U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 294269, updated on 2-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    RT1-Daprovided by RGD
    Official Full Name
    RT1 class II, locus Daprovided by RGD
    Primary source
    RGD:1593283
    See related
    EnsemblRapid:ENSRNOG00000032844 AllianceGenome:RGD:1593283
    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
    DA1; H2-Ea; RT1-u
    Summary
    Predicted to enable several functions, including MHC class II protein complex binding activity; T cell receptor binding activity; and peptide antigen binding activity. Predicted to be involved in several processes, including antigen processing and presentation of endogenous peptide antigen via MHC class II; antigen processing and presentation of exogenous peptide antigen via MHC class II; and regulation of T cell differentiation. Predicted to act upstream of or within immunoglobulin mediated immune response. Predicted to be located in external side of plasma membrane; immunological synapse; and lysosome. Predicted to be part of MHC class II protein complex. Predicted to be active in late endosome membrane and lysosomal membrane. Biomarker of prediabetes syndrome. Human ortholog(s) of this gene implicated in Parkinson's disease (multiple); allergic disease; asthma; and autoimmune disease (multiple). Orthologous to human HLA-DRA (major histocompatibility complex, class II, DR alpha). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Spleen (RPKM 5146.2), Thymus (RPKM 2676.3) and 6 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See RT1-Da 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 (4515393..4520387)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (4513464..4518457)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (4127644..4132616, complement)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108349035 Neighboring gene butyrophilin-like 3 Neighboring gene butyrophilin-like 2 Neighboring gene RT1 class II, locus Db2 Neighboring gene arrestin, beta 2, pseudogene Neighboring gene RT1 class II, locus Db1

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. The complete sequence of the MHC class II chain RT.1D alpha u of the diabetic BB rat: mRNA levels of RT1.D alpha in lymphocytes. Holowachuk EW, et al. Nucleic Acids Res, 1987 Dec 23. PMID 3122183, Free PMC Article
    2. Decreased monocyte human leukocyte antigen-DR expression after severe burn injury: Correlation with severity and secondary septic shock. Venet F, et al. Crit Care Med, 2007 Aug. PMID 17568330
    3. Peptide motif for the rat MHC class II molecule RT1.Da: similarities to the multiple sclerosis-associated HLA-DRB1*1501 molecule. Duyar H, et al. Immunogenetics, 2005 Apr. PMID 15711804
    4. HLA-DMB gene and HLA-DRA promoter region polymorphisms in Australian multiple sclerosis patients. Bennetts BH, et al. Hum Immunol, 1999 Sep. PMID 10527398
    5. Inflammation and epithelial cell injury in AIDS enteropathy: involvement of endoplasmic reticulum stress. Maingat F, et al. FASEB J, 2011 Jul. PMID 21427211, Free PMC Article

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Peptide binding motif for the MHC class II molecule RT1.Da.
      Title: Peptide motif for the rat MHC class II molecule RT1.Da: similarities to the multiple sclerosis-associated HLA-DRB1*1501 molecule.
    Submit: New GeneRIF Correction

    Pathways from PubChem

    Go to the top of the page

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • MGC112637

    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 T cell receptor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables peptide antigen binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables peptide antigen binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables polysaccharide binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in antigen processing and presentation of endogenous peptide antigen via MHC class II 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 antigen processing and presentation of exogenous peptide antigen via MHC class II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in antigen processing and presentation of peptide or polysaccharide antigen via MHC class II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in cognition ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within immunoglobulin mediated immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in myeloid dendritic cell antigen processing and presentation 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 peptide antigen assembly with MHC class II protein complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of CD4-positive, alpha-beta T cell activation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of T cell activation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of T cell mediated cytotoxicity ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of memory T cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of T-helper 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
    		  
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in external side of plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in immunological synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in late endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosomal membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lysosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    RT1 class II, locus Da
    Names
    MHC RT1.u-D-alpha chain
    MHC class II RT1D alpha chain antigen
    MHC class II antigen RT1.D alpha chain
    RT1-D alpha
    RT1-Du alpha
    histocompatibility 2, class II antigen E alpha

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001008847.2 → NP_001008847.1  RT1 class II, locus Da precursor

      See identical proteins and their annotated locations for NP_001008847.1

      Status: VALIDATED

      Source sequence(s)
      BC098677, FM048166
      UniProtKB/TrEMBL
      A0A023IKG5, A0A023IM59, Q6MG98, Q6T4R6
      Related
      ENSRNOP00000048774.2, ENSRNOT00000048332.6
      Conserved Domains (2) summary
      pfam00993
      Location:29 → 107
      MHC_II_alpha; Class II histocompatibility antigen, alpha domain
      cd05767
      Location:110 → 204
      IgC1_MHC_II_alpha; Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains

    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
      4515393..4520387
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039098493.2 → XP_038954421.1  RT1 class II, locus Da isoform X1

      UniProtKB/TrEMBL
      A0A023IKG5, A0A023IM59, Q6MG98, Q6T4R6
      Conserved Domains (2) summary
      pfam00993
      Location:29 → 107
      MHC_II_alpha; Class II histocompatibility antigen, alpha domain
      cd05767
      Location:110 → 204
      IgC1_MHC_II_alpha; Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous