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PMID: 15289480 Published · ppublish English Comparative Study Journal Article Validation Study

A non-EST-based method for exon-skipping prediction.

Genome research ·Vol. 14 ·No. 8 ·2004-08-00 ·Pages 1617-23

Sorek R, Shemesh R, Cohen Y, Basechess O, Ast G, Shamir R

Abstract

It is estimated that between 35% and 74% of all human genes can undergo alternative splicing. Currently, the most efficient methods for large-scale detection of alternative splicing use expressed sequence tags (ESTs) or microarray analysis. As these methods merely sample the transcriptome, splice variants that do not appear in deeply sampled tissues have a low probability of being detected. We present a new method by which we can predict that an internal exon is skipped (namely whether it is a cassette-exon) merely based on its naked genomic sequence and on the sequence of its mouse ortholog. No other data, such as ESTs, are required for the prediction. Using our method, which was experimentally validated, we detected hundreds of novel splice variants that were not detectable using ESTs. We show that a substantial fraction of the splice variants in the human genome could not be identified through current human EST or cDNA data.

MeSH Terms
Alternative Splicing Animals Computational Biology/methods Databases, Nucleic Acid Exons Expressed Sequence Tags Genome, Human Humans Introns Mice Models, Genetic RNA, Messenger/genetics
Chemicals
RNA, Messenger
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Sorek Rotem
Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel. rotem@compugen.co.il
Shemesh Ronen
Cohen Yuval
Basechess Ortal
Ast Gil
Shamir Ron
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.2572604
Email
rotem@compugen.co.il
Published
2004-08-00
Pages
1617-23
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC509271
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.2572604 PMC Full Text View journal details
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