Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence

Background: Alternative splicing of pre-mature RNA is an important process eukaryotes utilize to increase their repertoire of different protein products. Several types of different alternative splice forms exist including exon skipping, differential splicing of exons at their 3’- or 5’-end, intron retention, and mutually exclusive splicing. The latter term is used for clusters of internal exons that are spliced in a mutually exclusive manner. Results: We have implemented an extension to the WebScipio software to search for mutually exclusive exons. Here, the search is based on the precondition that mutually exclusive exons encode regions of the same structural part of the protein product. This precondition provides restrictions to the search for candidate exons concerning their length, splice site conservation and reading frame preservation, and overall homology. Mutually exclusive exons that are not homologous and not of about the same length will not be found. Using the new algo...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Holger Pillmann, Klas Hatje, Florian Odronitz, Bjorn Hammesfahr, Martin Kollmar
• Keywords: Ab Initio, Biometrics, BMCBI 2011, Drosophila Melanogaster, Internal Exons