Question: What is the difference between " ENSG00000002586.1" and "ENSG00000002586.19_PAR_Y" in Ensembl ID ?
0
gravatar for taoi2
11 months ago by
taoi210
taoi210 wrote:

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,

rna-seq ensembl genome • 502 views
ADD COMMENTlink modified 4 months ago by schwill840 • written 11 months ago by taoi210

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

ADD REPLYlink written 4 months ago by schwill840
4
gravatar for Jean-Karim Heriche
11 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche23k wrote:

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.

ADD COMMENTlink written 11 months ago by Jean-Karim Heriche23k
1
gravatar for Emily_Ensembl
11 months ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k wrote:

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.

ADD COMMENTlink modified 11 months ago • written 11 months ago by Emily_Ensembl21k
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