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. 2012 Nov;22(11):2219–2229. doi: 10.1101/gr.133249.111

Figure 5.

Figure 5.

Dual coding in C11orf48 locus. (A) Subcodon profile and mRNA-seq for RefSeq mRNA NM_024099 (left) and predicted Ensembl transcript ENST00000524958 (right). (B) ORF organization of NM_024099 mRNA (left) and ENST00000524958 (right). (C) Comparative sequence analysis of corresponding genomic alignments from 15 vertebrate species for RefSeq mRNA NM_024099. (D) Exon organization of the C11orf48 locus. For detailed description, see legend to Figure 4. The higher density of mRNA-seq reads for NM_024099 (fourth row panel A, left) in the shaded pink area indicates that RNA-seq reads are being generated from an additional transcript variant corresponding to Ensembl transcript ENST00000524958. In panel C, it can be seen that for most of the predicted CDS, codon substitutions are consistent with RefSeq CDS predictions (the area is greener in the zero-frame). However, for the pink shaded area, substitutions are consistent with protein coding evolutionary signatures in the +1 frame. It can be seen that the coding likelihood for the +1 frame exceeds the threshold in the area of dual decoding. The conservation plot of synonymous codon positions, shown above the 0 frame, shows that conservation of synonymous positions is significantly higher in the shaded pink area. This is consistent with the purifying selection acting on protein coding sequences in two frames in this region.