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: Used to study graft-versus-host disease. Human ortholog(s) of this gene implicated in several diseases, including arthritis (multiple); asthma (multiple); eye disease (multiple); inner ear disease (multiple); and vasculitis (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-F (major histocompatibility complex, class I, F); 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 Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,907,139 - 4,910,798 (+)NCBIGRCr8GRCr8GRCr8
mRatBN7.2204,905,309 - 4,914,593 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.0205,414,463 - 5,418,012 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,351,605 - 5,421,098 (+)Ensemblrn6Rnor6.0
Rnor_5.0207,474,607 - 7,478,550 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4205,056,763 - 5,060,280 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera206,489,030 - 6,492,547 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

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

Cellular Component

Molecular Function

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
463 total Variants
miRNA Target Status (No longer updated)

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 (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-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

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 161 91 90 59 92 59 6 356 192 11 140 81 92 31 15 15

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

Ensembl Acc Id: ENSRNOT00000041590   ⟹   ENSRNOP00000039088
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,351,621 - 5,418,012 (+)Ensembl
Ensembl 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
Ensembl 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
Ensembl Acc Id: ENSRNOT00000081240   ⟹   ENSRNOP00000074602
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,351,621 - 5,418,013 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000082538   ⟹   ENSRNOP00000072208
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,351,621 - 5,421,098 (+)Ensembl
Ensembl 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:
Ensembl Acc Id: ENSRNOP00000072208   ⟸   ENSRNOT00000082538
Ensembl Acc Id: ENSRNOP00000039088   ⟸   ENSRNOT00000041590
Ensembl Acc Id: ENSRNOP00000073206   ⟸   ENSRNOT00000089306
Ensembl Acc Id: ENSRNOP00000071804   ⟸   ENSRNOT00000080900
Ensembl Acc Id: ENSRNOP00000074602   ⟸   ENSRNOT00000081240
Ensembl 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
- UniProtKB: A0A2P1NRV5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135034   ⟸   XM_063278964
- Peptide Label: isoform X4
- UniProtKB: A0A2P1NRV5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135032   ⟸   XM_063278962
- Peptide Label: isoform X1
- UniProtKB: A0A2P1NRV5 (UniProtKB/TrEMBL)
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
  ENSRNOG00000069209 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000116105 ENTREZGENE
  ENSRNOT00000116105.3 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_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:24973 UniProtKB/TrEMBL
NCBI Gene 24973 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-A1 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000038999 RatGTEx
  ENSRNOG00000069209 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A2P1NRV5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZMP3_RAT 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_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
2006-11-20 RT1-A1  RT1 class Ia, locus A1      Symbol and Name status set to provisional 70820 PROVISIONAL
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