Conversion tool from ENST(ensembl) transcript to NM transcript(NCBI)

Question

[gmora]

So I have hundreds ensemble gene transcripts which needs to be converted to NCBI transcripts. I am worried about their being position changes in known mutations. I think one of reasons for this change is to have consecutive exons numbering (1,2,3 etc) instead of (1b,2,3,5) that is found in ensembl.

Gene Transcript Location Position Type Nuc Change AA Change Nuc Name AA Name
A ENST0001 exon 1 69aa c G-->C A-->P(150) c.448G>C p.Ala150Pro

This is roughly what the file looks like before conversion. I think between the formats the Position (AA or nucleotide) will change as will the Nuc Name. * denotes likely area's of change.

Any help would be appreciated

Answer 1

[Devon Ryan]

Use biomart. I've never seen a 1b exon in an Ensembl annotation. Not all Ensembl transcripts will have a RefSeq counterpart, but those that do should be the same.

As an aside, there's apparently a small bug in Ensembl biomart at the moment where occasionally nuccore yeast gene ID's are returned rather than refseq IDs. I'll report that so it gets fixed, though it's trivial to filter thankfully (they don't start with NM_).

[Denise CS]

Please report this to our helpdesk, so that it can be fixed.

Answer 2

[Denise CS]

You can use BioMart to convert ENST into NMs. Check our tutorial page. Under 'filters', you input your list of ENSTs and under 'attributes' you select NM from the 'External' field. You will then get the correspondence between them. In Ensembl, we assign stable IDs to exons such as ENSE00001184784, and their numbers are consecutive, rather than things such as 1b, 2, 3, 5. See this example. 'Ala150Pro' notations are from HGVS. See this post. If you have your variants in HGVS notation such as ENST00000415952.1:c.-149-34206G>T, 7:g.24926827C>A, you can use the Ensembl VEP to find out where they map to in both RefSeq and Ensembl genes.