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

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Gene: RT1-A3 (RT1 class I, locus A3) Rattus norvegicus
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Symbol: RT1-A3
Name: RT1 class I, locus A3
RGD ID: 1359610
Description: INVOLVED IN antigen processing and presentation (inferred); antigen processing and presentation of peptide antigen via MHC class I (inferred); immune response (inferred); PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; FOUND IN lumenal side of endoplasmic reticulum membrane (inferred); membrane (inferred); MHC class I protein complex (inferred); 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: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,849,410 - 4,853,233 (+)NCBIGRCr8GRCr8GRCr8
mRatBN7.2204,847,518 - 4,851,344 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_WKY_Bbb_1.0205,444,065 - 5,447,816 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
RGSC_v3.4204,998,645 - 5,002,204 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
RGSC_v3.1204,998,871 - 5,002,431 (+)NCBI
Cytogenetic Map20p12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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
382 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)20418947649189476Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015332005306452Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124164241Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)2016693431Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20127341128Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129193376Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129193376Rat
7175096Tcs1T cell selection QTL 1T cell selection trait (VT:0004917)expression2047282825026446Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2016693431Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20126925056Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126128279Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
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)20134066551Rat
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)20362632310078622Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129193376Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036263239244918Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129193376Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129193376Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20114100378Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat

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

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
7 1 15 42 67 131 88 7 45 36 32 14 14

Sequence


RefSeq Acc Id: NM_001008830   ⟹   NP_001008830
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,849,451 - 4,853,230 (+)NCBI
mRatBN7.2204,847,562 - 4,851,341 (+)NCBI
RGSC_v3.4204,998,645 - 5,002,204 (+)RGD
RefSeq Acc Id: XM_039098676   ⟹   XP_038954604
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,849,410 - 4,853,233 (+)NCBI
mRatBN7.2204,847,518 - 4,851,344 (+)NCBI
RefSeq Acc Id: NP_001008830   ⟸   NM_001008830
- Peptide Label: precursor
- UniProtKB: Q9JHM2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038954604   ⟸   XM_039098676
- Peptide Label: isoform X1
Protein Domains
Ig-like

Transcriptome

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


Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-4533 BioCyc
Ensembl Genes ENSRNOG00000071249 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000120568 ENTREZGENE
  ENSRNOT00000120568.2 UniProtKB/TrEMBL
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_class-I_related 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 HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, C ALPHA CHAIN 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
RatGTEx ENSRNOG00000071249 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0ABK0KVX6_RAT UniProtKB/TrEMBL
  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