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Aliases for CX3CR1 Gene

Aliases for CX3CR1 Gene

  • C-X3-C Motif Chemokine Receptor 1 2 3 5
  • Chemokine (C-X3-C Motif) Receptor 1 2 3
  • Beta Chemokine Receptor-Like 1 3 4
  • Chemokine (C-X3-C) Receptor 1 2 3
  • G-Protein Coupled Receptor 13 3 4
  • Fractalkine Receptor 3 4
  • C-X3-C CKR-1 3 4
  • CMK-BRL-1 3 4
  • CMK-BRL1 3 4
  • CMKBRL1 3 4
  • GPR13 3 4
  • V28 3 4
  • Chemokine (C-C) Receptor-Like 1 3
  • CX3C Chemokine Receptor 1 3
  • CMKDR1 3
  • GPRV28 3
  • CCRL1 3

External Ids for CX3CR1 Gene

Previous HGNC Symbols for CX3CR1 Gene

  • GPR13

Previous GeneCards Identifiers for CX3CR1 Gene

  • GC03M038644
  • GC03M038538
  • GC03M039118
  • GC03M039265

Summaries for CX3CR1 Gene

Entrez Gene Summary for CX3CR1 Gene

  • Fractalkine is a transmembrane protein and chemokine involved in the adhesion and migration of leukocytes. The protein encoded by this gene is a receptor for fractalkine. The encoded protein also is a coreceptor for HIV-1, and some variations in this gene lead to increased susceptibility to HIV-1 infection and rapid progression to AIDS. Four transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]

GeneCards Summary for CX3CR1 Gene

CX3CR1 (C-X3-C Motif Chemokine Receptor 1) is a Protein Coding gene. Diseases associated with CX3CR1 include Macular Degeneration, Age-Related, 12 and Coronary Artery Disease. Among its related pathways are Akt Signaling and Chemokine Superfamily Pathway: Human/Mouse Ligand-Receptor Interactions. GO annotations related to this gene include G-protein coupled receptor activity and chemokine receptor activity. An important paralog of this gene is CCR2.

UniProtKB/Swiss-Prot for CX3CR1 Gene

  • Receptor for the CX3C chemokine fractalkine (CX3CL1); binds to CX3CL1 and mediates both its adhesive and migratory functions (PubMed:9390561, PubMed:23125415). Acts as coreceptor with CD4 for HIV-1 virus envelope protein (in vitro) (PubMed:9726990). Isoform 2 and isoform 3 seem to be more potent HIV-1 coreceptors than isoform 1 (PubMed:14607932).

Gene Wiki entry for CX3CR1 Gene

Additional gene information for CX3CR1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CX3CR1 Gene

Genomics for CX3CR1 Gene

Regulatory Elements for CX3CR1 Gene

Enhancers for CX3CR1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03H039106 1.1 ENCODE 21.7 +174.1 174141 2.7 HDGF PKNOX1 ARID4B SIN3A ZNF2 YY1 SLC30A9 ZNF143 SP3 SP5 CX3CR1 TTC21A GORASP1 CSRNP1 MOBP SCN11A PIR55888 GC03M039097
GH03H039175 1.6 Ensembl ENCODE dbSUPER 11.7 +101.7 101689 8.7 HDGF FOXA2 ARID4B SIN3A YBX1 YY1 FOS SP3 SP5 ZHX2 GORASP1 CSRNP1 CX3CR1 TTC21A RPSA PIR56273 XIRP1
GH03H039361 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10.4 -80.3 -80272 1.6 MAX BATF RELA ZNF316 GATA3 POLR2A EGR1 EED NR2F6 ETV6 RPSA HNRNPA1P21 CCR8 SNORA6 CX3CR1 XIRP1 SLC25A38 WDR48 EEF1A1P24 GC03P039372
GH03H039447 1.2 Ensembl ENCODE dbSUPER 13.8 -166.3 -166267 0.4 CTCF TFAP4 ZNF654 FOXA2 TRIM22 REST ZNF501 RAD21 TEAD3 ZNF217 CX3CR1 SNORA6 RPSA LOC105377038 GC03P039422
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CX3CR1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for CX3CR1 Gene

Genomic Locations for CX3CR1 Gene
18,242 bases
Minus strand

Genomic View for CX3CR1 Gene

Genes around CX3CR1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CX3CR1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CX3CR1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CX3CR1 Gene

Proteins for CX3CR1 Gene

  • Protein details for CX3CR1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    CX3C chemokine receptor 1
    Protein Accession:
    Secondary Accessions:
    • A0N0N6
    • B2R5Z4
    • J3KP17

    Protein attributes for CX3CR1 Gene

    355 amino acids
    Molecular mass:
    40396 Da
    Quaternary structure:
    • Interacts with human respiratory syncytial virus (HRSV) protein G; this interaction modulates host immune response. Interacts with HIV-1 envelope polyprotein gp160. Found in a ternary complex with CX3CL1 and ITGAV:ITGB3 or ITGA4:ITGB1 (PubMed:23125415).

    Alternative splice isoforms for CX3CR1 Gene


neXtProt entry for CX3CR1 Gene

Post-translational modifications for CX3CR1 Gene

  • This protein is not N-glycosylated which is unusual for G-protein-coupled receptors.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CX3CR1 Gene

Domains & Families for CX3CR1 Gene

Gene Families for CX3CR1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • G-protein coupled receptors
  • Plasma proteins
  • Potential drug targets
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for CX3CR1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the G-protein coupled receptor 1 family.
  • Belongs to the G-protein coupled receptor 1 family.
genes like me logo Genes that share domains with CX3CR1: view

Function for CX3CR1 Gene

Molecular function for CX3CR1 Gene

GENATLAS Biochemistry:
fractalkine receptor CX3CR1,expressed in T lymphocytes,polynuclear,G protein coupled receptor superfamily,mediating leukocyte migration and adhesion
UniProtKB/Swiss-Prot Function:
Receptor for the CX3C chemokine fractalkine (CX3CL1); binds to CX3CL1 and mediates both its adhesive and migratory functions (PubMed:9390561, PubMed:23125415). Acts as coreceptor with CD4 for HIV-1 virus envelope protein (in vitro) (PubMed:9726990). Isoform 2 and isoform 3 seem to be more potent HIV-1 coreceptors than isoform 1 (PubMed:14607932).

Phenotypes From GWAS Catalog for CX3CR1 Gene

Gene Ontology (GO) - Molecular Function for CX3CR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004871 signal transducer activity IEA --
GO:0004896 cytokine receptor activity IEA --
GO:0004930 G-protein coupled receptor activity IEA --
GO:0004950 chemokine receptor activity TAS 10754298
GO:0005515 protein binding IPI 9931005
genes like me logo Genes that share ontologies with CX3CR1: view
genes like me logo Genes that share phenotypes with CX3CR1: view

Animal Models for CX3CR1 Gene

MGI Knock Outs for CX3CR1:

Animal Model Products

miRNA for CX3CR1 Gene

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CX3CR1 Gene

Localization for CX3CR1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CX3CR1 Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

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 CX3CR1 gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytoskeleton 1
peroxisome 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for CX3CR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 9390561
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0032809 neuronal cell body membrane IEA --
genes like me logo Genes that share ontologies with CX3CR1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CX3CR1 Gene

Pathways & Interactions for CX3CR1 Gene

genes like me logo Genes that share pathways with CX3CR1: view

SIGNOR curated interactions for CX3CR1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for CX3CR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002052 positive regulation of neuroblast proliferation IEA --
GO:0002282 microglial cell activation involved in immune response IEA --
GO:0002881 negative regulation of chronic inflammatory response to non-antigenic stimulus IEA --
GO:0006935 chemotaxis TAS 10754298
GO:0006968 cellular defense response TAS 10754298
genes like me logo Genes that share ontologies with CX3CR1: view

Drugs & Compounds for CX3CR1 Gene

(7) Drugs for CX3CR1 Gene - From: DGIdb, IUPHAR, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
[<sup>125</sup>I]CX<sub>3</sub>CL1 (human) Pharma Full agonist, Agonist 0
CX<sub>3</sub>CL1 Pharma Full agonist, Agonist 0

(4) Additional Compounds for CX3CR1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CX3CR1: view

Transcripts for CX3CR1 Gene

Unigene Clusters for CX3CR1 Gene

Chemokine (C-X3-C motif) receptor 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CX3CR1 Gene

No ASD Table

Relevant External Links for CX3CR1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CX3CR1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CX3CR1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CX3CR1 Gene

This gene is overexpressed in Whole Blood (x13.5), Brain - Spinal cord (cervical c-1) (x6.6), and Brain - Substantia nigra (x5.5).

Protein differential expression in normal tissues from HIPED for CX3CR1 Gene

This gene is overexpressed in Adrenal (26.8), Lung (15.5), and Liver (13.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CX3CR1 Gene

NURSA nuclear receptor signaling pathways regulating expression of CX3CR1 Gene:


SOURCE GeneReport for Unigene cluster for CX3CR1 Gene:


mRNA Expression by UniProt/SwissProt for CX3CR1 Gene:

Tissue specificity: Expressed in lymphoid and neural tissues.

Evidence on tissue expression from TISSUES for CX3CR1 Gene

  • Nervous system(4.9)
  • Blood(4.7)
  • Spleen(2.7)
  • Lymph node(2.6)
  • Eye(2.1)
  • Lung(2)
genes like me logo Genes that share expression patterns with CX3CR1: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CX3CR1 Gene

Orthologs for CX3CR1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CX3CR1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CX3CR1 33 34
  • 99.34 (n)
(Canis familiaris)
Mammalia CX3CR1 33 34
  • 86.99 (n)
(Bos Taurus)
Mammalia CX3CR1 33 34
  • 84.62 (n)
(Mus musculus)
Mammalia Cx3cr1 33 16 34
  • 80.72 (n)
(Rattus norvegicus)
Mammalia Cx3cr1 33
  • 79.87 (n)
(Monodelphis domestica)
Mammalia CX3CR1 34
  • 63 (a)
(Ornithorhynchus anatinus)
Mammalia CX3CR1 34
  • 58 (a)
(Gallus gallus)
Aves CX3CR1 33 34
  • 61.35 (n)
(Anolis carolinensis)
Reptilia CX3CR1 34
  • 47 (a)
Species where no ortholog for CX3CR1 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)
  • 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)
  • 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 CX3CR1 Gene

Gene Tree for CX3CR1 (if available)
Gene Tree for CX3CR1 (if available)

Paralogs for CX3CR1 Gene

Variants for CX3CR1 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for CX3CR1 Gene

Variations in CX3CR1 are associated with rapid progression to AIDS [MIM:609423]. Increased susceptibility to HIV infection and rapid progression to AIDS are associated with the Ile-249/Met-280 haplotype.

Sequence variations from dbSNP and Humsavar for CX3CR1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs3732378 Pathogenic 39,265,671(+) CAACC(A/G)TCTCA reference, missense
rs3732379 Pathogenic 39,265,765(+) CATAA(C/T)GTTGT reference, missense
rs137854870 untested 39,265,725(-) CTTCT(C/T)TCCCA reference, missense
rs1000324850 -- 39,280,993(+) AGGCC(C/T)CTCTG intron-variant, upstream-variant-2KB
rs1000377638 -- 39,268,468(+) TGTCA(C/G)AGAGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CX3CR1 Gene

Variant ID Type Subtype PubMed ID
nsv3772 CNV insertion 18451855

Variation tolerance for CX3CR1 Gene

Residual Variation Intolerance Score: 92.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.09; 75.37% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CX3CR1 Gene

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

Disorders for CX3CR1 Gene

MalaCards: The human disease database

(8) MalaCards diseases for CX3CR1 Gene - From: HGMD, OMIM, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
macular degeneration, age-related, 12
  • age related macular degeneration 12
coronary artery disease
  • coronary artery anomaly
  • aids, slow progression to
retinal vasculitis
  • retinal vasculitis nos
cerebrovascular disease
  • stroke
- elite association - COSMIC cancer census association via MalaCards


  • Macular degeneration, age-related, 12 (ARMD12) [MIM:613784]: A form of age-related macular degeneration, a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane. {ECO:0000269 PubMed:15208270}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Relevant External Links for CX3CR1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CX3CR1: view

No data available for Genatlas for CX3CR1 Gene

Publications for CX3CR1 Gene

  1. Identification of CX3CR1. A chemotactic receptor for the human CX3C chemokine fractalkine and a fusion coreceptor for HIV-1. (PMID: 9726990) Combadiere C … Murphy PM (The Journal of biological chemistry 1998) 2 3 4 22 60
  2. Cloning, chromosomal localization, and RNA expression of a human beta chemokine receptor-like gene. (PMID: 7646814) Combadiere C … Murphy PM (DNA and cell biology 1995) 2 3 4 22 60
  3. Relationship between CX3CR1 genetic polymorphism and carotid atherosclerosis. (PMID: 20047517) Zhao R … Sun Y (Artificial cells, blood substitutes, and immobilization biotechnology 2010) 3 22 45 60
  4. Fractalkine receptor/ligand genetic variants and carotid intima-media thickness. (PMID: 19372452) Debette S … Markus HS (Stroke 2009) 3 22 45 60
  5. Search for an association between V249I and T280M CX3CR1 genetic polymorphisms, endothelial injury and preeclampsia: the ECLAXIR study. (PMID: 19587779) Stepanian A … ECLAXIR study group (PloS one 2009) 3 22 45 60

Products for CX3CR1 Gene

Sources for CX3CR1 Gene

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