Table 2.
Results of analysis for reading-frame conservation (RFC)
| Species | Set † | Number with significantly conserved reading frame †† |
| Human | Human-specific relative to chimp | 10/40 (25%) |
| Others in human, that were formed since divergence from dog | 49/171 (29%) | |
| Other older PRs | 162/378 (43%) | |
| TOTAL | 221/589 (38%) | |
| Mouse | Mouse-specific relative to rat | 35/240 (15%) |
| Others in mouse, that were formed since divergence from dog | 17/58 (29%) | |
| Other older PRs | 123/233 (53%) | |
| TOTAL | 175/531 (33%) |
† These are the sets illustrated in Figure 4. All of the PRs that pass the local gene order test, allowing for Nhomologs ≤ 1 were analysed for reading-frame conservation.
†† For PRs formed since divergence from dog, RFC simulations were performed using ancestral sequences calculated using PAML [20]. For PRs formed before divergence from dog, RFC simulations were conservatively performed to half of the nucleotide-level divergence between the PR and its assigned parent sequence.