H-DBAS: human-transcriptome database for alternative splicing: update 2010.
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.
Takeda
Jun-ichi
J
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.
Suzuki
Yutaka
Y
Sakate
Ryuichi
R
Sato
Yoshiharu
Y
Gojobori
Takashi
T
Imanishi
Tadashi
T
Sugano
Sumio
S
D000465:Algorithms; D017398:Alternative Splicing; D002467:Cell Nucleus / Q000378:metabolism; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D003593:Cytoplasm / Q000378:metabolism; D018076:DNA, Complementary / Q000378:metabolism; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D023281:Genomics; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D011132:Polyribosomes / Q000378:metabolism; D012313:RNA / Q000737:chemistry*; D012984:Software
D018076:DNA, Complementary; D012313:RNA