Abstract
A comprehensive survey of alternate splicing across 42 eukaryotes so as to gain insight into how spliceosomal introns are recognized.
Highlights
Variations in transcript splicing can reveal how eukaryotes recognize intronic splice sites
All eukaryotes exhibit splice variation We found that splice variation is present in all organisms we analyzed
Using expressed sequence tag (EST) and cDNA data from 42 organisms, we find the prevalence of retained intron (RI) and cassette exon (CE) to vary significantly across major eukaryotic groups, strongly suggesting that the underlying mode of splice site recognition (ID versus exon definition (ED)) varies in prevalence across eukaryotes
Summary
Variations in transcript splicing can reveal how eukaryotes recognize intronic splice sites. We have performed a comprehensive survey of alternative splicing across 42 eukaryotes to gain insight into how spliceosomal introns are recognized. There is substantial range in splicing frequency [1,2]. 5% of genes are spliced in Saccharomyces cerevisiae [3], a yeast, while the average number of introns per gene among other fungi is generally low Genome Biology 2008, Volume 9, Issue 3, Article R50 McGuire et al R50.2 exceptions). Their average intron density ranges from just over one in Schizosaccharomyces pombe to approximately five in Cryptococcus neoformans [4]. Multicellular animals often have large numbers of introns (over seven per gene in vertebrates), while plants have intermediate numbers of introns (approximately four per gene in Oryza sativa and Arabidopsis thaliana)
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