Skip Navigation

Nucleic Acids Research 2005 33(Database Issue):D80-D85; doi:10.1093/nar/gki129
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (643K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Citing Articles
Right arrowScopus Links
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Huang, H.-D.
Right arrow Articles by Huang, C.-C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Huang, H.-D.
Right arrow Articles by Huang, C.-C.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

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/.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
A. Bhasi, R. V. Pandey, S. P. Utharasamy, and P. Senapathy
EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes
Bioinformatics, July 15, 2007; 23(14): 1815 - 1823.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
V. Shepelev and A. Fedorov
Advances in the Exon-Intron Database (EID)
Brief Bioinform, June 1, 2006; 7(2): 178 - 185.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
L. Florea
Bioinformatics of alternative splicing and its regulation
Brief Bioinform, March 1, 2006; 7(1): 55 - 69.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Stamm, J.-J. Riethoven, V. Le Texier, C. Gopalakrishnan, V. Kumanduri, Y. Tang, N. L. Barbosa-Morais, and T. A. Thanaraj
ASD: a bioinformatics resource on alternative splicing
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D46 - D55.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Holste, G. Huo, V. Tung, and C. B. Burge
HOLLYWOOD: a comparative relational database of alternative splicing
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D56 - D62.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. de la Grange, M. Dutertre, N. Martin, and D. Auboeuf
FAST DB: a website resource for the study of the expression regulation of human gene products
Nucleic Acids Res., July 28, 2005; 33(13): 4276 - 4284.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Y. Galperin
The Molecular Biology Database Collection: 2005 update
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D5 - D24.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.