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... See more...

Aliases for CX3CL1 Gene

Aliases for CX3CL1 Gene

  • C-X3-C Motif Chemokine Ligand 1 2 3 5
  • Small Inducible Cytokine Subfamily D (Cys-X3-Cys), Member 1 (Fractalkine, Neurotactin) 2 3
  • Chemokine (C-X3-C Motif) Ligand 1 2 3
  • CX3C Membrane-Anchored Chemokine 3 4
  • Small-Inducible Cytokine D1 3 4
  • C-X3-C Motif Chemokine 1 3 4
  • Neurotactin 3 4
  • Fractalkine 3 4
  • SCYD1 3 4
  • NTT 3 4
  • Small Inducible Cytokine Subfamily D (Cys-X3-Cys), Member-1 3
  • C3Xkine 3
  • ABCD-3 3
  • CXC3C 3
  • CXC3 3
  • NTN 3
  • FKN 4

External Ids for CX3CL1 Gene

Previous HGNC Symbols for CX3CL1 Gene

  • SCYD1

Previous GeneCards Identifiers for CX3CL1 Gene

  • GC16P047801
  • GC16P057466
  • GC16P057140
  • GC16P057181
  • GC16P057162
  • GC16P055963
  • GC16P057406
  • GC16P043274

Summaries for CX3CL1 Gene

Entrez Gene Summary for CX3CL1 Gene

  • 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]

CIViC Summary for CX3CL1 Gene

GeneCards Summary for CX3CL1 Gene

CX3CL1 (C-X3-C Motif Chemokine Ligand 1) is a Protein Coding gene. Diseases associated with CX3CL1 include Pityriasis Rosea and Vasculitis. Among its related pathways are CCR5 Pathway in Macrophages and Direct p53 effectors. Gene Ontology (GO) annotations related to this gene include signaling receptor binding and chemokine activity. An important paralog of this gene is CCL21.

UniProtKB/Swiss-Prot Summary for CX3CL1 Gene

  • Acts as a ligand for both CX3CR1 and integrins. Binds to CX3CR1 (PubMed:23125415, PubMed:9931005, PubMed:21829356). Binds to integrins ITGAV:ITGB3 and ITGA4:ITGB1. Can activate integrins in both a CX3CR1-dependent and CX3CR1-independent manner. In the presence of CX3CR1, activates integrins by binding to the classical ligand-binding site (site 1) in integrins. In the absence of CX3CR1, binds to a second site (site 2) in integrins which is distinct from site 1 and enhances the binding of other integrin ligands to site 1 (PubMed:23125415, PubMed:24789099). The soluble form is chemotactic for T-cells and monocytes and not for neutrophils. The membrane-bound form promotes adhesion of those leukocytes to endothelial cells. May play a role in regulating leukocyte adhesion and migration processes at the endothelium (PubMed:9024663, PubMed:9177350).

Gene Wiki entry for CX3CL1 Gene

Additional gene information for CX3CL1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CX3CL1 Gene

Genomics for CX3CL1 Gene

GeneHancer (GH) Regulatory Elements for CX3CL1 Gene

Promoters and enhancers for CX3CL1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J057371 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 500.7 +0.6 599 3.4 EP300 POLR2G NCOR1 CTCF ZIC2 KDM6A TCF7 RELA ZBTB25 ZNF740 CX3CL1 RSPRY1 CIAPIN1 ENSG00000261270 CCL17
GH16J057482 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 10.1 +112.4 112360 5.3 ZBTB40 EP300 NRF1 POLR2G NCOR1 ZFX ZIC2 POLR2A KDM6A ZBTB10 DOK4 CIAPIN1 COQ9 LOC105371286 POLR2C CX3CL1 CCL22 USB1 lnc-CIAPIN1-2
GH16J057298 Promoter/Enhancer 1.8 ENCODE CraniofacialAtlas dbSUPER 11.8 -72.4 -72382 2.8 FOXK2 ZBTB40 ZNF217 EP300 CTCF TCF12 NRF1 SP1 BCLAF1 NCOR1 TRL-CAG2-1 TRL-CAG2-2 POLR2C LOC101927556 PSME3IP1 NUP93 CCL22 CCDC102A CX3CL1 RSPRY1
GH16J057303 Enhancer 1.3 Ensembl ENCODE dbSUPER 12 -68.1 -68060 3.2 EP300 TCF12 POLR2G NCOR1 KDM6A ZNF623 RELA ZBTB25 TGIF2 RAD21 CCL22 CX3CL1 ARL2BP TRL-CAG2-2 lnc-CCL22-2 RPL23AP91
GH16J057341 Enhancer 0.8 ENCODE 17 -31.0 -30964 1.4 EP300 RELA CTBP1 TRIM22 BCL11A TCF12 NFIC ZBTB17 CBFB FOS CX3CL1 CIAPIN1 RSPRY1 CNGB1 ENSG00000271456 lnc-PLLP-2 CCL22
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CX3CL1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CX3CL1

Top Transcription factor binding sites by QIAGEN in the CX3CL1 gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • NF-kappaB
  • NF-kappaB1

Genomic Locations for CX3CL1 Gene

Genomic Locations for CX3CL1 Gene
chr16:57,372,461-57,385,048
(GRCh38/hg38)
Size:
12,588 bases
Orientation:
Plus strand
chr16:57,406,370-57,418,960
(GRCh37/hg19)
Size:
12,591 bases
Orientation:
Plus strand

Genomic View for CX3CL1 Gene

Genes around CX3CL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CX3CL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CX3CL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CX3CL1 Gene

Proteins for CX3CL1 Gene

  • Protein details for CX3CL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P78423-X3CL1_HUMAN
    Recommended name:
    Fractalkine
    Protein Accession:
    P78423
    Secondary Accessions:
    • O00672

    Protein attributes for CX3CL1 Gene

    Size:
    397 amino acids
    Molecular mass:
    42203 Da
    Quaternary structure:
    • Monomer (PubMed:9931005). Interacts with pox virus crmD; this inhibits cell migration mediated by CX3CL1 (PubMed:21829356). Forms a ternary complex with CX3CR1 and ITGAV:ITGB3 or ITGA4:ITGB1 (PubMed:23125415).

    Three dimensional structures from OCA and Proteopedia for CX3CL1 Gene

neXtProt entry for CX3CL1 Gene

Post-translational modifications for CX3CL1 Gene

  • A soluble short 95 kDa form may be released by proteolytic cleavage from the long membrane-anchored form.
  • O-glycosylated with core 1 or possibly core 8 glycans.
  • Glycosylation at Asn33, Thr183, Ser253, Thr318, and Thr329
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • X3CL1_HUMAN (698)

Other Protein References for CX3CL1 Gene

Antibody Products

  • Abcam antibodies for CX3CL1

Assay Products

  • Abcam assays for CX3CL1

No data available for DME Specific Peptides for CX3CL1 Gene

Domains & Families for CX3CL1 Gene

Gene Families for CX3CL1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted membrane proteins
  • Predicted secreted proteins

Protein Domains for CX3CL1 Gene

Blocks:
  • Fractalkine/neurotactin precursor signature
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CX3CL1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ94424, Homo sapiens chemokine (C-X3-C motif) ligand 1 (CX3CL1), mRNA (A0N0N7_HUMAN)
  • CX3CL1 protein (Q6I9S9_HUMAN)
  • Small-inducible cytokine D1 (X3CL1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P78423

UniProtKB/Swiss-Prot:

X3CL1_HUMAN :
  • Belongs to the intercrine delta family.
Family:
  • Belongs to the intercrine delta family.
genes like me logo Genes that share domains with CX3CL1: view

Function for CX3CL1 Gene

Molecular function for CX3CL1 Gene

UniProtKB/Swiss-Prot Function:
Acts as a ligand for both CX3CR1 and integrins. Binds to CX3CR1 (PubMed:23125415, PubMed:9931005, PubMed:21829356). Binds to integrins ITGAV:ITGB3 and ITGA4:ITGB1. Can activate integrins in both a CX3CR1-dependent and CX3CR1-independent manner. In the presence of CX3CR1, activates integrins by binding to the classical ligand-binding site (site 1) in integrins. In the absence of CX3CR1, binds to a second site (site 2) in integrins which is distinct from site 1 and enhances the binding of other integrin ligands to site 1 (PubMed:23125415, PubMed:24789099). The soluble form is chemotactic for T-cells and monocytes and not for neutrophils. The membrane-bound form promotes adhesion of those leukocytes to endothelial cells. May play a role in regulating leukocyte adhesion and migration processes at the endothelium (PubMed:9024663, PubMed:9177350).
UniProtKB/Swiss-Prot Induction:
By TNF and IL1/interleukin-1 in pulmonary endothelial cells and umbilical vein endothelial cells.

Phenotypes From GWAS Catalog for CX3CL1 Gene

Gene Ontology (GO) - Molecular Function for CX3CL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 signaling receptor binding TAS 12714508
GO:0005125 cytokine activity IEA --
GO:0005178 integrin binding IDA 23125415
GO:0005515 protein binding IPI 9931005
GO:0008009 chemokine activity IEA,TAS 12714508
genes like me logo Genes that share ontologies with CX3CL1: view
genes like me logo Genes that share phenotypes with CX3CL1: view

Animal Models for CX3CL1 Gene

MGI Knock Outs for CX3CL1:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CX3CL1 Gene

Localization for CX3CL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CX3CL1 Gene

Cell membrane; Single-pass type I membrane protein.
[Processed fractalkine]: Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CX3CL1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
mitochondrion 3
cytoskeleton 2
peroxisome 2
nucleus 2
endoplasmic reticulum 2
endosome 2
cytosol 2
lysosome 2
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CX3CL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA,TAS --
GO:0005615 extracellular space IBA 21873635
GO:0005623 cell IEA --
GO:0005886 plasma membrane IEA,TAS 24352739
GO:0009986 cell surface IEA,IDA 12714508
genes like me logo Genes that share ontologies with CX3CL1: view

Pathways & Interactions for CX3CL1 Gene

PathCards logo

SuperPathways for CX3CL1 Gene

SuperPathway Contained pathways
1 PEDF Induced Signaling
.94
.94
.73
.71
.62
.61
.47
.46
2 Chemokine Superfamily Pathway: Human/Mouse Ligand-Receptor Interactions
3 ERK Signaling
.61
.61
.51
4 Peptide ligand-binding receptors
5 CCR5 Pathway in Macrophages
.33
genes like me logo Genes that share pathways with CX3CL1: view

SIGNOR curated interactions for CX3CL1 Gene

Activates:

Gene Ontology (GO) - Biological Process for CX3CL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001774 microglial cell activation ISS --
GO:0001954 positive regulation of cell-matrix adhesion TAS 24352739
GO:0002052 positive regulation of neuroblast proliferation ISS --
GO:0002523 leukocyte migration involved in inflammatory response IMP 23125415
GO:0002548 monocyte chemotaxis IBA 21873635
genes like me logo Genes that share ontologies with CX3CL1: view

Drugs & Compounds for CX3CL1 Gene

(5) Drugs for CX3CL1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for CX3CL1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CX3CL1: view

Transcripts for CX3CL1 Gene

mRNA/cDNA for CX3CL1 Gene

2 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CX3CL1 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b
SP1:
SP2: -

Relevant External Links for CX3CL1 Gene

GeneLoc Exon Structure for
CX3CL1

Expression for CX3CL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CX3CL1 Gene

mRNA differential expression in normal tissues according to GTEx for CX3CL1 Gene

This gene is overexpressed in Breast - Mammary Tissue (x4.4).

Protein differential expression in normal tissues from HIPED for CX3CL1 Gene

This gene is overexpressed in Bone (57.4) and Heart (10.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CX3CL1 Gene



Protein tissue co-expression partners for CX3CL1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CX3CL1

SOURCE GeneReport for Unigene cluster for CX3CL1 Gene:

Hs.531668

mRNA Expression by UniProt/SwissProt for CX3CL1 Gene:

P78423-X3CL1_HUMAN
Tissue specificity: Expressed in the seminal plasma, endometrial fluid and follicular fluid (at protein level). Small intestine, colon, testis, prostate, heart, brain, lung, skeletal muscle, kidney and pancreas. Most abundant in the brain and heart.

Evidence on tissue expression from TISSUES for CX3CL1 Gene

  • Nervous system(4.9)
  • Lung(2.9)
  • Heart(2.6)
  • Blood(2.5)
  • Kidney(2.3)
  • Muscle(2.3)
  • Lymph node(2)
genes like me logo Genes that share expression patterns with CX3CL1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for CX3CL1 Gene

Orthologs for CX3CL1 Gene

This gene was present in the common ancestor of mammals.

Orthologs for CX3CL1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CX3CL1 31 30
  • 99.16 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CX3CL1 31 30
  • 77.58 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Cx3cl1 30
  • 74.66 (n)
mouse
(Mus musculus)
Mammalia Cx3cl1 17 31 30
  • 73.33 (n)
cow
(Bos Taurus)
Mammalia CX3CL1 31 30
  • 71.43 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CX3CL1 31
  • 39 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CX3CL1 31
  • 39 (a)
OneToOne
Species where no ortholog for CX3CL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for CX3CL1 Gene

ENSEMBL:
Gene Tree for CX3CL1 (if available)
TreeFam:
Gene Tree for CX3CL1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CX3CL1: view image

Paralogs for CX3CL1 Gene

(17) SIMAP similar genes for CX3CL1 Gene using alignment to 6 proteins:

  • X3CL1_HUMAN
  • A0N0N7_HUMAN
  • H3BSR6_HUMAN
  • H3BV86_HUMAN
  • J3QRA1_HUMAN
  • Q6I9S9_HUMAN
genes like me logo Genes that share paralogs with CX3CL1: view

Variants for CX3CL1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CX3CL1 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
711165 Benign: not provided 57,382,414(+) C/T SYNONYMOUS_VARIANT
716483 Benign: not provided 57,382,093(+) G/A SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
717037 Benign: not provided 57,382,618(+) G/A SYNONYMOUS_VARIANT
734681 Benign: not provided 57,382,192(+) C/T SYNONYMOUS_VARIANT
735956 Likely Benign: not provided 57,382,315(+) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for CX3CL1 Gene

Variation tolerance for CX3CL1 Gene

Residual Variation Intolerance Score: 58.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.08; 22.06% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CX3CL1 Gene

Human Gene Mutation Database (HGMD)
CX3CL1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CX3CL1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for CX3CL1 Gene

Disorders for CX3CL1 Gene

MalaCards: The human disease database

(17) MalaCards diseases for CX3CL1 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
pityriasis rosea
  • pityriasis circinata
vasculitis
  • autoimmune vasculitis
chorioretinitis
  • retinochoroiditis
ischemia
  • acute coronary syndrome
microscopic polyangiitis
  • mpa
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CX3CL1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CX3CL1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CX3CL1 Gene

Publications for CX3CL1 Gene

  1. Neurotactin, a membrane-anchored chemokine upregulated in brain inflammation. (PMID: 9177350) Pan Y … Gearing D (Nature 1997) 2 3 4 23 54
  2. A new class of membrane-bound chemokine with a CX3C motif. (PMID: 9024663) Bazan JF … Schall TJ (Nature 1997) 2 3 4 23 54
  3. Fractalkine receptor/ligand genetic variants and carotid intima-media thickness. (PMID: 19372452) Debette S … Markus HS (Stroke 2009) 3 23 41 54
  4. Polymorphisms of Fractalkine receptor CX3CR1 and plasma levels of its ligand CX3CL1 in colorectal cancer patients. (PMID: 17611763) Dimberg J … Wågsäter D (International journal of colorectal disease 2007) 3 23 41 54
  5. Solution structure and dynamics of the CX3C chemokine domain of fractalkine and its interaction with an N-terminal fragment of CX3CR1. (PMID: 9931005) Mizoue LS … Handel TM (Biochemistry 1999) 3 4 23 54

Products for CX3CL1 Gene

Sources for CX3CL1 Gene