Genome-Wide Survey for Biologically Functional Pseudogenes
Figure 9
Recognizing Pseudogenes by Inspecting Their Alignment
(A) An alignment, visualized with TeXshade [34], of the processed copies to the ATXN7L3 human and mouse protein-coding genes. The human as well as the mouse ATXN7L3 contains 12 exons, which are all present in the respective duplicates. Approximate exon borders are shown in yellow.
The most interesting part consists of columns 1–468 (boxed green), which according to several EST and mRNA sequences is the only segment expressed. It consists of a highly conserved part, 1–288 (red), which is a potential open reading frame, followed by part 289–468 with pseudogenic disablements.
(B) Selected parts of the alignment of the ATX1 copies which are also processed. The protein-coding genes contain eight exons of which only parts of the last two code for protein. The entire segment of the pseudogenes corresponding to the protein-coding parts of the genes is expressed. The possibility that the processed copies are protein-coding cannot not be completely ruled out, however. Indeed, each pseudogene consists of one single 2,068-bp-long open reading frame. However, the frame induced by the alignments to the protein-coding genes contains several pseudogenic disablements.