sato Y, Gojobori T, Imanishi T, Sugano S.

    Source

    Integrated Database and Systems Biology Team, Biomedicinal Information Research Center National Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research Bldg Aomi 2-4-7, Koto-ku, Tokyo 135-0064, Japan.

    Abstract

    H-DBAS (http://h-invitational.jp/h-dbas/) is a specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. In this update, for better annotations of AS events, we correlated RNA-Seq tag information to the AS exons and splice junctions. We generated a total of 148,376,598 RNA-Seq tags from RNAs extracted from cytoplasmic, nuclear and polysome fractions. Analysis of the RNA-Seq tags allowed us to identify 90,900 exons that are very likely to be used for protein synthesis. On the other hand, 254 AS junctions of human RefSeq transcripts are unique to nuclear RNA and may not have any translational consequences. We also present a new comparative genomics viewer so that users can empirically understand the evolutionary turnover of AS. With the unique experimental data closely connected with intensively curated cDNA information, H-DBAS provides a unique platform for the analysis of complex AS.

    PMID:
    19969536
    [PubMed - indexed for MEDLINE]
    PMCID:
    PMC2808982
    Free PMC Article

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