Characterization and prediction of alternative splice sites.
Human alternative isoform, cryptic, skipped, and constitutive splice sites from the ALTEXTRON database were analysed regarding splice site strength, composition, GC content, position and binding site strength of polypyrimidine tract and branch site. Several features were identified which distinguish alternative isoform and cryptic splice sites, but not skipped splice sites from constitutive ones. These include splice site strength, introns GC content, U2AF35 binding site score, and oligonucleotide frequencies. For the predictive classification of splice sites, pattern recognition models for different splicing factor binding sites and oligonucleotide frequency models (OFMs) were combined using backpropagation networks. 67.45% of acceptor sites and 71.23% of donor sites are correctly classified by networks trained for classification of constitutive and alternative isoform/cryptic splice sites. A web-application for the prediction of alternative splice sites is available at http://es.embnet.org/~mwang/assp.html .
Wang
Magnus
M
Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avenida de Reina Mercedes 6, E-41012 Sevilla, Spain. mwang@es.embnet.org
Marín
Antonio
A
D017398:Alternative Splicing / Q000235:genetics*; D001665:Binding Sites / Q000235:genetics; D030561:Databases, Nucleic Acid; D006801:Humans; D009687:Nuclear Proteins / Q000235:genetics*; D022821:RNA Splice Sites / Q000235:genetics*; D012261:Ribonucleoproteins / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D000072668:Splicing Factor U2AF
D009687:Nuclear Proteins; D022821:RNA Splice Sites; D012261:Ribonucleoproteins; D000072668:Splicing Factor U2AF; C000607494:U2AF2 protein, human