ArticleProceedings of the National Academy of Sciences of the United States of America1998
Relationship between "proto-splice sites" and intron phases: evidence from dicodon analysis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 1998. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed, 112 citations in OpenAlex.
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- Architecture and Distribution of Introns in Core Genes of FourG3 (Bethesda, Md.) · 2017Article
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- Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process.BMC evolutionary biology · 2013Article
- Cryptic splice sites and split genes.Nucleic acids research · 2011Article
- Evolutionary dynamics of spliceosomal intron revealed by in silico analyses of the P-Type ATPase superfamily genes.Molecular biology reports · 2011Article
- Does drive toward canonic exonic splicing sites exist in mammals?Journal of molecular evolution · 2010Article
- Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts.Genome biology · 2010Article
- Oscheius tipulae as an example of eEF1A gene diversity in nematodes.Journal of molecular evolution · 2008Article
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- An overabundance of phase 0 introns immediately after the start codon in eukaryotic genes.BMC genomics · 2006Article
- Phase distribution of spliceosomal introns: implications for intron origin.BMC evolutionary biology · 2006Article
- The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?Biology direct · 2006Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The coding sequence at the boundaries of exons flanking nuclear introns shows some degree of conservation. To the extent that such sequences might be recognized by the splicing machinery, this conservation may be a derived result of evolution for efficient splicing. Alternatively, such conserved sequences might be remnants of proto-splice sites, which might have existed early in eukaryotic genes and served as the targets for the insertion of introns, as has been proposed by the introns-late theory. The distribution of intron phases, the position of the intron within a codon, is biased with an over-representation of phase 0 introns. Could any distribution of proto-splice sites account for today's intron phase distribution? Here, we examine the dicodon usage in six model organisms, based on current sequences in the GenBank database, and predict the phase distribution that would be expected if introns had been inserted into proto-splice sites. However, these predictions differ between the various model organisms and disagree with the observed intron phase distributions. Thus, we reject the hypothesis that introns are inserted into hypothetical proto-splice sites. Finally, we analyze the sequences around the splice sites of introns in all six of the species to show that the actual conservation of sequence in exon regions near introns is very small and differs considerably between these species, which is inconsistent with a general proto-splice sites model.
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