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    RT1-S3 RT1 class Ib, locus S3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 294228, updated on 29-Feb-2024

    Summary

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    Official Symbol
    RT1-S3provided by RGD
    Official Full Name
    RT1 class Ib, locus S3provided by RGD
    Primary source
    RGD:735037
    See related
    Ensembl:ENSRNOG00000000777 AllianceGenome:RGD:735037
    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
    RTBM1; H2-T23; RT-BM1; RT1-BM1
    Summary
    Predicted to enable beta-2-microglobulin binding activity; peptide antigen binding activity; and signaling receptor binding activity. Predicted to be involved in several processes, including positive regulation of gene expression; positive regulation of lymphocyte proliferation; and regulation of leukocyte mediated cytotoxicity. Predicted to act upstream of or within antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent and inner ear development. Predicted to be located in cell surface and plasma membrane. Predicted to be part of MHC class I protein complex and MHC class Ib protein complex. Predicted to be active in external side of plasma membrane and extracellular space. Human ortholog(s) of this gene implicated in occupational asthma. Orthologous to human HLA-E (major histocompatibility complex, class I, E). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Spleen (RPKM 513.9), Lung (RPKM 420.3) and 9 other tissues See more
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    Genomic context

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    See RT1-S3 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 (2675463..2680229)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (2670654..2675411)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (3176124..3180825)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene RT1 class Ib, locus O1 like 1 Neighboring gene uncharacterized LOC134483846 Neighboring gene RT1 class Ib, locus S2 Neighboring gene RT1 class Ib, locus O1 Neighboring gene RT1 class Ib, locus N3 Neighboring gene RT1 class I, locus T24, gene 4 Neighboring gene class I gene fragment 2361 Neighboring gene ribosomal protein L41, pseudogene 1

    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. Comparison of RT-BM1 sequences from six different rat major histocompatibility complex haplotypes reveals limited variation, and alternate splicing in the 3' untranslated region. Lau P, et al. Immunogenetics, 2000 Feb. PMID 10663577
    2. Structural organization, sequence analysis, and physical mapping of the Grc-linked class Ib gene RT1.S3 in the rat. Salgar SK, et al. Immunogenetics, 1998 Jun. PMID 9601949
    3. A rat class I cDNA clone with an Alu-like sequence and mapping to two genes in RT1.C/E. Parker KE, et al. Immunogenetics, 1990. PMID 1969387
    4. Distinct HLA-E Peptide Complexes Modify Antibody-Driven Effector Functions of Adaptive NK Cells. Rölle A, et al. Cell Rep, 2018 Aug 21. PMID 30134159
    5. Pathogen-derived HLA-E bound epitopes reveal broad primary anchor pocket tolerability and conformationally malleable peptide binding. Walters LC, et al. Nat Commun, 2018 Aug 7. PMID 30087334, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables peptide antigen binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables signaling receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    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 positive regulation of T cell mediated cytotoxicity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    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
    		  

    General protein information

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    Preferred Names
    RT1 class Ib, locus S3
    Names
    MHC class Ib RT1.S3
    RT1 class Ib, locus BM1
    histocompatibility 2, T region locus 23

    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_001008886.2 → NP_001008886.2  RT1 class Ib, locus S3 precursor

      See identical proteins and their annotated locations for NP_001008886.2

      Status: VALIDATED

      Source sequence(s)
      AJ243976, BX883048, CK599963
      UniProtKB/TrEMBL
      F1LQF2, O78105, O78106
      Related
      ENSRNOP00000001036.6, ENSRNOT00000001036.8
      Conserved Domains (2) summary
      cd07698
      Location:205 → 297
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam00129
      Location:24 → 201
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

    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
      2675463..2680229
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006255917.5 → XP_006255979.1  RT1 class Ib, locus S3 isoform X1

      See identical proteins and their annotated locations for XP_006255979.1

      UniProtKB/TrEMBL
      F1LQF2, O78105, O78106
      Conserved Domains (2) summary
      cd07698
      Location:205 → 297
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam00129
      Location:24 → 201
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    Nucleotide Protein Strain
    Heading Accession and Version

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