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RT1-CE3 RT1 class I, locus CE3 [ Rattus norvegicus (Norway rat) ]

Gene ID: 414793, updated on 2-Nov-2024

Summary

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Official Symbol
RT1-CE3provided by RGD
Official Full Name
RT1 class I, locus CE3provided by RGD
Primary source
RGD:1598231
See related
AllianceGenome:RGD:1598231
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/E3
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 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, Nov 2024]
Expression
Biased expression in Spleen (RPKM 1127.8), Lung (RPKM 1014.5) and 9 other tissues See more
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Genomic context

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See RT1-CE3 in Genome Data Viewer
Location:
20p12
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (3521323..3525218, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (3516647..3520938, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (4918047..4943603, complement)

Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene RT1 class I, locus CE4 Neighboring gene uncharacterized LOC134483853 Neighboring gene Cdk2ap1-ps3 pseudogene Neighboring gene LOC224733l-3 pseudogene Neighboring gene uncharacterized LOC134483855 Neighboring gene Cdk2ap1-ps2 pseudogene

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 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

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 I, locus CE3
Names
MHC class I protein
MHC class I protein-like

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_001008841.2 → NP_001008841.1  RT1 class I, locus CE3 precursor

    See identical proteins and their annotated locations for NP_001008841.1

    Status: VALIDATED

    Source sequence(s)
    BX883046
    UniProtKB/TrEMBL
    F1LQG7, Q6MG38, Q861Q2
    Conserved Domains (2) 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

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
    3521323..3525218 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039098965.2 → XP_038954893.1  RT1 class I, locus CE3 isoform X2

    UniProtKB/TrEMBL
    A0A2P1NRX8, Q861Q2
    Conserved Domains (3) summary
    pfam00129
    Location:25 → 203
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    cd00096
    Location:208 → 216
    Ig; Ig strand A [structural motif]
    cl11960
    Location:205 → 298
    Ig; Immunoglobulin domain

  2. XM_039098964.2 → XP_038954892.1  RT1 class I, locus CE3 isoform X1

    UniProtKB/TrEMBL
    Q861Q2
    Conserved Domains (3) summary
    pfam00129
    Location:25 → 203
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    cd00096
    Location:208 → 216
    Ig; Ig strand A [structural motif]
    cl11960
    Location:205 → 298
    Ig; Immunoglobulin domain

  3. XM_039098967.2 → XP_038954895.1  RT1 class I, locus CE3 isoform X3

    Conserved Domains (1) summary
    cd07698
    Location:45 → 136
    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_063279420.1 → XP_063135490.1  RT1 class I, locus CE3 isoform X4

RNA

  1. XR_010060753.1 RNA Sequence

  2. XR_010060752.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

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