oaioai:CiteSeerX.psu:10.1.1.569.8013

The importance of being divisible by three in alternative splicing

Abstract

Alternative splicing events that are conserved in orthologous genes in different species are commonly viewed as reliable evidence of authentic, functionally significant alternative splicing events. Several recent bioinformatic analyses have shown that con-served alternative exons possess several features that distinguish them from alternative exons that are species-specific. One of the most striking differ-ences between conserved and species-specific alternative exons is the high percentage of exons that preserve the reading frame (exons whose length is an exact multiple of 3, termed symmetrical exons) among the conserved alternative exons. Here, we examined conserved alternative exons and found several features that differentiate between symmetrical and non-symmetrical alternative exons. We show that symmetrical alternative exons have a strong tendency not to disrupt protein domain structures, whereas the tendency of non-symmetrical alternative exons to overlap with different fractions of protein domains is similar to that of constitutive exons. Additionally, skipping isoforms of non-symmetrical alternative exons are strongly underrepresented, compared with their including isoforms, suggesting that skipping of a large fraction of non-symmetrical alternative exons produces transcripts that are degraded by the nonsense-mediated mRNA decay mechanism. Non-symmetrical alternative exons also show a tendency to reside in the 50 half of the CDS. These findings suggest that alternative splicing of symmet-rical and non-symmetrical exons is governed by different selective pressures and serves different purposes

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oaioai:CiteSeerX.psu:10.1.1.569.8013Last time updated on 10/29/2017

This paper was published in CiteSeerX.

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