Coordinates Of Par Regions On Ensembl Y Chromosome

Question

[Bio_X2Y]

How can you find out the coordinates of the PAR1 and PAR2 regions on chromosomes X and Y in the Ensembl human reference genome? As far as I can tell, these regions are masked with Ns on Ensembl (but not UCSC).

[Bio_X2Y]

Thanks to the folks below for answers. The PAR regions (as well as haplotypes) are defined in the assembly_exception table of the Ensembl human core mysql database.

Answer 1

[biobot 0.0.77.a.1099]

In Ensembl, PAR regions are stored as Bio::EnsEMBL::AssemblyExceptionFeatures. You can fetch these via a Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor.

# get DB adaptor $dba by usual means
my $aefa = $dba->get_AssemblyExceptionFeatureAdaptor();

# get $slice e.g. per chromosome
my @aefs = @{$aefa->fetch_all_by_Slice($slice)};

AssemblyExceptionFeatures also include haplotypes, so you may need to filter the features.

[Bio_X2Y]

Thanks for this. Do you know if there is a formal way of getting at this information outside of using BioPerl, etc. Something through a conventional download or an online mysql database?

[biobot 0.0.77.a.1099]

There is a public Ensembl MySQL database at http://www.ensembl.org/info/data/mysql.html and file downloads at http://www.ensembl.org/info/data/ftp/index.html . If you use the MySQL instance, you will need to understand the database schema (which is documented). The Perl API hides the schema details.

Answer 2

[Shigeta]

UCSC also documents them on their genome build page.

Here's human.

Answer 3

[lh3]

Go to this page and click "X" on the chromosome view image.

Answer 4

[Andrew Su]

If you're just doing one-off queries, why not just go directly to Ensembl? For example, for my favorite test gene CDK2:

http://uswest.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000123374

Clearly shows the genomic position at the top:

Chromosome 12: 56,360,556-56,366,565 forward strand

Now, the hard part (for me) is knowing the Ensembl gene IDs for PAR1 and PAR2, since PAR2 is apparently not an official gene human gene symbol, and the PAR1 in Entrez Gene doesn't have a match in Ensembl. But presumably you can find your Ensembl Gene ID more easily?

(Incidentally, NCBI Entrez Gene also will give genomic coordinates, and they use the same assembly as Ensembl...)

[Bio_X2Y]

Thanks Andrew, but when I said PAR1 and PAR2 I was referring to the Pseudo-Autosomal Regions rather than genes (http://en.wikipedia.org/wiki/Pseudoautosomal_region). Apologies for being unclear!

[Andrew Su]

Ahh, never mind then...