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    CX3CL1 C-X3-C motif chemokine ligand 1 [ Homo sapiens (human) ]

    Gene ID: 6376, updated on 9-Dec-2024

    Summary

    Official Symbol
    CX3CL1provided by HGNC
    Official Full Name
    C-X3-C motif chemokine ligand 1provided by HGNC
    Primary source
    HGNC:HGNC:10647
    See related
    Ensembl:ENSG00000006210 MIM:601880; AllianceGenome:HGNC:10647
    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
    NTN; NTT; CXC3; CXC3C; SCYD1; ABCD-3; C3Xkine; fractalkine; neurotactin
    Summary
    This gene belongs to the CX3C subgroup of chemokines, characterized by the number of amino acids located between the conserved cysteine residues. This is the only member of the CX3C subgroup, which contains three amino acids between cysteine residues, resulting in a Cys-X-X-X-Cys configuration. The encoded protein contains an extended mucin-like stalk with a chemokine domain on top, and exists in both a membrane-anchored form where it acts as a binding molecule, or, in soluble form, as a chemotactic cytokine. The mature form of this protein can be cleaved at the cell surface, yielding different soluble forms that can interact with the G-protein coupled receptor, C-X3-C motif chemokine receptor 1 gene product. This gene plays a role in a wide range of diseases, including cancer, vasculitis, neuropathies, atherosclerosis, inflammatory diseases, and in human immunodeficiency virus infections. [provided by RefSeq, Sep 2017]
    Expression
    Broad expression in brain (RPKM 40.1), lung (RPKM 37.8) and 21 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CX3CL1 in Genome Data Viewer
    Location:
    16q21
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (57372490..57385044)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (63167607..63180165)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (57406402..57418956)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein L23a pseudogene 91 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:57396657-57396838 Neighboring gene C-C motif chemokine ligand 22 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:57412503-57413083 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10891 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57417624-57418314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57418315-57419004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10894 Neighboring gene C-C motif chemokine ligand 17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10895 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57450029-57450544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57450545-57451060 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57451577-57452091 Neighboring gene cytokine induced apoptosis inhibitor 1 Neighboring gene Sharpr-MPRA regulatory region 5957

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 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 Upregulation of the human proteins CCL2, CX3CL1, IL-1beta, and CXCL10 by HIV-1 gp120 involves CB2 receptor in mesencephalic neuronal/glial culture model PubMed
    env Chemokines such as fractalkine, macrophage-derived chemokine (MDC), RANTES, and SDF-1alpha are able to block gp120-induced apoptosis of hippocampal neurons; both fractalkine and MDC activate ERK-1/2, while SDF-1alpha activates CREB PubMed
    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
    Tat tat HIV-1 Tat-mediated downregulation of CX3CR1 inhibits CX3CL1-induced migration of microglia PubMed
    tat Pretreatment of microglia with HIV-1 Tat followed by treatment with CX3CL1 results in inhibition of CX3CL1-mediated activation of ERK1/2 and JNK MAPKs compared to cells not treated with Tat PubMed
    tat Fractalkine-CX3CR1 signaling contributes to the inhibition of the synergistic neurotoxic effects by opioids and HIV-1 Tat PubMed
    tat Fractalkine is neuroprotective to cultured neurons when co-administered with HIV-1 Tat, a viral protein that induces neuronal apoptosis 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 CCR chemokine receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables CX3C chemokine receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables CX3C chemokine receptor binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables CX3C chemokine receptor binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables CXCR1 chemokine receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables chemoattractant activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables chemokine activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chemokine activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chemokine activity IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    enables chemokine activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables integrin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables signaling receptor binding TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in G protein-coupled receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in angiogenesis involved in wound healing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in antimicrobial humoral immune response mediated by antimicrobial peptide IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in autocrine signaling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell adhesion IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    involved_in cell chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell-cell adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell-cell adhesion TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cell-cell signaling TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in chemokine-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in chemokine-mediated signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in chemokine-mediated signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in chemotaxis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cytokine-mediated signaling pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in defense response TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in eosinophil chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in extrinsic apoptotic signaling pathway in absence of ligand IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in immune response TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in inflammatory response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in integrin activation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in leukocyte adhesive activation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in leukocyte chemotaxis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in leukocyte migration involved in inflammatory response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lymphocyte chemotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in macrophage chemotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in microglial cell activation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in microglial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of apoptotic signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in negative regulation of cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cell-substrate adhesion NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of extrinsic apoptotic signaling pathway in absence of ligand IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of glutamate receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of hippocampal neuron apoptotic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in negative regulation of interleukin-1 alpha production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of interleukin-1 beta production TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of interleukin-6 production TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of microglial cell activation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of neuron migration TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of tumor necrosis factor production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of tumor necrosis factor production TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in neuron cellular homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neuron remodeling TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in neutrophil chemotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive chemotaxis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of ERK1 and ERK2 cascade TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of MAPK cascade IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of actin filament bundle assembly IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of calcium-independent cell-cell adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of canonical NF-kappaB signal transduction IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of canonical NF-kappaB signal transduction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell-matrix adhesion TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of inflammatory response IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in positive regulation of microglial cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of neuroblast proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of release of sequestered calcium ion into cytosol IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of smooth muscle cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transforming growth factor beta1 production IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of lipopolysaccharide-mediated signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of neurogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of synaptic plasticity TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in response to ischemia ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in synapse pruning TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cell projection ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular region IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular region IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in extracellular region ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in neuron projection IEA
    Inferred from Electronic Annotation
    more info
     
    located_in neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in perinuclear region of cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    fractalkine
    Names
    C-X3-C motif chemokine 1
    CX3C membrane-anchored chemokine
    chemokine (C-X3-C motif) ligand 1
    small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin)
    small inducible cytokine subfamily D (Cys-X3-Cys), member-1
    small-inducible cytokine D1

    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.

    mRNA and Protein(s)

    1. NM_001304392.3NP_001291321.1  fractalkine isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 5' end and initiates translation at an alternate start codon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AC009052, BC001163, CA396869, HY114023
      UniProtKB/TrEMBL
      J3QRA1
      Conserved Domains (2) summary
      PRK10263
      Location:44217
      PRK10263; DNA translocase FtsK; Provisional
      cl00134
      Location:115
      Chemokine; small cytokines, including a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; distinguished from other cytokines by their receptors, which are G-protein coupled receptors; divided into 4 ...
    2. NM_002996.6NP_002987.1  fractalkine isoform 1 precursor

      See identical proteins and their annotated locations for NP_002987.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC009052, BC001163, HY114023
      Consensus CDS
      CCDS10779.1
      UniProtKB/Swiss-Prot
      O00672, P78423
      UniProtKB/TrEMBL
      A0N0N7, Q53H89, Q6I9S9
      Related
      ENSP00000006053.6, ENST00000006053.7
      Conserved Domains (3) summary
      PRK12323
      Location:169342
      PRK12323; DNA polymerase III subunit gamma/tau
      cd00274
      Location:25100
      Chemokine_CX3C; 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteines; differ structurally from the other subgroups in that they are attached to a membrane-spanning domain via a mucin-like stalk and can be proteolytically cleaved to a ...
      NF033804
      Location:102243
      Streccoc_I_II; antigen I/II family LPXTG-anchored adhesin

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      57372490..57385044
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      63167607..63180165
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)