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    RT1-CE1 RT1 class I, locus1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 309603, updated on 9-Dec-2024

    Summary

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    Symbol
    RT1-CE1provided by RGD
    Full Name
    RT1 class I, locus1provided by RGD
    Primary source
    RGD:1595869
    See related
    EnsemblRapid:ENSRNOG00000071235 AllianceGenome:RGD:1595869
    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/E1; RT1-CE12
    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 located in lumenal side of endoplasmic reticulum membrane and phagocytic vesicle membrane. Predicted to be active in external side of plasma membrane and extracellular space. 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 Lung (RPKM 928.6), Spleen (RPKM 917.9) and 9 other tissues See more
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    Genomic context

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    See RT1-CE1 in Genome Data Viewer
    Location:
    20p12
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (3560455..3564428, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (3555779..3559487, complement)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene RT1 class I, locus CE2 Neighboring gene VPS52 subunit of GARP complex, pseudogene 3 Neighboring gene DExD-box helicase 39B Neighboring gene Small nucleolar RNA SNORD83 Neighboring gene small nucleolar RNA SNORD83

    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. RT1-U: identification of a novel, active, class Ib alloantigen of the rat MHC. Leong LY, et al. J Immunol, 1999 Jan 15. PMID 9916694
    2. 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
    3. 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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    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
    		  
    located_in lumenal side of endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in phagocytic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    RT1 class I, locus CE1
    Names
    MHC class I protein
    RT1 class I, CE12

    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_001008832.2 → NP_001008832.1  RT1 class I, locus CE1 precursor

      See identical proteins and their annotated locations for NP_001008832.1

      Status: VALIDATED

      Source sequence(s)
      BX883046
      UniProtKB/TrEMBL
      A0A2P1NRX5, Q861Q4
      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:343 → 374
      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
      3560455..3564428 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039098654.2 → XP_038954582.1  RT1 class I, locus CE1 isoform X1

      UniProtKB/TrEMBL
      A0A2P1NRX5
      Conserved Domains (3) summary
      pfam00129
      Location:25 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      pfam06623
      Location:343 → 367
      MHC_I_C; MHC_I C-terminus
      cd21016
      Location:204 → 299
      IgC1_MHC_Ib_T10_T22_like; Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains

    2. XM_063279101.1 → XP_063135171.1  RT1 class I, locus CE1 isoform X3

      UniProtKB/TrEMBL
      A0A0G2K4S5
      Related
      ENSRNOP00000098086.2, ENSRNOT00000120404.2

    3. XM_063279100.1 → XP_063135170.1  RT1 class I, locus CE1 isoform X2

      UniProtKB/TrEMBL
      A0A2P1NRX5

    4. XM_063279102.1 → XP_063135172.1  RT1 class I, locus CE1 isoform X4

      UniProtKB/TrEMBL
      A0A2P1NRX5

    5. XM_063279103.1 → XP_063135173.1  RT1 class I, locus CE1 isoform X5

      UniProtKB/TrEMBL
      O62933

    6. XM_063279105.1 → XP_063135175.1  RT1 class I, locus CE1 isoform X6

      UniProtKB/TrEMBL
      O62933

    7. XM_063279106.1 → XP_063135176.1  RT1 class I, locus CE1 isoform X6

      UniProtKB/TrEMBL
      O62933

    8. XM_063279104.1 → XP_063135174.1  RT1 class I, locus CE1 isoform X5

      UniProtKB/TrEMBL
      O62933
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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