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#399 Mouse strains - Human ortho

GDxBase
open
Premanand Achuthan
None
5
2013-05-21
2013-05-16
Premanand Achuthan
No

Click Mouse Strains Search from Menu
Click on the first example Idd3 Idd region
In the Strain summary table click on View in Gbrowse for the first strain 'NOD.B6(PL)-Idd3C57BL/6/MrkTacJ'
Look at the Mouse regions track, says has Human 4q27 Orthologous Region. Click on the link.
Get message 'No locus was found for id 1283. Please enter an identifier in the search box. '
Same behaviour in live site.
Note: Mouse strains is still in NCBIM37 as decided earlier.

Discussion

  • Premanand Achuthan

    Premanand Achuthan - 2013-05-16

    Need to reload T1DRegions in strainsdb.

    Reassign Olly -> Prem

     

  • Premanand Achuthan

    Premanand Achuthan - 2013-05-16
    • assigned_to: Olly Burren --> Premanand Achuthan
     

  • Olly Burren

    Olly Burren - 2013-05-16

    I guess the strain database need updating with the latest set of regions of b37 and that would fix this issue. Human Ortho 4q27 has an id of 1623

     

  • Olly Burren

    Olly Burren - 2013-05-16

    perhaps look at altering database so that regions and genes are retrieved from core gbrowse databases

     

  • Premanand Achuthan

    Premanand Achuthan - 2013-05-21
    • Priority: 9 --> 5
     

  • Premanand Achuthan

    Premanand Achuthan - 2013-05-21

    Even if we point the strandb to the latest set of regions of mm37, the link to locus pages will not link correctly as we don't store the orthologous regions of older builds. Needs further discussion. Reducing it to 5 and will leave it open.

     
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