Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse

Christina L. Zheng, F. U. Xiang-Dong, Michael Gribskov

Research output: Contribution to journalArticlepeer-review

54 Scopus citations

Abstract

Alternative splicing is a major contributor to genomic complexity, disease, and development. Previous studies have captured some of the characteristics that distinguish alternative splicing from constitutive splicing. However, most published work only focuses on skipped exons and/or a single species. Here we take advantage of the highly curated data in the MAASE database (see related paper in this issue) to analyze features that characterize different modes of splicing. Our analysis confirms previous observations about alternative splicing, including weaker splicing signals at alternative splice sites, higher sequence conservation surrounding orthologous alternative exons, shorter exon length, and more frequent reading frame maintenance in skipped exons. In addition, our study reveals potentially novel regulatory principles underlying distinct modes of alternative splicing and a role of a specific class of repeat elements (transposons) in the origin/evolution of alternative exons. These features suggest diverse regulatory mechanisms and evolutionary paths for different modes of alternative splicing.

Original languageEnglish (US)
Pages (from-to)1777-1787
Number of pages11
JournalRNA
Volume11
Issue number12
DOIs
StatePublished - Dec 2005
Externally publishedYes

Keywords

  • Alternative splicing
  • Constitutive splicing
  • Evolution of alternative splicing
  • MAASE database
  • Regulatory motifs
  • Transposable elements

ASJC Scopus subject areas

  • Molecular Biology

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