An alternative-exon database and its statistical analysis

Stamm, S., Zhu, J., Nakai, K., Stoilov, P., Stoss, O., Zhang, M. Q. (December 2000) An alternative-exon database and its statistical analysis. DNA and Cell Biology, 19 (12). pp. 739-756. ISSN 1044-5498

URL: http://www.ncbi.nlm.nih.gov/pubmed/11177572

Abstract

We compiled a comprehensive database of alternative exons from the literature and analyzed them statistically, Most alternative exons are cassette exons and are expressed in more than two tissues. Of all exons whose expression was reported to be specific for a certain tissue, the majority were expressed in the brain. Whereas the length of constitutive exons follows a normal distribution, the distribution of alternative exons is skewed toward smaller ones. Furthermore, alternative-exon splice sites deviate more from the consensus: their 3' splice sites are characterized by a higher purine content in the polypyrimidine stretch, and their 5' splice sites deviate from the consensus sequence mostly at the +4 and +5 positions. Furthermore, for exons expressed in a single tissue, adenosine is more frequently used at the -3 position of the 3' splice site, In addition to the known AC-rich and purine-rich exonic sequence elements, sequence comparison using a Gibbs algorithm identified several moths in exons surrounded by weak splice sites and in tissue-specific exons, Together, these data indicate a combinatorial effect of weak splice sites, atypical nucleotide usage at certain positions, and functional enhancers as an important contribution to alternative-exon regulation.

Item Type: Paper
Uncontrolled Keywords: PRE-MESSENGER-RNA SPLICE-SITE SELECTION SR PROTEINS IN-VIVO HUMAN GENES ENHANCER RECOGNITION SEQUENCES IDENTIFICATION TRANSCRIPTION
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > databases
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > exons > exon splicing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > exons
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > pre-mRNA
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: Matt Covey
Date: December 2000
Date Deposited: 31 Jan 2014 20:35
Last Modified: 31 Jan 2014 20:35
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29349

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