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Nucleic Acids Research 2005 33(Database Issue):D80-D85; doi:10.1093/nar/gki129
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Nucleic Acids Research, 2005, Vol. 33, Database issue D80-D85
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

SpliceInfo: an information repository for mRNA alternative splicing in human genome

Hsien-Da Huang, Jorng-Tzong Horng1,2,*, Feng-Mao Lin1, Yu-Chung Chang3 and Chen-Chia Huang1

Department of Biological Science and Technology, Institute of Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan, 1 Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan, 2 Department of Life Science, National Central University, Chung-Li 320, Taiwan and 3 Department of Biotechnology, Ming Chuan University, Taoyuan 333, Taiwan

* To whom correspondence should be addressed. Tel: +886 3 4227151 (Ext. 34307); Fax: +886 3 4222681; Email: horng{at}db.csie.ncu.edu.tw

Received August 15, 2004; Revised and Accepted October 25, 2004

We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5'-alternative splicing, 3'-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein sequences available for a given gene for evidence of AS. Additional features such as the tissue specificity of the mRNA, the protein domain contained by exons, the GC-ratio of exons, the repeats contained within the exons, and the Gene Ontology are annotated computationally for each exonic region that is alternatively spliced. Motivated by a previous investigation of AS-related motifs such as exonic splicing enhancer and exonic splicing silencer, this resource also provides a means of identifying motifs candidates and this should help to identify potential regulatory mechanisms within a particular exonic sequence set and its two flanking intronic sequence sets. This is carried out using motif discovery tools to identify motif candidates related to alternative splicing regulation and together with a secondary structure prediction tool, will help in the identification of the structural properties of such regulatory motifs. The integrated resource is now available on http://SpliceInfo.mbc.NCTU.edu.tw/.

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