[ensembl-dev] HG883_PATCH

[mag]

Hi Enrico,

HG883_PATCH is indeed a patch.
The human reference assembly contains fix patches, which attempt to 
correct sequencing errors in the primary assembly, as well as novel 
patches, or haplotypes.
More information here:
http://www.ensembl.org/Help/Glossary?id=297

HG883_PATCH is located on chromosome 17, as can be seen on this view:
http://www.ensembl.org/Homo_sapiens/Location/View?db=core;r=HG883_PATCH:26729129-26731068
If you click outside of the green region, it will tell you which 
chromosome you are on.

LRGs are Locus Reference Genomic.
These provide an assembly-independent gene location and are mainly used 
by the diagnostic community.
More information here:
http://www.ensembl.org/Help/Glossary?id=406

To ensure the uniqueness of a sequence, you should align it against the 
primary assembly, hence excluding all alternative sequences.
On our ftp site 
(ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna), the 
sequence is called Homo_sapiens.GRCh37.75.dna_sm.primary_assembly.fa


Hope that helps,
Magali

On 24/03/2014 05:33, Enrico Rubagotti wrote:
> Hi all,
> I wish to ensure the uniqueness of ENST00000003834 in the human genome.
> To achieve this objective  I blasted ENST00000003834 (identity value 
> =100%) over the entire GRCh37.p13 and the result was aligned to the 
> Chr 17, and HG883_PATCH and LRG_183.
> HG883_PATCH looks like a patch of the human genome, to which 
> chromosome it refers?
> What is LRG_183?
>
> Please find below the result from blast
>
> Query=  ENSG00000004139|ENST00000003834|26691378|26728065|17
> Length=2916
> Score     E
> Sequences producing significant alignments: (Bits)  Value
>
> ENSG00000004139|ENST00000003834|26691378|26728065|17 5385    0.0
> LRG_183|LRG_183t1|5001|16567|LRG_183 3701    0.0
> ENSG00000076351|ENST00000583295|26721661|26734215|17 3701    0.0
> ENSG00000076351|ENST00000584729|26721661|26734215|17 3701    0.0
> ENSG00000267556|ENST00000591663|26691378|26725182|HG883_PATCH 1615    0.0
> ENSG00000267556|ENST00000585482|26691378|26725182|HG883_PATCH 1242    0.0
> ENSG00000004139|ENST00000578128|26691378|26728065|17 1242    0.0
> ENSG00000004139|ENST00000579593|26691378|26728065|17 1227    0.0
> ENSG00000267556|ENST00000585569|26691378|26725182|HG883_PATCH 660    0.0
> ENSG00000004139|ENST00000577870|26691378|26728065|17 660    0.0
> ENSG00000267556|ENST00000589014|26691378|26725182|HG883_PATCH 278    
> 2e-72
> ENSG00000004139|ENST00000582323|26691378|26728065|17 278    2e-72
> ENSG00000267556|ENST00000591907|26691378|26725182|HG883_PATCH 154    
> 3e-35
>
> Kind regards,
>
> Enrico
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: 
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/