Transcript ID

Question

[cheong]

Hi guys how are you?

came across something and i saw

ENST00000001008.6-0_ENSG00000004478.8

ENST00000001008.6_ENSG00000004478.8

i believe ENSG00000004478.8 is the ensembl and ENST00000001008 is the transcript id, where .6 is the version.

However, are ENST00000001008.6-0 and ENST00000001008.6 the same? ( with that -0 at the end?)

thank you.

[ATpoint]

Hi, yes ENSG is gene and T is transcript. The -0 is (to me knowledge) no Ensembl standard so it is probably custom. Maybe some context?

[cheong]

Hi ATpoinrt,

Thank you!

I saw this in the results generated by a software called flair (https://doi.org/10.1038/s41467-020-15171-6)

the transcripts were quantified and in the results i saw a lot of similar situations as mentioned above. So I was wondering if that represents the transcript and a variation of the transcript (with -0 at the end) ? I tend to believe they are different because the counts are different... but how are they related....

[Arup Ghosh]

It seems the numbers followed by a dash(-*) are being used to denote transcript isoforms.

Ref: https://github.com/BrooksLabUCSC/flair/blob/74c04368b9acfd4afed613a685c11b3142bc4428/src/flair/identify_gene_isoform.py#L20