Ambiguity in Ensembl results for IRGM gene

Question

[nazaninhoseinkhan]

Dear all, I am confused about transcripts results for a gene (IRGM).

In Ensembl there are two genes with the name IRGM with the same location but the different sizes.

One of these genes has 3 transcripts and the other has 2 transcripts. One of the transcripts is shared between two (4 transcripts in total).

However in UCSC genome browser, only 3 transcripts has been reported for IRGM.

Can anyone help me to understand this discrepancy?

I am looking forward your response

Nazanin

[Jean-Karim Heriche]

Each resource has its own way of annotating genomes so they should not be assumed to be identical. In the current EnsEMBL (v89), I see only one human IRGM gene with three transcripts.

[nazaninhoseinkhan]

please see this link:

http://www.ensembl.org/Human/Search/Results?q=IRGM;site=ensembl;facet_species=Human

Please check the result number 1 and 5.

[Emily]

What species is this in? Can you please post us some links showing us what you're looking at. Like Jean-Karim, I can only see one IRGM in human.

[nazaninhoseinkhan]

I am looking for human IRGM.

Please check this link:

http://www.ensembl.org/Human/Search/Results?q=IRGM;site=ensembl;facet_species=Human

Please check results number 1 and 5

Answer 1

[Jean-Karim Heriche]

The second gene down the list (item number 5, numbers2-4 are the transcripts of number 1) is from NCBI RefSeq, not EnsEMBL. Resources like EnsEMBL provide links to other annotation resources but that doesn't mean they all agree on what a gene is. When looking at a gene in EnsEMBL, you should view the corresponding summary page like the one I linked to. The best way is to work with IDs. They are unambiguous.