publication . Article . Review . 2009

Human Splicing Finder: an online bioinformatics tool to predict splicing signals

Desmet, F.-O.; Hamroun, D.; Lalande, M.; Collod-Beroud, G.; Claustres, M.; Beroud, C.;
Open Access English
  • Published: 01 May 2009 Journal: NUCLEIC ACIDS RESEARCH, volume 37, issue 9, pages e67-e67 (issn: 0305-1048, eissn: 1362-4962, Copyright policy)
  • Publisher: OXFORD UNIV PRESS
International audience; Thousands of mutations are identified yearly. Although many directly affect protein expression, an increasing proportion of mutations is now believed to influence mRNA splicing. They mostly affect existing splice sites, but synonymous, non-synonymous or nonsense mutations can also create or disrupt splice sites or auxiliary cis-splicing sequences. To facilitate the analysis of the different mutations, we designed Human Splicing Finder (HSF), a tool to predict the effects of mutations on splicing signals or to identify splicing motifs in any human sequence. It contains all available matrices for auxiliary sequence prediction as well as new...
free text keywords: Methods Online, [SDV.GEN]Life Sciences [q-bio]/Genetics
Related Organizations
Funded by
Genotype-To-Phenotype Databases: A Holistic Solution
  • Funder: European Commission (EC)
  • Project Code: 200754
  • Funding stream: FP7 | SP1 | HEALTH
103 references, page 1 of 7

1. Berget,S.M., Moore,C. and Sharp,P.A. (1977) Spliced segments at the 50 terminus of adenovirus 2 late mRNA. Proc. Natl Acad. Sci. USA, 74, 3171-3175. [OpenAIRE]

2. Nilsen,T.W. (2003) The spliceosome: the most complex macromolecular machine in the cell? Bioessays, 25, 1147-1149.

3. Zhou,Z., Licklider,L.J., Gygi,S.P. and Reed,R. (2002) Comprehensive proteomic analysis of the human spliceosome. Nature, 419, 182-185.

4. Breitbart,R.E., Nguyen,H.T., Medford,R.M., Destree,A.T., Mahdavi,V. and Nadal-Ginard,B. (1985) Intricate combinatorial patterns of exon splicing generate multiple regulated troponin T isoforms from a single gene. Cell, 41, 67-82.

5. Maniatis,T. and Tasic,B. (2002) Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature, 418, 236-243.

6. Cartegni,L., Chew,S.L. and Krainer,A.R. (2002) Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat. Rev. Genet., 3, 285-298.

7. Robberson,B.L., Cote,G.J. and Berget,S.M. (1990) Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol. Cell Biol., 10, 84-94. [OpenAIRE]

8. Jacob,M. and Gallinaro,H. (1989) The 50 splice site: phylogenetic evolution and variable geometry of association with U1RNA. Nucleic Acids Res., 17, 2159-2180.

9. Blencowe,B.J. (2000) Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends Biochem Sci., 25, 106-110.

10. Zhu,J., Mayeda,A. and Krainer,A.R. (2001) Exon identity established through differential antagonism between exonic splicing silencer-bound hnRNP A1 and enhancer-bound SR proteins. Mol. Cell, 8, 1351-1361.

11. Zhang,X.H., Leslie,C.S. and Chasin,L.A. (2005) Computational searches for splicing signals. Methods, 37, 292-305.

12. Bhasi,A., Pandey,R.V., Utharasamy,S.P. and Senapathy,P. (2007) EuSplice: A unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes. Bioinformatics, 23, 1815-1823.

13. Churbanov,A., Rogozin,I.B., Deogun,J.S. and Ali,H. (2006) Method of predicting splice sites based on signal interactions. Biol. Direct., 1, 10.

14. Dunckley,M.G., Manoharan,M., Villiet,P., Eperon,I.C. and Dickson,G. (1998) Modification of splicing in the dystrophin gene in cultured Mdx muscle cells by antisense oligoribonucleotides. Hum. Mol. Genet., 7, 1083-1090.

15. Wilton,S.D. and Fletcher,S. (2005) RNA splicing manipulation: strategies to modify gene expression for a variety of therapeutic outcomes. Curr. Gene. Ther., 5, 467-483.

103 references, page 1 of 7
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publication . Article . Review . 2009

Human Splicing Finder: an online bioinformatics tool to predict splicing signals

Desmet, F.-O.; Hamroun, D.; Lalande, M.; Collod-Beroud, G.; Claustres, M.; Beroud, C.;