Pseudoautosomal regions (PAR) coordinates in different species, where and how?

Question

[R.Blues]

Hello all,

I am trying to find the coordinates of pseudoautosomal regions (PAR) in different species, such as human, mouse and rat.

So far I have just found the coordinates for human, in hg19, via http://genome.ucsc.edu/cgi-bin/hgGateway. But... how can I find the coordinates for other species such as mouse? Or does someone can provide me of the coordinates for mouse and rat?

I would really appreciate some help.

[GenoMax]

See if this paper helps.

[R.Blues]

Wow, it is really nice. At least I know that I cannot expect to know the PAR in rat!

However, there are no coordinates or supplementary material in the paper. Do you know where could I find this information?

Thank you very much for your help.

Answer 1

[Tommy Carstensen]

Here I got the assembly ID for species Mus musculus (GCA_000001635): http://www.ensembl.org/Mus_musculus/Info/Index

curl -s ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.7_GRCm38.p5/GCA_000001635.7_GRCm38.p5_assembly_regions.txt | grep ^PAR
PAR X   169969759   170931299   PAR na  na  na
PAR Y   90745845    91644698    PAR na  na  na

Similar for species Homo sapiens:

curl -s ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.14_GRCh37.p13/GCA_000001405.14_GRCh37.p13_assembly_regions.txt | grep PAR
PAR#1   X   60001   2699520 PAR na  na  na
PAR#2   X   154931044   155260560   PAR na  na  na
PAR#1   Y   10001   2649520 PAR na  na  na
PAR#2   Y   59034050    59363566    PAR na  na  na

Answer 2

[Santosh Anand]

The Genome Reference Consortium (GRC), which provides the reference assembly of genomes, annotates the PAR regions for human and mouse at least. You can try checking the status of others.

GRC Human

GRC Mouse