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RT1-DOa RT1 class II, locus DOa [ Rattus norvegicus (Norway rat) ]

Gene ID: 24984, updated on 5-Mar-2024

Summary

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Official Symbol
RT1-DOaprovided by RGD
Official Full Name
RT1 class II, locus DOaprovided by RGD
Primary source
RGD:3477
See related
Ensembl:ENSRNOG00000026762 AllianceGenome:RGD:3477
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
H2-Oa
Summary
Predicted to enable MHC class II protein complex binding activity. Predicted to be involved in several processes, including antigen processing and presentation of exogenous peptide antigen via MHC class II; negative regulation of antigen processing and presentation of peptide antigen via MHC class II; and peptide antigen assembly with MHC class II protein complex. Predicted to act upstream of or within antigen processing and presentation and regulation of T cell differentiation. Predicted to be integral component of membrane. Predicted to be part of MHC class II protein complex. Human ortholog(s) of this gene implicated in occupational asthma. Orthologous to human HLA-DOA (major histocompatibility complex, class II, DO alpha). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Spleen (RPKM 126.7), Thymus (RPKM 60.3) and 3 other tissues See more
Orthologs
human mouse all
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Genomic context

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See RT1-DOa 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 (4755287..4758491, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (4753587..4756590, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (3889106..3892360)

Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene bromodomain containing 2 like Neighboring gene bromodomain containing 2 Neighboring gene RT1 class II, locus Ha Neighboring gene RT1 class II, locus Hb, 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. Cloning and analysis of a new rat major histocompatibility complex class II gene, RT1.DOa. Arimura Y, et al. Immunogenetics, 1995. PMID 7607708
  2. Genetic variants in the major histocompatibility complex class I and class II genes are associated with diisocyanate-induced Asthma. Yucesoy B, et al. J Occup Environ Med, 2014 Apr. PMID 24709764, Free PMC Article
  3. Altered major histocompatibility complex class II peptide loading in H2-O-deficient mice. Perraudeau M, et al. Eur J Immunol, 2000 Oct. PMID 11069069
  4. Mapping the HLA-DO/HLA-DM complex by FRET and mutagenesis. Yoon T, et al. Proc Natl Acad Sci U S A, 2012 Jul 10. PMID 22733780, Free PMC Article
  5. The major histocompatibility complex of the rat (Rattus norvegicus). Günther E, et al. Immunogenetics, 2001 Sep. PMID 11685465

See all (8) 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 MHC class II protein complex binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables MHC class II protein complex binding ISO
Inferred from Sequence Orthology
more info
  
enables peptide antigen binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in adaptive immune response IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within antigen processing and presentation ISO
Inferred from Sequence Orthology
more info
  
involved_in antigen processing and presentation of exogenous peptide antigen via MHC class II IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within antigen processing and presentation of exogenous peptide antigen via MHC class II ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of antigen processing and presentation of peptide antigen via MHC class II ISO
Inferred from Sequence Orthology
more info
  
involved_in peptide antigen assembly with MHC class II protein complex IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of T cell activation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within regulation of T cell differentiation ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of MHC class II protein complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of MHC class II protein complex ISO
Inferred from Sequence Orthology
more info
  
is_active_in late endosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in lysosomal membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
RT1 class II, locus DOa
Names
histocompatibility 2, O region alpha locus

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_183051.2 → NP_898874.2  RT1 class II, locus DOa precursor

    See identical proteins and their annotated locations for NP_898874.2

    Status: VALIDATED

    Source sequence(s)
    BX883042
    UniProtKB/TrEMBL
    A6JJF2, F7F5V5, Q31289, Q6MGB0
    Conserved Domains (2) summary
    cd05767
    Location:112 → 205
    IgC_MHC_II_alpha; Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    pfam00993
    Location:30 → 108
    MHC_II_alpha; Class II histocompatibility antigen, alpha domain

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
    4755287..4758491 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017601546.3 → XP_017457035.1  RT1 class II, locus DOa isoform X2

    UniProtKB/TrEMBL
    Q31289

  2. XM_006255914.5 → XP_006255976.1  RT1 class II, locus DOa isoform X1

    See identical proteins and their annotated locations for XP_006255976.1

    UniProtKB/TrEMBL
    A6JJF2, F7F5V5, Q31289, Q6MGB0
    Related
    ENSRNOP00000034452.2
    Conserved Domains (2) summary
    cd05767
    Location:112 → 205
    IgC_MHC_II_alpha; Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    pfam00993
    Location:30 → 108
    MHC_II_alpha; Class II histocompatibility antigen, alpha domain
Nucleotide Protein Strain
Heading Accession and Version

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