Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids

► Structure prediction reveals thousands of loci with evidence of stabilizing selection. ► Predictions of protein-coding regions uncover thousands of unannotated novel exons. ► Coding regions found in dicistronic transcripts and functional read-through products. ► About 9% of the RNAz hits overlap CDS, so there may be ∼1000 loci with dual functions. ► Available comparative genomics methods cannot produce accurate maps of dual loci.