CX3CL1 (C-X3-C motif chemokine ligand 1)

Gene

• Entrez ID: 6376
• Gene name: C-X3-C motif chemokine ligand 1
• Gene symbol: CX3CL1
• Synonyms: ABCD-3, C3Xkine, CXC3, CXC3C, NTN, NTT, SCYD1, fractalkine, neurotactin
• Chromosome: 16
• Chromosome location: 16q21
• 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, res

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT725028	hsa-miR-605-5p	HITS-CLIP	19536157
MIRT725027	hsa-miR-2681-3p	HITS-CLIP	19536157
MIRT725026	hsa-miR-3688-3p	HITS-CLIP	19536157
MIRT725025	hsa-miR-490-5p	HITS-CLIP	19536157
MIRT725024	hsa-miR-4308	HITS-CLIP	19536157
MIRT725023	hsa-miR-4292	HITS-CLIP	19536157
MIRT725022	hsa-miR-6791-5p	HITS-CLIP	19536157
MIRT725021	hsa-miR-7152-3p	HITS-CLIP	19536157
MIRT725020	hsa-miR-5093	HITS-CLIP	19536157
MIRT725028	hsa-miR-605-5p	HITS-CLIP	19536157
MIRT725027	hsa-miR-2681-3p	HITS-CLIP	19536157
MIRT725026	hsa-miR-3688-3p	HITS-CLIP	19536157
MIRT725025	hsa-miR-490-5p	HITS-CLIP	19536157
MIRT725024	hsa-miR-4308	HITS-CLIP	19536157
MIRT725023	hsa-miR-4292	HITS-CLIP	19536157
MIRT725022	hsa-miR-6791-5p	HITS-CLIP	19536157
MIRT725021	hsa-miR-7152-3p	HITS-CLIP	19536157
MIRT725020	hsa-miR-5093	HITS-CLIP	19536157
MIRT917501	hsa-miR-1185	CLIP-seq
MIRT917502	hsa-miR-1262	CLIP-seq
MIRT917503	hsa-miR-1264	CLIP-seq
MIRT917504	hsa-miR-1293	CLIP-seq
MIRT917505	hsa-miR-1343	CLIP-seq
MIRT917506	hsa-miR-2110	CLIP-seq
MIRT917507	hsa-miR-214	CLIP-seq
MIRT917508	hsa-miR-27a	CLIP-seq
MIRT917509	hsa-miR-27b	CLIP-seq
MIRT917510	hsa-miR-3124-3p	CLIP-seq
MIRT917511	hsa-miR-3176	CLIP-seq
MIRT917512	hsa-miR-3189-3p	CLIP-seq
MIRT917513	hsa-miR-3605-5p	CLIP-seq
MIRT917514	hsa-miR-3613-3p	CLIP-seq
MIRT917515	hsa-miR-3614-3p	CLIP-seq
MIRT917516	hsa-miR-3616-3p	CLIP-seq
MIRT917517	hsa-miR-3619-5p	CLIP-seq
MIRT917518	hsa-miR-3679-5p	CLIP-seq
MIRT917519	hsa-miR-3685	CLIP-seq
MIRT917520	hsa-miR-384	CLIP-seq
MIRT917521	hsa-miR-3919	CLIP-seq
MIRT917522	hsa-miR-3922-3p	CLIP-seq
MIRT917523	hsa-miR-3925-5p	CLIP-seq
MIRT917524	hsa-miR-4271	CLIP-seq
MIRT917525	hsa-miR-4291	CLIP-seq
MIRT917526	hsa-miR-432	CLIP-seq
MIRT917527	hsa-miR-4436b-3p	CLIP-seq
MIRT917528	hsa-miR-4443	CLIP-seq
MIRT917529	hsa-miR-4447	CLIP-seq
MIRT917530	hsa-miR-4472	CLIP-seq
MIRT917531	hsa-miR-4483	CLIP-seq
MIRT917532	hsa-miR-4651	CLIP-seq
MIRT917533	hsa-miR-4667-5p	CLIP-seq
MIRT917534	hsa-miR-4700-5p	CLIP-seq
MIRT917535	hsa-miR-4701-3p	CLIP-seq
MIRT917536	hsa-miR-4725-3p	CLIP-seq
MIRT917537	hsa-miR-4757-5p	CLIP-seq
MIRT917538	hsa-miR-4773	CLIP-seq
MIRT917539	hsa-miR-483-5p	CLIP-seq
MIRT917540	hsa-miR-513a-5p	CLIP-seq
MIRT917541	hsa-miR-542-5p	CLIP-seq
MIRT917542	hsa-miR-548al	CLIP-seq
MIRT917543	hsa-miR-608	CLIP-seq
MIRT917544	hsa-miR-761	CLIP-seq
MIRT917545	hsa-miR-922	CLIP-seq
MIRT917502	hsa-miR-1262	CLIP-seq
MIRT917504	hsa-miR-1293	CLIP-seq
MIRT917512	hsa-miR-3189-3p	CLIP-seq
MIRT917529	hsa-miR-4447	CLIP-seq
MIRT917530	hsa-miR-4472	CLIP-seq
MIRT917531	hsa-miR-4483	CLIP-seq
MIRT917532	hsa-miR-4651	CLIP-seq
MIRT917535	hsa-miR-4701-3p	CLIP-seq
MIRT917543	hsa-miR-608	CLIP-seq
MIRT1972050	hsa-miR-1182	CLIP-seq
MIRT1972051	hsa-miR-1207-5p	CLIP-seq
MIRT1972052	hsa-miR-1233	CLIP-seq
MIRT1972053	hsa-miR-1972	CLIP-seq
MIRT917512	hsa-miR-3189-3p	CLIP-seq
MIRT917527	hsa-miR-4436b-3p	CLIP-seq
MIRT1972054	hsa-miR-4488	CLIP-seq
MIRT1972055	hsa-miR-4687-5p	CLIP-seq
MIRT1972056	hsa-miR-4697-5p	CLIP-seq
MIRT1972057	hsa-miR-4763-3p	CLIP-seq
MIRT1972050	hsa-miR-1182	CLIP-seq
MIRT2207770	hsa-miR-1183	CLIP-seq
MIRT917501	hsa-miR-1185	CLIP-seq
MIRT2207771	hsa-miR-1206	CLIP-seq
MIRT1972051	hsa-miR-1207-5p	CLIP-seq
MIRT2207772	hsa-miR-1224-3p	CLIP-seq
MIRT2207773	hsa-miR-1226	CLIP-seq
MIRT2207774	hsa-miR-125a-5p	CLIP-seq
MIRT2207775	hsa-miR-125b	CLIP-seq
MIRT2207776	hsa-miR-1260	CLIP-seq
MIRT2207777	hsa-miR-1260b	CLIP-seq
MIRT917502	hsa-miR-1262	CLIP-seq
MIRT2207778	hsa-miR-1273f	CLIP-seq
MIRT2207779	hsa-miR-1278	CLIP-seq
MIRT2207780	hsa-miR-1280	CLIP-seq
MIRT2207781	hsa-miR-1286	CLIP-seq
MIRT917504	hsa-miR-1293	CLIP-seq
MIRT2207782	hsa-miR-143	CLIP-seq
MIRT2207783	hsa-miR-1909	CLIP-seq
MIRT917507	hsa-miR-214	CLIP-seq
MIRT2207784	hsa-miR-2467-3p	CLIP-seq
MIRT2207785	hsa-miR-3169	CLIP-seq
MIRT917512	hsa-miR-3189-3p	CLIP-seq
MIRT2207786	hsa-miR-3194-5p	CLIP-seq
MIRT2207787	hsa-miR-342-5p	CLIP-seq
MIRT917513	hsa-miR-3605-5p	CLIP-seq
MIRT917517	hsa-miR-3619-5p	CLIP-seq
MIRT2207788	hsa-miR-3678-3p	CLIP-seq
MIRT917518	hsa-miR-3679-5p	CLIP-seq
MIRT2207789	hsa-miR-3689a-3p	CLIP-seq
MIRT2207790	hsa-miR-3689c	CLIP-seq
MIRT2207791	hsa-miR-4260	CLIP-seq
MIRT2207792	hsa-miR-4283	CLIP-seq
MIRT2207793	hsa-miR-4319	CLIP-seq
MIRT917527	hsa-miR-4436b-3p	CLIP-seq
MIRT917529	hsa-miR-4447	CLIP-seq
MIRT917530	hsa-miR-4472	CLIP-seq
MIRT917531	hsa-miR-4483	CLIP-seq
MIRT1972054	hsa-miR-4488	CLIP-seq
MIRT2207794	hsa-miR-4489	CLIP-seq
MIRT2207795	hsa-miR-4492	CLIP-seq
MIRT2207796	hsa-miR-4498	CLIP-seq
MIRT2207797	hsa-miR-4505	CLIP-seq
MIRT2207798	hsa-miR-4530	CLIP-seq
MIRT2207799	hsa-miR-4641	CLIP-seq
MIRT917532	hsa-miR-4651	CLIP-seq
MIRT2207800	hsa-miR-4661-3p	CLIP-seq
MIRT2207801	hsa-miR-4664-5p	CLIP-seq
MIRT1972056	hsa-miR-4697-5p	CLIP-seq
MIRT917535	hsa-miR-4701-3p	CLIP-seq
MIRT2207802	hsa-miR-4708-5p	CLIP-seq
MIRT2207803	hsa-miR-4728-5p	CLIP-seq
MIRT2207804	hsa-miR-4731-5p	CLIP-seq
MIRT2207805	hsa-miR-4733-3p	CLIP-seq
MIRT2207806	hsa-miR-4755-3p	CLIP-seq
MIRT1972057	hsa-miR-4763-3p	CLIP-seq
MIRT2207807	hsa-miR-4770	CLIP-seq
MIRT917539	hsa-miR-483-5p	CLIP-seq
MIRT2207808	hsa-miR-541	CLIP-seq
MIRT917541	hsa-miR-542-5p	CLIP-seq
MIRT917542	hsa-miR-548al	CLIP-seq
MIRT917543	hsa-miR-608	CLIP-seq
MIRT2207809	hsa-miR-654-5p	CLIP-seq
MIRT917544	hsa-miR-761	CLIP-seq
MIRT2207810	hsa-miR-762	CLIP-seq
MIRT917545	hsa-miR-922	CLIP-seq
MIRT917502	hsa-miR-1262	CLIP-seq
MIRT917504	hsa-miR-1293	CLIP-seq
MIRT2207784	hsa-miR-2467-3p	CLIP-seq
MIRT917512	hsa-miR-3189-3p	CLIP-seq
MIRT917527	hsa-miR-4436b-3p	CLIP-seq
MIRT917529	hsa-miR-4447	CLIP-seq
MIRT917530	hsa-miR-4472	CLIP-seq
MIRT917531	hsa-miR-4483	CLIP-seq
MIRT2207795	hsa-miR-4492	CLIP-seq
MIRT2207796	hsa-miR-4498	CLIP-seq
MIRT2207797	hsa-miR-4505	CLIP-seq
MIRT2207798	hsa-miR-4530	CLIP-seq
MIRT917532	hsa-miR-4651	CLIP-seq
MIRT917535	hsa-miR-4701-3p	CLIP-seq
MIRT917543	hsa-miR-608	CLIP-seq
MIRT2207810	hsa-miR-762	CLIP-seq
MIRT917510	hsa-miR-3124-3p	CLIP-seq
MIRT2447841	hsa-miR-4469	CLIP-seq
MIRT2447842	hsa-miR-4777-3p	CLIP-seq
MIRT2447843	hsa-miR-642a	CLIP-seq
MIRT917510	hsa-miR-3124-3p	CLIP-seq
MIRT2447841	hsa-miR-4469	CLIP-seq
MIRT2447842	hsa-miR-4777-3p	CLIP-seq
MIRT2447843	hsa-miR-642a	CLIP-seq
MIRT917510	hsa-miR-3124-3p	CLIP-seq
MIRT2447841	hsa-miR-4469	CLIP-seq
MIRT2447842	hsa-miR-4777-3p	CLIP-seq
MIRT2447843	hsa-miR-642a	CLIP-seq
MIRT917510	hsa-miR-3124-3p	CLIP-seq
MIRT2447841	hsa-miR-4469	CLIP-seq
MIRT2447842	hsa-miR-4777-3p	CLIP-seq
MIRT2447843	hsa-miR-642a	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
WT1	Unknown	17430890

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001774	Process	Microglial cell activation	ISS
GO:0001954	Process	Positive regulation of cell-matrix adhesion	TAS	24352739
GO:0002052	Process	Positive regulation of neuroblast proliferation	ISS
GO:0002523	Process	Leukocyte migration involved in inflammatory response	IMP	23125415
GO:0002548	Process	Monocyte chemotaxis	IBA	21873635
GO:0002931	Process	Response to ischemia	ISS
GO:0005102	Function	Signaling receptor binding	TAS	12714508
GO:0005178	Function	Integrin binding	IDA	23125415
GO:0005515	Function	Protein binding	IPI	9931005, 23125415, 24789099, 25745166
GO:0005576	Component	Extracellular region	IDA	10415068, 12714508
GO:0005576	Component	Extracellular region	IMP	10899174
GO:0005576	Component	Extracellular region	ISS
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	IBA	21873635
GO:0005886	Component	Plasma membrane	TAS	24352739
GO:0006935	Process	Chemotaxis	IDA	21829356
GO:0006935	Process	Chemotaxis	IMP	23125415
GO:0006952	Process	Defense response	TAS	12714508
GO:0006954	Process	Inflammatory response	IBA	21873635
GO:0006955	Process	Immune response	TAS	12714508
GO:0007155	Process	Cell adhesion	IPI	10187784
GO:0007186	Process	G protein-coupled receptor signaling pathway	IBA	21873635
GO:0007186	Process	G protein-coupled receptor signaling pathway	ISS
GO:0007186	Process	G protein-coupled receptor signaling pathway	TAS
GO:0007267	Process	Cell-cell signaling	TAS	24352739
GO:0007568	Process	Aging	ISS
GO:0008009	Function	Chemokine activity	IBA	21873635
GO:0008009	Function	Chemokine activity	IDA	21829356
GO:0008009	Function	Chemokine activity	IGI	10415068
GO:0008009	Function	Chemokine activity	TAS	12714508, 24352739
GO:0008284	Process	Positive regulation of cell population proliferation	IMP	24294368
GO:0009986	Component	Cell surface	IDA	12714508
GO:0010812	Process	Negative regulation of cell-substrate adhesion	NAS	24352739
GO:0010976	Process	Positive regulation of neuron projection development	ISS
GO:0016020	Component	Membrane	IDA	10899174
GO:0016020	Component	Membrane	ISS
GO:0016021	Component	Integral component of membrane	IDA	12714508
GO:0016322	Process	Neuron remodeling	TAS	20920788
GO:0019221	Process	Cytokine-mediated signaling pathway	TAS	11777952
GO:0030336	Process	Negative regulation of cell migration	IDA	25435433
GO:0030593	Process	Neutrophil chemotaxis	IBA	21873635
GO:0030595	Process	Leukocyte chemotaxis	TAS	11777952
GO:0031664	Process	Regulation of lipopolysaccharide-mediated signaling pathway	IDA	10652441
GO:0031737	Function	CX3C chemokine receptor binding	IDA	10415068, 23125415
GO:0031737	Function	CX3C chemokine receptor binding	NAS	20018408
GO:0031737	Function	CX3C chemokine receptor binding	TAS	24352739
GO:0032233	Process	Positive regulation of actin filament bundle assembly	IGI	10415068
GO:0032690	Process	Negative regulation of interleukin-1 alpha production	ISS
GO:0032691	Process	Negative regulation of interleukin-1 beta production	TAS	20018408
GO:0032715	Process	Negative regulation of interleukin-6 production	TAS	20018408
GO:0032720	Process	Negative regulation of tumor necrosis factor production	IDA	10652441
GO:0032720	Process	Negative regulation of tumor necrosis factor production	TAS	20018408
GO:0033622	Process	Integrin activation	IMP	23125415
GO:0035425	Process	Autocrine signaling	ISS
GO:0042056	Function	Chemoattractant activity	IMP	10899174
GO:0042995	Component	Cell projection	ISS
GO:0043025	Component	Neuronal cell body	ISS
GO:0043066	Process	Negative regulation of apoptotic process	IMP	24294368
GO:0043123	Process	Positive regulation of I-kappaB kinase/NF-kappaB signaling	ISS
GO:0043410	Process	Positive regulation of MAPK cascade	IGI	10415068
GO:0043547	Process	Positive regulation of GTPase activity	IBA	21873635
GO:0045237	Function	CXCR1 chemokine receptor binding	IPI	10187784
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	ISS
GO:0048020	Function	CCR chemokine receptor binding	IBA	21873635
GO:0048167	Process	Regulation of synaptic plasticity	TAS	24352739
GO:0048245	Process	Eosinophil chemotaxis	IBA	21873635
GO:0048247	Process	Lymphocyte chemotaxis	IBA	21873635
GO:0048471	Component	Perinuclear region of cytoplasm	ISS
GO:0048661	Process	Positive regulation of smooth muscle cell proliferation	ISS
GO:0050729	Process	Positive regulation of inflammatory response	IEP	11777952
GO:0050767	Process	Regulation of neurogenesis	TAS	24352739
GO:0050902	Process	Leukocyte adhesive activation	TAS	12714508
GO:0050918	Process	Positive chemotaxis	IMP	10899174
GO:0051041	Process	Positive regulation of calcium-independent cell-cell adhesion	IDA	12714508
GO:0051092	Process	Positive regulation of NF-kappaB transcription factor activity	IGI	10869418
GO:0051281	Process	Positive regulation of release of sequestered calcium ion into cytosol	IGI	10415068, 10869418
GO:0051897	Process	Positive regulation of protein kinase B signaling	IGI	10415068, 10869418
GO:0051897	Process	Positive regulation of protein kinase B signaling	ISS
GO:0060326	Process	Cell chemotaxis	IDA	10415068
GO:0061518	Process	Microglial cell proliferation	IMP	12125082
GO:0070050	Process	Neuron cellular homeostasis	ISS
GO:0070098	Process	Chemokine-mediated signaling pathway	IBA	21873635
GO:0070098	Process	Chemokine-mediated signaling pathway	IDA	10415068
GO:0070374	Process	Positive regulation of ERK1 and ERK2 cascade	IBA	21873635
GO:0070374	Process	Positive regulation of ERK1 and ERK2 cascade	TAS	24352739
GO:0071346	Process	Cellular response to interferon-gamma	IBA	21873635
GO:0071347	Process	Cellular response to interleukin-1	IBA	21873635
GO:0071356	Process	Cellular response to tumor necrosis factor	IBA	21873635
GO:0098609	Process	Cell-cell adhesion	ISS
GO:0098609	Process	Cell-cell adhesion	TAS	24352739
GO:0098883	Process	Synapse pruning	TAS	20920788
GO:0110091	Process	Negative regulation of hippocampal neuron apoptotic process	IGI	10869418
GO:1900450	Process	Negative regulation of glutamate receptor signaling pathway	ISS
GO:1903721	Process	Positive regulation of I-kappaB phosphorylation	IGI	10869418
GO:1903979	Process	Negative regulation of microglial cell activation	ISS
GO:1904141	Process	Positive regulation of microglial cell migration	IDA	10415068
GO:2001223	Process	Negative regulation of neuron migration	TAS	24352739
GO:2001234	Process	Negative regulation of apoptotic signaling pathway	IGI	10869418

Other IDs

• MIM: 601880
• HGNC: 10647
• e!Ensembl: ENSG00000006210

Protein

• UniProt ID: P78423
• Protein name: Fractalkine (C-X3-C motif chemokine 1) (CX3C membrane-anchored chemokine) (Neurotactin) (Small-inducible cytokine D1) [Cleaved into: Processed fractalkine]
• Protein function: Chemokine that acts as a ligand for both CX3CR1 and integrins ITGAV:ITGB3 and ITGA4:ITGB1 (PubMed:12055230, PubMed:21829356, PubMed:23125415, PubMed:9782118, PubMed:9931005). The CX3CR1-CX3CL1 signaling exerts distinct functions in different tis
• PDB: 1B2T, 1F2L, 3ONA, 4XT1, 4XT3, 5WB2, 7RKF, 7RKM, 7RKN, 7XBX
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00048	IL8	31 → 89	Small cytokines (intecrine/chemokine), interleukin-8 like	Domain

• Sequence:

  MAPISLSWLLRLATFCHLTVLLAGQHHGVTKCNITCSKMTSKIPVALLIHYQQNQASCGK
  RAIILETRQHRLFCADPKEQWVKDAMQHLDRQAAALTRNGGTFEKQIGEVKPRTTPAAGG
  MDESVVLEPEATGESSSLEPTPSSQEAQRALGTSPELPTGVTGSSGTRLPPTPKAQDGGP
  VGTELFRVPPVSTAATWQSSAPHQPGPSLWAEAKTSEAPSTQDPSTQASTASSPAPEENA
  PSEGQRVWGQGQSPRPENSLEREEMGPVPAHTDAFQDWGPGSMAHVSVVPVSSEGTPSRE
  PVASGSWTPKAEEPIHATMDPQRLGVLITPVPDAQAATRRQAVGLLAFLGLLFCLGVAMF
  TYQSLQGCPRKMAGEMAEGLRYIPRSCGSNSYVLVPV

• Sequence length: 397

Pathways

KEGG:

Cytokine-cytokine receptor interaction
Viral protein interaction with cytokine and cytokine receptor
Chemokine signaling pathway
Efferocytosis
TNF signaling pathway
Human cytomegalovirus infection

Reactome:

Chemokine receptors bind chemokines
G alpha (i) signalling events

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Prostate cancer	Malignant neoplasm of prostate	rs121909139, rs121909140, rs121909141, rs121909142, rs121909143, rs606231169, rs606231170, rs137852584, rs137852578, rs137852580, rs137852581, rs137852582	17199135

Unknown
Disease name	Disease term	dbSNP ID	References
Myocardial ischemia	Myocardial Ischemia		16214533
Prostatic neoplasms	Prostatic Neoplasms		17199135