[ensembl-dev] Strange positions on chrY in homo_sapiens_otherfeatures_96_38

[Jerome Roy]

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,
-- 
Jerome Roy
WuXiNextCODE
https://www.wuxinextcode.com/