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Intrinsic Splicing Profile of Human Genes Undergoing Simple Cassette Exon Events

  • Andigoni Malousi
  • Vassilis Koutkias
  • Sofia Kouidou
  • Nicos Maglaveras
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4345)

Abstract

Alternative pre-mRNA splicing presides over protein diversity and organism complexity. Alternative splicing isoforms in human have been associated with specific developmental stages, tissue-specific expressions and disease-causing factors. In this study, we identified and analysed intrinsic features that discriminate non-conserved human genes that undergo a single internal cassette exon event from constitutively spliced exons. Context-based analysis revealed a guanine-rich track at the donor of the cassette’s upstream intronic region that is absent in the constitutive dataset, as well as significant differences in the distribution of CpG and A3/G3 sequences between the alternative and the constitutive intronic regions. Interestingly, introns flanking cassette exons are larger than the constitutive ones, while exon lengths do not vary significantly. Splice sites flanking cassette exons are less identifiable, while splice sites at the outer ends are ‘stronger’ than constitutive introns. The results indicate that specific intrinsic features are linked with the inclusion/excision of internal exons which are indicative of the underlying selection rules.

Keywords

Alternative splicing cassette exons splice sites intrinsic features 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Andigoni Malousi
    • 1
  • Vassilis Koutkias
    • 1
  • Sofia Kouidou
    • 2
  • Nicos Maglaveras
    • 1
  1. 1.Lab. of Medical Informatics, Faculty of MedicineAristotle University of ThessalonikiThessalonikiGreece
  2. 2.Dept. of Biological Chemistry, Faculty of MedicineAristotle University of ThessalonikiThessalonikiGreece

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