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    RT1-CE5 RT1 class I, locus CE5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 309607, updated on 3-Apr-2024

    Summary

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    Official Symbol
    RT1-CE5provided by RGD
    Official Full Name
    RT1 class I, locus CE5provided by RGD
    Primary source
    RGD:1595868
    See related
    AllianceGenome:RGD:1595868
    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-E2; rt1-El; RT1-CE7; RT1-C/E5
    Summary
    Predicted to enable several functions, including 14-3-3 protein binding activity; TAP binding activity; and beta-2-microglobulin 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 regulation of lymphocyte mediated immunity. Predicted to be located in several cellular components, including bounding membrane of organelle; cell surface; and endoplasmic reticulum. Predicted to be part of MHC class Ib protein complex. Predicted to be active in external side of plasma membrane and extracellular space. Human ortholog(s) of this gene implicated in several diseases, including asthma (multiple); autoimmune disease (multiple); eye disease (multiple); human immunodeficiency virus infectious disease (multiple); and inner ear disease (multiple). Orthologous to several human genes including HLA-F (major histocompatibility complex, class I, F). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Spleen (RPKM 1103.6), Lung (RPKM 1023.1) and 9 other tissues See more
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    Genomic context

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    See RT1-CE5 in Genome Data Viewer
    Location:
    20p12
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (3407880..3484130, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (3403418..3479476, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (4892702..4896993, complement)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120098828 Neighboring gene uncharacterized LOC120098832 Neighboring gene RT1 class I, locus CE11 Neighboring gene LOC224733l-7 pseudogene Neighboring gene RT1 class I, locus CE10 Neighboring gene RT1 class I, locus CE9, pseudogene 1 Neighboring gene RT1 class I, locus CE8, pseudogene 1 Neighboring gene LOC224733l-6 pseudogene Neighboring gene Cdk2ap1-ps4 pseudogene Neighboring gene uncharacterized LOC120098833 Neighboring gene LOC224733l-5 pseudogene Neighboring gene RT1 class I, locus CE4 Neighboring gene RT1 class I, locus CE7 Neighboring gene Sacm2l-ps4 pseudogene Neighboring gene RT1 class I, locus CE6 Neighboring gene uncharacterized LOC134483853 Neighboring gene LOC224733l-4 pseudogene Neighboring gene Cdk2ap1-ps3 pseudogene

    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. Characterisation of RT1-E2, a multigenic family of highly conserved rat non-classical MHC class I molecules initially identified in cells from immunoprivileged sites. Lau P, et al. BMC Immunol, 2003 Jul 1. PMID 12837137, Free PMC Article
    2. Physical map and expression profile of genes of the telomeric class I gene region of the rat MHC. Ioannidu S, et al. J Immunol, 2001 Mar 15. PMID 11238641
    3. HLA-F and MHC-I open conformers cooperate in a MHC-I antigen cross-presentation pathway. Goodridge JP, et al. J Immunol, 2013 Aug 15. PMID 23851683, Free PMC Article
    4. HLA-F is a surface marker on activated lymphocytes. Lee N, et al. Eur J Immunol, 2010 Aug. PMID 20865824, Free PMC Article
    5. Selective export of HLA-F by its cytoplasmic tail. Boyle LH, et al. J Immunol, 2006 Jun 1. PMID 16709803

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC112896

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables 14-3-3 protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables TAP1 binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables TAP2 binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables beta-2-microglobulin 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 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 antigen processing and presentation of endogenous peptide antigen via MHC class Ib ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in antigen processing and presentation of exogenous peptide antigen via MHC class Ib ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of T cell cytokine production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of natural killer cell cytokine production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of natural killer cell degranulation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of natural killer cell mediated cytotoxicity ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of T cell mediated cytotoxicity 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 natural killer cell cytokine production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of natural killer cell degranulation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of MHC class I protein complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of MHC class Ib protein complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in early endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  
    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
    		  
    located_in lumenal side of endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosomal membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in phagocytic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    RT1 class I, locus CE5
    Names
    MHC class I protein
    MHC class Ib antigen
    RT1 class I, CE7

    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_001008843.2 → NP_001008843.1  RT1 class I, locus CE5 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001008843.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).
      Source sequence(s)
      AJ537417, BC098841
      UniProtKB/TrEMBL
      A6KUT7, Q861Q0
      Conserved Domains (3) summary
      cd07698
      Location:207 → 299
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam00129
      Location:25 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      pfam06623
      Location:343 → 369
      MHC_I_C; MHC_I C-terminus

    2. NM_001033986.1 → NP_001029158.1  RT1 class I, locus CE5 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001029158.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. This results in a longer protein (isoform 2) compared to isoform 1.
      Source sequence(s)
      BC098841
      UniProtKB/TrEMBL
      A6KUT7, F7FP91, Q95II0
      Conserved Domains (4) summary
      pfam00129
      Location:25 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      pfam06623
      Location:349 → 372
      MHC_I_C; MHC_I C-terminus
      cd00096
      Location:208 → 216
      Ig; Ig strand A [structural motif]
      cl11960
      Location:205 → 299
      Ig; Immunoglobulin 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
      3407880..3484130 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063279109.1 → XP_063135179.1  RT1 class I, locus CE5 isoform X3

    2. XM_063279111.1 → XP_063135181.1  RT1 class I, locus CE5 isoform X4

    3. XM_063279116.1 → XP_063135186.1  RT1 class I, locus CE5 isoform X14

      UniProtKB/TrEMBL
      D3ZLE6

    4. XM_039098665.2 → XP_038954593.1  RT1 class I, locus CE5 isoform X9

      Conserved Domains (5) summary
      pfam00129
      Location:25 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      pfam06623
      Location:338 → 363
      MHC_I_C; MHC_I C-terminus
      cd00096
      Location:208 → 216
      Ig; Ig strand A [structural motif]
      cl11960
      Location:205 → 299
      Ig; Immunoglobulin domain
      cl41775
      Location:299 → 341
      JMTM_Notch_APP; juxtamembrane and transmembrane (JMTM) domain found in Notch and APP family proteins

    5. XM_063279114.1 → XP_063135184.1  RT1 class I, locus CE5 isoform X10

    6. XM_063279108.1 → XP_063135178.1  RT1 class I, locus CE5 isoform X2

    7. XM_063279107.1 → XP_063135177.1  RT1 class I, locus CE5 isoform X1

    8. XM_063279113.1 → XP_063135183.1  RT1 class I, locus CE5 isoform X8

    9. XM_063279110.1 → XP_063135180.1  RT1 class I, locus CE5 isoform X4

    10. XM_039098673.2 → XP_038954601.1  RT1 class I, locus CE5 isoform X14

      UniProtKB/TrEMBL
      D3ZLE6
      Conserved Domains (4) summary
      pfam00129
      Location:25 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      cd00096
      Location:208 → 216
      Ig; Ig strand A [structural motif]
      cl11960
      Location:205 → 299
      Ig; Immunoglobulin domain
      cl41775
      Location:299 → 341
      JMTM_Notch_APP; juxtamembrane and transmembrane (JMTM) domain found in Notch and APP family proteins

    11. XM_039098664.2 → XP_038954592.1  RT1 class I, locus CE5 isoform X10

      Conserved Domains (5) summary
      pfam00129
      Location:25 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      pfam06623
      Location:338 → 363
      MHC_I_C; MHC_I C-terminus
      cd00096
      Location:208 → 216
      Ig; Ig strand A [structural motif]
      cl11960
      Location:205 → 299
      Ig; Immunoglobulin domain
      cl41775
      Location:299 → 341
      JMTM_Notch_APP; juxtamembrane and transmembrane (JMTM) domain found in Notch and APP family proteins

    12. XM_039098672.2 → XP_038954600.1  RT1 class I, locus CE5 isoform X13

      UniProtKB/TrEMBL
      D3ZLE6
      Conserved Domains (4) summary
      pfam00129
      Location:25 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      cd00096
      Location:208 → 216
      Ig; Ig strand A [structural motif]
      cl11960
      Location:205 → 299
      Ig; Immunoglobulin domain
      cl41775
      Location:299 → 341
      JMTM_Notch_APP; juxtamembrane and transmembrane (JMTM) domain found in Notch and APP family proteins

    13. XM_039098660.2 → XP_038954588.1  RT1 class I, locus CE5 isoform X5

      UniProtKB/TrEMBL
      A6KUT7, F7FP91, Q95II0
      Conserved Domains (4) summary
      pfam00129
      Location:25 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      pfam06623
      Location:349 → 372
      MHC_I_C; MHC_I C-terminus
      cd00096
      Location:208 → 216
      Ig; Ig strand A [structural motif]
      cl11960
      Location:205 → 299
      Ig; Immunoglobulin domain

    14. XM_039098663.2 → XP_038954591.1  RT1 class I, locus CE5 isoform X6

      Conserved Domains (4) summary
      pfam00129
      Location:25 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      pfam06623
      Location:345 → 370
      MHC_I_C; MHC_I C-terminus
      cd00096
      Location:208 → 216
      Ig; Ig strand A [structural motif]
      cl11960
      Location:205 → 301
      Ig; Immunoglobulin domain

    15. XM_039098667.2 → XP_038954595.1  RT1 class I, locus CE5 isoform X11

      UniProtKB/TrEMBL
      A6KUT7
      Conserved Domains (3) summary
      pfam00129
      Location:25 → 203
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
      cd00096
      Location:208 → 216
      Ig; Ig strand A [structural motif]
      cl11960
      Location:205 → 299
      Ig; Immunoglobulin domain

    16. XM_063279115.1 → XP_063135185.1  RT1 class I, locus CE5 isoform X12

    17. XM_063279112.1 → XP_063135182.1  RT1 class I, locus CE5 isoform X7

      UniProtKB/TrEMBL
      Q861Q0

    RNA

    1. XR_010060670.1 RNA Sequence

    2. XR_010060674.1 RNA Sequence

    3. XR_010060672.1 RNA Sequence

    4. XR_010060669.1 RNA Sequence

    5. XR_010060671.1 RNA Sequence

    6. XR_010060673.1 RNA Sequence

    7. XR_005497231.2 RNA Sequence

    8. XR_005497232.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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