Table 4. Estimates of selective constraint in coding, intronic, and intergenic DNA of rodents, and contributions to the genomic deleterious mutation rate (U) per diploid genome per generation
DNA category Nucleotide sites per locus Mean constraint, SEM Contribution to U
Coding 1,125* 0.87 (0.009) 0.22
5′ intronic splice regions 44.4 0.73 (0.027) 0.0071
3′ intronic splice regions 222 0.29 (0.024) 0.012
Intron 1, 5′ end 3,307 0.10 (0.017) 0.049
5′ intergenic 5,596§ 0.093 (0.013) 0.074
3′ intergenic 5,271§ 0.12 (0.015) 0.079
  • Estimates were made under the assumption that there are 35,000 protein coding loci in the mouse genome (10, 11).

  • * The average length of rodent coding sequences is ≈ 1,500 nt, and about three-quarters of sites in coding sequences generate an amino acid change if mutated.

  • Blocks totaling 6 and 30 nt near 5′ and 3′ splice junction sites, respectively, show significant evidence of selective constraint (Table 1), and there are an average of 7.4 introns per locus (11).

  • Blocks of up to 6,000 bp (excludes splice control regions).

  • § Blocks of up to 6,000 bp upstream or downstream from the coding sequence were analyzed.

  • Estimate based on ref. 8, but assuming 35,000 rather than 80,000 loci, calculated under the assumption that mice and rats diverged 13 million years ago (24) and have two generations per year (8).