Rates of Transition and Transversion in Coding Sequences since the Human-Rodent Divergence

Protein-coding sequences of 337 human genes were compared with those of homologous genes from rodent (mouse or rat). A composite alignment containing 477,189 nucleotide positions was constructed, and 21,570 amino acid replacements were inferred. The rates of transitional and transversional silent substitutions in fourfold degenerate sites are estimated as 1.71 × 10 -9 and 1.22 × 10 -9 site -1 year -1, respectively. Rates of substitutions in replacement sites, subject to selective constraints mediated by the genetic code, are lower, but also reflect a transitional bias. The amino acid exchange rejected least often during evolution is Asp/Glu, which is fixed at 30% the rate of transversions in silent sites. The most mutable amino acids in this survey are threonine and serine; serine coded by AGY is more mutable than serine coded by TCN. A scoring matrix for evaluating amino acid similarity was derived from this study.