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

Summary

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Official Symbol: CX3CL1provided by HGNC
Official Full Name: chemokine (C-X3-C motif) ligand 1provided by HGNC
Primary source: HGNC:10647
Locus tag: A-152E5.2
See related: Ensembl:ENSG00000006210; HPRD:03529; MIM:601880; Vega:OTTHUMG00000133469
Gene type: protein coding
RefSeq status: PROVISIONAL
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

Genomic context

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Location :: 16q13

Sequence :: Chromosome: 16; NC_000016.9 (57406414..57418956)

See CX3CL1 in Epigenomics, MapViewer

Chromosome 16 - NC_000016.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Bibliography

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GeneRIFs: Gene References Into Functions What's a GeneRIF?

Fractalkine was a significant predictor of all-cause mortality in patients with advanced heart failure. Fractalkine improves risk prediction beyond NT-proBNP and might therefore help to identify high risk patients who need special care.
Title: Fractalkine is an independent predictor of mortality in patients with advanced heart failure.
In the present coronary artery disease population, no differences in circulating levels of fractalkine or expression levels of CX3CR1 were observed between patients with and without T2DM, or with and without metabolic syndrome.
Title: Fractalkine and its receptor (CX3CR1) in patients with stable coronary artery disease and diabetes mellitus.
CX3CL1 expression in the conjunctiva is increased in immune cell trafficking during toxic ocular surface inflammation.
Title: CX3CL1 expression in the conjunctiva is involved in immune cell trafficking during toxic ocular surface inflammation.
Fibroblast growth factor receptor 1 activation leads to induction of CX3CL1 in a tumor setting.
Title: Fibroblast growth factor receptor 1 activation in mammary tumor cells promotes macrophage recruitment in a CX3CL1-dependent manner.
Chemokine fractalkine receptor (CX3CL1) binds directly to integrins alpha4beta1 and alphav4beta3 at a very high affinity.
Title: Integrins αvβ3 and α4β1 act as coreceptors for fractalkine, and the integrin-binding defective mutant of fractalkine is an antagonist of CX3CR1.
Fractalkine is a potential local inflammatory mediator which influences platelet activation in the setting of atherosclerosis. Review.
Title: Fractalkine--a local inflammatory marker aggravating platelet activation at the vulnerable plaque.
Suggest that Ang-II induces functional CX(3)CL1 expression in arterial but not in venous endothelial cells.
Title: Arterial and venous endothelia display differential functional fractalkine (CX3CL1) expression by angiotensin-II.
MCP-1, RANTES and fractalkine independently participate in the pathogenesis of plaque vulnerability and subsequent plaque rupture.
Title: Independent roles of monocyte chemoattractant protein-1, regulated on activation, normal T-cell expressed and secreted and fractalkine in the vulnerability of coronary atherosclerotic plaques.
Hypoxic release of endothelial CX3CL1 induced SMC phenotypic switching from the contractile to the proliferative state. Inhibition of CX3CR1 prevented CX3CL1 stimulation of SMC proliferation and monolayer expansion.
Title: Hypoxia-induced endothelial CX3CL1 triggers lung smooth muscle cell phenotypic switching and proliferative expansion.
Upregulation of glomerular and urinary fractalkine suggests an involvement of the CX3CR1-fractalkine axis in the exacerbation of gross hematuria in patients with IgA nephropathy.
Title: Activated innate immunity and the involvement of CX3CR1-fractalkine in promoting hematuria in patients with IgA nephropathy.

Submit: New GeneRIF Correction See all (131)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

HIV-1 protein interactions

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Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	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, p14	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 Protein Interaction Database

Interactions

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Products	Interactant	Other Gene	Source	Pubs	Description
P78423	P78423	CX3CL1	HPRD	PubMed
P78423	P49238	CX3CR1	HPRD	PubMed
BioGRID:112278	BioGRID:112278	CX3CL1	BioGRID	PubMed	Co-crystal Structure
BioGRID:112278	BioGRID:107904	CX3CR1	BioGRID	PubMed	Co-crystal Structure

Pathways from BioSystems

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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 ...
Direct p53 effectors, organism-specific biosystem (from Pathway Interaction Database)
Direct p53 effectors, organism-specific biosystem
Direct p53 effectors
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...
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...

General gene information

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Markers

RH86440 (e-PCR)
- UniSTS:90134

D8S2279 (e-PCR)
- UniSTS:473907

RH79608 (e-PCR)
- UniSTS:86368

D1S1423 (e-PCR)
- UniSTS:149619

D11S3114 (e-PCR)
- UniSTS:152207

RH67976 (e-PCR)
- UniSTS:57255

D16S2589E (e-PCR)
- UniSTS:51897

Homology

Homologs of the CX3CL1 gene: The CX3CL1 gene is conserved in chimpanzee, Rhesus monkey, dog, mouse, and rat.
Map Viewer (Mouse, Rat)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
chemokine activity	IDA Inferred from Direct Assay more info
chemokine activity	TAS Traceable Author Statement more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed
receptor binding	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
angiogenesis involved in wound healing	IEA Inferred from Electronic Annotation more info
cell adhesion	IEA Inferred from Electronic Annotation more info
chemotaxis	IDA Inferred from Direct Assay more info
cytokine-mediated signaling pathway	TAS Traceable Author Statement more info	PubMed
defense response	TAS Traceable Author Statement more info	PubMed
immune response	TAS Traceable Author Statement more info	PubMed
leukocyte adhesive activation	TAS Traceable Author Statement more info	PubMed
leukocyte chemotaxis	TAS Traceable Author Statement more info	PubMed
lymphocyte chemotaxis	IEA Inferred from Electronic Annotation more info
macrophage chemotaxis	IEA Inferred from Electronic Annotation more info
negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
neutrophil chemotaxis	IEA Inferred from Electronic Annotation more info
positive regulation of angiogenesis	IEA Inferred from Electronic Annotation more info
positive regulation of calcium-independent cell-cell adhesion	IDA Inferred from Direct Assay more info	PubMed
positive regulation of inflammatory response	IEP Inferred from Expression Pattern more info	PubMed
positive regulation of transforming growth factor beta1 production	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
cell surface	IDA Inferred from Direct Assay more info	PubMed
extracellular region	IDA Inferred from Direct Assay more info	PubMed
extracellular space	IEA Inferred from Electronic Annotation more info
integral to membrane	IDA Inferred from Direct Assay more info	PubMed
plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: fractalkine

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

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)

NM_002996.3 → NP_002987.1 fractalkine precursor

Status: PROVISIONAL

Source sequence(s)

BC001163

Consensus CDS

CCDS10779.1

UniProtKB/TrEMBL

A0N0N7

UniProtKB/Swiss-Prot

P78423

Related

ENSP00000006053, OTTHUMP00000164674, ENST00000006053, OTTHUMT00000257345

Conserved Domains (1) summary

cd00274
Location:25 – 100
Blast Score: 395

Chemokine_CX3C; 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 ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

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

Reference GRCh37.p10 Primary Assembly

Genomic

NC_000016.9 Reference GRCh37.p10 Primary Assembly

Range

57406414..57418956

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000148.1 Alternate HuRef

Range

43274294..43286836

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.0

Genomic

NC_018927.1 Alternate CHM1_1.0

Range

58419560..58432105

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	ABBA01025270.1 (21002..33544)	None
genomic	AC004382.1	AAC24307.1
genomic	AC009052.8 (70218..82760)	None
genomic	AMYH01007699.1 (32140..44685)	None
genomic	CH471092.1	EAW82919.1
genomic	EF064745.1	ABK41928.1
mRNA	AB209037.1	BAD92274.1
mRNA	AK222692.1	BAD96412.1
mRNA	AK223351.1	BAD97071.1
mRNA	AK313806.1	BAG36542.1
mRNA	BC001163.1	AAH01163.1
mRNA	BC016164.1	AAH16164.1
mRNA	CR457426.1	CAG33707.1
mRNA	GU047346.1	None
mRNA	U84487.1	AAB49679.1
mRNA	U91835.1	AAB50014.1
other-genetic	DQ890704.2	ABM81630.1
other-genetic	DQ891871.2	ABM82797.1
other-genetic	DQ893888.2	ABM84814.1
other-genetic	DQ895059.2	ABM85985.1