[ensembl-dev] Strange positions on chrY in homo_sapiens_otherfeatures_96_38

[Thibaut Hourlier]

Hi Jerome,

This should not have happened. The Y chromosome is a strange case as it 
has PAR regions like the X chromosome. It looks like the coordinates for 
all the genes/transcripts/... have been shifted outside of the chromosome.

The data will be fixed in release 99 which should be available before 
the end of the year.

Apologies for the problems caused by this bug.

Regards,
Thibaut

On 31/10/2019 14:25, Jerome Roy wrote:
> Hi,
>
> I am (still) looking at refseq data in the mysql database and found strange positions for chrY:
> for example, looking at the TTTY3 gene I'm expecting the start to be at 25,728,490 (https://www.ncbi.nlm.nih.gov/gene/114760)
> But I don't get this position for ensembl 96/97/98:
>
> With ensembl95:
>> select seq_region_id,seq_region_start,seq_region_end,description from homo_sapiens_otherfeatures_95_38.gene where description like '%114760%';
> +---------------+------------------+----------------+-------------------------------------------------------------------------------------------+
> | seq_region_id | seq_region_start | seq_region_end | description                                                                               |
> +---------------+------------------+----------------+-------------------------------------------------------------------------------------------+
> | 131553        | 25728490         | 25733388       | testis-specific transcript, Y-linked 3 (non-protein coding) [Source:NCBI gene;Acc:114760] |
> +---------------+------------------+----------------+-------------------------------------------------------------------------------------------+
>
>
> With ensembl96:
>> select seq_region_id,seq_region_start,seq_region_end,description from homo_sapiens_otherfeatures_96_38.gene where description like '%114760%';
> +---------------+------------------+----------------+----------------------------------------------------------------------+
> | seq_region_id | seq_region_start | seq_region_end | description                                                          |
> +---------------+------------------+----------------+----------------------------------------------------------------------+
> | 131553        | 82945905         | 82950803       | testis-specific transcript, Y-linked 3 [Source:NCBI gene;Acc:114760] |
> +---------------+------------------+----------------+----------------------------------------------------------------------+
>
> I don't get why this position has changed to 82,945,905.
> The position in homo_sapiens_core_95_38 has not changed.
>
> I get the same for all genes I looked at, they are all above position 60,184,233.
>
> Is this related to changes in refseq data handling in ensembl96?
>
> Thanks
> Best regards,