There are a small number of genes that have mass spectrometry evidence for a mature protein product but which are also unambiguously pseudogenes.
The best example I have seen of this is C08F11.14
It has two clear frameshifts (in introns 5 and 7) which resulted in the gene being reclassified as a pseudogene.
The trace reads for the genomic sequence in the area of the frameshifts appear to have good quality.
One EST (yk791b06.3) aligns perfectly across most of the area of one of the frameshifts indicating that there is no genomic sequencing error there.
It has about 20 mass spec peptides found from multiple experiments indicating that it has a mature protein expressed as high levels.
Is this an example of RNA editing?
???
I’m puzzled by this one.
Gary