What is the difference between " ENSG00000002586.1" and "ENSG00000002586.19_PAR_Y" in Ensembl ID ?

Question

[taoi2]

Hello !

I don't know what the difference between " ENSG00000002586.1" and "ENSG00000002586.19_PAR_Y" in Ensembl gene/transcripts ID means.

How do you deal with these ID with "_PAR_Y" in RNA-seq mapping process ?

Thanks,

[schwill84]

Hi,

I would like to make the following suggestion:

Since by normal definitions there is no Y chromosome in female tissue, PAR_Y quantifications should be ignored (excluding special cases such as intersex syndrome).

In male, however, I would suggest making the sum of counts for the X and PAR_Y transcripts. Since alternative splicing may generate different variants of the same "Ensembl-ID" transcript, quantification should account for the total of the isoforms.

Best

Answer 1

[Jean-Karim Heriche]

It means the gene has multiple copies in the pseudoautosomal regions. The '.1' part is the version number.
How you deal with them most likely depends on whether you care about these regions.

Answer 2

[Emily]

Just found out that these suffixes are added in the GENCODE annotation files. We need to discuss how we deal with these because we can't be putting out IDs with one hand and not providing tools that can interpret them with the other hand.

I'm sorry for any confusion.