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    CX3CR1 chemokine (C-X3-C motif) receptor 1 [ Homo sapiens (human) ]

    Gene ID: 1524, updated on 29-Aug-2015
    Official Symbol
    CX3CR1provided by HGNC
    Official Full Name
    chemokine (C-X3-C motif) receptor 1provided by HGNC
    Primary source
    HGNC:HGNC:2558
    See related
    Ensembl:ENSG00000168329; HPRD:03277; MIM:601470; Vega:OTTHUMG00000156249
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    V28; CCRL1; GPR13; CMKDR1; GPRV28; CMKBRL1
    Summary
    Fractalkine is a transmembrane protein and chemokine involved in the adhesion and migration of leukocytes. The protein encoded by this gene is a receptor for fractalkine. The encoded protein also is a coreceptor for HIV-1, and some variations in this gene lead to increased susceptibility to HIV-1 infection and rapid progression to AIDS. Four transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]
    Orthologs
    See CX3CR1 in Epigenomics, MapViewer
    Location:
    3p21.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    107 current GRCh38.p2 (GCF_000001405.28) 3 NC_000003.12 (39263494..39281735, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (39304985..39323226, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene destrin (actin depolymerizing factor) pseudogene 4 Neighboring gene uncharacterized LOC102724104 Neighboring gene adenosine deaminase domain containing 1 (testis-specific) pseudogene 1 Neighboring gene chemokine (C-C motif) receptor 8

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Fractalkine (CX3CL1) protects hippocampal neurons from the neurotoxicity induced by the HIV-1 envelope protein gp120, and neuronal CX(3)CR1 receptors and Akt activation are responsible for the neuroprotective effects of fractalkine PubMed
    env HIV-1 gp120 from CXCR4-tropic subtype E viruses isolated in Thailand associates with and uses at least one of the following coreceptors for virus entry: CCR8, CCR1, CCR2b, or CX3CR1 PubMed
    Tat tat Inhibition of NF-kappaB and YY1 reverses HIV-1 Tat-mediated downregulation of CX3CR1 in microglia PubMed
    tat HIV-1 Tat-mediated downregulation of CX3CR1 inhibits CX3CL1-induced migration of microglia PubMed
    tat HIV-1 Tat upregulates chemokine (C-X3-C motif) receptor 1 (CX3CR1) in HEK 293 cells PubMed
    tat Fractalkine-CX3CR1 signaling contributes to the inhibition of the synergistic neurotoxic effects by opioids and HIV-1 Tat PubMed

    Go to the HIV-1, Human Interaction Database

    • Chemokine receptors bind chemokines, organism-specific biosystem (from REACTOME)
      Chemokine receptors bind chemokines, organism-specific biosystemChemokine receptors are cytokine receptors found on the surface of certain cells, which interact with a type of cytokine called a chemokine. Following interaction, these receptors trigger a flux of i...
    • Chemokine signaling pathway, organism-specific biosystem (from KEGG)
      Chemokine signaling pathway, organism-specific biosystemInflammatory immune response requires the recruitment of leukocytes to the site of inflammation upon foreign insult. Chemokines are small chemoattractant peptides that provide directional cues for th...
    • Chemokine signaling pathway, conserved biosystem (from KEGG)
      Chemokine signaling pathway, conserved biosystemInflammatory immune response requires the recruitment of leukocytes to the site of inflammation upon foreign insult. Chemokines are small chemoattractant peptides that provide directional cues for th...
    • Class A/1 (Rhodopsin-like receptors), organism-specific biosystem (from REACTOME)
      Class A/1 (Rhodopsin-like receptors), organism-specific biosystemRhodopsin-like receptors (class A/1) are the largest group of GPCRs and are the best studied group from a functional and structural point of view. They show great diversity at the sequence level and ...
    • Cytokine-cytokine receptor interaction, organism-specific biosystem (from KEGG)
      Cytokine-cytokine receptor interaction, organism-specific biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
    • Cytokine-cytokine receptor interaction, conserved biosystem (from KEGG)
      Cytokine-cytokine receptor interaction, conserved biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
    • GPCR ligand binding, organism-specific biosystem (from REACTOME)
      GPCR ligand binding, organism-specific biosystemThere are more than 800 G-protein coupled receptor (GPCRs) in the human genome, making it the largest receptor superfamily. GPCRs are also the largest class of drug targets, involved in virtually all...
    • GPCRs, Class A Rhodopsin-like, organism-specific biosystem (from WikiPathways)
      GPCRs, Class A Rhodopsin-like, organism-specific biosystemThis pathway was created using the GPCRDB (Horn et al., 1998), http://www.cmbi.kun.nl/7tm/. The groupings are based on the GPCR phylogenetic tree available from the GPCRDB and the training sets used ...
    • Peptide GPCRs, organism-specific biosystem (from WikiPathways)
      Peptide GPCRs, organism-specific biosystem
      Peptide GPCRs
    • Peptide ligand-binding receptors, organism-specific biosystem (from REACTOME)
      Peptide ligand-binding receptors, organism-specific biosystemThese receptors, a subset of the Class A/1 (Rhodopsin-like) family, all bind peptide ligands which include the chemokines, opioids and somatostatins.
    • Signal Transduction, organism-specific biosystem (from REACTOME)
      Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
    • Signaling by GPCR, organism-specific biosystem (from REACTOME)
      Signaling by GPCR, organism-specific biosystemG protein-coupled receptors (GPCRs; 7TM receptors; seven transmembrane domain receptors; heptahelical receptors; G protein-linked receptors [GPLR]) are the largest family of transmembrane receptors i...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    C-X3-C chemokine receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    chemokine receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    G-protein coupled receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    cellular defense response TAS
    Traceable Author Statement
    more info
    PubMed 
    cellular response to lipopolysaccharide IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to transforming growth factor beta stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    cerebral cortex cell migration IEA
    Inferred from Electronic Annotation
    more info
     
    chemokine-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    chemokine-mediated signaling pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    chemotaxis TAS
    Traceable Author Statement
    more info
    PubMed 
    macrophage chemotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    memory IEA
    Inferred from Electronic Annotation
    more info
     
    microglial cell activation involved in immune response IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of cell migration IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of chronic inflammatory response to non-antigenic stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of extrinsic apoptotic signaling pathway in absence of ligand IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of long-term synaptic potentiation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of neuroblast proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    response to wounding TAS
    Traceable Author Statement
    more info
    PubMed 
    viral process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    integral component of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    neuron projection IEA
    Inferred from Electronic Annotation
    more info
     
    neuronal cell body membrane IEA
    Inferred from Electronic Annotation
    more info
     
    perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    CX3C chemokine receptor 1
    Names
    C-X3-C CKR-1
    CMK-BRL-1
    CMK-BRL1
    G protein-coupled receptor 13
    G-protein coupled receptor 13
    beta chemokine receptor-like 1
    chemokine (C-C) receptor-like 1
    chemokine (C-X3-C) receptor 1
    fractalkine receptor

    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.

    Genomic

    1. NG_016362.1 RefSeqGene

      Range
      5001..23242
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001171171.1NP_001164642.1  CX3C chemokine receptor 1 isoform b

      See identical proteins and their annotated locations for NP_001164642.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2, 3, and 4 all encode the same isoform.
      Source sequence(s)
      AC092053, AI400350, BC028078, DA406242
      Consensus CDS
      CCDS43069.1
      UniProtKB/Swiss-Prot
      P49238
      Related
      ENSP00000439140, ENST00000541347
      Conserved Domains (1) summary
      pfam00001
      Location:54293
      7tm_1; 7 transmembrane receptor (rhodopsin family)
    2. NM_001171172.1NP_001164643.1  CX3C chemokine receptor 1 isoform b

      See identical proteins and their annotated locations for NP_001164643.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2, 3, and 4 all encode the same isoform.
      Source sequence(s)
      AC092053, AI400350, BC028078, DA396634, DB274136
      Consensus CDS
      CCDS43069.1
      UniProtKB/Swiss-Prot
      P49238
      Related
      ENSP00000444928, ENST00000542107
      Conserved Domains (1) summary
      pfam00001
      Location:54293
      7tm_1; 7 transmembrane receptor (rhodopsin family)
    3. NM_001171174.1NP_001164645.1  CX3C chemokine receptor 1 isoform a

      See identical proteins and their annotated locations for NP_001164645.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as clone 10) encodes the longer isoform (a).
      Source sequence(s)
      AC092053, AI400350, BC028078
      Consensus CDS
      CCDS54571.1
      UniProtKB/Swiss-Prot
      P49238
      Related
      ENSP00000351059, ENST00000358309
      Conserved Domains (1) summary
      pfam00001
      Location:86325
      7tm_1; 7 transmembrane receptor (rhodopsin family)
    4. NM_001337.3NP_001328.1  CX3C chemokine receptor 1 isoform b

      See identical proteins and their annotated locations for NP_001328.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4, also known as V28) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2, 3, and 4 all encode the same isoform.
      Source sequence(s)
      AC092053, BG541473, U20350
      Consensus CDS
      CCDS43069.1
      UniProtKB/Swiss-Prot
      P49238
      Related
      ENSP00000382166, OTTHUMP00000209587, ENST00000399220, OTTHUMT00000343613
      Conserved Domains (1) summary
      pfam00001
      Location:54293
      7tm_1; 7 transmembrane receptor (rhodopsin family)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p2 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p2 Primary Assembly

      Range
      39263494..39281735
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018914.2 Alternate CHM1_1.1

      Range
      39256125..39274344
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)