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RGD DISEASE ONTOLOGY - ANNOTATIONS

RGD uses the Human Disease Ontology (DO, https://disease-ontology.org/) for disease curation across species. RGD automatically downloads each new release of the ontology on a monthly basis. Some additional terms which are required for RGD's curation purposes but are not currently covered in the official version of DO have been added. As corresponding terms are added to DO, these custom terms are retired and the DO terms substituted in existing annotations and subsequently used for curation.

Term:Urinary Calculi
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Accession:DOID:9003311 term browser browse the term
Definition:Low-density crystals or stones in any part of the URINARY TRACT. Their chemical compositions often include CALCIUM OXALATE, magnesium ammonium phosphate (struvite), CYSTINE, or URIC ACID.
Synonyms:exact_synonym: Urinary Calculus;   Urinary Stone;   Urinary Stones;   Urinary Tract Stone;   Urinary Tract Stones
 primary_id: MESH:D014545
For additional species annotation, visit the Alliance of Genome Resources.



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Urinary Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Add3 adducin 3 IEP RGD PMID:15329129 RGD:2317717 NCBI chr 1:252,147,341...252,255,126
Ensembl chr 1:252,147,386...252,255,124
JBrowse link
G F2 coagulation factor II ISO RGD PMID:22494008 RGD:6893519 NCBI chr 3:77,596,196...77,609,486
Ensembl chr 3:77,596,198...77,609,486
JBrowse link
G Il1rn interleukin 1 receptor antagonist susceptibility ISO DNA:repeats, haplotype:intron:IVS2+914_1000dup IL1RN*1, IL1RN*2 IL1RN*3 (human) RGD PMID:18186699 RGD:6907399 NCBI chr 3:7,111,567...7,127,451
Ensembl chr 3:7,111,550...7,127,445
JBrowse link
G Spp1 secreted phosphoprotein 1 no_association ISO DNA:polymorphism: :p.R9402H (human)
DNA:polymorphism: :p.N9171S (human)
RGD PMID:16145474 PMID:16145474 RGD:1581368, RGD:1581368 NCBI chr14:5,308,885...5,315,120
Ensembl chr14:5,308,885...5,315,162
JBrowse link
G Vdr vitamin D receptor ISO GAD PMID:15118671 RGD:1331525 NCBI chr 7:128,987,981...129,037,677
Ensembl chr 7:128,987,981...129,037,677
JBrowse link
bladder calculus term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ahr aryl hydrocarbon receptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:22232670 NCBI chr 6:52,234,089...52,271,568
Ensembl chr 6:52,234,089...52,271,568
JBrowse link
Kidney Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bglap bone gamma-carboxyglutamate protein ISO RGD PMID:12674322 RGD:7207412 NCBI chr 2:173,838,518...173,839,495
Ensembl chr 2:173,838,518...173,839,495
JBrowse link
G Car2 carbonic anhydrase 2 IEP RGD PMID:10977795 RGD:1600710 NCBI chr 2:86,741,625...86,756,766
Ensembl chr 2:86,741,626...86,756,818
JBrowse link
G Cat catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 3:89,842,393...89,874,577
Ensembl chr 3:89,842,399...89,874,478
JBrowse link
G Cd44 CD44 molecule (Indian blood group) IEP RGD PMID:16850024 RGD:2289370 NCBI chr 3:89,155,850...89,244,615
Ensembl chr 3:89,157,058...89,244,620
JBrowse link
G Cldn14 claudin 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chr11:33,232,281...33,329,440
Ensembl chr11:33,232,220...33,329,171
JBrowse link
G F2 coagulation factor II susceptibility ISO DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chr 3:77,596,196...77,609,486
Ensembl chr 3:77,596,198...77,609,486
JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 1:201,337,762...201,340,230
Ensembl chr 1:201,321,672...201,340,226
JBrowse link
G Ifng interferon gamma ISO associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chr 7:53,903,339...53,907,375
Ensembl chr 7:53,903,337...53,907,375
JBrowse link
G Mgp matrix Gla protein IDA RGD PMID:10460895 RGD:1582511 NCBI chr 4:169,766,290...169,769,612
Ensembl chr 4:169,766,279...169,769,667
JBrowse link
G Mpo myeloperoxidase ISO protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chr10:72,594,458...72,608,862
Ensembl chr10:72,594,661...72,604,819
JBrowse link
G Pomc proopiomelanocortin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chr 6:26,939,844...26,945,666
Ensembl chr 6:26,939,837...26,945,664
JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:29,456,673...29,462,249
Ensembl chr11:29,456,558...29,462,249
JBrowse link
G Spp1 secreted phosphoprotein 1 ISO
IEP
CTD Direct Evidence: marker/mechanism CTD
RGD
PMID:8325891 PMID:10890885 PMID:15954903 PMID:21378157 PMID:16105024 RGD:1581372, RGD:6903839, RGD:1581334 NCBI chr14:5,308,885...5,315,120
Ensembl chr14:5,308,885...5,315,162
JBrowse link
G Trpm7 transient receptor potential cation channel, subfamily M, member 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chr 3:114,046,258...114,134,799
Ensembl chr 3:114,046,258...114,135,190
JBrowse link
prostate calculus term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ltf lactotransferrin ISO RGD PMID:19202053 RGD:7243107 NCBI chr 8:110,999,948...111,022,795
Ensembl chr 8:110,999,948...111,022,795
JBrowse link
Renal Hypouricemia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Slc22a12 solute carrier family 22 member 12 ISO ClinVar Annotator: match by term: Dalmatian hypouricemia
CTD Direct Evidence: marker/mechanism
OMIM
ClinVar
CTD
PMID:12024214 PMID:14655203 PMID:14694169 PMID:15054642 PMID:15327384 More... NCBI chr 1:203,845,039...203,852,496
Ensembl chr 1:203,845,048...203,853,555
JBrowse link
G Slc2a9 solute carrier family 2 member 9 ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Dalmatian hypouricemia
CTD
ClinVar
PMID:18989453 PMID:22132990 NCBI chr14:72,328,334...72,461,981
Ensembl chr14:72,328,320...72,461,981
JBrowse link
Ureteral Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cat catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 3:89,842,393...89,874,577
Ensembl chr 3:89,842,399...89,874,478
JBrowse link
G Gsr glutathione-disulfide reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr16:58,482,209...58,525,256
Ensembl chr16:58,482,505...58,525,661
JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 1:201,337,762...201,340,230
Ensembl chr 1:201,321,672...201,340,226
JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:29,456,673...29,462,249
Ensembl chr11:29,456,558...29,462,249
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 18215
    Pathological Conditions, Signs and Symptoms 11356
      Anatomical Pathological Conditions 2263
        Calculi 38
          Urinary Calculi 31
            Kidney Calculi + 20
            Renal Hypouricemia 2
            Ureteral Calculi 4
            lower urinary tract calculus + 2
Path 2
Term Annotations click to browse term
  disease 18215
    disease of anatomical entity 17576
      Urogenital Diseases 4728
        urinary system disease 2409
          urolithiasis 71
            Urinary Calculi 31
              Kidney Calculi + 20
              Renal Hypouricemia 2
              Ureteral Calculi 4
              lower urinary tract calculus + 2
paths to the root