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 ?