title: Alternative splicing of mutually exclusive exons--a review.
abstract: Alternative splicing (AS) of pre-mRNAs in higher eukaryotes and several viruses is one major source of protein diversity. Usually, the following major subtypes of AS are distinguished: exon skipping, intron retention, and alternative 3' and 5' splice sites. Moreover, mutually exclusive exons (MXEs) represent a rare subtype. In the splicing of MXEs, two (or more) splicing events are not independent anymore, but are executed or disabled in a coordinated manner. In this review, several bioinformatics approaches for analyzing MXEs are presented and discussed. In particular, we revisit suitable definitions and nomenclatures, and bioinformatics tools for finding MXEs, adjacent and non-adjacent MXEs, clustered and grouped MXEs. Moreover, the molecular mechanisms for splicing MXEs proposed in the literature are reviewed and discussed.
authors.affiliation: Department of Bioinformatics, Friedrich Schiller University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany. m.pohl@uni-jena.de
authors.forename: Martin
authors.initials: M
authors.lastname: Pohl
authors.forename: Ralf H
authors.initials: RH
authors.lastname: Bortfeldt
authors.forename: Konrad
authors.initials: K
authors.lastname: Grützmann
authors.forename: Stefan
authors.initials: S
authors.lastname: Schuster
mesh_terms: D017398:Alternative Splicing / Q000235:genetics* / Q000502:physiology*; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics*; D008957:Models, Genetic; D012322:RNA Precursors / Q000235:genetics*; D022821:RNA Splice Sites / Q000235:genetics; D009626:Terminology as Topic
chemical_list: D012322:RNA Precursors; D022821:RNA Splice Sites
keywords: AS; Alternative splicing; Drosophila Down Syndrome Cell Adhesion Molecule; Dscam; EST; Exon clusters; MXE; Mutually exclusive exons; NMD; Non-sense mediated decay; ORF; Splicing mechanisms; alternative splicing or alternatively spliced; expressed sequence tag; mutually exclusive exon; nonsense mediated mRNA decay; open reading frame