Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes

Wang, J., Smith, P. J., Krainer, A. R., Zhang, M. Q. (2005) Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res, 33 (16). pp. 5053-62. ISSN 1362-4962 (Electronic)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/16147989
DOI: 10.1093/nar/gki810

Abstract

Exonic splicing enhancers (ESEs) are pre-mRNA cis-acting elements required for splice-site recognition. We previously developed a web-based program called ESEfinder that scores any sequence for the presence of ESE motifs recognized by the human SR proteins SF2/ASF, SRp40, SRp55 and SC35 (http://rulai.cshl.edu/tools/ESE/). Using ESEfinder, we have undertaken a large-scale analysis of ESE motif distribution in human protein-coding genes. Significantly higher frequencies of ESE motifs were observed in constitutive internal protein-coding exons, compared with both their flanking intronic regions and with pseudo exons. Statistical analysis of ESE motif frequency distributions revealed a complex relationship between splice-site strength and increased or decreased frequencies of particular SR protein motifs. Comparison of constitutively and alternatively spliced exons demonstrated slightly weaker splice-site scores, as well as significantly fewer ESE motifs, in the alternatively spliced group. Our results underline the importance of ESE-mediated SR protein function in the process of exon definition, in the context of both constitutive splicing and regulated alternative splicing.

Item Type: Paper
Uncontrolled Keywords: Alternative Splicing Computational Biology Exons Humans Proteins genetics RNA Precursors chemistry RNA Splice Sites RNA Splicing RNA, Messenger chemistry RNA-Binding Proteins metabolism Regulatory Sequences, Ribonucleic Acid Sequence Analysis RNA Software
Subjects: bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > cis-regulatory elements
bioinformatics > genomics and proteomics > computers > computer software
bioinformatics > genomics and proteomics > databases > databases
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > splicing factor
CSHL Authors:
Communities: CSHL labs > Krainer lab
CSHL labs > Zhang lab
Depositing User: CSHL Librarian
Date: 2005
Date Deposited: 21 Dec 2011 16:07
Last Modified: 09 Apr 2014 16:17
PMCID: PMC1201331
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22730

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