GFF end coordinate used by mappers to determine gene transcription termination

Question

[emurb]

Hello,

I would like to know which information of a GFF file mappers (STAR in my case) use to determine the end of a gene. I can see in my GFF that I have a line of type "gene", with start and end coordinates. But sometimes, I can see a line of type "three_prime_UTR".

If I want to shift a gene end to detect transcription termination problems (read through), should I modify a "gene" line ? or a "three_prime_UTR" line ? What to do when I don't have "three_prime_UTR" line ?

Thank you

[PoGibas]

Not all genes have 3'UTR. I guess you should use gene end coordinate.

Answer 1

[Devon Ryan]

3'UTRs are within gene entries, so just modify the gene entry. Note, though, that you must add an exon entry to go with the extension, since that's what things actually look at (i.e., they see if reads intersect with exons, and then see which genes the resulting set of exons comes from).