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Cd84 CD84 molecule [ Rattus norvegicus (Norway rat) ]

Gene ID: 501872, updated on 27-Nov-2024

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, Nov 2024]
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

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

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000013

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

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000013
    UniProtKB/TrEMBL
    A0A0G2K3N2, A6JG09
    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

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

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

  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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