[ensembl-dev] GRCh37 chrY sequence ?

[usman Ali]

sir would like to recieve more information from you regarding human Y
chromosome

On Mon, Jun 11, 2012 at 6:27 PM, Bert Overduin <bert at ebi.ac.uk> wrote:

> Hi Bron,
>
> The sentence "but it's a string of 1000 Ns (Pseudoautosomal region)" does
> not make sense to me. First, the region is 10000, not 1000 bp long, second,
> this is not a pseudo autosomal region, but the regions that are identical
> to X are.
>
> Cheers,
> Bert
>
> On Mon, Jun 11, 2012 at 1:35 PM, Bronwen Aken <ba1 at sanger.ac.uk> wrote:
>
>> Hi Hiram,
>>
>>
>> For the human Y chromosome in Ensembl, we have included DNA sequence
>> (A/G/C/T) for only the unique region. The rest of the chromosome is masked
>> with Ns, which explains how the length of the chromosome matches the GRC
>> chromosome but the composition of the sequence is shifted. The reason we
>> only include the unique region of Y is to make sure that we represent each
>> region of the genome only once.
>>
>> grep \> Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa
>> >Y dna:chromosome chromosome:GRCh37:Y:2649521:59034049:1
>>
>>
>> To add a bit more detail, the Y chromosome has four regions, two of which
>> are unique to Y and two of which are shared with X.
>> chromosome:GRCh37:Y:1 - 10000 is unique to Y but it's a string of 1000 Ns
>> (Pseudoautosomal region)
>> chromosome:GRCh37:Y:10001 - 2649520 is shared with X
>> chromosome:GRCh37:Y:2649521- 59034049  is unique to Y
>> chromosome:GRCh37:Y:59034050 - 59373566 is shared with X
>>
>> We store sequence for only the 2 unique regions of Y in our database. The
>> full chromosome Y can be generated on-the-fly by our API, where we stitch
>> in the shared sequence from X. By default our API will fetch only the
>> unique regions of Y however you can request to stitch in the X sequence by
>> setting the 4th argument in the SliceAdaptor to '1' :
>> $slice_adaptor->fetch_all('toplevel', undef,0,1)};
>> The relationship between the shared regions of X and Y are stored in the
>> assembly_exception table.
>>
>>
>> Hope that helps.
>>
>> Cheers,
>> Bronwen
>>
>>
>> On 8 Jun 2012, at 17:29, Hiram Clawson wrote:
>>
>> Good Morning Ensembl:
>>
>> A user reported to UCSC that the GRCh37/hg19 chrY sequence at UCSC is
>> different from the chrY sequence at Ensembl.  I picked up the v67
>> chrY sequence from Ensembl and compared it to the UCSC chrY and
>> the GRCh37 chrY sequence and Ensembl has a different sequence.
>> I checked previous versions of chrY from Ensembl and they remain
>> the same, so it isn't a patched sequence.  Anyone know what
>> the story is here ?
>>
>> --Hiram
>>
>> faCount composition measure of chrY sequence from genbank, UCSC and
>> Ensembl:
>>
>> #seq           len     A       C       G       T       N       cpg
>> CM000686.1 59373566 7667625 5099171 5153288 7733482 33720000 217906
>> hg19.chrY  59373566 7667625 5099171 5153288 7733482 33720000 217906
>> Y.v67      59373566 6965778 4475138 4518436 7025177 36389037 163434
>>
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>>
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>>
>
>
> --
> Bert Overduin, Ph.D.
> Vertebrate Genomics Team
>
> EMBL - European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge CB10 1SD
> United Kingdom
>
> http://www.ebi.ac.uk/~bert
>
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