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

Gene ID: 6376, updated on 2-May-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
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Genomic context

Location:
16q21
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (57372490..57385044)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (63167607..63180165)
105.20220307 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 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 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 GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of I-kappaB phosphorylation IGI
Inferred from Genetic Interaction
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 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_2023_10

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)