What is the difference between " ENSG00000002586.1" and "ENSG00000002586.19_PAR_Y" in Ensembl ID ?
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,
• 6,955 views
•
link
updated
by
schwill84 •
•
written
by
taoi2 •
•
written
by
taoi2 •
2 answers
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.
• 0 views
•
link
written
by
Jean-Karim Heriche
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.
Log in to answer this question.
More posts like this
-
Gene-based and transcriptome-based profiling
written by Chris •
-
gene name of DEG ID
written by m.esmaeilpour •
-
Diffrent between design co-Expression network with RNA-Seq data and micoarray data
written by askari.arezou94 •
-
Ensembl ID mapping using Biomart
written by prithvi.mastermind •
-
How to deal with the case that one gene symbol matches multiple ensembl ids?
written by dz2353
-
Mapping GRCh38 to ENSEMBL / UCSC ,Gene, transcript , cDNA and Protein IDs and Sequence
written by inambioinfo •
-
Ensembl transcripts sequence start with "N"
written by Feng Xie •
-
ID Conversion within ENSEMBL?
written by bbmisraccb •
-
Difference between NCBI mRNA sequences and RNA-seq assembled sequences
written by Kurban
-
how to read gene expression RNA seq
written by Am.A •
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