H-DBAS: Human-transcriptome database for alternative splicing: Update 2010

Jun ichi Takeda; Yutaka Suzuki; Ryuichi Sakate; Yoshiharu Sato; Takashi Gojobori; Tadashi Imanishi; Sumio Sugano

doi:10.1093/nar/gkp984

H-DBAS: Human-transcriptome database for alternative splicing: Update 2010

Jun ichi Takeda, Yutaka Suzuki, Ryuichi Sakate, Yoshiharu Sato, Takashi Gojobori, Tadashi Imanishi^*, Sumio Sugano

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

30 Scopus citations

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.

Original language	English (US)
Article number	gkp984
Pages (from-to)	D86-D90
Journal	NUCLEIC ACIDS RESEARCH
Volume	38
Issue number	SUPPL.1
DOIs	https://doi.org/10.1093/nar/gkp984
State	Published - Dec 7 2009
Externally published	Yes

ASJC Scopus subject areas

Genetics

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title = "H-DBAS: Human-transcriptome database for alternative splicing: Update 2010",

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.",

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AU - Takeda, Jun ichi

AU - Suzuki, Yutaka

AU - Sakate, Ryuichi

AU - Sato, Yoshiharu

AU - Gojobori, Takashi

AU - Imanishi, Tadashi

AU - Sugano, Sumio

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H-DBAS: Human-transcriptome database for alternative splicing: Update 2010

Abstract

ASJC Scopus subject areas

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