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

    Gene ID: 24986, updated on 9-Dec-2024

    Summary

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    Symbol
    RT1-Haprovided by RGD
    Full Name
    RT1 class II, locus Haprovided by RGD
    Primary source
    RGD:1595921
    See related
    EnsemblRapid:ENSRNOG00000045908 AllianceGenome:RGD:1595921
    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
    RT1.Ha
    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; peptide antigen assembly with MHC class II protein complex; and positive regulation of type II interferon production. Predicted to be located in cell surface and intracellular membrane-bounded organelle. 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 several diseases, including Crohn's disease; asthma (multiple); hepatitis B; liver disease (multiple); and onchocerciasis. Orthologous to human HLA-DPA1 (major histocompatibility complex, class II, DP alpha 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 69.3), Spleen (RPKM 49.1) and 1 other tissue See more
    Orthologs
    human all
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    Genomic context

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    See RT1-Ha 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 (4762425..4772439, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (4760631..4770662, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (3875478..3885140)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene bromodomain containing 2 Neighboring gene RT1 class II, locus DOa Neighboring gene RT1 class II, locus Hb, pseudogene 1 Neighboring gene collagen type XI alpha 2 chain

    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. Distinct Relapse Rates and Risk Predictors After Discontinuing Tenofovir and Entecavir Therapy. Su TH, et al. J Infect Dis, 2018 Mar 28. PMID 29300980
    2. HLA-DP and susceptibility to insulin-dependent diabetes mellitus in an ethnically mixed population. Associations with other HLA-alleles. Balducci-Silano PL, et al. J Autoimmun, 1995 Jun. PMID 7576003
    3. Met-11 of HLA class II DP alpha 1 first domain associated with onchocerciasis. Meyer CG, et al. Exp Clin Immunogenet, 1996. PMID 8854084
    4. HLA-DR-DQ alleles and HLA-DP alleles are independently associated with susceptibility to different stages of post-schistosomal hepatic fibrosis in the Chinese population. Hirayama K, et al. Tissue Antigens, 1999 Mar. PMID 10203020
    5. Effect of HLA-DPA1 alleles on chronic hepatitis B prognosis and treatment response. Katrinli S, et al. North Clin Istanb, 2016. PMID 28275747, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC116352

    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 peptide antigen binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables peptide antigen 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 exogenous peptide antigen via MHC class II IBA
    Inferred from Biological aspect of Ancestor
    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 cellular response to type II interferon 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 T cell activation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of T cell proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of type II interferon production 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 intracellular membrane-bounded organelle 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 Ha
    Names
    HLA class II histocompatibility antigen, DP alpha 1 chain-like
    RLA class II histocompatibility antigen, DP alpha-1 chain-like
    major histocompatibility complex class II H-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_001008848.2 → NP_001008848.1  RT1 class II, locus Ha precursor

      See identical proteins and their annotated locations for NP_001008848.1

      Status: VALIDATED

      Source sequence(s)
      BX883042
      UniProtKB/TrEMBL
      F7FN89, Q31287, Q6MGB1
      Conserved Domains (3) summary
      cd05767
      Location:111 → 204
      IgC_MHC_II_alpha; Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam00993
      Location:30 → 107
      MHC_II_alpha; Class II histocompatibility antigen, alpha domain
      pfam16196
      Location:202 → 253
      C1-set_C; C1-set C-terminal 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
      4762425..4772439 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006255916.5 → XP_006255978.2  RT1 class II, locus Ha isoform X1

      See identical proteins and their annotated locations for XP_006255978.2

      UniProtKB/TrEMBL
      Q31287
      Related
      ENSRNOP00000033818.5, ENSRNOT00000036900.6
      Conserved Domains (3) summary
      cd05767
      Location:153 → 246
      IgC_MHC_II_alpha; Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam00993
      Location:72 → 149
      MHC_II_alpha; Class II histocompatibility antigen, alpha domain
      pfam16196
      Location:244 → 295
      C1-set_C; C1-set C-terminal domain
    Nucleotide Protein Strain
    Heading Accession and Version

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