RT1-A1 (RT1 class Ia, locus A1) - Rat Genome Database

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Gene: RT1-A1 (RT1 class Ia, locus A1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-A1
Name: RT1 class Ia, locus A1
RGD ID: 1595924
Description: Enables beta-2-microglobulin binding activity and peptide binding activity. Involved in T cell tolerance induction; negative regulation of natural killer cell mediated cytotoxicity; and positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. Predicted to be located in lumenal side of endoplasmic reticulum membrane and phagocytic vesicle membrane. Predicted to be part of MHC class I protein complex. Predicted to be active in external side of plasma membrane and extracellular space. Used to study graft-versus-host disease. Human ortholog(s) of this gene implicated in several diseases, including artery disease (multiple); asthma (multiple); autoimmune disease (multiple); eye disease (multiple); and inner ear disease (multiple). Orthologous to several human genes including HLA-B (major histocompatibility complex, class I, B); HLA-C (major histocompatibility complex, class I, C); and HLA-E (major histocompatibility complex, class I, E); PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; ammonium acetate.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: RT1 class I gene (A-1); RT1 class Ia, A1n; RT1 class Ia, locus A (A1); RT1 class Ia, locus A1 (mapped); RT1-A; RT1-A1_mapped; RT1-A1n; RT1.A1(N); RT1A-1
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,907,139 - 4,910,798 (+)NCBIGRCr8
mRatBN7.2204,905,309 - 4,914,593 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.0205,414,463 - 5,418,012 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,351,605 - 5,421,098 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0207,474,607 - 7,478,550 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,056,763 - 5,060,280 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera206,489,030 - 6,492,547 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Self-MHC class Ia (RT1-A(n)) protects cells co-expressing the activatory allogeneic MHC class Ib molecule (RT1-E(u)) from NK lysis. Backman-Petersson E, etal., Int Immunol. 2000 Jun;12(6):843-50.
2. Donor-derived soluble MHC antigens plus low-dose cyclosporine induce transplantation unresponsiveness independent of the thymus by down-regulating T cell-mediated alloresponses in a rat transplantation model. Behrens D, etal., Transplantation. 2001 Dec 27;72(12):1974-82.
3. Recombinant dimeric MHC antigens protect cardiac allografts from rejection and visualize alloreactive T cells. Fried A, etal., J Leukoc Biol. 2005 Sep;78(3):595-604. Epub 2005 Jul 6.
4. 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.
5. 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.
6. Use of allochimeric proteins to mitigate graft-versus-host and host-versus-graft immune responses to rat small bowel allografts. Okamoto M, etal., Transplantation. 2000 Oct 15;70(7):1060-7.
7. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
8. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
9. GOA pipeline RGD automated data pipeline
10. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Expression of the rat MHC class I gene in the human B lymphoblastoid cell line Hmy 2 CIR. Salgar SK, etal., Eur J Immunogenet. 1995 Dec;22(6):479-83.
13. Peptide specificity of RT1-A1(c), an inhibitory rat major histocompatibility complex class I natural killer cell ligand. Stevens J, etal., J Biol Chem. 2000 Sep 22;275(38):29217-24.
14. Oral feeding of an immunodominant MHC donor-derived synthetic class I peptide prolongs graft survival of heterotopic cardiac allografts in a high-responder rat strain combination. Zavazava N, etal., J Leukoc Biol. 2000 Jun;67(6):793-800.
Additional References at PubMed
PMID:2420472   PMID:2784569   PMID:8046333   PMID:8617941   PMID:8881041   PMID:9443915   PMID:9754572   PMID:11685465   PMID:15004152   PMID:15045471   PMID:15056662   PMID:18502829  
PMID:20008523   PMID:20946353   PMID:21841133   PMID:22031944   PMID:22321387   PMID:22562814   PMID:23646949   PMID:24586191   PMID:29531166  


Genomics

Variants

.
Variants in RT1-A1
848 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:408
Count of miRNA genes:220
Interacting mature miRNAs:255
Transcripts:ENSRNOT00000041590
Prediction methods:Microtar, 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
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-D1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,908,501 - 4,908,657 (+)MAPPERmRatBN7.2
Rnor_6.0205,417,603 - 5,417,758NCBIRnor6.0
Rnor_5.0207,477,747 - 7,477,902UniSTSRnor5.0
RGSC_v3.4205,059,871 - 5,060,026UniSTSRGSC3.4
Celera206,492,138 - 6,492,293UniSTS
Celera20685,255 - 685,411UniSTS
Celera205,715,355 - 5,715,511UniSTS
Cytogenetic Map20p12UniSTS
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
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
Medium 3 15 49 33 19 33 3 7 17 23 11
Low 26 8 8 8 8 8 63 16 17 8
Below cutoff 2 4 2 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001008827 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098424 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AJ243580 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX883042 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212678 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214333 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228888 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231496 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233575 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235186 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC222922 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MG963095 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U50448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X90375 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSRNOT00000041590   ⟹   ENSRNOP00000039088
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,351,621 - 5,418,012 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078972   ⟹   ENSRNOP00000075633
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,353,443 - 3,358,533 (-)Ensembl
Rnor_6.0 Ensembl205,414,448 - 5,418,015 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080900   ⟹   ENSRNOP00000071804
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,350,937 - 3,380,362 (-)Ensembl
Rnor_6.0 Ensembl205,414,457 - 5,418,019 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000081240   ⟹   ENSRNOP00000074602
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,351,621 - 5,418,013 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082538   ⟹   ENSRNOP00000072208
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,351,621 - 5,421,098 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089306   ⟹   ENSRNOP00000073206
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,351,605 - 5,418,011 (+)Ensembl
RefSeq Acc Id: NM_001008827   ⟹   NP_001008827
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,907,209 - 4,910,798 (+)NCBI
mRatBN7.2204,905,325 - 4,908,914 (+)NCBI
Rnor_6.0205,414,495 - 5,418,012 (+)NCBI
Rnor_5.0207,474,607 - 7,478,550 (+)NCBI
RGSC_v3.4205,056,763 - 5,060,280 (+)RGD
Celera206,489,030 - 6,492,547 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256099   ⟹   XP_006256161
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,907,139 - 4,910,798 (+)NCBI
mRatBN7.2204,905,309 - 4,908,914 (+)NCBI
Rnor_6.0205,414,463 - 5,418,012 (+)NCBI
Rnor_5.0207,474,607 - 7,478,550 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039098424   ⟹   XP_038954352
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,907,139 - 4,910,798 (+)NCBI
mRatBN7.2204,905,309 - 4,908,374 (+)NCBI
RefSeq Acc Id: XM_063278962   ⟹   XP_063135032
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,907,139 - 4,910,258 (+)NCBI
RefSeq Acc Id: XM_063278963   ⟹   XP_063135033
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,907,139 - 4,910,798 (+)NCBI
RefSeq Acc Id: XM_063278964   ⟹   XP_063135034
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,907,139 - 4,910,798 (+)NCBI
RefSeq Acc Id: NP_001008827   ⟸   NM_001008827
- Peptide Label: precursor
- UniProtKB: Q6MGB9 (UniProtKB/TrEMBL),   A0A2P1NRV5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256161   ⟸   XM_006256099
- Peptide Label: isoform X5
- UniProtKB: A0A2P1NRV5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072208   ⟸   ENSRNOT00000082538
RefSeq Acc Id: ENSRNOP00000039088   ⟸   ENSRNOT00000041590
RefSeq Acc Id: ENSRNOP00000073206   ⟸   ENSRNOT00000089306
RefSeq Acc Id: ENSRNOP00000071804   ⟸   ENSRNOT00000080900
RefSeq Acc Id: ENSRNOP00000074602   ⟸   ENSRNOT00000081240
RefSeq Acc Id: ENSRNOP00000075633   ⟸   ENSRNOT00000078972
RefSeq Acc Id: XP_038954352   ⟸   XM_039098424
- Peptide Label: isoform X2
- UniProtKB: A0A2P1NRV5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135033   ⟸   XM_063278963
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063135034   ⟸   XM_063278964
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063135032   ⟸   XM_063278962
- Peptide Label: isoform X1
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K1E1-F1-model_v2 AlphaFold A0A0G2K1E1 1-382 view protein structure

Transcriptome

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

Promoters
RGD ID:13701407
Promoter ID:EPDNEW_R11931
Type:single initiation site
Name:RT1-A1_1
Description:RT1 class Ia, locus A1
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_6.0205,414,475 - 5,414,535EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595924 AgrOrtholog
BioCyc Gene G2FUF-4523 BioCyc
Ensembl Genes ENSRNOG00000038999 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000080900.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.30.500.10 UniProtKB/TrEMBL
InterPro Ig-like 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:24973 UniProtKB/TrEMBL
NCBI Gene 24973 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-A1 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000038999 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A0G2K1E1_RAT UniProtKB/TrEMBL
  A0A2P1NRV5 ENTREZGENE, UniProtKB/TrEMBL
  Q6MGB9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-04-12 RT1-A1  RT1 class Ia, locus A1  RT1-A1_mapped  RT1 class Ia, locus A1 (mapped)  Data merged from RGD:3465 737654 APPROVED
2006-11-20 RT1-A1  RT1 class Ia, locus A1      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 RT1-A1_mapped  RT1 class Ia, locus A1(mapped)  RT1-A1  RT1 class Ia, locus A1  Symbol set to symbol_mapped, name set to name (mapped) 1582166 APPROVED
2004-02-13 RT1-A1  RT1 class Ia, locus A1  RT1A-1  RT1 class I gene (A-1)  Data merged from RGD:3509 737654 APPROVED
2004-02-11 RT1-A1  RT1 class Ia, locus A1      Symbol and Name status set to approved 625702 APPROVED
2002-06-10 RT1-A1  RT1 class Ia, locus A (A1)      Symbol and Name status set to approved 70586 APPROVED