An audit of the PeptideAtlas database uncovers evidence for repurposed pseudogenes and co-opted retroviral ORFs

CONCLUSIONS: Our analysis shows that proteomics data can be used in conjunction with evolutionary evidence to confirm the existence of new coding genes. The evidence suggests that both testis and placenta are the tissues most likely to express still to be identified coding genes, and that there may be other transposon-derived ORF that have been co-opted as coding genes. The strong evidence for the translation of regions under dysregulated conditions has important implications for the annotation...