A sequence compilation and comparison of exons that are alternatively spliced in neurons

Stamm, S., Zhang, M. Q., Marr, T. G., Helfman, D. M. (1994) A sequence compilation and comparison of exons that are alternatively spliced in neurons. Nucleic Acids Res, 22 (9). pp. 1515-26. ISSN 0305-1048 (Print)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/8202349
DOI: 10.1093/nar/22.9.1515

Abstract

Alternative splicing is an important regulatory mechanism to create protein diversity. In order to elucidate possible regulatory elements common to neuron specific exons, we created and statistically analysed a database of exons that are alternatively spliced in neurons. The splice site comparison of alternatively and constitutively spliced exons reveals that some, but not all alternatively spliced exons have splice sites deviating from the consensus sequence, implying diverse patterns of regulation. The deviation from the consensus is most evident at the -3 position of the 3' splice site and the +4 and -3 position of the 5' splice site. The nucleotide composition of alternatively and constitutively spliced exons is different, with alternatively spliced exons being more AU rich. We performed overlapping k-tuple analysis to identify common motifs. We found that alternatively and constitutively spliced exons differ in the frequency of several trinucleotides that cannot be explained by the amino acid composition and may be important for splicing regulation.

Item Type: Paper
Uncontrolled Keywords: Alternative Splicing Animals Base Sequence Comparative Study Dna Exons Information Systems Molecular Sequence Data Neurons/ metabolism Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > Alternative Splicing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > exons > exon splicing
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons
CSHL Authors:
Communities: CSHL labs > Helfman lab
Depositing User: Matt Covey
Date Deposited: 01 May 2015 19:51
Last Modified: 08 Nov 2017 16:03
PMCID: PMC308024
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31470

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