Stable Ensembl Ids
2
1
Entering edit mode
4.9 years ago
BAGeno ▴ 190

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?

gene ensembl • 1.4k views
ADD COMMENT
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
4.9 years ago

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
3
Entering edit mode

ADD REPLY
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode
6 days ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 2147 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