Identification of rodent-specific unitary pseudogenes. (a) Evolution of rodent-specific pseudogenized bifunctional transcripts. An ancestral transcript encoding a functional (shown by the exclamation mark) protein (vertical lines indicate an intact open reading frame (ORF)) and with a role as a miRNA decoy (mRD) has accumulated one or more mutations disabling its ORF (red cross) on the lineage leading to rodents. As a result the mouse or rat unitary pseudogene (green) has lost its coding potential while retaining its function as a competitive endogenous RNA while both functions are conserved in the protein-coding loci (blue) in human or dog. MYA, million years ago. (b) Flowchart for identifying rodent-specific losses of human protein-coding genes. (c) Genome browser view of the transmap annotation (green block) for the mouse unitary pseudogene of human carboxypeptidase O (CPO). This unitary pseudogene is located in an intergenic region of the mouse genome (chr1:63,950,645-63,982,545, mm9). Protein-coding genes downstream (Fastkd2) and upstream (Klf7) of this sequence are conserved between mouse and human as illustrated by the overlap between transmap and the UCSC protein coding gene annotations (in blue). The mammalian conservation track on the bottom (UCSC genome browser) shows the degree of placental mammal base pair conservation (20 species). (d) Portion of pairwise alignment between the human CPO peptide (blue) and the syntenic sequence in mouse (green). Highlighted in red are a frame shifting deletion at the start of exon 3 and the resulting downstream premature stop codon.
Marques et al. Genome Biology 2012 13:R102 doi:10.1186/gb-2012-13-11-r102