Multiple sequence alignment and phylogenetic analysis of a human transcribed pseudogene that has orthologs in the ≥2 other mammals. (a) Multiple sequence alignment of conceptually-translated ortholog sequences (urn:lsid:pseudogene.org:9606.Pseudogene:4346; see Additional file 2: Table S2) from different mammals along with the human parental protein sequence (human ADP-ribose pyrophosphatase, swissprot accession id: NUDT9_HUMAN). The positions of stop codons in the alignment are denoted by 'X' and frameshifts denoted as 'B'. (b) A rooted phylogenetic tree constructed from the most conserved segment from a multiple nucleotide sequence alignment between ortholog sequences (human parental protein sequence - ADP-ribose pyrophosphatase, swissprot accession id: NUDT9_HUMAN). As an outgroup, we chose a protein sequence from C.elegans from the 'nudix' hydrolase family but belonging to another subfamily (NDX2_CAEEL) identified based on BLAST matching. PHYLIP Bootstrap support values out of 1000 iterations are indicated at each node.
Khachane and Harrison BMC Genomics 2009 10:435 doi:10.1186/1471-2164-10-435