[ensembl-dev] what happened to the rest of human chrY?

Nicole Washington nlwashington at lbl.gov
Tue Feb 26 19:07:44 GMT 2013


I'm just starting out learning the ENSEMBL API.  I've written a simple script to fetch the human chromosomes and print out a count of the genes for each one.  I am not a human-genome expert, so the answer to my question may very well be due to nuances in the human genome.

Quite simply, I do:

my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' );
my $slices = $slice_adaptor->fetch_all('chromosome');

and then iterate over the list of slices, printing out some details about each.

Chr Y behaves differently than the rest of the human chromosomes.  All other chromosomes (1..22, X, MT) go from 1-max_length.  But, it seems that there are two chrY toplevel elements retrieved, neither of which extends the complete length from 1..59,373,566.  They only span 1..10,000 and 2,649,521..59,034,049, completely skipping over the range 10,000..2,649,52.  It also seems that chrY is the only chromosome that is split into two toplevel features.

Does anyone know why this is?  Am I missing something very simple here?

Here the output from my script for ChrY:

Fetching genes for Y...Properties for this chromosome
 ID: chromosome:GRCh37:Y:1:10000:1
 Length: 59373566
 Build: 27507
 Coords: 1..10000
found 0 genes.
Fetching genes for Y...Properties for this chromosome
 ID: chromosome:GRCh37:Y:2649521:59034049:1
 Length: 59373566
 Build: 27507
 Coords: 2649521..59034049
found 501 genes.

Thanks for any help you can provide.


Nicole Washington
Research Scientist
Lawrence Berkeley National Laboratory
Genomics Division
1 Cyclotron Rd. MS64-121
Berkeley, CA 94720
NLWashington at lbl.gov
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