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RT1-A1 RT1 class Ia, locus A1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 24973, updated on 13-Apr-2024

Summary

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Official Symbol
RT1-A1provided by RGD
Official Full Name
RT1 class Ia, locus A1provided by RGD
Primary source
RGD:1595924
See related
AllianceGenome:RGD:1595924
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
RT1-A; RT1A-1; RT1-A1n; RT1.A1(N)
Summary
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 integral component of membrane. Predicted to be active in external side of plasma membrane and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Spleen (RPKM 1410.0), Lung (RPKM 1210.9) and 9 other tissues See more
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Genomic context

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Location:
20p12
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (4907139..4910798)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (4905309..4914593)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (5414463..5418012)

Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene Cdk2ap1-pseudogene 1 Neighboring gene LOC224733l-1 pseudogene Neighboring gene VPS52 subunit of GARP complex Neighboring gene U6 spliceosomal RNA Neighboring gene ribosomal protein S18

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Recombinant dimeric MHC antigens protect cardiac allografts from rejection and visualize alloreactive T cells. Fried A, et al. J Leukoc Biol, 2005 Sep. PMID 16000395
  2. The rat RT1-A1c MHC molecule is a xenogeneic ligand recognized by the mouse activating Ly-49W and inhibitory Ly-49G receptors. Lavender KJ, et al. J Immunol, 2004 Mar 15. PMID 15004152
  3. 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, et al. Transplantation, 2001 Dec 27. PMID 11773898
  4. Use of allochimeric proteins to mitigate graft-versus-host and host-versus-graft immune responses to rat small bowel allografts. Okamoto M, et al. Transplantation, 2000 Oct 15. PMID 11045643
  5. 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, et al. J Leukoc Biol, 2000 Jun. PMID 10857851

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Induction of the MHCI antigen processing and presentation pathway in hippocampal neurons and glia may contribute to age-related hippocampal dysfunction by increasing neuroimmune signaling or altering synaptic homeostasis.
    Title: Neuroglial expression of the MHCI pathway and PirB receptor is upregulated in the hippocampus with advanced aging.
  2. the identity of the P2 peptide anchor residue is an integral component of MHC-I recognition by Ly49i2
    Title: Recognition of class I MHC by a rat Ly49 NK cell receptor is dependent on the identity of the P2 anchor amino acid of bound peptide.
  3. The class I major histocompatibility complex molecule RT1-A1c is a xenogeneic ligand for murine Ly-49W activating and Ly-49G inhibitory receptors.
    Title: The rat RT1-A1c MHC molecule is a xenogeneic ligand recognized by the mouse activating Ly-49W and inhibitory Ly-49G receptors.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables beta-2-microglobulin binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables peptide antigen binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables peptide binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-containing complex binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables signaling receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in T cell tolerance induction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class Ib IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of natural killer cell mediated cytotoxicity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of T cell mediated cytotoxicity IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of T cell mediated cytotoxicity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of tolerance induction to nonself antigen IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of MHC class I protein complex IEA
Inferred from Electronic Annotation
more info
  
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in lumenal side of endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  
located_in phagocytic vesicle membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
RT1 class Ia, locus A1
Names
RT1 class I gene (A-1)
RT1 class Ia, A1n
RT1 class Ia, locus A (A1)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001008827.2 → NP_001008827.1  RT1 class Ia, locus A1 precursor

    See identical proteins and their annotated locations for NP_001008827.1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000020
    UniProtKB/TrEMBL
    A0A2P1NRV5, Q6MGB9
    Conserved Domains (3) summary
    cd07698
    Location:207 → 299
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    pfam00129
    Location:25 → 203
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    pfam06623
    Location:342 → 368
    MHC_I_C; MHC_I C-terminus

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086038.1 Reference GRCr8

    Range
    4907139..4910798
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063278963.1 → XP_063135033.1  RT1 class Ia, locus A1 isoform X3

  2. XM_063278964.1 → XP_063135034.1  RT1 class Ia, locus A1 isoform X4

  3. XM_039098424.2 → XP_038954352.1  RT1 class Ia, locus A1 isoform X2

    UniProtKB/TrEMBL
    A0A2P1NRV5
    Conserved Domains (3) summary
    pfam00129
    Location:25 → 203
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    pfam06623
    Location:342 → 366
    MHC_I_C; MHC_I C-terminus
    cd21015
    Location:205 → 299
    IgC1_MHC_Ia_RT1-Aa; Class Ia major histocompatibility complex (MHC) immunoglobulin domain of RT1-Aa; member of the C1-set of Ig superfamily (IgSF) domains

  4. XM_006256099.5 → XP_006256161.1  RT1 class Ia, locus A1 isoform X5

    UniProtKB/TrEMBL
    A0A2P1NRV5
    Conserved Domains (2) summary
    cd07698
    Location:207 → 299
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    pfam00129
    Location:25 → 203
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

  5. XM_063278962.1 → XP_063135032.1  RT1 class Ia, locus A1 isoform X1

Nucleotide Protein Strain
Heading Accession and Version

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