Figure 2

Exon 11b and exon 7b are highly conserved but disrupted in murids. A) The murid exon 11b sequence has experienced multiple catastrophic defects, including frameshifting deletions and mutation of acceptor (mouse), donor (rat) and lariat branch (both species) sites. Red boxes - probable deleterious mutations. Yellow box - exon 11b. Arrow - unusual pyrimidine at +3 position. Broad taxonomy is shown at left; E - superorder Euarchontoglires; L - order Lagomorphia; R - order Rodentia; M - family Muridae. B) Selected phylogeny of superorder Euarchontoglires (based on Huchon et al. [61]), showing species in which exon 7b and exon 11b are known to be intact (bold lines) or disrupted (faint lines). Red star indicates most parsimonious time of mutation of both elements. C) Disruption of murid exon 7b by retroviral insertion. The upper panel shows the exon structure present in most mammals (to scale), while the lower shows that found in murids. Large horizontal arrow - majority transcriptional start site observed in non-murid transcript sequences. Red cross - donor splice site mutation. Small vertical arrows - murid-specific substitutions in exon 7. A detailed annotated alignment of this mammalian genomic region appears in Additional file 3.