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    RT1-M5 RT1 class Ib, locus M5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 499400, updated on 9-Dec-2024

    Summary

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    Official Symbol
    RT1-M5provided by RGD
    Official Full Name
    RT1 class Ib, locus M5provided by RGD
    Primary source
    RGD:1595816
    See related
    EnsemblRapid:ENSRNOG00000033136 AllianceGenome:RGD:1595816
    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
    Hla-f; RT1.M5; RGD1560260
    Summary
    Predicted to enable peptide antigen binding activity and signaling receptor binding activity. Predicted to be involved in several processes, including antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent; antigen processing and presentation of endogenous peptide antigen via MHC class Ib; and positive regulation of T cell mediated cytotoxicity. Predicted to be active in external side of plasma membrane and extracellular space. Human ortholog(s) of this gene implicated in several diseases, including Stevens-Johnson syndrome; 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 Thymus (RPKM 11.3), Testes (RPKM 5.4) and 6 other tissues See more
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    Genomic context

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    See RT1-M5 in Genome Data Viewer
    Location:
    20p12
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (1551751..1554015, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (1546496..1548948, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (2038158..2040422, complement)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene gamma-aminobutyric acid type B receptor subunit 1 Neighboring gene myelin oligodendrocyte glycoprotein Neighboring gene zinc finger protein 57 Neighboring gene RT1 class Ib, locus M4 Neighboring gene ribosomal protein S15, 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. HLA-B27 subtypes in Turkish patients with ankylosing spondylitis and healthy controls. Acar M, et al. Rheumatol Int, 2012 Oct. PMID 21927904
    2. Novel HLA B*2714 and B*2708 allele associations in seronegative spondarthritis patients and haemophilia patients with chronic synovitis in India. Shankarkumar U, et al. Tissue Antigens, 2003 Aug. PMID 12889998
    3. Clinical phenotype is related to HLA genotype in the peripheral arthropathies of inflammatory bowel disease. Orchard TR, et al. Gastroenterology, 2000 Feb. PMID 10648455
    4. Lack of association of HLA-B*51 with a severe disease course in Behçet's disease. Gül A, et al. Rheumatology (Oxford), 2001 Jun. PMID 11426025
    5. Structure and expression of MHC class Ib genes of the central M region in rat and mouse: M4, M5, and M6. Lambracht-Washington D, et al. Immunogenetics, 2008 Apr. PMID 18324395

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    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 M5
    Names
    MHC class Ib antigen RT1.M5 long isoform
    MHC class Ib antigen RT1.M5 short isoform
    major histocompatibility complex, class I, F

    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_001048045.2 → NP_001041510.2  RT1 class Ib, locus M5 isoform 2 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region compared to variant 1. The resulting protein (isoform 2) is shorter but has the same N- and C-termini compared to isoform 1.
      Source sequence(s)
      BX883052
      UniProtKB/TrEMBL
      Q0PKT2
      Related
      ENSRNOP00000098015.2, ENSRNOT00000120325.2
      Conserved Domains (2) summary
      cd07698
      Location:208 → 300
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam00129
      Location:26 → 204
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

    2. NM_001168353.1 → NP_001161825.1  RT1 class Ib, locus M5 isoform 1 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      BX883052
      UniProtKB/TrEMBL
      F1MAR7, Q0PKT2
      Related
      ENSRNOP00000045665.4, ENSRNOT00000052311.6
      Conserved Domains (2) summary
      cd07698
      Location:208 → 300
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam00129
      Location:26 → 204
      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
      1551751..1554015 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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