PTC positions in transcripts

Question

[jsw940]

Hello, I have a question about Ensembl genome data.

There are lots of transcripts annotated as "nonsense_mediated_decay" in ensembl data.

Then, I think that PTC(premature termination codon) must be in that transcript. So, how can I know the position and kinds of PTC which is the evidence of annotation?

I used to try to find PTCs based on ORF. But because there are number of cases, I couldn't find PTC.

How could I find it?

Thank you.

Answer 1

[i.sudbery]

This depends on how you define a PTC (which in turn depends on how the cell detects a termination codon as a PTC). The usual theory is that a cell detects a stop codon as a premature stop codon if there are exon junctions downstream of the stop. Thus Ensembl will mark any gene which has an intron after the stop codon as "nonsense_mediated_decay", and the supposed "PTC" is the one at the end of the ORF.