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    Cd84 CD84 molecule [ Rattus norvegicus (Norway rat) ]

    Gene ID: 501872, updated on 4-Jan-2025

    Summary

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    Official Symbol
    Cd84provided by RGD
    Official Full Name
    CD84 moleculeprovided by RGD
    Primary source
    RGD:1564553
    See related
    EnsemblRapid:ENSRNOG00000022884 AllianceGenome:RGD:1564553
    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
    RGD1564553
    Summary
    Predicted to enable identical protein binding activity. Predicted to be involved in several processes, including regulation of cytokine production; regulation of leukocyte activation; and regulation of signal transduction. Predicted to be located in intracellular membrane-bounded organelle and plasma membrane. Predicted to be active in external side of plasma membrane. Orthologous to human CD84 (CD84 molecule). [provided by Alliance of Genome Resources, Jan 2025]
    Expression
    Biased expression in Spleen (RPKM 90.7), Thymus (RPKM 38.8) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Cd84 in Genome Data Viewer
    Location:
    13q24
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (86859979..86899984)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (84327580..84367153)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (90241369..90283625)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene Cd48 molecule Neighboring gene uncharacterized LOC103692288 Neighboring gene signaling lymphocytic activation molecule family member 1 Neighboring gene SLAM family member 6 Neighboring gene ribosomal protein S15, pseudogene 16

    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. CD84 negatively regulates IgE high-affinity receptor signaling in human mast cells. Álvarez-Errico D, et al. J Immunol, 2011 Dec 1. PMID 22068234, Free PMC Article
    2. Mouse CD84 is a pan-leukocyte cell-surface molecule that modulates LPS-induced cytokine secretion by macrophages. Sintes J, et al. J Leukoc Biol, 2010 Oct. PMID 20628063, Free PMC Article
    3. Structure of CD84 provides insight into SLAM family function. Yan Q, et al. Proc Natl Acad Sci U S A, 2007 Jun 19. PMID 17563375, Free PMC Article
    4. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. Prunotto M, et al. J Proteomics, 2013 Apr 26. PMID 23376485
    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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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in T cell activation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of granulocyte macrophage colony-stimulating factor production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of interleukin-10 production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of interleukin-18 production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of interleukin-6 production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of mast cell activation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of mast cell degranulation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of MAPK cascade ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of NF-kappaB transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of monocyte chemotactic protein-1 production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of tumor necrosis factor production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of lipopolysaccharide-mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of macrophage activation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of store-operated calcium entry ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in intracellular membrane-bounded organelle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle 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
    SLAM family member 5
    Names
    CD84 antigen

    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_001412898.1 → NP_001399827.1  SLAM family member 5 isoform 3 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000013
      UniProtKB/TrEMBL
      F1M0B5

    2. NM_001412899.1 → NP_001399828.1  SLAM family member 5 isoform 4 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000013
      UniProtKB/TrEMBL
      F1M0B5

    3. NM_001412900.1 → NP_001399829.1  SLAM family member 5 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000013
      UniProtKB/TrEMBL
      A0A0G2K3N2, A6JG09, F1M0B5
      Related
      ENSRNOP00000072708.2, ENSRNOT00000078162.3

    4. NM_001412901.1 → NP_001399830.1  SLAM family member 5 isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000013
      UniProtKB/TrEMBL
      F1M0B5

    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_086031.1 Reference GRCr8

      Range
      86859979..86899984
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017598907.3 → XP_017454396.1  SLAM family member 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K3N2, A6JG09, F1M0B5
      Conserved Domains (2) summary
      cd05775
      Location:32 → 128
      Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
      pfam13927
      Location:133 → 196
      Ig_3; Immunoglobulin domain

    2. XM_017598906.3 → XP_017454395.1  SLAM family member 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K3N2, A6JG09, F1M0B5
      Conserved Domains (2) summary
      cd05775
      Location:32 → 128
      Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
      pfam13927
      Location:133 → 196
      Ig_3; Immunoglobulin domain

    3. XM_039091002.2 → XP_038946930.1  SLAM family member 5 isoform X4

      Conserved Domains (3) summary
      cd00096
      Location:148 → 155
      Ig; Ig strand B [structural motif]
      cd16842
      Location:28 → 128
      Ig_SLAM-like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family
      cl11960
      Location:149 → 207
      Ig; Immunoglobulin domain

    4. XM_039091003.1 → XP_038946931.1  SLAM family member 5 isoform X5

      Conserved Domains (3) summary
      cd00096
      Location:148 → 155
      Ig; Ig strand B [structural motif]
      cd16842
      Location:28 → 128
      Ig_SLAM-like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family
      cl11960
      Location:149 → 207
      Ig; Immunoglobulin domain

    5. XM_063272556.1 → XP_063128626.1  SLAM family member 5 isoform X2

      UniProtKB/TrEMBL
      F1M0B5

    6. XM_063272555.1 → XP_063128625.1  SLAM family member 5 isoform X2

      UniProtKB/TrEMBL
      F1M0B5

    7. XM_008769757.4 → XP_008767979.1  SLAM family member 5 isoform X3

      UniProtKB/TrEMBL
      F1M0B5
      Conserved Domains (3) summary
      cd00096
      Location:121 → 128
      Ig; Ig strand B [structural motif]
      cd16842
      Location:1 → 101
      Ig_SLAM-like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family
      cl11960
      Location:122 → 180
      Ig; Immunoglobulin domain

    8. XM_039091004.2 → XP_038946932.1  SLAM family member 5 isoform X6

      Conserved Domains (2) summary
      cd00096
      Location:28 → 35
      Ig; Ig strand B [structural motif]
      cl11960
      Location:29 → 87
      Ig; Immunoglobulin domain

    9. XM_039091006.2 → XP_038946934.1  SLAM family member 5 isoform X7

      Conserved Domains (1) summary
      cl11960
      Location:29 → 87
      Ig; Immunoglobulin domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001192006.1: Suppressed sequence

      Description
      NM_001192006.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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