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Ambiguity in Ensembl results for IRGM gene

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

ensembl transcripts ambiguity
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written by nazaninhoseinkhan nazaninhoseinkhan

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.

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written by Jean-Karim Heriche Jean-Karim Heriche

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.

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written by Emily Emily

1 answer

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.

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written by Jean-Karim Heriche Jean-Karim Heriche

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