RT1-A3 (RT1 class I, locus A3) - Rat Genome Database

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Gene: RT1-A3 (RT1 class I, locus A3) Rattus norvegicus
Analyze
Symbol: RT1-A3
Name: RT1 class I, locus A3
RGD ID: 1359610
Description: PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 3-chloropropane-1,2-diol
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: MHC class I antigen; MHC class I protein; RT1; RT1 class I, A3; RT1 class Ia, A3n; RT1-A; RT1-A3n; RT1.A3
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,847,518 - 4,851,344 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_WKY_Bbb_1.0205,444,065 - 5,447,816 (+)NCBIRnor_WKY
RGSC_v3.4204,998,645 - 5,002,204 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1204,998,871 - 5,002,431 (+)NCBI
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. A novel instance of class I modification (cim) affecting two of three rat class I RT1-A molecules within one MHC haplotype. Gonzalez-Munoz AL, etal., J Immunol. 2003 Jul 1;171(1):274-84.
2. RT1-U: identification of a novel, active, class Ib alloantigen of the rat MHC. Leong LY, etal., J Immunol 1999 Jan 15;162(2):743-52.
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Physical mapping and evolution of the centromeric class I gene-containing region of the rat MHC. Walter L and Gunther E, Immunogenetics 2000 Aug;51(10):829-37.
7. Nucleotide sequences of three distinct clones coding for rat heavy chain class I major histocompatibility antigens. Wang M, etal., Immunogenetics 1996;43(5):318-20.
Additional References at PubMed
PMID:22562814   PMID:29531166  


Genomics

Variants

.
Variants in RT1-A3
361 total Variants

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
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
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2046066076691706Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
7175096Tcs1T cell selection QTL 1T cell selectionexpression2047270785024580Rat

Markers in Region
H2-Q6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,905,718 - 4,906,260 (+)MAPPERmRatBN7.2
Rnor_6.0205,414,820 - 5,415,361NCBIRnor6.0
Rnor_5.0207,474,964 - 7,475,505UniSTSRnor5.0
RGSC_v3.4205,057,088 - 5,057,629UniSTSRGSC3.4
RGSC_v3.4204,998,963 - 4,999,507UniSTSRGSC3.4
Celera206,489,355 - 6,489,896UniSTS
Celera206,447,813 - 6,448,357UniSTS
Cytogenetic Map20p12UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: NM_001008830   ⟹   NP_001008830
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,847,589 - 4,851,320 (+)NCBI
RGSC_v3.4204,998,645 - 5,002,204 (+)RGD
RefSeq Acc Id: XM_039098676   ⟹   XP_038954604
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,847,518 - 4,851,344 (+)NCBI
RefSeq Acc Id: XM_039098677   ⟹   XP_038954605
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,847,518 - 4,851,344 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001008830   ⟸   NM_001008830
- Peptide Label: precursor
- UniProtKB: Q9JHM2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038954605   ⟸   XM_039098677
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038954604   ⟸   XM_039098676
- Peptide Label: isoform X1
Protein Domains
Ig-like


Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-4533 BioCyc
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.30.500.10 UniProtKB/TrEMBL
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-like_Ag-recog UniProtKB/TrEMBL
  MHC_I-like_Ag-recog_sf UniProtKB/TrEMBL
  MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  MHC_I_a_a1/a2 UniProtKB/TrEMBL
  MHC_I_a_C UniProtKB/TrEMBL
KEGG Report rno:309627 UniProtKB/TrEMBL
NCBI Gene 309627 ENTREZGENE
PANTHER CLASS IB MHC ANTIGEN QA-2-RELATED UniProtKB/TrEMBL
  MHC CLASS I-RELATED UniProtKB/TrEMBL
Pfam C1-set UniProtKB/TrEMBL
  MHC_I UniProtKB/TrEMBL
  MHC_I_C UniProtKB/TrEMBL
PhenoGen RT1-A3 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt Q9JHM2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-15 RT1-A3  RT1 class I, locus A3  RT1-A3  RT1 class I, A3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 RT1-A3  RT1 class I, A3      Symbol and Name status set to provisional 70820 PROVISIONAL