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

Gene ID: 294269, updated on 22-May-2022

Summary

Official Symbol
RT1-Daprovided by RGD
Official Full Name
RT1 class II, locus Daprovided by RGD
Primary source
RGD:1593283
See related
Ensembl: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 be located in bounding membrane of organelle; cell surface; and immunological synapse. Predicted to be part of MHC class II protein complex. 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, Apr 2022]
Expression
Biased expression in Spleen (RPKM 5146.2), Thymus (RPKM 2676.3) and 6 other tissues See more
Orthologs
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Genomic context

See RT1-Da in Genome Data Viewer
Location:
20p12
Exon count:
5
Annotation release Status Assembly Chr Location
108 current 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_051355.1Genomic 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

Expression

  • 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

Pathways from PubChem

General gene information

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
PubMed 
enables T cell receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables molecular_function ND
No biological Data available
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 adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
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
PubMed 
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 immunoglobulin production involved in immunoglobulin-mediated immune response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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
PubMed 
involved_in positive regulation of T cell mediated cytotoxicity ISO
Inferred from Sequence Orthology
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
PubMed 
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
 
is_active_in cellular_component ND
No biological Data available
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
 
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
located_in late endosome membrane ISO
Inferred from Sequence Orthology
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

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)

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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_001008847.2NP_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
    Q6MG98
    Related
    ENSRNOP00000048774.2, ENSRNOT00000048332.5
    Conserved Domains (2) summary
    pfam00993
    Location:29107
    MHC_II_alpha; Class II histocompatibility antigen, alpha domain
    cd05767
    Location:110204
    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: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051355.1 Reference mRatBN7.2 Primary Assembly

    Range
    4513464..4518457
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (2) summary
    pfam00993
    Location:29107
    MHC_II_alpha; Class II histocompatibility antigen, alpha domain
    cd05767
    Location:110204
    IgC1_MHC_II_alpha; Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains