Table 1.
CDSs/UTRs |
Upstream intron |
Downstream intron |
||||
---|---|---|---|---|---|---|
Ka | Ks or Ku | 3′_50 | Central | 5′_50 | Central | |
Mouse–rat | ||||||
Exon 11 | — | 0.116 | — | — | 0.131 | 0.199 |
Exon 1 | 0.031 | 0.118 | 0.110 | 0.173 | 0.114 | 0.136 |
Exon 13 | — | 0.146 | 0.109 | 0.177 | 0.063 | 0.171 |
Exon 2 | 0.004 | 0.317 | 0.134 | 0.171 | 0.041 | 0.129 |
Exon 3 | 0.005 | 0.316 | 0.131 | 0.129 | 0.185 | 0.173 |
Exon 18 | 0.079a | 0.176/0.113a | 0.161 | 0.187 | 0.087 | 0.165 |
Human–Macaca | ||||||
Exon 11 | — | 0.040 | — | — | — | 0.068 |
Exon 1 | 0.014 | 0.014 | 0.020 | 0.068 | 0.064 | 0.062 |
Exon 13 | — | 0.071 | 0.109 | 0.064 | 0.064 | 0.074 |
Exon 2 | 0.004 | 0.051 | 0.085 | 0.074 | 0.041 | 0.057 |
Exon 3 | 0.005 | 0.069 | 0.042 | 0.057 | 0.054 | |
Exon 18 | — | 0.063 | 0.041 | 0.069 | 0.020 | 0.065 |
Mouse–human | ||||||
Exon 11 | — | 0.378 | — | — | 0.458 | 0.632 |
Exon 1 | 0.100 | 0.465 | 0.218 | 0.632 | 0.579 | 0.773 |
Exon 13 | — | 0.433 | 0.352 | 0.502 | 0.667 | 0.608 |
Exon 2 | 0.007 | 0.563 | 0.517 | 0.608 | 0.420 | 0.481 |
Exon 3 | 0.011 | 0.903 | 0.240 | 0.481 | 0.574 | 0.530 |
Exon 18 | — | 0.847 | 0.134 | 0.535 | 0.383 | 0.579 |
Evolutionary rates at non-synonymous (Ka) and synonymous (Ks) sites were calculated for coding exons by PAML (69). Evolutionary rates at non-coding exons (Ku) and for intronic sequences (Ki) were calculated using Kimura’s two-parameter model (70). The Ki values for central parts and for the end 50 nucleotide regions (3′_50 and 5′_50) of introns were calculated separately, because ∼50 nucleotide sequences at each end of an intron are thought to be subject to weak purifying selection that stems from the involvement of these sequences in splicing (39,78).
aFor partially coding exons, Ka and Ks were calculated for cording parts and Ku was calculated for non-coding sequences.