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    RT1-N3 RT1 class Ib, locus N3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 24750, updated on 9-Dec-2024

    Summary

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    Official Symbol
    RT1-N3provided by RGD
    Official Full Name
    RT1 class Ib, locus N3provided by RGD
    Primary source
    RGD:1598370
    See related
    EnsemblRapid:ENSRNOG00000000795 AllianceGenome:RGD:1598370
    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
    Summary
    Predicted to enable peptide antigen binding activity and signaling receptor binding activity. Predicted to be involved in several processes, including antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent; antigen processing and presentation of endogenous peptide antigen via MHC class Ib; and positive regulation of T cell mediated cytotoxicity. Predicted to be active in external side of plasma membrane and extracellular space. Human ortholog(s) of this gene implicated in several diseases, including Stevens-Johnson syndrome; asthma (multiple); autoimmune disease (multiple); eye disease (multiple); and inner ear disease (multiple). Orthologous to human HLA-B (major histocompatibility complex, class I, B); HLA-C (major histocompatibility complex, class I, C); and HLA-E (major histocompatibility complex, class I, E). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 380.4), Spleen (RPKM 114.9) and 8 other tissues See more
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    Genomic context

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    See RT1-N3 in Genome Data Viewer
    Location:
    20p12
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (2666469..2670355)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (2659132..2665536)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (3166793..3170945)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene RT1 class Ib, locus O1 like 1 Neighboring gene uncharacterized LOC134483846 Neighboring gene RT1 class Ib, locus S2 Neighboring gene ribosomal protein S2, pseudogene 1 Neighboring gene RT1 class Ib, locus O1 Neighboring gene RT1 class Ib, locus S3 Neighboring gene RT1 class I, locus T24, gene 4 Neighboring gene class I gene fragment 2361

    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. Multiple TL-like loci in the grc-G/C region of the rat. Kirisits MJ, et al. Immunogenetics, 1994. PMID 8168848
    2. Can a "fishbone" prevent peritonitis? Kurtin PS, et al. Nephrol News Issues, 1992 Nov. PMID 1300431
    3. The genomic sequence and comparative analysis of the rat major histocompatibility complex. Hurt P, et al. Genome Res, 2004 Apr. PMID 15060004, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables peptide antigen binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables signaling receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in antigen processing and presentation of endogenous peptide antigen via MHC class Ib IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of T cell mediated cytotoxicity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    RT1 class Ib, locus N3
    Names
    RT1 class Ib gene, H2-TL-like, grc region (N3)

    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_001008855.2 → NP_001008855.1  RT1 class Ib, locus N3

      See identical proteins and their annotated locations for NP_001008855.1

      Status: VALIDATED

      Source sequence(s)
      BC158567, FM122995
      UniProtKB/TrEMBL
      A0A023GRW5, F6PT03, G5EBE1, H7C829, I1SB24, L7N646, Q31280, Q6MG01, U3KRG4, V9HVV1
      Related
      ENSRNOP00000001035.5, ENSRNOT00000001035.7
      Conserved Domains (2) summary
      cd07698
      Location:207 → 299
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      cl08246
      Location:33 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

    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
      2666469..2670355
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039098420.2 → XP_038954348.1  RT1 class Ib, locus N3 isoform X2

      UniProtKB/TrEMBL
      F6PT03
      Conserved Domains (3) summary
      cd00096
      Location:208 → 216
      Ig; Ig strand A [structural motif]
      cl08246
      Location:33 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      cl11960
      Location:204 → 299
      Ig; Immunoglobulin domain

    2. XM_006255908.5 → XP_006255970.1  RT1 class Ib, locus N3 isoform X1

      UniProtKB/TrEMBL
      F6PT03
      Conserved Domains (2) summary
      cd07698
      Location:207 → 299
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      cl08246
      Location:33 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

    3. XM_006255909.5 → XP_006255971.1  RT1 class Ib, locus N3 isoform X4

      UniProtKB/TrEMBL
      F6PT03
      Conserved Domains (2) summary
      cd07698
      Location:207 → 299
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      cl08246
      Location:33 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

    4. XM_039098421.2 → XP_038954349.1  RT1 class Ib, locus N3 isoform X3

      UniProtKB/TrEMBL
      F6PT03
      Related
      ENSRNOP00000074505.3, ENSRNOT00000084770.4
      Conserved Domains (3) summary
      cd00096
      Location:208 → 216
      Ig; Ig strand A [structural motif]
      cl08246
      Location:33 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      cl11960
      Location:204 → 299
      Ig; Immunoglobulin domain
    Nucleotide Protein Strain
    Heading Accession and Version

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