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    RT1-CE4 RT1 class I, locus CE4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 414783, updated on 4-Jan-2025

    Summary

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    Official Symbol
    RT1-CE4provided by RGD
    Official Full Name
    RT1 class I, locus CE4provided by RGD
    Primary source
    RGD:1598234
    See related
    EnsemblRapid:ENSRNOG00000071228 AllianceGenome:RGD:1598234
    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-C/E4
    Summary
    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, Jan 2025]
    Expression
    Biased expression in Thymus (RPKM 1094.4), Spleen (RPKM 936.5) and 9 other tissues See more
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    Genomic context

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    See RT1-CE4 in Genome Data Viewer
    Location:
    20p12
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (3436182..3509236, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (3431509..3504535, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (4918523..4921339, complement)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene RT1 class I, locus CE5 Neighboring gene LOC224733l-6 pseudogene Neighboring gene Cdk2ap1-ps4 pseudogene Neighboring gene uncharacterized LOC120098833 Neighboring gene LOC224733l-5 pseudogene Neighboring gene RT1 class I, locus CE7 Neighboring gene RT1 class I, locus CE6 Neighboring gene VPS52 subunit of GARP complex, pseudogene 4 Neighboring gene uncharacterized LOC134483853 Neighboring gene LOC224733l-4 pseudogene Neighboring gene Cdk2ap1-ps3 pseudogene Neighboring gene LOC224733l-3 pseudogene Neighboring gene RT1 class I, locus CE3

    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. Identification of MHC Class Ib Ligands for Stimulatory and Inhibitory Ly49 Receptors and Induction of Potent NK Cell Alloresponses in Rats. Dai KZ, et al. J Immunol, 2018 Apr 15. PMID 29531166, Free PMC Article
    2. 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 I, locus CE4
    Names
    MHC class I protein

    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_001008842.2 → NP_001008842.1  RT1 class I, locus CE4 precursor

      See identical proteins and their annotated locations for NP_001008842.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000020
      UniProtKB/TrEMBL
      A0A2P1NRX4, E9PT10, Q861Q1
      Related
      ENSRNOP00000098054.1, ENSRNOT00000120366.2
      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:346 → 371
      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
      3436182..3509236 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039098960.2 → XP_038954888.1  RT1 class I, locus CE4 isoform X2

      UniProtKB/TrEMBL
      A0A2P1NRX4
      Conserved Domains (2) summary
      pfam00129
      Location:25 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      cd07698
      Location:207 → 298
      IgC1_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains

    2. XM_063279388.1 → XP_063135458.1  RT1 class I, locus CE4 isoform X3

      UniProtKB/TrEMBL
      A0A2P1NRX4

    3. XM_039098961.2 → XP_038954889.1  RT1 class I, locus CE4 isoform X4

      UniProtKB/TrEMBL
      A0A2P1NRX4
      Conserved Domains (3) summary
      pfam00129
      Location:25 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      pfam06623
      Location:299 → 322
      MHC_I_C; MHC_I C-terminus
      cd07698
      Location:207 → 298
      IgC1_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains

    4. XM_039098959.2 → XP_038954887.1  RT1 class I, locus CE4 isoform X1

      UniProtKB/TrEMBL
      A0A2P1NRX4
      Conserved Domains (2) summary
      pfam00129
      Location:25 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      cd07698
      Location:207 → 298
      IgC1_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains

    RNA

    1. XR_010060745.1 RNA Sequence

    2. XR_010060744.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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