Query with exons and exons_hg19 both returns the same coordinates
oyvindbusk opened this issue · comments
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"
}
@oyvindbusk thanks for letting us know, we will look into this and fix it, very likely the upstream data source changed data or structure.
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.
This should have been fixed in the latest data release.