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. 2010 Jan;38(Database issue):D86-90.
doi: 10.1093/nar/gkp984. Epub 2009 Dec 7.

H-DBAS: Human-Transcriptome Database for Alternative Splicing: Update 2010

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Free PMC article

H-DBAS: Human-Transcriptome Database for Alternative Splicing: Update 2010

Jun-ichi Takeda et al. Nucleic Acids Res. .
Free PMC article

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.

Figures

Figure 1.
Figure 1.
Screenshot of RNA-Seq viewer. Genomic regions in caspase 4, an apoptosis-related cysteine peptidase (CASP4) and the estimated junctions with the two or more supporting RNA-Seq tags mapped to the corresponding genomic regions. (A) AS variants of RefSeq are represented. Annotated protein-coding regions and untranslated regions are indicated by green and yellow boxes, respectively. (B) Junctions estimated by the mapped RNA-Seq tags derived from cytoplasmic, nuclear and polysome cellular fractions are shown in cyan, navy and brown, respectively. If the AS junction of RefSeq transcript is expressed in unique sub-cellular fraction (nuclear in this figure), it is shown in red. The gray boxes indicate the assembled exonic regions of RefSeq transcripts. (C) RNA-Seq tags which support the junction are represented. Two or more RNA-Seq tags mapped on the splice sites are shown by each sub-cellular fraction. The represented colors are the same as (B).
Figure 2.
Figure 2.
Screenshot of comparative genomic viewer. AS variants in the phosphatidylinositol 3-kinase regulatory subunit alpha (PI3-kinase p85 subunit alpha) gene are shown both in humans and mice. The exon structures of the human AS variants and the mouse full-length cDNAs are shown in the upper and lower panels, respectively, across the human–mouse genome alignment. In this view option (Exon view), constitutively spliced introns of the transcripts are omitted. Mutually equally spliced variants in humans and mice are indicated by blue and orange arrows, respectively.

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