What does the decimal ending of a transcript id mean?
1
2
Entering edit mode
8.8 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 • 5.0k views
ADD COMMENT
3
Entering edit mode
8.8 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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2058 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6