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

    Gene ID: 24984, updated on 9-Dec-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
    EnsemblRapid: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 and peptide antigen 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 part of MHC class II protein complex. Predicted to be active in late endosome membrane and lysosomal membrane. 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, Dec 2024]
    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 ISO
    Inferred from Sequence Orthology
    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
    		  
    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
    		  
    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 ISO
    Inferred from Sequence Orthology
    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
      ENSRNOP00000098018.2, ENSRNOT00000120328.2
      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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