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RT1-S3 RT1 class Ib, locus S3 [ Rattus norvegicus (Norway rat) ]

Gene ID: 294228, updated on 27-Nov-2024

Summary

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Official Symbol
RT1-S3provided by RGD
Official Full Name
RT1 class Ib, locus S3provided by RGD
Primary source
RGD:735037
See related
EnsemblRapid:ENSRNOG00000085024 AllianceGenome:RGD:735037
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
RTBM1; H2-T23; RT-BM1; RT1-BM1
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 occupational asthma. Orthologous to human HLA-E (major histocompatibility complex, class I, E). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Spleen (RPKM 513.9), Lung (RPKM 420.3) and 9 other tissues See more
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Genomic context

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See RT1-S3 in Genome Data Viewer
Location:
20p12
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (2675463..2680229)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (2670654..2675411)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (3176124..3180825)

Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene RT1 class Ib, locus O1 like 1 Neighboring gene uncharacterized LOC134483846 Neighboring gene RT1 class Ib, locus S2 Neighboring gene RT1 class Ib, locus O1 Neighboring gene RT1 class Ib, locus N3 Neighboring gene RT1 class I, locus T24, gene 4 Neighboring gene class I gene fragment 2361 Neighboring gene ribosomal protein L41, 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. A rat class I cDNA clone with an Alu-like sequence and mapping to two genes in RT1.C/E. Parker KE, et al. Immunogenetics, 1990. PMID 1969387
  2. Structural organization, sequence analysis, and physical mapping of the Grc-linked class Ib gene RT1.S3 in the rat. Salgar SK, et al. Immunogenetics, 1998 Jun. PMID 9601949
  3. Comparison of RT-BM1 sequences from six different rat major histocompatibility complex haplotypes reveals limited variation, and alternate splicing in the 3' untranslated region. Lau P, et al. Immunogenetics, 2000 Feb. PMID 10663577
  4. Pathogen-derived HLA-E bound epitopes reveal broad primary anchor pocket tolerability and conformationally malleable peptide binding. Walters LC, et al. Nat Commun, 2018 Aug 7. PMID 30087334, Free PMC Article
  5. Cutting edge: the human cytomegalovirus UL40 gene product contains a ligand for HLA-E and prevents NK cell-mediated lysis. Ulbrecht M, et al. J Immunol, 2000 May 15. PMID 10799855

See all (24) citations in PubMed

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 Ib, locus S3
Names
MHC class Ib RT1.S3
RT1 class Ib, locus BM1
histocompatibility 2, T region locus 23

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_001008886.2 → NP_001008886.2  RT1 class Ib, locus S3 precursor

    See identical proteins and their annotated locations for NP_001008886.2

    Status: VALIDATED

    Source sequence(s)
    AJ243976, BX883048, CK599963
    UniProtKB/TrEMBL
    F1LQF2, O78105, O78106
    Related
    ENSRNOP00000096812.3, ENSRNOT00000120072.3
    Conserved Domains (2) summary
    cd07698
    Location:205 → 297
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    pfam00129
    Location:24 → 201
    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
    2675463..2680229
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006255917.5 → XP_006255979.1  RT1 class Ib, locus S3 isoform X1

    See identical proteins and their annotated locations for XP_006255979.1

    UniProtKB/TrEMBL
    F1LQF2, O78105, O78106
    Conserved Domains (2) summary
    cd07698
    Location:205 → 297
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    pfam00129
    Location:24 → 201
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
Nucleotide Protein Strain
Heading Accession and Version

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