[ensembl-dev] Missmatch from database and website

[Mahmood Naderan]

I have an update that may shed a light but I cannot figure out.
With the command in my previous email, I see that the stableID is
ENSG00000259634. As I enter this ID in the web site, I see

Gene: RP11-529H20.5 ENSG00000259634  . Location  Chromosome 14:
92,524,896-92,525,877 reverse strand.

As you can see the start and end numbers matches with my previous email and
its name is not ATXN3 which I requested in the command. So, the question is
that why fetch_all_by_external_name("atxn3") returns that.

In my previous questions, Emily pointed that function may returns LRGs. For
me it is hard to understand since I am not an expert in that field. I want
to the get the main gene and not anything else.

Regards,
Mahmood



On Sat, Jul 15, 2017 at 2:15 PM, Mahmood Naderan <mahmood.nt at gmail.com>
wrote:

> Hi,
> With this code
>
>   my @genes = @{ $gene_adaptor->fetch_all_by_external_name("atxn3) };
>   my $gene  = @genes[0];
>   my $start = $gene->start();
>   my $end   = $gene->end();
>
> I see that
>   start=92524896
>   end=92525877
>
> However, from the website, I see
>   Chromosome 14: 92,524,896-92,572,965
>
> As you can see, the end numbers are different.
> http://grch37.ensembl.org/Homo_sapiens/Gene/Sequence?db=
> core;g=ENSG00000066427;r=14:92524896-92572965
>
>
> Is there any reason for that?
>
> Regards,
> Mahmood
>
>
>
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