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

    Gene ID: 1524, updated on 10-Dec-2024

    Summary

    Official Symbol
    CX3CR1provided by HGNC
    Official Full Name
    C-X3-C motif chemokine receptor 1provided by HGNC
    Primary source
    HGNC:HGNC:2558
    See related
    Ensembl:ENSG00000168329 MIM:601470; AllianceGenome:HGNC:2558
    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]
    Expression
    Biased expression in brain (RPKM 21.4), lung (RPKM 6.4) and 12 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CX3CR1 in Genome Data Viewer
    Location:
    3p22.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (39263494..39292966, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (39276418..39305868, complement)
    RS_2024_09 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 ATAC-STARR-seq lymphoblastoid silent region 14223 Neighboring gene DSTN pseudogene 4 Neighboring gene uncharacterized LOC102724104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19696 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19697 Neighboring gene adenosine deaminase domain containing 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19701 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 21 Neighboring gene C-C motif chemokine receptor 8

    Genomic regions, transcripts, and products

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables C-C chemokine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables C-C chemokine receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables C-X3-C chemokine binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables C-X3-C chemokine binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables C-X3-C chemokine receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables CX3C chemokine receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables G protein-coupled peptide receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables G protein-coupled receptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables chemokine receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in G protein-coupled receptor signaling pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in adaptive immune response ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in antifungal innate immune response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in antifungal innate immune response ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in autocrine signaling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in brain development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in calcium-mediated signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell-cell signaling TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cellular defense response TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cellular response to lipopolysaccharide ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular response to transforming growth factor beta stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to tumor necrosis factor IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in central nervous system maturation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in chemokine-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chemotaxis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in host-mediated regulation of intestinal microbiota composition ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in immune response ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in innate immune response IC
    Inferred by Curator
    more info
    PubMed 
    involved_in leukocyte chemotaxis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in leukocyte tethering or rolling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in memory IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in microglial cell activation involved in immune response ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in modulation of chemical synaptic transmission ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in multiple spine synapse organization, single dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of apoptotic signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of cell migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of hippocampal neuron apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of interleukin-1 beta production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of long-term synaptic potentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of microglial cell mediated cytotoxicity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in phospholipase C-activating G protein-coupled receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of canonical NF-kappaB signal transduction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cytosolic calcium ion concentration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of microglial cell migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of monocyte chemotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of neuroblast proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of neurogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of microglial cell migration TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of neurogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of nitric oxide biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of synaptic plasticity TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of tumor necrosis factor production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in response to ischemia ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in response to wounding TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in social behavior ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in synapse maturation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in synapse pruning IC
    Inferred by Curator
    more info
     
    involved_in synapse pruning ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cell surface ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in cell surface TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in dendritic tree ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in macropinosome membrane TAS
    Traceable Author Statement
    more info
     
    located_in neuron projection ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in neuronal cell body membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in perinuclear region of cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    CX3C chemokine receptor 1
    Names
    C-X3-C CKR-1
    CMK-BRL-1
    CMK-BRL1
    G-protein coupled receptor 13
    beta chemokine receptor-like 1
    chemokine (C-C) receptor-like 1
    chemokine (C-X3-C motif) receptor 1
    chemokine (C-X3-C) receptor 1
    fractalkine receptor

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_016362.2 RefSeqGene

      Range
      17930..34470
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001171171.2NP_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
      A0N0N6, B2R5Z4, J3KP17, P49238
      Related
      ENSP00000439140.1, ENST00000541347.5
      Conserved Domains (1) summary
      pfam00001
      Location:48293
      7tm_1; 7 transmembrane receptor (rhodopsin family)
    2. NM_001171172.2NP_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
      A0N0N6, B2R5Z4, J3KP17, P49238
      Related
      ENSP00000444928.1, ENST00000542107.5
      Conserved Domains (1) summary
      pfam00001
      Location:48293
      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
      ENSP00000351059.3, ENST00000358309.3
      Conserved Domains (1) summary
      pfam00001
      Location:80325
      7tm_1; 7 transmembrane receptor (rhodopsin family)
    4. NM_001337.4NP_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
      A0N0N6, B2R5Z4, J3KP17, P49238
      Related
      ENSP00000382166.3, ENST00000399220.3
      Conserved Domains (1) summary
      pfam00001
      Location:48293
      7tm_1; 7 transmembrane receptor (rhodopsin family)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      39263494..39292966 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047447538.1XP_047303494.1  CX3C chemokine receptor 1 isoform X1

      UniProtKB/Swiss-Prot
      A0N0N6, B2R5Z4, J3KP17, P49238

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      39276418..39305868 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054345424.1XP_054201399.1  CX3C chemokine receptor 1 isoform X1