Abstract
Biased usage of amino acids near exon-intron boundaries is phylogenetically widespread and characteristic of species for which there are expected to be problems defining exons.
Highlights
In mammals, splice-regulatory domains impose marked trends on the relative abundance of certain amino acids near exon-intron boundaries
Trends in other species, do we repeatedly see the same amino acids avoided or preferred or are trends largely unique to each species? are mammals unusual in showing a tight correlation between 5' and 3' trends, and may divergent results bear implications for the workings of the splicing machinery? do we find more skews in species that a priori are Preference trends are widespread in multicellular species Exons from eight metazoan species (Human (Hs), mouse expected to have a harder time identifying exons, that is, (Mm), Danio rerio (Dr), Caenorrhabditis elegans (Ce), those in which exons are relatively small islands in a sea of Caenorrhabditis briggsae (Cb), Anopheles gambiae (Ag), Q
As splice site signals can extend into exons and our focus is on exonic splicing regulation, we removed the first full codon at the exon-intron boundary
Summary
Splice-regulatory domains impose marked trends on the relative abundance of certain amino acids near exon-intron boundaries. Is this a mammalian particularity or symptomatic of exonic splicing regulation across taxa? Genome Biology 2008, Volume 9, Issue 2, Article R29 Warnecke et al R29.2 being suboptimally designed as far as their immediate function is concerned. The need to encode, in exonic sequence, information relevant for correct splicing is another factor with the potential to influence protein composition [2]. Playing a critical role in constitutive as well as alternative splicing [4], they function at multiple stages of spliceosome assembly by interacting with corresponding RNA recognition motifs in a number of different trans-factors [4]. SR proteins appear critical for establishing, in conjunction with other proteins, cross-exon complexes that enable faithful communication between splice sites [3]
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