Question: Coordinates Of Par Regions On Ensembl Y Chromosome
5
gravatar for Bio_X2Y
8.4 years ago by
Bio_X2Y3.6k
Ireland
Bio_X2Y3.6k wrote:

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).

ensembl coordinates • 5.0k views
ADD COMMENTlink written 8.4 years ago by Bio_X2Y3.6k

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.

ADD REPLYlink written 8.4 years ago by Bio_X2Y3.6k
4
gravatar for iw9oel_ad
8.4 years ago by
iw9oel_ad6.0k
iw9oel_ad6.0k wrote:

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.

ADD COMMENTlink modified 8.4 years ago • written 8.4 years ago by iw9oel_ad6.0k

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?

ADD REPLYlink written 8.4 years ago by Bio_X2Y3.6k

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.

ADD REPLYlink written 8.4 years ago by iw9oel_ad6.0k

There is a public Ensembl MySQL database described at ensembl.org/info/data/mysql.html and file downloads at 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. – Keith James 0 secs ago

ADD REPLYlink written 8.4 years ago by iw9oel_ad6.0k

There is a public Ensembl MySQL database described at ensembl.org/info/data/mysql.html and file downloads at 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.

ADD REPLYlink written 8.4 years ago by iw9oel_ad6.0k

There is a public Ensembl MySQL database described 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.

ADD REPLYlink written 8.4 years ago by iw9oel_ad6.0k
3
gravatar for Shigeta
8.3 years ago by
Shigeta460
Berkeley, CA
Shigeta460 wrote:

UCSC also documents them on their genome build page.

Here's human: http://genome.ucsc.edu/cgi-bin/hgGateway

ADD COMMENTlink written 8.3 years ago by Shigeta460
1
gravatar for lh3
8.3 years ago by
lh331k
United States
lh331k wrote:

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

ADD COMMENTlink written 8.3 years ago by lh331k
0
gravatar for Andrew Su
8.4 years ago by
Andrew Su4.8k
San Diego, CA
Andrew Su4.8k wrote:

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...)

ADD COMMENTlink written 8.4 years ago by Andrew Su4.8k

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!

ADD REPLYlink written 8.4 years ago by Bio_X2Y3.6k

Ahh, never mind then...

ADD REPLYlink written 8.4 years ago by Andrew Su4.8k
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