What does the decimal ending of a transcript id mean?
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Entering edit mode
8.3 years ago
amviot ▴ 20

When working with alternative transcripts, I see a decimal ending to the transcript id. What does the decimal value add to the transcript meaning? For example, a mutation, BRAF p.V600M is annotated by VEP with:

csn="ENST00000479537.1:c.82G>A_p.Val28Met"

hgvsc="ENST00000479537.1:c.82G>A"

transcript_id="ENST00000479537"

&

csn="ENST00000288602.6:c.1798G>A_p.Val600Met"

hgvsc="ENST00000288602.6:c.1798G>A"

transcript_id="ENST00000288602"

I see the transcript IDs for BRAF listed at Ensembl as they are given in the "transcript_id" fields above. What does the ".1" and ".6" mean for each transcript above?

genome alignment • 4.7k views
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8.3 years ago

They are version numbers. They're not useful for most practical purposes because if the sequence changes significantly, then the ID itself is changed. See here for an explanation of versioning in Ensembl.

EDIT: update link

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can it be ignored safely then when mapping genes against a transcriptome using one of the state-of-the-art mappers like Salmon?

The link (with the further explanations, presumably) is currently dead, unfortunately

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I've updated the link. Whether to care about transcript versioning depends on whether you care about the changes associated with the versions. In practice, I would just pick one Ensembl genome version as reference and stick to it because transcript version numbers only change during re-annotations which are indicated by a change in Ensembl genome version.

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