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Molecular Biology and Evolution 19:521-252 (2002)
© 2002 Society for Molecular Biology and Evolution

Do Introns Favor or Avoid Regions of Amino Acid Conservation?

Toshinori Endo, Alexei Fedorov, Sandro J. de Souza and Walter Gilbert

*The Biological Laboratories, Harvard University;
{dagger}Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University;
{ddagger}Laboratory of Computational Biology, Ludwig Institute for Cancer Research, São Paulo branch

Are intron positions correlated with regions of high amino acid conservation? For a set of ancient conserved proteins, with intronless prokaryotic but intron-containing eukaryotic homologs, multiple sequence alignments identified residues invariant throughout evolution. Intron positions between codons show no preferences. However, introns lying after the first base of a codon prefer conserved regions, markedly in glycines. Because glycines are in excess in conserved regions, this behavior could reflect phase-one introns entering glycine residues randomly in the ancestral sequences. Examination of intron positions within codons of evolutionarily invariable amino acids showed that roughly 50% of these introns are bordered by guanines at both 5'- and 3'-ends, 25% have a G only before the intron, and 5% have a G only after the intron, whereas about 20% are bordered by nonguanine bases.


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A. Fedorov, A. F. Merican, and W. Gilbert
Large-scale comparison of intron positions among animal, plant, and fungal genes
PNAS, December 10, 2002; 99(25): 16128 - 16133.
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