Source for `transcript_name` in GTFs

Question

[gernophil]

Hey, does anyone know the official source for transcript_name used in GENCODE and Ensembl GTFs? I don't find much about it. Just that it's gene name plus transcript number. But who assigns these numbers?

Answer 1

[Jorge - Ensembl]

Hi! Transcript naming is part of the Ensembl gene annotation pipeline. There will be further review for species annotated both by Ensembl and Havana which includes GENCODE Human and Mouse. More info on the GENCODE GTFs is here.

Answer 2

[GenoMax]

Manual annotation is done by HAVANA group from Ensembl: https://www.ensembl.org/info/genome/genebuild/manual_havana.html It would be fair to assume that they are responsible for the transcript_names. You can email Ensembl helpdesk and confirm.