Dual-specificity splice sites function alternatively as 5 ' and 3 ' splice sites

Zhang, C. L., Hastings, M. L., Krainer, A. R., Zhang, M. Q. (September 2007) Dual-specificity splice sites function alternatively as 5 ' and 3 ' splice sites. Proceedings of the National Academy of Sciences of the United States of America, 104 (38). pp. 15028-15033. ISSN 0027-8424

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URL: http://www.ncbi.nlm.nih.gov/pubmed/17848517
DOI: 10.1073/pnas.0703773104

Abstract

As a result of large-scale sequencing projects and recent splicing-microarray studies, estimates of mammalian genes expressing multiple transcripts continue to increase. This expansion of transcript information makes it possible to better characterize alternative splicing events and gain insights into splicing mechanisms and regulation. Here, we describe a class of splice sites that we call dual-specificity splice sites, which we identified through genome-wide, high-quality alignment of mRNA/EST and genome sequences and experimentally verified by RT-PCR. These splice sites can be alternatively recognized as either 5' or 3' splice sites, and the dual splicing is conceptually similar to a pair of mutually exclusive exons separated by a zero-length intron. The dual-splice-site sequences are essentially a composite of canonical 5' and 3' splice-site consensus sequences, with a CAG\GURAG core. The relative use of a dual site as a 5' or 3' splice site can be accurately predicted by assuming competition for specific binding between spliceosomal components involved in recognition of 5' and 3' splice sites, respectively. Dual-specificity splice sites exist in human and mouse, and possibly in other vertebrate species, although most sites are not conserved, suggesting that their origin is recent. We discuss the implications of this unusual splicing pattern for the diverse mechanisms of exon recognition and for gene evolution.

Item Type: Paper
Uncontrolled Keywords: alternative splicing competition mRNA/EST HUMAN GENOME MOUSE TRANSCRIPTS MECHANISMS NONSENSE SEQUENCE INTRONS GENE
Subjects: bioinformatics > quantitative biology
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > computers > computer software
organism description > animal > mammal > rodent > mouse
CSHL Authors:
Communities: CSHL labs > Krainer lab
CSHL labs > Zhang lab
Depositing User: CSHL Librarian
Date: September 2007
Date Deposited: 30 Aug 2011 13:25
Last Modified: 31 Mar 2014 20:58
PMCID: PMC1986607
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15292

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