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

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Gene: RT1-Da (RT1 class II, locus Da) Rattus norvegicus
Analyze
Symbol: RT1-Da
Name: RT1 class II, locus Da
RGD ID: 1593283
Description: Predicted to enable several functions, including MHC class II protein complex binding activity; T cell receptor binding activity; and peptide antigen binding activity. Predicted to be involved in several processes, including antigen processing and presentation of endogenous peptide antigen via MHC class II; antigen processing and presentation of exogenous peptide antigen via MHC class II; and regulation of T cell differentiation. Predicted to act upstream of or within immunoglobulin mediated immune response. Predicted to be located in external side of plasma membrane; immunological synapse; and lysosome. Predicted to be part of MHC class II protein complex. Predicted to be active in late endosome membrane and lysosomal membrane. Biomarker of prediabetes syndrome. Human ortholog(s) of this gene implicated in Parkinson's disease (multiple); allergic disease; asthma; and autoimmune disease (multiple). Orthologous to human HLA-DRA (major histocompatibility complex, class II, DR alpha); PARTICIPATES IN interleukin-12 signaling pathway; allograft rejection pathway; antigen processing and presentation pathway; INTERACTS WITH 1,2,4-trimethylbenzene; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: DA1; H2-Ea; histocompatibility 2, class II antigen E alpha; MGC112637; MHC class II antigen RT1.D alpha chain; MHC class II RT1D alpha chain antigen; MHC RT1.u-D-alpha chain; RT1 class II, locus Da (mapped); RT1-D alpha; RT1-Da_mapped; RT1-Daa; RT1-Dab; RT1-Dac; RT1-Dad; RT1-Daf; RT1-Dah; RT1-Dak; RT1-Dal; RT1-Dam; RT1-Dan; RT1-Du alpha; RT1-u
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,513,464 - 4,518,457 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl204,512,911 - 4,518,455 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx205,276,067 - 5,281,031 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0204,637,807 - 4,642,772 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0205,110,863 - 5,115,835 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0204,127,644 - 4,132,616 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,127,644 - 4,132,616 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,207,782 - 6,212,754 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,636,310 - 4,641,282 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera206,115,646 - 6,120,618 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2,4-trimethylbenzene  (EXP)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4,6-trinitrotoluene  (EXP)
2-nitrofluorene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4-amino-2,6-dinitrotoluene  (EXP)
5-azacytidine  (ISO)
acetamide  (EXP)
all-trans-retinoic acid  (ISO)
amitriptyline  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
bexarotene  (EXP)
bisphenol A  (EXP)
bortezomib  (ISO)
buspirone  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chrysin  (ISO)
clofibric acid  (EXP)
cocaine  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diethylstilbestrol  (EXP)
dimethyl fumarate  (ISO)
dimethyl sulfoxide  (ISO)
dimethylarsinic acid  (EXP)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
entinostat  (ISO)
folic acid  (ISO)
genistein  (ISO)
gentamycin  (EXP)
graphite  (ISO)
hexachlorobenzene  (EXP)
ionomycin  (EXP)
iopromide  (ISO)
lead diacetate  (EXP,ISO)
lipopolysaccharide  (ISO)
losartan  (EXP)
mercury dichloride  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
mevalonic acid  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
nickel atom  (ISO)
nimesulide  (EXP)
oxaliplatin  (EXP)
ozone  (EXP,ISO)
paracetamol  (ISO)
paraquat  (ISO)
perfluorohexanesulfonic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
PhIP  (EXP)
phorbol 13-acetate 12-myristate  (EXP)
pirinixic acid  (EXP,ISO)
progesterone  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
selenium atom  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
tamibarotene  (ISO)
tamoxifen  (EXP)
temozolomide  (ISO)
testosterone  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
topotecan  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
ursodeoxycholic acid  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. HLA-DMB gene and HLA-DRA promoter region polymorphisms in Australian multiple sclerosis patients. Bennetts BH, etal., Hum Immunol. 1999 Sep;60(9):886-93.
2. Coexpression of susceptible and resistant HLA class II transgenes in murine experimental autoimmune thyroiditis: DQ8 molecules downregulate DR3-mediated thyroiditis. Flynn JC, etal., J Autoimmun. 2002 May;18(3):213-20.
3. 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.
4. HLA rs3129882 variant in Chinese Han patients with late-onset sporadic Parkinson disease. Guo Y, etal., Neurosci Lett. 2011 Sep 1;501(3):185-7. Epub 2011 Jul 20.
5. Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease. Hamza TH, etal., Nat Genet. 2010 Sep;42(9):781-5. Epub 2010 Aug 15.
6. Elevated mRNA levels of major histocompatibility complex class II genes in lymphocytes of autoimmune BB rats. Holowachuk EW, etal., Diabetes. 1988 Dec;37(12):1637-40.
7. Replication of CD58 and CLEC16A as genome-wide significant risk genes for multiple sclerosis. Hoppenbrouwers IA, etal., J Hum Genet. 2009 Nov;54(11):676-80. Epub 2009 Oct 16.
8. HLA-DR4-IE chimeric class II transgenic, murine class II-deficient mice are susceptible to experimental allergic encephalomyelitis. Ito K, etal., J Exp Med. 1996 Jun 1;183(6):2635-44.
9. HLA-DRA polymorphisms associated with risk of nasal polyposis in asthmatic patients. Kim JH, etal., Am J Rhinol Allergy. 2012 Jan-Feb;26(1):12-7. doi: 10.2500/ajra.2012.26.3692.
10. Elucidating the molecular physiopathology of acute respiratory distress syndrome in severe acute respiratory syndrome patients. Kong SL, etal., Virus Res. 2009 Nov;145(2):260-9. Epub 2009 Jul 25.
11. Genome-wide association study of asthma identifies RAD50-IL13 and HLA-DR/DQ regions. Li X, etal., J Allergy Clin Immunol. 2010 Feb;125(2):328-335.e11. doi: 10.1016/j.jaci.2009.11.018.
12. Inflammation and epithelial cell injury in AIDS enteropathy: involvement of endoplasmic reticulum stress. Maingat F, etal., FASEB J. 2011 Jul;25(7):2211-20. Epub 2011 Mar 22.
13. Dermatophagoides farinae-1-derived peptides and HLA molecules recognized by T cells from atopic individuals. Matsuoka T, etal., Int Arch Allergy Immunol. 1997 Apr;112(4):365-70.
14. Genome-wide expression analysis detects eight genes with robust alterations specific to bipolar I disorder: relevance to neuronal network perturbation. Nakatani N, etal., Hum Mol Genet. 2006 Jun 15;15(12):1949-62. Epub 2006 May 10.
15. Messenger RNA expression of major histocompatibility complex class II genes in whole blood from septic shock patients. Pachot A, etal., Crit Care Med. 2005 Jan;33(1):31-8; discussion 236-7.
16. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
17. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
18. GOA pipeline RGD automated data pipeline
19. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
21. Comprehensive gene review and curation RGD comprehensive gene curation
22. T-cell tolerance by dendritic cells and macrophages as a mechanism for the major histocompatibility complex-linked resistance to autoimmune diabetes. Thiessen S, etal., Diabetes. 2002 Feb;51(2):325-38.
23. Decreased monocyte human leukocyte antigen-DR expression after severe burn injury: Correlation with severity and secondary septic shock. Venet F, etal., Crit Care Med. 2007 Aug;35(8):1910-7.
Additional References at PubMed
PMID:1300424   PMID:1448172   PMID:3122183   PMID:3865897   PMID:7477400   PMID:7606781   PMID:8890155   PMID:9354468   PMID:9745012   PMID:11487543   PMID:12136338   PMID:12477932  
PMID:12519789   PMID:12879310   PMID:15517241   PMID:15711804   PMID:18305173   PMID:19056867   PMID:19117940   PMID:19199708   PMID:20458337   PMID:21502329   PMID:22733780   PMID:23227193  
PMID:23376485   PMID:24586191  


Genomics

Comparative Map Data
RT1-Da
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,513,464 - 4,518,457 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl204,512,911 - 4,518,455 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx205,276,067 - 5,281,031 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0204,637,807 - 4,642,772 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0205,110,863 - 5,115,835 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0204,127,644 - 4,132,616 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,127,644 - 4,132,616 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,207,782 - 6,212,754 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,636,310 - 4,641,282 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera206,115,646 - 6,120,618 (+)NCBICelera
Cytogenetic Map20p12NCBI
HLA-DRA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38632,439,887 - 32,445,046 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl632,439,878 - 32,445,046 (+)EnsemblGRCh38hg38GRCh38
GRCh37632,407,664 - 32,412,823 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36632,515,625 - 32,520,801 (+)NCBINCBI36Build 36hg18NCBI36
Build 34632,515,624 - 32,520,799NCBI
Celera633,973,612 - 33,978,821 (+)NCBICelera
Cytogenetic Map6p21.32NCBI
HuRef632,160,529 - 32,165,737 (+)NCBIHuRef
CHM1_1632,410,098 - 32,415,302 (+)NCBICHM1_1
T2T-CHM13v2.0632,292,811 - 32,297,976 (+)NCBIT2T-CHM13v2.0
H2-Ea
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391734,560,926 - 34,563,619 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1734,560,926 - 34,563,618 (-)EnsemblGRCm39 Ensembl
GRCm381734,341,952 - 34,344,645 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1734,341,959 - 34,344,645 (-)EnsemblGRCm38mm10GRCm38
MGSCv371734,478,902 - 34,484,492 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361734,479,157 - 34,481,590 (-)NCBIMGSCv36mm8
Celera1737,104,259 - 37,109,038 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1717.98NCBI
LOC102019320
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554371,109,713 - 1,114,802 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554371,109,735 - 1,114,742 (+)NCBIChiLan1.0ChiLan1.0
LOC100987081
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1642,882,622 - 42,887,781 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0632,105,421 - 32,110,579 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1632,982,228 - 32,987,417 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl632,982,228 - 32,987,417 (+)Ensemblpanpan1.1panPan2
DLA-DRA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1122,133,026 - 2,137,825 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl122,132,499 - 2,168,975 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha122,282,352 - 2,285,906 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0122,409,388 - 2,414,180 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl122,409,425 - 2,449,778 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1122,132,677 - 2,136,225 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0122,213,826 - 2,217,378 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0122,287,866 - 2,291,417 (+)NCBIUU_Cfam_GSD_1.0
LOC101969065
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494637,016,438 - 37,021,225 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936727540,217 - 545,036 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936727540,225 - 544,968 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLA-DRA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl724,825,054 - 24,835,158 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1724,825,037 - 24,830,650 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2729,036,552 - 29,042,147 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap7q1.1NCBI
MHC-DRA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11739,623,324 - 39,628,464 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1739,622,402 - 39,629,261 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604432,311,484 - 32,316,629 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
LOC101706353
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475424,079,366 - 24,084,512 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475424,079,459 - 24,086,342 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in RT1-Da
89 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:37
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000048332
Prediction methods:Miranda, Rnahybrid
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
RH130473  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,518,304 - 4,518,455 (-)MAPPERmRatBN7.2
Rnor_6.0204,127,646 - 4,127,796NCBIRnor6.0
Rnor_5.0206,207,784 - 6,207,934UniSTSRnor5.0
RGSC_v3.4204,641,130 - 4,641,280UniSTSRGSC3.4
Celera206,120,466 - 6,120,616UniSTS
RH 3.4 Map2057.34UniSTS
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 3
Medium 3 12 32 17 16 17 6 8 19 9 11 6
Low 15 13 12 12 2 3 25 10 23 2
Below cutoff 6 8 8 8 25 6 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001008847 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AJ002991 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ002992 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ002993 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ002994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ002995 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ002996 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ002997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ002998 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ002999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ003000 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ003001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ305304 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ554216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY436750 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626210 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626211 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626212 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626213 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626214 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626215 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626218 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY701539 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC098677 (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
  D16225 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM048166 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218406 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218574 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220966 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226848 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227693 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230207 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232717 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232757 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233042 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233454 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233943 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234684 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235025 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC222932 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC222933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC222934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC222935 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC222936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M15562 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y00480 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSRNOT00000048332   ⟹   ENSRNOP00000048774
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,513,485 - 4,518,455 (+)Ensembl
Rnor_6.0 Ensembl204,127,644 - 4,132,616 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077630   ⟹   ENSRNOP00000074986
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,131,722 - 4,132,604 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081202
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,128,701 - 4,129,503 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115035   ⟹   ENSRNOP00000095893
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,512,911 - 4,518,455 (+)Ensembl
RefSeq Acc Id: NM_001008847   ⟹   NP_001008847
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,513,485 - 4,518,457 (+)NCBI
Rnor_6.0204,127,644 - 4,132,616 (-)NCBI
Rnor_5.0206,207,782 - 6,212,754 (-)NCBI
RGSC_v3.4204,636,310 - 4,641,282 (+)RGD
Celera206,115,646 - 6,120,618 (+)RGD
Sequence:
RefSeq Acc Id: XM_039098493   ⟹   XP_038954421
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,513,464 - 4,518,457 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001008847 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954421 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41609 (Get FASTA)   NCBI Sequence Viewer  
  AAH98677 (Get FASTA)   NCBI Sequence Viewer  
  AAR87772 (Get FASTA)   NCBI Sequence Viewer  
  AAV40639 (Get FASTA)   NCBI Sequence Viewer  
  AAV40640 (Get FASTA)   NCBI Sequence Viewer  
  AAV40641 (Get FASTA)   NCBI Sequence Viewer  
  AAV40642 (Get FASTA)   NCBI Sequence Viewer  
  AAV40643 (Get FASTA)   NCBI Sequence Viewer  
  AAV40644 (Get FASTA)   NCBI Sequence Viewer  
  AAV40645 (Get FASTA)   NCBI Sequence Viewer  
  AAV40646 (Get FASTA)   NCBI Sequence Viewer  
  AAV40647 (Get FASTA)   NCBI Sequence Viewer  
  AAV40648 (Get FASTA)   NCBI Sequence Viewer  
  AAW28800 (Get FASTA)   NCBI Sequence Viewer  
  AGV39029 (Get FASTA)   NCBI Sequence Viewer  
  AGV39030 (Get FASTA)   NCBI Sequence Viewer  
  AGV39031 (Get FASTA)   NCBI Sequence Viewer  
  AGV39032 (Get FASTA)   NCBI Sequence Viewer  
  AGV39033 (Get FASTA)   NCBI Sequence Viewer  
  CAA05782 (Get FASTA)   NCBI Sequence Viewer  
  CAA05783 (Get FASTA)   NCBI Sequence Viewer  
  CAA05784 (Get FASTA)   NCBI Sequence Viewer  
  CAA05785 (Get FASTA)   NCBI Sequence Viewer  
  CAA05786 (Get FASTA)   NCBI Sequence Viewer  
  CAA05787 (Get FASTA)   NCBI Sequence Viewer  
  CAA05788 (Get FASTA)   NCBI Sequence Viewer  
  CAA05789 (Get FASTA)   NCBI Sequence Viewer  
  CAA05790 (Get FASTA)   NCBI Sequence Viewer  
  CAA05791 (Get FASTA)   NCBI Sequence Viewer  
  CAA05792 (Get FASTA)   NCBI Sequence Viewer  
  CAA68540 (Get FASTA)   NCBI Sequence Viewer  
  CAC28142 (Get FASTA)   NCBI Sequence Viewer  
  CAD86939 (Get FASTA)   NCBI Sequence Viewer  
  CAE83948 (Get FASTA)   NCBI Sequence Viewer  
  EDL96796 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000048774
  ENSRNOP00000048774.2
  ENSRNOP00000095893.1
RefSeq Acc Id: NP_001008847   ⟸   NM_001008847
- Peptide Label: precursor
- UniProtKB: Q6MG98 (UniProtKB/TrEMBL),   A0A023IKG5 (UniProtKB/TrEMBL),   A0A023IM59 (UniProtKB/TrEMBL),   Q6T4R6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000048774   ⟸   ENSRNOT00000048332
RefSeq Acc Id: ENSRNOP00000074986   ⟸   ENSRNOT00000077630
RefSeq Acc Id: XP_038954421   ⟸   XM_039098493
- Peptide Label: isoform X1
- UniProtKB: Q6MG98 (UniProtKB/TrEMBL),   A0A023IKG5 (UniProtKB/TrEMBL),   A0A023IM59 (UniProtKB/TrEMBL),   Q6T4R6 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000095893   ⟸   ENSRNOT00000115035
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6MG98-F1-model_v2 AlphaFold Q6MG98 1-255 view protein structure

Transcriptome

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

Promoters
RGD ID:13701332
Promoter ID:EPDNEW_R11854
Type:multiple initiation site
Name:RT1-Da_1
Description:RT1 class II, locus Da
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_6.0204,132,599 - 4,132,659EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1593283 AgrOrtholog
BioCyc Gene G2FUF-4566 BioCyc
Ensembl Genes ENSRNOG00000032844 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048332 ENTREZGENE
  ENSRNOT00000048332.5 UniProtKB/TrEMBL
  ENSRNOT00000115035.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7373701 IMAGE-MGC_LOAD
InterPro Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig/MHC_CS UniProtKB/TrEMBL
  Ig_C1-set UniProtKB/TrEMBL
  MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  MHC_II_a/b_N UniProtKB/TrEMBL
  MHC_II_a_N UniProtKB/TrEMBL
KEGG Report rno:294269 UniProtKB/TrEMBL
MGC_CLONE MGC:112637 IMAGE-MGC_LOAD
NCBI Gene 294269 ENTREZGENE
PANTHER HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN-RELATED UniProtKB/TrEMBL
  MHC CLASS II-RELATED UniProtKB/TrEMBL
Pfam C1-set UniProtKB/TrEMBL
  MHC_II_alpha UniProtKB/TrEMBL
PhenoGen RT1-Da PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000032844 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
  MHC_II_alpha UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A023IKG5 ENTREZGENE, UniProtKB/TrEMBL
  A0A023IM59 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AUC1_RAT UniProtKB/TrEMBL
  Q6MG98 ENTREZGENE, UniProtKB/TrEMBL
  Q6T4R6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-14 RT1-Da   RT1 class II, locus Da  H2-Ea  histocompatibility 2, class II antigen E alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 H2-Ea  histocompatibility 2, class II antigen E alpha  RT1-Da  RT1 class II, locus Da  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-04-12 RT1-Da  RT1 class II, locus Da  RT1-Da_mapped  RT1 class II, locus Da (mapped)  Data merged from RGD:3479 737654 APPROVED
2006-11-20 RT1-Da_mapped  RT1 class II, locus Da(mapped)  RT1-Da  RT1 class II, locus Da  Symbol set to symbol_mapped, name set to name (mapped) 1582166 APPROVED
2006-11-20 RT1-Da  RT1 class II, locus Da      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-02-11 RT1-Da  RT1 class II, locus Da      Symbol and Name status set to approved 625702 APPROVED
2002-06-10 RT1-Da  RT1 class II, locus Da      Symbol and Name status set to approved 70586 APPROVED