Source for `transcript_name` in GTFs
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?
• 1,063 views
•
link
updated
by
Jorge - Ensembl •
•
written
by
gernophil •
•
written
by
gernophil •
2 answers
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.
• 0 views
•
link
written
by
Jorge - Ensembl •
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.
Log in to answer this question.
More posts like this
-
SpliceAI custom gene annotation file
written by ClkElf •
-
Reference panel of normals for ensembl named refgenome
written by gernophil •
-
Difference between ENSEMBL releases
written by gernophil •
-
Non-coding transcript on NCBI
written by Sammy •
-
Ensembl transcript id, mismatch between ensembl_transcript_id_version and ensembl_transcript_id
written by hardervidertsie •
-
Rn28s1 28S ribosomal RNA [ Mus musculus] annotation in GTF file
written by efratk •
-
Multiple Ensembl gene IDs for the same gene symbol (not haplotypic regions)
written by TheBlackDonut •
-
What does Ensembl/Genecode gene_type "processed_gene" really mean?
written by james.lloyd
-
Does ENSEMBL have a descriptor for 'full length' transcript
written by george.wiggins •
-
What's the number at the begining of some lines of transcriptome GTF file means ?
written by jack
