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    RT1-M4 RT1 class Ib, locus M4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 309584, updated on 9-Dec-2024

    Summary

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    Official Symbol
    RT1-M4provided by RGD
    Official Full Name
    RT1 class Ib, locus M4provided by RGD
    Primary source
    RGD:1562593
    See related
    EnsemblRapid:ENSRNOG00000081704 AllianceGenome:RGD:1562593
    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.M4
    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 human 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 4.0), Testes (RPKM 3.3) and 9 other tissues See more
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    Genomic context

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    See RT1-M4 in Genome Data Viewer
    Location:
    20p12
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (1557312..1561063)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (1552072..1555823)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (2043710..2048575)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene myelin oligodendrocyte glycoprotein Neighboring gene zinc finger protein 57 Neighboring gene RT1 class Ib, locus M5 Neighboring gene ribosomal protein S15, pseudogene 1 Neighboring gene RT1 class I, locus M6, gene 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. 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
    2. Active MHC class Ib genes in rat are pseudogenes in the mouse. Lambracht-Washington D, et al. Immunogenetics, 2004 May. PMID 15069589
    3. The major histocompatibility complex of the rat (Rattus norvegicus). Günther E, et al. Immunogenetics, 2001 Sep. PMID 11685465
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    General protein information

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    Preferred Names
    RT1 class Ib, locus M4
    Names
    MHC class Ib antigen

    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_001168343.1 → NP_001161815.1  RT1 class Ib, locus M4 precursor

      See identical proteins and their annotated locations for NP_001161815.1

      Status: VALIDATED

      Source sequence(s)
      BX883052
      UniProtKB/TrEMBL
      F1LSU0
      Related
      ENSRNOP00000100825.1, ENSRNOT00000145301.1
      Conserved Domains (2) summary
      cd07698
      Location:207 → 299
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      cl08246
      Location:25 → 203
      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
      1557312..1561063
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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