Unusual protein-coding structures identified by evolutionary signatures. (A) A well-conserved 30-aa ORF immediately following the stop codon in the gene Caki suggests translational readthrough. Note the perfect conservation of the putative readthrough stop codon, the “wobble” of the downstream stop codon, and the precipitous loss of conservation following the downstream stop codon, typical of a true translation stop. (B) A well-conserved ORF within the annotated 3′ UTR of CG4468 suggests a dicistronic transcript structure. Note the region of poor conservation that extends precisely from the upstream stop codon to the downstream start codon, suggesting separate translation of the two ORFs. (C) An abrupt change in the reading frame upon which selection appears to act within an exon of CG14047 is suggestive of a “programmed” translational frameshift (see also Supplemental Fig. 2).
