Interaction between mutation process and selection pressure in exons overlapping and non-overlapping with CGIs. In coding exons the substitution rate at synonymous sites is approximately 10-fold greater than at nonsynonymous sites. The mCpG → TG transition rate is about 10-fold greater than AG -> GG transition rate. CpG islands protect CpG dinucleotides from methylation, decreasing the transition rate from CG to TG. CpG dinucleotides in CGIs may be under stronger selection than CpG dinucleotides not overlapping within CGIs.