Fig. 6.

Sequence features of the ancestral ORF, which is annotated as a pseudogene in Drosophila yakuba. Start codons of the annotated pseudogene and of the shorter putative TRG in the simulans–sechellia–melanogaster clade are in green, well-conserved regions in yellow, frame-shift causing indels in blue, repetitive DNA in orange, and stop codons in black. We use the following frame numbering convention: the start codon of the putative pseudogene is denoted the +1 frame, the other two frames on the same strand are denoted +2 and +3 frames. The numbers in parentheses indicate how many more nucleotides (modulo 3) the species it is marked in has. The frames of the stop codons are not marked due to uncertainty about frame created by the repeat region. The two stop codons shown are located in the same frame.