title: Do introns favor or avoid regions of amino acid conservation?
abstract: 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.
authors.affiliation: The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA.
authors.forename: Toshinori
authors.initials: T
authors.lastname: Endo
authors.forename: Alexei
authors.initials: A
authors.lastname: Fedorov
authors.forename: Sandro J
authors.initials: SJ
authors.lastname: de Souza
authors.forename: Walter
authors.initials: W
authors.lastname: Gilbert
mesh_terms: D017398:Alternative Splicing; D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D017124:Conserved Sequence; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics; D005998:Glycine / Q000737:chemistry / Q000378:metabolism*; D006147:Guanine / Q000737:chemistry; D007438:Introns / Q000235:genetics*; D007448:Invertebrates / Q000235:genetics; D008954:Models, Biological; D011506:Proteins / Q000235:genetics*; D014714:Vertebrates / Q000235:genetics
chemical_list: D000596:Amino Acids; D011506:Proteins; D006147:Guanine; D005998:Glycine