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MyGene.info: A BioThings API for gene annotations
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Query with exons and exons_hg19 both returns the same coordinates #118

Closed oyvindbusk closed 2 years ago

oyvindbusk commented 2 years ago

Hi,

I wanted to flag that exons_hg19 is now returning GRCh38-coordinates.

In the following query: https://mygene.info/v3/gene/9150?fields=name,symbol,exons,exons_hg19 The returned exon coordinates for both exons and exons_hg19 are identical

This is not the expected behavior?

Thanks Øyvind

{
   "_id":"9150",
   "_version":1,
   "exons":[
      {
         "cdsend":79753790,
         "cdsstart":79695267,
         "chr":"18",
         "position":[
            [
               79681429,
               79681517
            ],
            [
               79695224,
               79695308
            ],
            [
               79695976,
               79696070
            ],
            [
               79697859,
               79697988
            ],
            [
               79704766,
               79704917
            ],
            [
               79710345,
               79710436
            ],
            [
               79712971,
               79713138
            ],
            [
               79714490,
               79715528
            ],
            [
               79717534,
               79717676
            ],
            [
               79717809,
               79718016
            ],
            [
               79728906,
               79729069
            ],
            [
               79736354,
               79736521
            ],
            [
               79753651,
               79754510
            ]
         ],
         "strand":1,
         "transcript":"NM_001202504",
         "txend":79754510,
         "txstart":79681429
      },
      {
         "cdsend":160649,
         "cdsstart":137900,
         "chr":"18_KI270863v1_alt",
         "position":[
            [
               124062,
               124150
            ],
            [
               137857,
               137941
            ],
            [
               138609,
               138703
            ],
            [
               140492,
               140621
            ],
            [
               147399,
               147550
            ],
            [
               152978,
               153069
            ],
            [
               155604,
               155771
            ],
            [
               157123,
               158161
            ],
            [
               160167,
               160309
            ],
            [
               160442,
               160649
            ]
         ],
         "strand":1,
         "transcript":"NM_001202504",
         "txend":160649,
         "txstart":124062
      },
      {
         "cdsend":160649,
         "cdsstart":122580,
         "chr":"18_KI270863v1_alt",
         "position":[
            [
               122435,
               122894
            ],
            [
               137857,
               137941
            ],
            [
               138609,
               138703
            ],
            [
               140492,
               140621
            ],
            [
               147399,
               147550
            ],
            [
               152978,
               153069
            ],
            [
               155604,
               155771
            ],
            [
               157123,
               158161
            ],
            [
               160167,
               160309
            ],
            [
               160442,
               160649
            ]
         ],
         "strand":1,
         "transcript":"NM_001318511",
         "txend":160649,
         "txstart":122435
      },
      {
         "cdsend":79753675,
         "cdsstart":79679947,
         "chr":"18",
         "position":[
            [
               79679802,
               79680261
            ],
            [
               79695224,
               79695308
            ],
            [
               79695976,
               79696070
            ],
            [
               79697859,
               79697988
            ],
            [
               79704766,
               79704917
            ],
            [
               79710345,
               79710436
            ],
            [
               79712971,
               79713138
            ],
            [
               79714490,
               79715528
            ],
            [
               79717534,
               79717676
            ],
            [
               79717809,
               79718016
            ],
            [
               79728906,
               79729069
            ],
            [
               79753651,
               79756625
            ]
         ],
         "strand":1,
         "transcript":"NM_001318511",
         "txend":79756625,
         "txstart":79679802
      },
      {
         "cdsend":79753790,
         "cdsstart":79679947,
         "chr":"18",
         "position":[
            [
               79679802,
               79680261
            ],
            [
               79695224,
               79695308
            ],
            [
               79695976,
               79696070
            ],
            [
               79697859,
               79697988
            ],
            [
               79704766,
               79704917
            ],
            [
               79710345,
               79710436
            ],
            [
               79712971,
               79713138
            ],
            [
               79714490,
               79715528
            ],
            [
               79717534,
               79717676
            ],
            [
               79717809,
               79718016
            ],
            [
               79728906,
               79729069
            ],
            [
               79736354,
               79736521
            ],
            [
               79753651,
               79754503
            ]
         ],
         "strand":1,
         "transcript":"NM_004715",
         "txend":79754503,
         "txstart":79679802
      },
      {
         "cdsend":160649,
         "cdsstart":122580,
         "chr":"18_KI270863v1_alt",
         "position":[
            [
               122435,
               122894
            ],
            [
               137857,
               137941
            ],
            [
               138609,
               138703
            ],
            [
               140492,
               140621
            ],
            [
               147399,
               147550
            ],
            [
               152978,
               153069
            ],
            [
               155604,
               155771
            ],
            [
               157123,
               158161
            ],
            [
               160167,
               160309
            ],
            [
               160442,
               160649
            ]
         ],
         "strand":1,
         "transcript":"NM_004715",
         "txend":160649,
         "txstart":122435
      },
      {
         "cdsend":79753671,
         "cdsstart":79679947,
         "chr":"18",
         "position":[
            [
               79679802,
               79680261
            ],
            [
               79695224,
               79695308
            ],
            [
               79695976,
               79696070
            ],
            [
               79697859,
               79697988
            ],
            [
               79704766,
               79704917
            ],
            [
               79710345,
               79710436
            ],
            [
               79712971,
               79713138
            ],
            [
               79714490,
               79715528
            ],
            [
               79717534,
               79717676
            ],
            [
               79717809,
               79718016
            ],
            [
               79736354,
               79736521
            ],
            [
               79753651,
               79756625
            ]
         ],
         "strand":1,
         "transcript":"NM_048368",
         "txend":79756625,
         "txstart":79679802
      },
      {
         "cdsend":160651,
         "cdsstart":122580,
         "chr":"18_KI270863v1_alt",
         "position":[
            [
               122435,
               122894
            ],
            [
               137857,
               137941
            ],
            [
               138609,
               138703
            ],
            [
               140492,
               140621
            ],
            [
               147399,
               147550
            ],
            [
               152978,
               153069
            ],
            [
               155604,
               155771
            ],
            [
               157123,
               158161
            ],
            [
               160167,
               160309
            ],
            [
               160442,
               160651
            ]
         ],
         "strand":1,
         "transcript":"NM_048368",
         "txend":160651,
         "txstart":122435
      }
   ],
   "exons_hg19":[
      {
         "cdsend":79753790,
         "cdsstart":79695267,
         "chr":"18",
         "position":[
            [
               79681429,
               79681517
            ],
            [
               79695224,
               79695308
            ],
            [
               79695976,
               79696070
            ],
            [
               79697859,
               79697988
            ],
            [
               79704766,
               79704917
            ],
            [
               79710345,
               79710436
            ],
            [
               79712971,
               79713138
            ],
            [
               79714490,
               79715528
            ],
            [
               79717534,
               79717676
            ],
            [
               79717809,
               79718016
            ],
            [
               79728906,
               79729069
            ],
            [
               79736354,
               79736521
            ],
            [
               79753651,
               79754510
            ]
         ],
         "strand":1,
         "transcript":"NM_001202504",
         "txend":79754510,
         "txstart":79681429
      },
      {
         "cdsend":160649,
         "cdsstart":137900,
         "chr":"18_KI270863v1_alt",
         "position":[
            [
               124062,
               124150
            ],
            [
               137857,
               137941
            ],
            [
               138609,
               138703
            ],
            [
               140492,
               140621
            ],
            [
               147399,
               147550
            ],
            [
               152978,
               153069
            ],
            [
               155604,
               155771
            ],
            [
               157123,
               158161
            ],
            [
               160167,
               160309
            ],
            [
               160442,
               160649
            ]
         ],
         "strand":1,
         "transcript":"NM_001202504",
         "txend":160649,
         "txstart":124062
      },
      {
         "cdsend":160649,
         "cdsstart":122580,
         "chr":"18_KI270863v1_alt",
         "position":[
            [
               122435,
               122894
            ],
            [
               137857,
               137941
            ],
            [
               138609,
               138703
            ],
            [
               140492,
               140621
            ],
            [
               147399,
               147550
            ],
            [
               152978,
               153069
            ],
            [
               155604,
               155771
            ],
            [
               157123,
               158161
            ],
            [
               160167,
               160309
            ],
            [
               160442,
               160649
            ]
         ],
         "strand":1,
         "transcript":"NM_001318511",
         "txend":160649,
         "txstart":122435
      },
      {
         "cdsend":79753675,
         "cdsstart":79679947,
         "chr":"18",
         "position":[
            [
               79679802,
               79680261
            ],
            [
               79695224,
               79695308
            ],
            [
               79695976,
               79696070
            ],
            [
               79697859,
               79697988
            ],
            [
               79704766,
               79704917
            ],
            [
               79710345,
               79710436
            ],
            [
               79712971,
               79713138
            ],
            [
               79714490,
               79715528
            ],
            [
               79717534,
               79717676
            ],
            [
               79717809,
               79718016
            ],
            [
               79728906,
               79729069
            ],
            [
               79753651,
               79756625
            ]
         ],
         "strand":1,
         "transcript":"NM_001318511",
         "txend":79756625,
         "txstart":79679802
      },
      {
         "cdsend":79753790,
         "cdsstart":79679947,
         "chr":"18",
         "position":[
            [
               79679802,
               79680261
            ],
            [
               79695224,
               79695308
            ],
            [
               79695976,
               79696070
            ],
            [
               79697859,
               79697988
            ],
            [
               79704766,
               79704917
            ],
            [
               79710345,
               79710436
            ],
            [
               79712971,
               79713138
            ],
            [
               79714490,
               79715528
            ],
            [
               79717534,
               79717676
            ],
            [
               79717809,
               79718016
            ],
            [
               79728906,
               79729069
            ],
            [
               79736354,
               79736521
            ],
            [
               79753651,
               79754503
            ]
         ],
         "strand":1,
         "transcript":"NM_004715",
         "txend":79754503,
         "txstart":79679802
      },
      {
         "cdsend":160649,
         "cdsstart":122580,
         "chr":"18_KI270863v1_alt",
         "position":[
            [
               122435,
               122894
            ],
            [
               137857,
               137941
            ],
            [
               138609,
               138703
            ],
            [
               140492,
               140621
            ],
            [
               147399,
               147550
            ],
            [
               152978,
               153069
            ],
            [
               155604,
               155771
            ],
            [
               157123,
               158161
            ],
            [
               160167,
               160309
            ],
            [
               160442,
               160649
            ]
         ],
         "strand":1,
         "transcript":"NM_004715",
         "txend":160649,
         "txstart":122435
      },
      {
         "cdsend":79753671,
         "cdsstart":79679947,
         "chr":"18",
         "position":[
            [
               79679802,
               79680261
            ],
            [
               79695224,
               79695308
            ],
            [
               79695976,
               79696070
            ],
            [
               79697859,
               79697988
            ],
            [
               79704766,
               79704917
            ],
            [
               79710345,
               79710436
            ],
            [
               79712971,
               79713138
            ],
            [
               79714490,
               79715528
            ],
            [
               79717534,
               79717676
            ],
            [
               79717809,
               79718016
            ],
            [
               79736354,
               79736521
            ],
            [
               79753651,
               79756625
            ]
         ],
         "strand":1,
         "transcript":"NM_048368",
         "txend":79756625,
         "txstart":79679802
      },
      {
         "cdsend":160651,
         "cdsstart":122580,
         "chr":"18_KI270863v1_alt",
         "position":[
            [
               122435,
               122894
            ],
            [
               137857,
               137941
            ],
            [
               138609,
               138703
            ],
            [
               140492,
               140621
            ],
            [
               147399,
               147550
            ],
            [
               152978,
               153069
            ],
            [
               155604,
               155771
            ],
            [
               157123,
               158161
            ],
            [
               160167,
               160309
            ],
            [
               160442,
               160651
            ]
         ],
         "strand":1,
         "transcript":"NM_048368",
         "txend":160651,
         "txstart":122435
      }
   ],
   "name":"CTD phosphatase subunit 1",
   "symbol":"CTDP1"
}
newgene commented 2 years ago

@oyvindbusk thanks for letting us know, we will look into this and fix it, very likely the upstream data source changed data or structure.

zcqian commented 2 years ago

We can confirm the upstream data has changed, and we are currently in the progress of fixing things on our end to adapt the upstream changes.

zcqian commented 2 years ago

This should have been fixed in the latest data release.