Genome vs. Transcriptome Annotation

Question

[arussell3483]

Hello,

I'm sure this is a basic question, but I'm having some trouble wrapping my head around it. If I had a genome annotation file in GTF format for a given organism, would that annotation also be applied to a transcriptome for the same organism? Or would there have to be a separate transcriptome annotation GTF file? Assuming the sequence identifiers are the same in all three files.

Thank you!!

Answer 1

[Ram]

GTF files contain annotation for only the coding regions (including regions that are not translated, such as UTRs and ncRNAs), so there is no "genome GTF", all GTF data addresses the transcriptome.

EDIT:

From this page: https://www.gencodegenes.org/human/, there seem to be a few categories that are not included in the principal GTF - poly A tails, certain pseudogenes, tRNAs, etc - I'm not sure if these are part of the transcriptome, but then transcriptome is ideally the full set of ALL transcripts in an organism, so it should include all sorts of features on all sorts of RNA. In practice though, GTF files include just "useful" features, so poly A tails and such can be ignored for the most part.

[arussell3483]

Thank you so much - that is what I figured, but then I started overthinking it. Thank you for the link as well!