Analysis of the role of retrotransposition in gene evolution in vertebrates

BMC Bioinformatics

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 N_homologs≤ 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.

ISSN: 1471-2105