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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:seminoma
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Accession:DOID:4440 term browser browse the term
Definition:A germinoma that has_material_basis_in cells that make sperm and eggs. (DO)
Synonyms:exact_synonym: pure seminoma;   seminomas
 primary_id: MESH:D018239
 xref: ICDO:9061/3
For additional species annotation, visit the Alliance of Genome Resources.

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seminoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ccnd2 cyclin D2 ISO mRNA, protein:increased expression:testis RGD PMID:15747581 RGD:2289154 NCBI chrNW_004955413:2,083,351...2,108,450
Ensembl chrNW_004955413:2,083,351...2,103,430 		JBrowse link
G Chek2 checkpoint kinase 2 ISO protein:decreased expression:testis RGD PMID:11593395 RGD:2298484 NCBI chrNW_004955455:2,969,113...3,008,004
Ensembl chrNW_004955455:2,969,270...3,003,173 		JBrowse link
G Entpd6 ectonucleoside triphosphate diphosphohydrolase 6 ISO CTD Direct Evidence: marker/mechanism CTD PMID:21519793 NCBI chrNW_004955415:31,219,909...31,245,107 JBrowse link
G Fas Fas cell surface death receptor ISO mRNA, protein:decreased expression:testis RGD PMID:17916181 RGD:2290049 NCBI chrNW_004955425:3,961,671...3,987,513
Ensembl chrNW_004955425:3,961,013...3,987,455 		JBrowse link
G Faslg Fas ligand ISO mRNA, protein:increased expression:testis RGD PMID:17916181 RGD:2290049 NCBI chrNW_004955406:13,098,479...13,107,045
Ensembl chrNW_004955406:13,098,662...13,107,389 		JBrowse link
G Fgfr3 fibroblast growth factor receptor 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19855393 NCBI chrNW_004955514:1,030,244...1,038,590
Ensembl chrNW_004955514:1,025,600...1,038,590 		JBrowse link
G Fhit fragile histidine triad diadenosine triphosphatase ISO protein:decreased expression::no expression observed in less mature seminomatous neoplastic tissues; re-expression seen in mature teratomatous tissues RGD PMID:12379753 RGD:2289879 NCBI chrNW_004955430:221,518...508,094 JBrowse link
G Hmbs hydroxymethylbilane synthase ISO mRNA:increased expression:tumor RGD PMID:15823405 RGD:2301683 NCBI chrNW_004955412:20,192,519...20,202,635
Ensembl chrNW_004955412:20,192,522...20,202,635 		JBrowse link
G Hras HRas proto-oncogene, GTPase ISO CTD Direct Evidence: marker/mechanism
DNA:mutations: :multiple (human)		 CTD
RGD		 PMID:19855393 RGD:2314832 NCBI chrNW_004955476:11,508,446...11,510,333
Ensembl chrNW_004955476:11,508,126...11,510,333 		JBrowse link
G Inha inhibin subunit alpha ISO protein:increased expression:tumor RGD PMID:11720904 RGD:2290380 NCBI chrNW_004955453:13,902,443...13,905,008
Ensembl chrNW_004955453:13,902,277...13,905,008 		JBrowse link
G Insr insulin receptor ISO mRNA:decreased expression:tumor:isoform B RGD PMID:15967097 RGD:2290460 NCBI chrNW_004955563:1,867,400...2,011,845
Ensembl chrNW_004955563:1,867,400...2,009,149 		JBrowse link
G Jup junction plakoglobin ISO mRNA:increased expression:tumor:relative to normal tissue (p<0.01) RGD PMID:11956097 RGD:2291872 NCBI chrNW_004955451:15,993,055...16,004,152
Ensembl chrNW_004955451:15,989,180...16,004,155 		JBrowse link
G Kcne1 potassium voltage-gated channel subfamily E regulatory subunit 1 ISO RGD PMID:15389592 RGD:1580497 NCBI chrNW_004955407:33,807,581...33,814,356
Ensembl chrNW_004955407:33,807,581...33,814,356 		JBrowse link
G Kcnq1 potassium voltage-gated channel subfamily Q member 1 ISO RGD PMID:15389592 RGD:1580497 NCBI chrNW_004955422:14,212,563...14,544,556
Ensembl chrNW_004955422:14,212,553...14,544,556 		JBrowse link
G Kit KIT proto-oncogene, receptor tyrosine kinase ISO DNA:transversion:CDS:2467G>C, amino acid D816H RGD PMID:10362788 RGD:2292181 NCBI chrNW_004955447:16,149,014...16,226,151
Ensembl chrNW_004955447:16,148,605...16,226,734 		JBrowse link
G Kras KRAS proto-oncogene, GTPase ISO RGD PMID:8816895 RGD:2314915 NCBI chrNW_004955413:20,298,852...20,328,756
Ensembl chrNW_004955413:20,298,824...20,328,758 		JBrowse link
G Pcna proliferating cell nuclear antigen disease_progression ISO RGD PMID:7474604 RGD:2315012 NCBI chrNW_004955415:15,744,601...15,748,910
Ensembl chrNW_004955415:15,744,601...15,749,673 		JBrowse link
G Pdgfra platelet derived growth factor receptor alpha ISO mRNA:splice variant:testis RGD PMID:8610136 RGD:2292154 NCBI chrNW_004955447:16,570,652...16,613,410
Ensembl chrNW_004955447:16,569,909...16,612,373 		JBrowse link
G Pdpn podoplanin ISO RGD PMID:17951198 RGD:2292234 NCBI chrNW_004955527:4,183,639...4,215,200 JBrowse link
G Pou5f1 POU class 5 homeobox 1 ISO mRNA, protein:increased expression:testis
DNA:hypomethylation:promoter
protein:increased expression:chest		 RGD PMID:17549357 PMID:17785371 PMID:18162782 RGD:2292429 RGD:2292432 RGD:2292433 NCBI chrNW_004955583:995,707...1,003,202 JBrowse link
G Prmt5 protein arginine methyltransferase 5 ISO protein:altered localization RGD PMID:17437848 RGD:2299953 NCBI chrNW_004955409:37,369,507...37,378,034
Ensembl chrNW_004955409:37,369,234...37,378,093 		JBrowse link
G Rb1 RB transcriptional corepressor 1 ISO protein:decreased expression:testis RGD PMID:12754735 RGD:2299891 NCBI chrNW_004955431:1,960,765...2,124,576
Ensembl chrNW_004955431:1,960,661...2,124,576 		JBrowse link
G Smad4 SMAD family member 4 ISO DNA, protein:insertion, decreased expression:1521insT RGD PMID:10706106 RGD:2299975 NCBI chrNW_004955402:35,956,080...36,001,746
Ensembl chrNW_004955402:35,961,165...35,994,538 		JBrowse link
G Tymp thymidine phosphorylase ISO protein:increased expression:testis RGD PMID:10886088 RGD:2293724 NCBI chrNW_004955413:33,505,424...33,509,095
Ensembl chrNW_004955413:33,505,446...33,508,748 		JBrowse link
G Vegfa vascular endothelial growth factor A disease_progression ISO protein:increased expression:testis RGD PMID:19288744 RGD:2315467 NCBI chrNW_004955437:9,527,445...9,541,908 JBrowse link
G Xrcc1 X-ray repair cross complementing 1 susceptibility ISO DNA:polymorphism: :p.R399Q RGD PMID:16596238 RGD:2302576 NCBI chrNW_004955555:1,293,416...1,315,839
Ensembl chrNW_004955555:1,293,416...1,315,839 		JBrowse link
spermatocytoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Fgfr3 fibroblast growth factor receptor 3 ISO ClinVar Annotator: match by term: Spermatocytic seminoma ClinVar PMID:7773297 PMID:8599935 PMID:8754806 PMID:9207791 PMID:9677066 More... NCBI chrNW_004955514:1,030,244...1,038,590
Ensembl chrNW_004955514:1,025,600...1,038,590 		JBrowse link
G Hras HRas proto-oncogene, GTPase ISO ClinVar Annotator: match by term: Spermatocytic seminoma ClinVar PMID:12727991 PMID:19855393 PMID:25157968 PMID:25741868 PMID:31775759 NCBI chrNW_004955476:11,508,446...11,510,333
Ensembl chrNW_004955476:11,508,126...11,510,333 		JBrowse link
G Lrrc56 leucine rich repeat containing 56 ISO ClinVar Annotator: match by term: Spermatocytic seminoma ClinVar PMID:12727991 PMID:19855393 PMID:25157968 PMID:25741868 PMID:31775759 NCBI chrNW_004955476:11,493,299...11,507,022
Ensembl chrNW_004955476:11,491,688...11,506,700 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 14320
    disease of cellular proliferation 6919
      cancer 5116
        cell type cancer 3409
          germ cell cancer 104
            seminoma 27
              extragonadal seminoma 0
              mediastinum seminoma 0
              spermatocytoma + 3
              testis seminoma + 0
Path 2
Term Annotations click to browse term
  disease 14320
    disease of anatomical entity 14026
      nervous system disease 12344
        central nervous system disease 11055
          brain disease 10380
            Brain Neoplasms 1279
              brain cancer 714
                germinoma 35
                  seminoma 27
                    extragonadal seminoma 0
                    mediastinum seminoma 0
                    spermatocytoma + 3
                    testis seminoma + 0
paths to the root