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

    Gene ID: 24973, updated on 9-Dec-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
    EnsemblRapid:ENSRNOG00000069209 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 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). [provided by Alliance of Genome Resources, Dec 2024]
    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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    See RT1-A1 in Genome Data Viewer
    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. Expression of the rat MHC class I gene in the human B lymphoblastoid cell line Hmy 2 CIR. Salgar SK, et al. Eur J Immunogenet, 1995 Dec. PMID 8597563
    2. Self-MHC class Ia (RT1-A(n)) protects cells co-expressing the activatory allogeneic MHC class Ib molecule (RT1-E(u)) from NK lysis. Bäckman-Petersson E, et al. Int Immunol, 2000 Jun. PMID 10837412
    3. Peptide specificity of RT1-A1(c), an inhibitory rat major histocompatibility complex class I natural killer cell ligand. Stevens J, et al. J Biol Chem, 2000 Sep 22. PMID 10856297
    4. 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
    5. 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

    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 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 
    Process Evidence Code Pubs
    involved_in T cell tolerance induction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 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 

    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
      Related
      ENSRNOP00000079066.3, ENSRNOT00000116105.3
      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

      UniProtKB/TrEMBL
      A0A2P1NRV5

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

      UniProtKB/TrEMBL
      A0A2P1NRV5

    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

      UniProtKB/TrEMBL
      A0A2P1NRV5
    Nucleotide Protein Strain
    Heading Accession and Version

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