H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-invitational

Jun Ichi Takeda; Yutaka Suzuki; Mitsuteru Nakao; Tsuyoshi Kuroda; Sumio Sugano; Takashi Gojobori; Tadashi Imanishi

doi:10.1093/nar/gkl854

H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-invitational

Jun Ichi Takeda, Yutaka Suzuki, Mitsuteru Nakao, Tsuyoshi Kuroda, Sumio Sugano, Takashi Gojobori, Tadashi Imanishi^*

^*Corresponding author for this work

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

36 Scopus citations

Abstract

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/.

Original language	English (US)
Pages (from-to)	D104-D109
Journal	NUCLEIC ACIDS RESEARCH
Volume	35
Issue number	SUPPL. 1
DOIs	https://doi.org/10.1093/nar/gkl854
State	Published - Jan 2007
Externally published	Yes

Bibliographical note

Funding Information:
We thank Y. Fujii, Y. Sato, T. Habara, H. Nakaoka, F. Todokoro, Y. Imamizu, M. Ogawa and C. Yamasaki for genome mapping, ORF prediction and functional annotation of the H-Invitational cDNA dataset. We are grateful to C.Gough for critical reading of the manuscript. This research was financially supported by the Ministry of Economy, Trade and Industry of Japan (METI), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Biological Informatics Consortium (JBIC). Funding to pay the Open Access publication charges for this article was provided by JBIC.

ASJC Scopus subject areas

Genetics

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@article{bc2db524832844fa82c012fc38030f08,

title = "H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-invitational",

abstract = "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/.",

author = "Takeda, {Jun Ichi} and Yutaka Suzuki and Mitsuteru Nakao and Tsuyoshi Kuroda and Sumio Sugano and Takashi Gojobori and Tadashi Imanishi",

note = "Funding Information: We thank Y. Fujii, Y. Sato, T. Habara, H. Nakaoka, F. Todokoro, Y. Imamizu, M. Ogawa and C. Yamasaki for genome mapping, ORF prediction and functional annotation of the H-Invitational cDNA dataset. We are grateful to C.Gough for critical reading of the manuscript. This research was financially supported by the Ministry of Economy, Trade and Industry of Japan (METI), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Biological Informatics Consortium (JBIC). Funding to pay the Open Access publication charges for this article was provided by JBIC.",

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AU - Takeda, Jun Ichi

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AU - Kuroda, Tsuyoshi

AU - Sugano, Sumio

AU - Gojobori, Takashi

AU - Imanishi, Tadashi

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ER -

H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-invitational

Abstract

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