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

    Gene ID: 309622, updated on 27-Dec-2024

    Summary

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    Official Symbol
    RT1-Bbprovided by RGD
    Official Full Name
    RT1 class II, locus Bbprovided by RGD
    Primary source
    RGD:3469
    See related
    EnsemblRapid:ENSRNOG00000032708 AllianceGenome:RGD:3469
    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
    Bb; RT1.B
    Summary
    Predicted to enable MHC class II protein complex binding activity and peptide antigen binding activity. Involved in several processes, including cellular response to dexamethasone stimulus; cellular response to morphine; and negative regulation of T cell proliferation. Located in cell surface. Used to study uveitis. Biomarker of pneumocystosis. Human ortholog(s) of this gene implicated in several diseases, including allergic disease (multiple); autoimmune disease (multiple); bacterial infectious disease (multiple); hematologic cancer (multiple); and liver disease (multiple). Orthologous to several human genes including HLA-DQB1 (major histocompatibility complex, class II, DQ beta 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 1663.0), Thymus (RPKM 1183.1) and 8 other tissues See more
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    Genomic context

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    See RT1-Bb in Genome Data Viewer
    Location:
    20p12
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (4598475..4604118, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (4596558..4602201, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (4043726..4049367)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene RT1 class II, locus Db1 Neighboring gene RT1 class II, locus Ba Neighboring gene RT1 class II, locus DOb Neighboring gene transporter 2, ATP binding cassette subfamily B member

    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. HLA-DQB1*0501-restricted Th1 type immune responses to Plasmodium falciparum liver stage antigen 1 protect against malaria anemia and reinfections. May J, et al. J Infect Dis, 2001 Jan 1. PMID 11076705
    2. The major histocompatibility complex genes impact pain response in DA and DA.1U rats. Guo Y, et al. Physiol Behav, 2015 Aug 1. PMID 25861730
    3. Association between HLA-DQB1 alleles and HAM/TSP patients in Khorasan Province. Tafreshian AR, et al. Iran J Basic Med Sci, 2014 Oct. PMID 25729550, Free PMC Article
    4. Significantly increased occurrence of HLA-DQB1*0301 allele in patients with ocular cicatricial pemphigoid. Chan LS, et al. J Invest Dermatol, 1997 Feb. PMID 9008223
    5. Human leukocyte antigen class II associations in patients with idiopathic dilated cardiomyopathy. Myocarditis Treatment Trial Investigators. Lozano MD, et al. J Card Fail, 1997 Jun. PMID 9220309

    See all (232) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The results of this study indicated that MHC genes might contribute to the difference in pain sensitivity
      Title: The major histocompatibility complex genes impact pain response in DA and DA.1U rats.
    2. MHC class II is considered to be involved in the initiation of PS-induced hepatic fibrosis in rats.
      Title: MHC class II-related genes expression in porcine-serum-induced rat hepatic fibrosis.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC94124

    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
    		  
    enables protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in T cell receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 antigen processing and presentation of exogenous peptide antigen via MHC class II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within antigen processing and presentation of peptide antigen ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in antigen processing and presentation of peptide or polysaccharide antigen via MHC class II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to dexamethasone stimulus IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in cellular response to glucocorticoid stimulus IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in cellular response to morphine IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in defense response to fungus IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in humoral immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of T cell proliferation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of MHC class II protein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of MHC class II protein complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of MHC class II protein complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cell surface IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in early endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in external side of plasma membrane 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
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in multivesicular body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    rano class II histocompatibility antigen, B-1 beta chain
    Names
    MHC class II antigen B beta chain
    RT1 class II histocompatibility antigen, B-1 beta chain
    RT1.B-beta(1)
    RT1.Bbeta 1

    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_001004084.3 → NP_001004084.1  rano class II histocompatibility antigen, B-1 beta chain precursor

      See identical proteins and their annotated locations for NP_001004084.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000020
      UniProtKB/Swiss-Prot
      P29826
      UniProtKB/TrEMBL
      A0A023ILS1, A6JJD7, Q5UT93, Q5UT99, Q6AYB1
      Related
      ENSRNOP00000000525.6, ENSRNOT00000000525.9
      Conserved Domains (2) summary
      cd05766
      Location:123 → 216
      IgC_MHC_II_beta; Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain
      pfam00969
      Location:40 → 112
      MHC_II_beta; Class II histocompatibility antigen, beta 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
      4598475..4604118 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P29826.1 GenPept UniProtKB/Swiss-Prot:P29826

    Gene LinkOut

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

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