RT1-Ba (RT1 class II, locus Ba) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: RT1-Ba (RT1 class II, locus Ba) Rattus norvegicus
Analyze
Symbol: RT1-Ba
Name: RT1 class II, locus Ba
RGD ID: 1595867
Description: Predicted to enable MHC class II protein complex binding activity and peptide antigen binding activity. Involved in cellular response to glucocorticoid stimulus and negative regulation of T cell proliferation. Predicted to be located in external side of plasma membrane and lysosome. Predicted to be part of MHC class II protein complex. Predicted to be active in late endosome membrane and lysosomal membrane. Used to study uveitis. Human ortholog(s) of this gene implicated in several diseases, including autoimmune disease (multiple); gastrointestinal system cancer (multiple); glomerulonephritis (multiple); hematologic cancer (multiple); and systemic scleroderma (multiple). Orthologous to human HLA-DQA1 (major histocompatibility complex, class II, DQ alpha 1) and HLA-DQA2 (major histocompatibility complex, class II, DQ alpha 2); PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; asthma pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: activated B cell RT1Bl alpha chain; BA1; MGC105667; MHC class I antigen; MHC class II antigen RT1.B alpha chain; Rano class II histocompatibility antigen, B alpha chain; RT1 class II antigen, Ba chain; RT1 class II, locus Ba (mapped); RT1-B alpha; RT1-Ba_mapped
RGD Orthologs
Human
Mouse
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,577,057 - 4,581,650 (+)NCBIGRCr8
mRatBN7.2204,575,134 - 4,579,727 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl204,575,134 - 4,579,744 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0204,066,133 - 4,070,726 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,066,132 - 4,070,721 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,146,271 - 6,150,864 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,697,971 - 4,702,564 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera206,176,966 - 6,181,559 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
abdominal aortic aneurysm  (ISO)
achalasia  (ISO)
acute lymphoblastic leukemia  (ISO)
allergic disease  (ISO)
alopecia areata  (ISO)
Amyopathic Dermatomyositis  (ISO)
ankylosing spondylitis  (ISO)
antiphospholipid syndrome  (ISO)
aplastic anemia  (ISO)
arthritis  (ISO)
aspirin-induced respiratory disease  (ISO)
asthma  (ISO)
autoimmune disease  (ISO)
autoimmune myocarditis  (ISO)
autoimmune polyendocrine syndrome  (ISO)
autoimmune polyendocrine syndrome type 2  (ISO)
autoimmune thyroiditis  (ISO)
brain infarction  (ISO)
breast cancer  (ISO)
celiac disease  (ISO)
Chemical and Drug Induced Liver Injury  (ISO)
choreatic disease  (ISO)
chronic fatigue syndrome  (ISO)
Chronic Hepatitis B  (ISO)
Chronic Hepatitis C  (ISO)
chronic myeloid leukemia  (ISO)
colon carcinoma  (ISO)
congenital toxoplasmosis  (ISO)
Delayed Hypersensitivity  (IDA)
dermatitis  (ISO)
diffuse scleroderma  (ISO)
dilated cardiomyopathy 1H  (ISO)
Discoid Lupus Erythematosus  (ISO)
Drug Eruptions  (ISO)
eosinophilia-myalgia syndrome  (ISO)
Experimental Autoimmune Encephalomyelitis  (IDA,IMP)
Experimental Liver Cirrhosis  (EXP)
extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue  (ISO)
factor VIII deficiency  (ISO)
gastric adenocarcinoma  (ISO)
glucose intolerance  (ISO)
Graves' disease  (ISO)
Hashimoto Disease  (ISO)
Helicobacter Infections  (ISO)
Henoch-Schoenlein purpura  (ISO)
hepatitis B  (ISO)
hepatitis C  (ISO)
hepatocellular carcinoma  (ISO)
human immunodeficiency virus infectious disease  (ISO)
hypertension  (ISO)
juvenile rheumatoid arthritis  (ISO)
lepromatous leprosy  (ISO)
liver cirrhosis  (ISO)
lupus nephritis  (ISO)
marginal zone lymphoma  (ISO)
melanoma  (ISO)
membranous glomerulonephritis  (ISO)
multiple sclerosis  (ISO)
myasthenia gravis  (ISO)
myositis  (ISO)
narcolepsy  (ISO)
Nasal Polyps  (ISO)
onchocerciasis  (ISO)
Oropharyngeal Neoplasms  (ISO)
pancreatitis  (ISO)
paroxysmal nocturnal hemoglobinuria  (ISO)
pemphigus  (ISO)
primary biliary cholangitis  (ISO)
proteasome-associated autoinflammatory syndrome 1  (ISO)
proteinuria  (ISO)
Pseudomonas Infections  (ISO)
psoriasis  (ISO)
rheumatic fever  (ISO)
rheumatic heart disease  (ISO)
rheumatoid arthritis  (ISO)
rhinitis  (ISO)
rhinoscleroma  (ISO)
Schistosomiasis Japonica  (ISO)
Sjogren's syndrome  (ISO)
Spinal Tuberculoses  (ISO)
stomach cancer  (ISO)
Stroke  (ISO)
Sudden Hearing Loss  (ISO)
systemic lupus erythematosus  (ISO)
systemic scleroderma  (ISO)
thrombophilia  (ISO)
tuberculosis  (ISO)
Tubulointerstitial Nephritis and Uveitis  (ISO)
type 1 diabetes mellitus  (ISO)
type 2 diabetes mellitus  (ISO)
uveitis  (IMP)
visceral leishmaniasis  (ISO)
vitiligo  (ISO)
Vogt-Koyanagi-Harada disease  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-dinitrobenzenesulfonic acid  (ISO)
2-butoxyethanol  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3,7-dihydropurine-6-thione  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP,ISO)
acetamide  (EXP)
alpha-Zearalanol  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (EXP)
auranofin  (ISO)
azathioprine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
Benzo[k]fluoranthene  (ISO)
bexarotene  (EXP)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buspirone  (EXP)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
capecitabine  (ISO)
captan  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
chloroprene  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
coumarin  (EXP)
DDT  (EXP)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dichloromethane  (EXP)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
diquat  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
ethylbenzene  (EXP)
flutamide  (EXP)
fluvastatin  (ISO)
folic acid  (ISO)
folpet  (ISO)
gentamycin  (EXP)
hydrazine  (ISO)
isoprenaline  (ISO)
lead diacetate  (ISO)
lumiracoxib  (ISO)
menadione  (ISO)
mercaptopurine  (ISO)
mercury atom  (ISO)
mercury dichloride  (EXP)
mercury(0)  (ISO)
N-(6-acetamidohexyl)acetamide  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
nimesulide  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
palladium  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
PCB138  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
propanal  (ISO)
propiconazole  (ISO)
purine-6-thiol  (ISO)
quercetin  (ISO)
quercitrin  (ISO)
rotenone  (EXP)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
tamoxifen  (EXP)
testosterone enanthate  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
toluene 2,4-diisocyanate  (ISO)
topotecan  (EXP)
tremolite asbestos  (ISO)
Tributyltin oxide  (ISO)
trichloroethene  (EXP)
triptonide  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Treatment of autoimmune anterior uveitis with recombinant TCR ligands. Adamus G, etal., Invest Ophthalmol Vis Sci. 2006 Jun;47(6):2555-61.
2. Association of HLA class II allele and haplotype frequencies with chronic myelogenous leukemia and age-at-onset of the disease. Amirzargar AA, etal., Pathol Oncol Res. 2007;13(1):47-51. Epub 2007 Mar 27.
3. Interrelationship of major histocompatibility complex class II alleles and autoantibodies in four ethnic groups with various forms of myositis. Arnett FC, etal., Arthritis Rheum. 1996 Sep;39(9):1507-18.
4. HLA class II polymorphism in cystic fibrosis. A possible modifier of pulmonary phenotype. Aron Y, etal., Am J Respir Crit Care Med. 1999 May;159(5 Pt 1):1464-8.
5. The role of the HLA-DQA1 gene in resistance to atrophic gastritis and gastric adenocarcinoma induced by Helicobacter pylori infection. Azuma T, etal., Cancer. 1998 Mar 15;82(6):1013-8. doi: 10.1002/(sici)1097-0142(19980315)82:6<1013::aid-cncr2>3.0.co;2-f.
6. Association of HLA-DQA1*0501 with Graves' disease in English Caucasian men and women. Barlow AB, etal., Clin Endocrinol (Oxf). 1996 Jan;44(1):73-7.
7. Prevalence and clinical characteristics of celiac disease in Downs syndrome in a US study. Book L, etal., Am J Med Genet. 2001 Jan 1;98(1):70-4.
8. Two-domain MHC class II molecules form stable complexes with myelin basic protein 69-89 peptide that detect and inhibit rat encephalitogenic T cells and treat experimental autoimmune encephalomyelitis. Burrows GG, etal., J Immunol. 1998 Dec 1;161(11):5987-96.
9. HLA class II gene polymorphisms in antiphospholipid syndrome: haplotype analysis in 83 Caucasoid patients. Caliz R, etal., Rheumatology (Oxford). 2001 Jan;40(1):31-6.
10. Tumour necrosis factor microsatellites and HLA-DRB1*, HLA-DQA1*, and HLA-DQB1* alleles in Peruvian patients with rheumatoid arthritis. Castro F, etal., Ann Rheum Dis. 2001 Aug;60(8):791-5.
11. Replication of genome wide association studies on hepatocellular carcinoma susceptibility loci in a Chinese population. Chen K, etal., PLoS One. 2013 Oct 28;8(10):e77315. doi: 10.1371/journal.pone.0077315. eCollection 2013.
12. Duration of chronic inflammation alters gene expression in muscle from untreated girls with juvenile dermatomyositis. Chen YW, etal., BMC Immunol. 2008 Jul 31;9:43.
13. Tumour necrosis factor-alpha single nucleotide polymorphisms are not independent of HLA class I in UK Caucasians with adult onset idiopathic inflammatory myopathies. Chinoy H, etal., Rheumatology (Oxford). 2007 Sep;46(9):1411-6. Epub 2007 Jun 22.
14. HLA-DR and HLA-DQ alleles in patients from the south of Brazil: markers for leprosy susceptibility and resistance. da Silva SA, etal., BMC Infect Dis. 2009 Aug 22;9:134.
15. Genetic response to an environmental pathogenic agent: HLA-DQ and onchocerciasis in northwestern Ecuador. De Angelis F, etal., Tissue Antigens. 2012 Feb;79(2):123-9. doi: 10.1111/j.1399-0039.2011.01811.x. Epub 2011 Nov 26.
16. Helicobacter pylori, parietal cell antibodies and autoimmune gastropathy in type 1 diabetes mellitus. De Block CE, etal., Aliment Pharmacol Ther. 2002 Feb;16(2):281-9.
17. Characterization of the encephalitogenic immune response in a model of multiple sclerosis. de Graaf KL, etal., Eur J Immunol. 2008 Jan;38(1):299-308.
18. Resistance to celiac disease in humanized HLA-DR3-DQ2-transgenic mice expressing specific anti-gliadin CD4+ T cells. de Kauwe AL, etal., J Immunol. 2009 Jun 15;182(12):7440-50.
19. Differential effects of DRB1*0301 and DQA1*0501-DQB1*0201 on the activation and progression of islet cell autoimmunity. Eller E, etal., Genes Immun. 2007 Dec;8(8):628-33. Epub 2007 Aug 30.
20. HLA-DRB and HLA-DQ genetic variability in patients with aspirin-exacerbated respiratory disease. Esmaeilzadeh H, etal., Am J Rhinol Allergy. 2015 May-Jun;29(3):e63-9. doi: 10.2500/ajra.2015.29.4154.
21. DQA1 and DQB1 association and nasal polyposis. Fajardo-Dolci G, etal., Otolaryngol Head Neck Surg. 2006 Aug;135(2):243-7.
22. Aspirin insensitive thrombophilia: transcript profiling of blood identifies platelet abnormalities and HLA restriction. Fallahi P, etal., Gene. 2013 May 15;520(2):131-8. doi: 10.1016/j.gene.2013.02.032. Epub 2013 Feb 27.
23. Association between chronic cutaneous lupus erythematosus and HLA class II alleles. Fischer GF, etal., Hum Immunol. 1994 Dec;41(4):280-4.
24. Identification of a highly promiscuous and an HLA allele-specific T-cell epitope in the birch major allergen Bet v 1: HLA restriction, epitope mapping and TCR sequence comparisons. Friedl-Hajek R, etal., Clin Exp Allergy. 1999 Apr;29(4):478-87.
25. Association between HLA-DQA1, -DQB1 gene polymorphisms and susceptibility to asthma in northern Chinese subjects. Gao J, etal., Chin Med J (Engl). 2003 Jul;116(7):1078-82.
26. Association of gastric cancer, HLA-DQA1, and infection with Helicobacter pylori CagA+ and VacA+ in a Mexican population. Garza-González E, etal., J Gastroenterol. 2004 Dec;39(12):1138-42. doi: 10.1007/s00535-004-1462-2.
27. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
28. Genome-Wide Analysis of Genetic Risk Factors for Rheumatic Heart Disease in Aboriginal Australians Provides Support for Pathogenic Molecular Mimicry. Gray LA, etal., J Infect Dis. 2017 Dec 12;216(11):1460-1470. doi: 10.1093/infdis/jix497.
29. High frequency of abnormal glucose tolerance in DQA1*0102/DQB1*0602 relatives identified as part of the Diabetes Prevention Trial--Type 1 Diabetes. Greenbaum CJ, etal., Diabetologia. 2005 Jan;48(1):68-74. Epub 2004 Dec 16.
30. [Correlation between Constitution of Yin Deficiency Syndrome and Polymorphism of HLA-DQA1/Treatment Response of Peg-IFNalpha Therapy in HBeAg Positive Chronic Hepatitis B Patients]. Guo JC, etal., Zhongguo Zhong Xi Yi Jie He Za Zhi. 2016 May;36(5):539-43.
31. [Association between asthma and the polymorphism of HLA-DQ genes]. Guo X, etal., Zhonghua Jie He He Hu Xi Za Zhi. 2001 Mar;24(3):139-41.
32. HLA-DQA1 gene expression profiling in oligoarticular JIA. Haas JP, etal., Autoimmunity. 2009 May;42(4):389-91.
33. DRB1, DQA1, DQB1 genes in Turkish children with rheumatic fever. Hallioglu O, etal., Clin Exp Rheumatol. 2005 Jan-Feb;23(1):117-20.
34. Human leukocyte antigen-DQ alleles and haplotypes and their associations with resistance and susceptibility to HIV-1 infection. Hardie RA, etal., AIDS. 2008 Apr 23;22(7):807-16.
35. Susceptibility alleles and haplotypes of human leukocyte antigen DRB1, DQA1, and DQB1 in autoimmune polyglandular syndrome type III in Japanese population. Hashimoto K, etal., Horm Res. 2005;64(5):253-60. Epub 2005 Oct 27.
36. HLA class II profile: a weak determinant of factor VIII inhibitor development in severe haemophilia A. UKHCDO Inhibitor Working Party. Hay CR, etal., Thromb Haemost. 1997 Feb;77(2):234-7.
37. Translation in Xenopus laevis oocytes of hybrid selected LEW rat RT1.B alpha- and beta-chain transcripts results in serologically discrete class II polypeptide chain complexes. Henkes W and Reske K, Mol Immunol. 1989 Feb;26(2):171-9.
38. gamma delta+ T cells regulate major histocompatibility complex class II(IA and IE)-dependent susceptibility to coxsackievirus B3-induced autoimmune myocarditis. Huber SA, etal., J Virol. 1999 Jul;73(7):5630-6. doi: 10.1128/JVI.73.7.5630-5636.1999.
39. Contradictory intrahepatic immune responses activated in high-load hepatitis C virus livers compared with low-load livers. Ishibashi M, etal., Arch Virol. 2018 Apr;163(4):855-865. doi: 10.1007/s00705-017-3675-8. Epub 2017 Dec 16.
40. Association between HLA class II gene and susceptibility or resistance to chronic hepatitis B. Jiang YG, etal., World J Gastroenterol. 2003 Oct;9(10):2221-5.
41. Ectopic expression of MHC class II genes (RT1.B(I) beta/alpha) in rat hepatocytes in vivo and in culture can be elicited by treatment with the pregnane X receptor agonists pregnenolone 16 alpha-carbonitrile and dexamethasone. Jimenez BD, etal., Life Sci. 2002 Jun 7;71(3):311-23.
42. HLA-DQA1 & DQB1 variants associated with hepatitis B virus-related chronic hepatitis, cirrhosis & hepatocellular carcinoma. Karra VK, etal., Indian J Med Res. 2018 Jun;147(6):573-580. doi: 10.4103/ijmr.IJMR_1644_15.
43. HLA-DQA1*0103-DQB1*0601 haplotype and Helicobacter pylori-positive gastric mucosa-associated lymphoid tissue lymphoma. Kawahara Y, etal., Clin Gastroenterol Hepatol. 2005 Sep;3(9):865-8.
44. HLA class II allele and haplotype frequencies in Iranian patients with leukemia. Khosravi F, etal., Iran J Allergy Asthma Immunol. 2007 Sep;6(3):137-42.
45. Major histocompatibility complex class II (DRB1*, DQA1*, and DQB1*) and DRB1*04 subtypes' associations of Hashimoto's thyroiditis in a Greek population. Kokaraki G, etal., Tissue Antigens. 2009 Mar;73(3):199-205.
46. HLA associations with multiple sclerosis in Greece. Kouri I, etal., J Neurol Sci. 2011 Jul 7.
47. Association between HLA-DQA1/DRB1 polymorphism and development of hepatocellular carcinoma during entecavir treatment. Kozuka R, etal., J Gastroenterol Hepatol. 2019 May;34(5):937-946. doi: 10.1111/jgh.14454. Epub 2018 Sep 26.
48. HLA-DQA1*0501 is associated with diffuse systemic sclerosis in Caucasian men. Lambert NC, etal., Arthritis Rheum. 2000 Sep;43(9):2005-10.
49. Immunogenetics of atopic asthma: association of DRB1*1101 DQA1*0501 DQB1*0301 haplotype with Dermatophagoides spp.-sensitive asthma in a sample of the Venezuelan population. Lara-Marquez ML, etal., Clin Exp Allergy 1999 Jan;29(1):60-71.
50. Celiac disease in children with autoimmune thyroid disease. Larizza D, etal., J Pediatr. 2001 Nov;139(5):738-40.
51. Common variants in the HLA-DRB1-HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis. LeishGEN Consortium, etal., Nat Genet. 2013 Feb;45(2):208-13. doi: 10.1038/ng.2518. Epub 2013 Jan 6.
52. Strong associations between specific HLA-DQ and HLA-DR alleles and the tubulointerstitial nephritis and uveitis syndrome. Levinson RD, etal., Invest Ophthalmol Vis Sci. 2003 Feb;44(2):653-7.
53. [Possible association between polymorphisms of human leukocyte antigen-DQ genes and susceptibility to trichloroethylene-induced severe generalized dermatitis]. Li HS, etal., Zhonghua Yu Fang Yi Xue Za Zhi. 2006 May;40(3):173-6.
54. GWAS identifies novel susceptibility loci on 6p21.32 and 21q21.3 for hepatocellular carcinoma in chronic hepatitis B virus carriers. Li S, etal., PLoS Genet. 2012;8(7):e1002791. doi: 10.1371/journal.pgen.1002791. Epub 2012 Jul 12.
55. [HLA-DQ molecules associated with myasthenia gravis in Chinese patients]. Li X, etal., Yi Chuan Xue Bao. 1999;26(4):295-300.
56. Association of polymorphisms of human leucocyte antigen-DQA1 and DQB1 alleles with chronic hepatitis B virus infection, liver cirrhosis and hepatocellular carcinoma in Chinese. Liu C and Cheng B, Int J Immunogenet. 2007 Oct;34(5):373-8. doi: 10.1111/j.1744-313X.2007.00702.x.
57. [Association of HLA-DQA1 and DQB1 alleles with Vogt-Koyanagi-Harada syndrome in Han Chinese population]. Liu Q, etal., Zhonghua Yan Ke Za Zhi. 1999 May;35(3):210-5.
58. HLA-DQA1, -DQB1 polymorphism and genetic susceptibility to idiopathic dilated cardiomyopathy in Hans of northern China. Liu W, etal., Ann Hum Genet. 2005 Jul;69(Pt 4):382-8.
59. Relationship between HLA-DQA1 polymorphism and genetic susceptibility to idiopathic dilated cardiomyopathy. Liu W, etal., Chin Med J (Engl). 2004 Oct;117(10):1449-52.
60. [Association of haplotype formed on HLA-DRB1 and HLA-DQA1 alleles with outcomes of hepatitis B virus infection]. Lu LP, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2006 Aug;23(4):427-30.
61. The same HLA-DQ alleles determine either susceptibility or resistance to different coxsackievirus-mediated autoimmune diseases. Luppi P, etal., J Biol Regul Homeost Agents. 1999 Jan-Mar;13(1):14-26.
62. Complex HLA-DR and -DQ interactions confer risk of narcolepsy-cataplexy in three ethnic groups. Mignot E, etal., Am J Hum Genet. 2001 Mar;68(3):686-99. Epub 2001 Feb 13.
63. HLA-DRB1, -DQA1, and -DQB1 genotypes in patients with nasal polyposis. Molnar-Gabor E, etal., Laryngoscope. 2000 Mar;110(3 Pt 1):422-5.
64. Effective detection of human leukocyte antigen risk alleles in celiac disease using tag single nucleotide polymorphisms. Monsuur AJ, etal., PLoS One. 2008 May 28;3(5):e2270.
65. Association of HLA class II alleles with childhood asthma and Total IgE levels. Movahedi M, etal., Iran J Allergy Asthma Immunol. 2008 Dec;7(4):215-20.
66. Human leukocyte antigen class II alleles in Caucasian women with primary biliary cirrhosis. Mullarkey ME, etal., Tissue Antigens. 2005 Feb;65(2):199-205. doi: 10.1111/j.1399-0039.2005.00351.x.
67. HLA DQ gene dosage and risk and severity of celiac disease. Murray JA, etal., Clin Gastroenterol Hepatol. 2007 Dec;5(12):1406-12. Epub 2007 Oct 24.
68. Combination of HLA-A24, -DQA1*03, and -DR9 contributes to acute-onset and early complete beta-cell destruction in type 1 diabetes: longitudinal study of residual beta-cell function. Nakanishi K and Inoko H, Diabetes. 2006 Jun;55(6):1862-8.
69. Identification of a specific HLA class II haplotype strongly associated with susceptibility to cyclosporine-dependent aplastic anemia. Nakao S, etal., Blood. 1994 Dec 15;84(12):4257-61.
70. Associations of MHC class II alleles in Norwegian primary Sjogren's syndrome patients: implications for development of autoantibodies to the Ro52 autoantigen. Nakken B, etal., Scand J Immunol. 2001 Oct;54(4):428-33.
71. Immunogenetic risk and protective factors for the idiopathic inflammatory myopathies: distinct HLA-A, -B, -Cw, -DRB1, and -DQA1 allelic profiles distinguish European American patients with different myositis autoantibodies. O'Hanlon TP, etal., Medicine (Baltimore). 2006 Mar;85(2):111-27.
72. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
73. HLA-DQA1 and -DQB1 genes and Helicobacter pylori infection in Italian patients with gastric adenocarcinoma. Perri F, etal., Tissue Antigens. 2002 Jan;59(1):55-7. doi: 10.1034/j.1399-0039.2002.590112.x.
74. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
75. HLA class II polymorphisms in Spanish melanoma patients: homozygosity for HLA-DQA1 locus can be a potential melanoma risk factor. Planelles D, etal., Br J Dermatol. 2006 Feb;154(2):261-6.
76. Nationwide collaborative study of HLA class II associations with distinct types of juvenile chronic arthritis (JCA) in Greece. Pratsidou-Gertsi P, etal., Eur J Immunogenet. 1999 Aug;26(4):299-310.
77. Association of the HLA-DQA1*0501 allele in multiple racial groups with juvenile dermatomyositis. Reed AM and Stirling JD, Hum Immunol. 1995 Nov;44(3):131-5.
78. Does HLA-dependent chimerism underlie the pathogenesis of juvenile dermatomyositis? Reed AM, etal., J Immunol. 2004 Apr 15;172(8):5041-6.
79. [Correlation between HLA-DQA1 allele and anaphylactoid purpura in juvenile Hans residing in Inner Mongolia]. Ren S, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2002 Feb;19(1):58-60.
80. Temporal trends of HLA genotype frequencies of type 1 diabetes patients in Sweden from 1986 to 2005 suggest altered risk. Resic-Lindehammer S, etal., Acta Diabetol. 2008 Dec;45(4):231-5. Epub 2008 Sep 4.
81. GOA pipeline RGD automated data pipeline
82. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
83. Comprehensive gene review and curation RGD comprehensive gene curation
84. Clinical, serologic, and immunogenetic features of familial idiopathic inflammatory myopathy. Rider LG, etal., Arthritis Rheum. 1998 Apr;41(4):710-9.
85. Myenteric antiplexus antibodies and class II HLA in achalasia. Ruiz-de-Leon A, etal., Dig Dis Sci. 2002 Jan;47(1):15-9.
86. Association of HLA class II alleles with hepatitis C virus clearance and persistence in thalassemia patients from Iran. Samimi-Rad K, etal., J Med Virol. 2015 Sep;87(9):1565-72. doi: 10.1002/jmv.24211. Epub 2015 May 12.
87. Association of HLA-DQA1*03011-DQB1*0301 haplotype with the development of respiratory scleroma. Sanchez-Marin LA, etal., Otolaryngol Head Neck Surg. 2007 Mar;136(3):481-3.
88. Sensitivity to bee venom antigen phospholipase A2: association with specific HLA class I and class II alleles and haplotypes in beekeepers and allergic patients. Sanchez-Velasco P, etal., Hum Immunol. 2005 Jul;66(7):818-25.
89. The combination of several polymorphic amino acid residues in the DQalpha and DQbeta chains forms a domain structure pattern and is associated with insulin-dependent diabetes mellitus. Sanjeevi CB, etal., Ann N Y Acad Sci. 2002 Apr;958:362-75.
90. HLA class II (DRB, DQA1 and DQB1) allele and haplotype frequencies in the patients with pemphigus vulgaris. Shams S, etal., J Clin Immunol. 2009 Mar;29(2):175-9. Epub 2008 Sep 9.
91. Evaluation of clinical and immunogenetic risk factors for the development of hepatotoxicity during antituberculosis treatment. Sharma SK, etal., Am J Respir Crit Care Med. 2002 Oct 1;166(7):916-9. doi: 10.1164/rccm.2108091.
92. Identification of HLA-DQA1 as a Susceptibility Gene for Spinal Tuberculosis by Exome Sequencing. Shen J, etal., Med Sci Monit. 2018 May 24;24:3442-3449. doi: 10.12659/MSM.907864.
93. [A study of the hereditary susceptibility of HLA-DQA1 to essential hypertension, athrothrombotic brain infarction and lacunar stroke]. Shen N, etal., Zhonghua Yi Xue Za Zhi. 2001 Mar 25;81(6):352-5.
94. HLA class II haplotype and quantitation of WT1 RNA in Japanese patients with paroxysmal nocturnal hemoglobinuria. Shichishima T, etal., Blood. 2002 Jul 1;100(1):22-8.
95. HLA-DQA1/B1 alleles as putative susceptibility markers in congenital toxoplasmosis. Shimokawa PT, etal., Virulence. 2016 May 18;7(4):456-64. doi: 10.1080/21505594.2016.1150401. Epub 2016 Feb 8.
96. A genome-wide study identifies HLA alleles associated with lumiracoxib-related liver injury. Singer JB, etal., Nat Genet. 2010 Aug;42(8):711-4. doi: 10.1038/ng.632. Epub 2010 Jul 18.
97. Association of chronic fatigue syndrome with human leucocyte antigen class II alleles. Smith J, etal., J Clin Pathol. 2005 Aug;58(8):860-3.
98. HLA-DQA1*02:01 is a major risk factor for lapatinib-induced hepatotoxicity in women with advanced breast cancer. Spraggs CF, etal., J Clin Oncol. 2011 Feb 20;29(6):667-73. Epub 2011 Jan 18.
99. Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy. Stanescu HC, etal., N Engl J Med. 2011 Feb 17;364(7):616-26.
100. HLA class II DR and DQ genotypes and haplotypes associated with rheumatic fever among a clinically homogeneous patient population of Latvian children. Stanevicha V, etal., Arthritis Res Ther. 2007;9(3):R58.
101. Risk of celiac disease in children with type 1 diabetes is modified by positivity for HLA-DQB1*02-DQA1*05 and TNF -308A. Sumnik Z, etal., Diabetes Care. 2006 Apr;29(4):858-63.
102. HLA-DQ polymorphisms modify the risk of thyroid autoimmunity in children with type 1 diabetes mellitus. Sumnik Z, etal., J Pediatr Endocrinol Metab. 2003 Jul-Aug;16(6):851-8.
103. HLA class II DPB1, DQA1, DQB1, and DRB1 genotypic associations with occupational allergic cough to Bunashimeji mushroom. Suzuki K, etal., Tissue Antigens. 2005 May;65(5):459-66.
104. Evidence that an HLA-DQA1-DQB1 haplotype influences susceptibility to childhood common acute lymphoblastic leukaemia in boys provides further support for an infection-related aetiology. Taylor GM, etal., Br J Cancer. 1998 Sep;78(5):561-5.
105. Evidence that the HLA DQA1*03 allele confers protection from chronic HCV-infection in Northern European Caucasoids. Tibbs C, etal., Hepatology. 1996 Dec;24(6):1342-5. doi: 10.1053/jhep.1996.v24.pm0008938158.
106. HLA-DQA is associated with abdominal aortic aneurysms in the Belgian population. Tromp G, etal., Ann N Y Acad Sci. 2006 Nov;1085:392-5.
107. A genome-wide association study of HCV-induced liver cirrhosis in the Japanese population identifies novel susceptibility loci at the MHC region. Urabe Y, etal., J Hepatol. 2013 May;58(5):875-82. doi: 10.1016/j.jhep.2012.12.024. Epub 2013 Jan 12.
108. IL10 GGC haplotype is positively and HLA-DQA1*05-DQB1*02 is negatively associated with radiographic progression in undifferentiated arthritis. Ursum J, etal., J Rheumatol. 2010 Jul;37(7):1431-8. Epub 2010 May 15.
109. Predictors of associated autoimmune diseases in families with type 1 diabetes: results from the Type 1 Diabetes Genetics Consortium. Wagner AM, etal., Diabetes Metab Res Rev. 2011 Jul;27(5):493-498. doi: 10.1002/dmrr.1189.
110. HLA-DQA1*0301-associated susceptibility for autoimmune polyglandular syndrome type II and III. Wallaschofski H, etal., Horm Metab Res. 2003 Feb;35(2):120-4.
111. Association between HLA class II locus and the susceptibility to Artemisia pollen-induced allergic rhinitis in Chinese population. Wang M, etal., Otolaryngol Head Neck Surg. 2004 Feb;130(2):192-6.
112. Clinical and immunogenetic prognostic factors for radiographic severity in ankylosing spondylitis. Ward MM, etal., Arthritis Rheum. 2009 Jul 15;61(7):859-66.
113. Autoimmune polyglandular syndrome type 2 shows the same HLA class II pattern as type 1 diabetes. Weinstock C, etal., Tissue Antigens. 2011 Apr;77(4):317-24. doi: 10.1111/j.1399-0039.2011.01634.x.
114. Association of HLA-DQA1 and DQB1 alleles with alolpecia areata in Chinese Hans. Xiao FL, etal., Arch Dermatol Res. 2005 Nov;297(5):201-9. Epub 2005 Nov 11.
115. [Association between HLA-DQA1 gene polymorphism and the outcomes of hepatitis B virus infection]. Xun YH, etal., Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi. 2009 Dec;23(6):430-3.
116. [Association between the polymorphism of HLA-DQA1 alleles and type 2 diabetes in Yi nationality of Yunnan] Yang HY, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2005 Dec;22(6):702-4.
117. Association of HLA-DQA1 and DQB1 genes with vitiligo in Chinese Hans. Yang S, etal., Int J Dermatol. 2005 Dec;44(12):1022-7.
118. HLA-DQA1 genotyping in patients with rheumatoid arthritis in Taiwan. Yen JH, etal., Kaohsiung J Med Sci. 2001 Apr;17(4):183-9.
119. Different distribution of HLA class II alleles according to response to corticosteroid therapy in sudden sensorineural hearing loss. Yeo SW, etal., Arch Otolaryngol Head Neck Surg. 2001 Aug;127(8):945-9.
120. Association of HLA-DQA1*0101/2 and DQB1*0502 with myasthenia gravis in southern Iranian patients. Yousefipour GA, etal., Iran J Immunol. 2009 Jun;6(2):99-102.
121. [Association of HLA-DQA1 gene rs9272346 polymorphism with clinical outcome of hepatitis B virus infection in ethnic Han population from Hubei]. Yu J, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2014 Feb;31(1):93-6. doi: 10.3760/cma.j.issn.1003-9406.2014.01.022.
122. Curative effects of interferon-alpha and HLA-DRB1 -DQA1 and -DQB1 alleles in chronic viral hepatitis B. Zang GQ, etal., World J Gastroenterol. 2004 Jul 15;10(14):2116-8. doi: 10.3748/wjg.v10.i14.2116.
123. Association between HLA class II alleles and protection from or susceptibility to chronic hepatitis C. Zavaglia C, etal., J Hepatol. 1998 Jan;28(1):1-7.
124. [Studies on the association of human leukocyte antigen class II alleles with advanced hepatosplenic schistosomiasis japonica]. Zhang JH, etal., Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi. 2005 Feb 28;23(1):6-9.
125. HLA-DQA1 and DQB1 alleles are associated with genetic susceptibility to psoriasis vulgaris in Chinese Han. Zhang X, etal., Int J Dermatol. 2004 Mar;43(3):181-7.
126. [The study on correlativity between HLA-DQ gene polymorphism and primary Sjogren's syndrome of the Han nationality in Shanxi province]. Zhang XY, etal., Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi. 2011 Feb;27(2):182-5.
Additional References at PubMed
PMID:2499874   PMID:3610254   PMID:6084802   PMID:6319276   PMID:7679955   PMID:7985028   PMID:8344727   PMID:8598040   PMID:8598041   PMID:8638109   PMID:9432982   PMID:9492004  
PMID:11027433   PMID:11069069   PMID:11148202   PMID:11465104   PMID:11685465   PMID:11714799   PMID:11854359   PMID:12477932   PMID:12879310   PMID:15517241   PMID:19946888   PMID:24586191  


Genomics

Comparative Map Data
RT1-Ba
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,577,057 - 4,581,650 (+)NCBIGRCr8
mRatBN7.2204,575,134 - 4,579,727 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl204,575,134 - 4,579,744 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0204,066,133 - 4,070,726 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,066,132 - 4,070,721 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,146,271 - 6,150,864 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,697,971 - 4,702,564 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera206,176,966 - 6,181,559 (+)NCBICelera
Cytogenetic Map20p12NCBI
HLA-DQA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38632,637,406 - 32,655,272 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl632,628,179 - 32,647,062 (+)EnsemblGRCh38hg38GRCh38
GRCh37632,605,183 - 32,611,461 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36632,713,161 - 32,719,407 (+)NCBINCBI36Build 36hg18NCBI36
Build 34632,713,160 - 32,719,407NCBI
Cytogenetic Map6p21.32NCBI
HuRef632,346,937 - 32,353,106 (+)NCBIHuRef
CHM1_1632,607,658 - 32,613,904 (+)NCBICHM1_1
T2T-CHM13v2.0632,466,412 - 32,472,812 (+)NCBIT2T-CHM13v2.0
H2-Aa
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391734,501,718 - 34,506,797 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1734,501,718 - 34,506,797 (-)EnsemblGRCm39 Ensembl
GRCm381734,282,744 - 34,287,823 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1734,282,744 - 34,287,823 (-)EnsemblGRCm38mm10GRCm38
MGSCv371734,419,696 - 34,424,716 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361733,891,091 - 33,896,110 (-)NCBIMGSCv36mm8
Celera1737,044,263 - 37,049,282 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1717.98NCBI
MHC-DQA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11739,422,445 - 39,428,777 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1739,420,134 - 39,428,871 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604432,455,961 - 32,462,315 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in RT1-Ba
508 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:188
Count of miRNA genes:133
Interacting mature miRNAs:148
Transcripts:ENSRNOT00000000523
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2026463954597031Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2026463954597031Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
737973Pia21Pristane induced arthritis QTL 214.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2036216564606812Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
7175099Tcs2T cell selection QTL 2T cell selectionexpression2045040024693102Rat

Markers in Region
D20Yum74  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,576,395 - 4,576,557 (-)MAPPERmRatBN7.2
Rnor_6.0204,069,303 - 4,069,464NCBIRnor6.0
Rnor_5.0206,149,441 - 6,149,602UniSTSRnor5.0
RGSC_v3.4204,699,233 - 4,699,394UniSTSRGSC3.4
Celera206,178,228 - 6,178,389UniSTS
Cytogenetic Map20p12UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 2 3
Medium 1 11 28 13 16 13 5 8 1 19 11 11 5
Low 14 15 14 14 3 3 28 10 22 3
Below cutoff 8 12 12 12 25 6 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001008831 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF307302 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH002251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ493030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ493031 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ493032 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ493033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ493034 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ493035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ554214 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626192 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626193 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626195 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626196 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626197 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626198 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY701537 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC086448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX883043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225318 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225365 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226209 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227679 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227967 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231104 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231505 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231715 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231789 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232205 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232339 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232809 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233023 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233515 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234577 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234579 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234771 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  K02815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC222945 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L11341 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M29311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X14879 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000000523   ⟹   ENSRNOP00000000523
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,575,134 - 4,579,727 (+)Ensembl
Rnor_6.0 Ensembl204,066,132 - 4,070,721 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077143   ⟹   ENSRNOP00000070569
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,575,196 - 4,579,730 (+)Ensembl
Rnor_6.0 Ensembl204,066,132 - 4,067,164 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091096
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,575,134 - 4,579,744 (+)Ensembl
Rnor_6.0 Ensembl204,066,732 - 4,067,931 (-)Ensembl
RefSeq Acc Id: NM_001008831   ⟹   NP_001008831
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,577,057 - 4,581,650 (+)NCBI
mRatBN7.2204,575,134 - 4,579,727 (+)NCBI
Rnor_6.0204,066,133 - 4,070,726 (-)NCBI
Rnor_5.0206,146,271 - 6,150,864 (-)NCBI
RGSC_v3.4204,697,971 - 4,702,564 (+)RGD
Celera206,176,966 - 6,181,559 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001008831 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41598 (Get FASTA)   NCBI Sequence Viewer  
  AAA41601 (Get FASTA)   NCBI Sequence Viewer  
  AAA42083 (Get FASTA)   NCBI Sequence Viewer  
  AAH86448 (Get FASTA)   NCBI Sequence Viewer  
  AAL67950 (Get FASTA)   NCBI Sequence Viewer  
  AAV40619 (Get FASTA)   NCBI Sequence Viewer  
  AAV40621 (Get FASTA)   NCBI Sequence Viewer  
  AAV40622 (Get FASTA)   NCBI Sequence Viewer  
  AAV40624 (Get FASTA)   NCBI Sequence Viewer  
  AAV40625 (Get FASTA)   NCBI Sequence Viewer  
  AAV40626 (Get FASTA)   NCBI Sequence Viewer  
  AAV40627 (Get FASTA)   NCBI Sequence Viewer  
  AAV40628 (Get FASTA)   NCBI Sequence Viewer  
  AAW28798 (Get FASTA)   NCBI Sequence Viewer  
  AGV39042 (Get FASTA)   NCBI Sequence Viewer  
  CAA33020 (Get FASTA)   NCBI Sequence Viewer  
  CAD37895 (Get FASTA)   NCBI Sequence Viewer  
  CAD37896 (Get FASTA)   NCBI Sequence Viewer  
  CAD37897 (Get FASTA)   NCBI Sequence Viewer  
  CAD37898 (Get FASTA)   NCBI Sequence Viewer  
  CAD37899 (Get FASTA)   NCBI Sequence Viewer  
  CAD37900 (Get FASTA)   NCBI Sequence Viewer  
  CAD86937 (Get FASTA)   NCBI Sequence Viewer  
  CAE83946 (Get FASTA)   NCBI Sequence Viewer  
  EDL96801 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000000523
  ENSRNOP00000000523.1
  ENSRNOP00000070569.2
  ENSRNOP00000076833.1
GenBank Protein P20037 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001008831   ⟸   NM_001008831
- Peptide Label: precursor
- UniProtKB: Q6MGA0 (UniProtKB/TrEMBL),   A6JJD5 (UniProtKB/TrEMBL),   Q8VI32 (UniProtKB/TrEMBL),   A0A023ILS4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070569   ⟸   ENSRNOT00000077143
RefSeq Acc Id: ENSRNOP00000000523   ⟸   ENSRNOT00000000523
Protein Domains
Ig-like   Ig-like C1-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P20037-F1-model_v2 AlphaFold P20037 1-256 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13701329
Promoter ID:EPDNEW_R11852
Type:initiation region
Name:RT1-Ba_1
Description:RT1 class II, locus Ba
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0204,070,718 - 4,070,778EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595867 AgrOrtholog
BioCyc Gene G2FUF-4562 BioCyc
Ensembl Genes ENSRNOG00000000451 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000523 ENTREZGENE
  ENSRNOT00000000523.5 UniProtKB/TrEMBL
  ENSRNOT00000077143.2 UniProtKB/TrEMBL
  ENSRNOT00000091096.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7304077 IMAGE-MGC_LOAD
InterPro Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig/MHC_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_C1-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_I/II-like_Ag-recog UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_II_a/b_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_II_a_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:309621 UniProtKB/TrEMBL
MGC_CLONE MGC:105667 IMAGE-MGC_LOAD
NCBI Gene 309621 ENTREZGENE
PANTHER HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DQ ALPHA 1 CHAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC CLASS II-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam C1-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_II_alpha UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen RT1-Ba PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_MHC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000451 RatGTEx
SMART IGc1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_II_alpha UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54452 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A023ILS4 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2JY95_RAT UniProtKB/TrEMBL
  A0A8I5XVG2_RAT UniProtKB/TrEMBL
  A6JJD5 ENTREZGENE
  HA2B_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q5UT85_RAT UniProtKB/TrEMBL
  Q6MGA0 ENTREZGENE, UniProtKB/TrEMBL
  Q8VI32 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A6JJD5 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-04-12 RT1-Ba  RT1 class II, locus Ba  RT1-Ba_mapped  RT1 class II, locus Ba (mapped)  Data merged from RGD:3468 737654 APPROVED
2006-11-20 RT1-Ba  RT1 class II, locus Ba      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 RT1-Ba_mapped  RT1 class II, locus Ba(mapped)  RT1-Ba  RT1 class II, locus Ba  Symbol set to symbol_mapped, name set to name (mapped) 1582166 APPROVED
2004-02-11 RT1-Ba  RT1 class II, locus Ba      Symbol and Name status set to approved 625702 APPROVED
2002-06-10 RT1-Ba  RT1 class II, locus Ba      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_mapping maps to the MHC RT1 complex 1300431
gene_physical_interaction alpha chain, with the RT1-Bb beta chain forms the Rt1-B MHC class II molecule 1300427