Stable Ensembl Ids

Question

[BAGeno]

Hi,

I want stable Ensembl ids of genes. I have used Hyperlink Management System. In output there are some genes which have more than one Ensembl ID. I want to ask that why genes have more than one Ensembl ID and which ID should be used for further processing?

[Devon Ryan]

It would help if you gave an example. In general, a "gene" is an abstract concept, which some sources (e.g., UCSC) will assign to multiple places on the genome. Such cases will result in the "same" gene having multiple IDs.

[BAGeno]

Like in case of ABCB11 there are two ensemble ids ENSG00000073734 and ENSG00000276582.

Answer 1

[Laura Luebbert]

You can search for genes using gget search and then check which chromosome the IDs are on (this will tell you whether they are different haplotypes) using gget info: https://github.com/pachterlab/gget

Answer 2

[Devon Ryan]

In your example, you can see that one is on chr2 and the other on an alternate haplotype. Consequently, it makes sense for there to be two IDs.

[BAGeno]

@Devon Ryan Can you please tell me alternate haplotype? I have searched it but found it confusing.

[Emily]

[Devon Ryan]

What part of it do you not understand? I'm not going to write some multi-paragraph reply when a single sentence will suffice.