CX3CR1 Gene (Protein Coding)

C-X3-C Motif Chemokine Receptor 1

GC03M039279
GIFtS:
45
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 dif... See more...

Aliases for CX3CR1 Gene

Aliases for CX3CR1 Gene

  • C-X3-C Motif Chemokine Receptor 1 2 3 5
  • V28 2 3 4
  • 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
  • CX3C Chemokine Receptor 1 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
  • CMKDR1 2 3
  • CCRL1 2 3
  • GPR13 3 4
  • Chemokine (C-C) Receptor-Like 1 3
  • GPRV28 3
  • CX3CR1 5

External Ids for CX3CR1 Gene

Previous HGNC Symbols for CX3CR1 Gene

  • GPR13
  • CMKBRL1

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 Human Immunodeficiency Virus Type 1. Among its related pathways are A-beta Pathways: Uptake and Degradation and Peptide ligand-binding receptors. Gene Ontology (GO) annotations related to this gene include G protein-coupled receptor activity and chemokine receptor activity. An important paralog of this gene is CCR4.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for CX3CR1 Gene

Genomics for CX3CR1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CX3CR1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CX3CR1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CX3CR1

Top Transcription factor binding sites by QIAGEN in the CX3CR1 gene promoter:
  • AREB6
  • Bach1
  • Brachyury
  • FOXJ2
  • FOXJ2 (long isoform)
  • GATA-1
  • HFH-1
  • PPAR-gamma1
  • PPAR-gamma2
  • RSRFC4

Genomic Locations for CX3CR1 Gene

Latest Assembly
chr3:39,263,494-39,281,735
(GRCh38/hg38)
Size:
18,242 bases
Orientation:
Minus strand

Previous Assembly
chr3:39,304,985-39,323,226
(GRCh37/hg19 by Entrez Gene)
Size:
18,242 bases
Orientation:
Minus strand

chr3:39,304,985-39,323,226
(GRCh37/hg19 by Ensembl)
Size:
18,242 bases
Orientation:
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 Structure • Gene Density

RefSeq DNA sequence for CX3CR1 Gene

Proteins for CX3CR1 Gene

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

    Protein Symbol:
    P49238-CX3C1_HUMAN
    Recommended name:
    CX3C chemokine receptor 1
    Protein Accession:
    P49238
    Secondary Accessions:
    • A0N0N6
    • B2R5Z4
    • J3KP17

    Protein attributes for CX3CR1 Gene

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

    Alternative splice isoforms for CX3CR1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CX3CR1 Gene

Protein Expression for CX3CR1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

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

Other Protein References for CX3CR1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for CX3CR1
  • Boster Bio Antibodies for CX3CR1
  • Santa Cruz Biotechnology (SCBT) Antibodies for CX3CR1

No data available for DME Specific Peptides for CX3CR1 Gene

Domains & Families for CX3CR1 Gene

Gene Families for CX3CR1 Gene

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

Protein Domains for CX3CR1 Gene

InterPro:
Blocks:
  • Chemokine receptor signature
  • Fractalkine receptor signature

Suggested Antigen Peptide Sequences for CX3CR1 Gene

GenScript: Design optimal peptide antigens:
  • V28 (CX3C1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P49238

UniProtKB/Swiss-Prot:

CX3C1_HUMAN :
  • Belongs to the G-protein coupled receptor 1 family.
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

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  6. Cell Lines for research

Molecular function for CX3CR1 Gene

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).
GENATLAS Biochemistry:
fractalkine receptor CX3CR1,expressed in T lymphocytes,polynuclear,G protein coupled receptor superfamily,mediating leukocyte migration and adhesion

Phenotypes From GWAS Catalog for CX3CR1 Gene

Gene Ontology (GO) - Molecular Function for CX3CR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004930 G protein-coupled receptor activity ISS --
GO:0004950 chemokine receptor activity IEA,TAS 10754298
GO:0005515 protein binding IPI 9931005
GO:0008528 G protein-coupled peptide receptor activity TAS 24352739
GO:0016493 C-C chemokine receptor activity IBA 21873635
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 Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CX3CR1

Clone products for research

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

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 CX3CR1 gene
Compartment Confidence
plasma membrane 5
extracellular 3
nucleus 3
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
endosome 2
cytosol 2
lysosome 2
peroxisome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (2)
See all subcellular structures

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:0009897 external side of plasma membrane IBA 21873635
GO:0009986 cell surface IEA,TAS 24352739
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with CX3CR1: view

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,ISS --
GO:0002931 response to ischemia IEA,ISS --
GO:0006935 chemotaxis IGI 16019082
GO:0006955 immune response IBA 21873635
GO:0006968 cellular defense response TAS 10754298
genes like me logo Genes that share ontologies with CX3CR1: view

Drugs & Compounds for CX3CR1 Gene

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(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 Agonist, Full agonist 0
CX<sub>3</sub>CL1 Pharma Agonist, Full 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

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mRNA/cDNA for CX3CR1 Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CX3CR1

Clone products for research

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

No ASD Table

Relevant External Links for CX3CR1 Gene

GeneLoc Exon Structure for
CX3CR1

Expression for CX3CR1 Gene

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

mRNA expression in normal human tissues for CX3CR1 Gene
mRNA expression by BioGPS for CX3CR1 GenemRNA expression by GTEx 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 and MOPED for CX3CR1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CX3CR1

SOURCE GeneReport for Unigene cluster for CX3CR1 Gene:

Hs.78913

mRNA Expression by UniProt/SwissProt for CX3CR1 Gene:

P49238-CX3C1_HUMAN
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(3.1)
  • Lymph node(3.1)
  • Intestine(2.5)
  • Bone marrow(2.5)
  • Lung(2.5)
  • Heart(2.4)
  • Eye(2.4)
  • Kidney(2.3)
  • Liver(2.3)
  • Skin(2.3)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with CX3CR1: view

Primer products for research

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
Chimpanzee
(Pan troglodytes)
 Mammalia CX3CR1 29 30
  • 99.34 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia CX3CR1 29 30
  • 86.99 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia CX3CR1 29 30
  • 84.62 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Cx3cr1 29 16 30
  • 80.72 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Cx3cr1 29
  • 79.87 (n)
Oppossum
(Monodelphis domestica)
 Mammalia CX3CR1 30
  • 63 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia CX3CR1 30
  • 58 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves CX3CR1 29 30
  • 61.35 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia CX3CR1 30
  • 47 (a)
 OneToOne
Species where no ortholog for CX3CR1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

ENSEMBL:
Gene Tree for CX3CR1 (if available)
TreeFam:
Gene Tree for CX3CR1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CX3CR1: view image
Alliance of Genome Resources:
Additional Orthologs for CX3CR1

Paralogs for CX3CR1 Gene

Paralogs for CX3CR1 Gene

(49) SIMAP similar genes for CX3CR1 Gene using alignment to 3 proteins:

  • CX3C1_HUMAN
  • C9JLM2_HUMAN
  • C9JN40_HUMAN
genes like me logo Genes that share paralogs with CX3CR1: view

Variants for CX3CR1 Gene

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Polymorphic Variants from UniProtKB/Swiss-Prot for CX3CR1 Gene

CX3C1_HUMAN-P49238
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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CX3CR1 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
992523 Uncertain Significance: Human immunodeficiency virus type 1, susceptibility to; Coronary heart disease 1; Age-related macular degeneration 12 39,281,686(-) G/C
NM_001171174.1(CX3CR1):c.10C>G (p.Pro4Ala) 		MISSENSE
rs137854870 Not Provided: not provided 39,265,725(-) A/G
NM_001171174.1(CX3CR1):c.881T>C (p.Phe294Ser) 		MISSENSE
rs139019894 Likely Benign: not provided 39,266,436(-) T/C
NM_001337.4(CX3CR1):c.74A>G (p.Asp25Gly) 		MISSENSE
rs1575205636 Likely Benign: not provided 39,265,685(-) G/A
NM_001337.4(CX3CR1):c.825C>T (p.Leu275=) 		SYNONYMOUS
rs17038679 Benign: not provided 39,266,054(-) G/A
NM_001337.4(CX3CR1):c.456C>T (p.Gly152=) 		SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CX3CR1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for CX3CR1 Gene

Human Gene Mutation Database (HGMD)
CX3CR1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CX3CR1
Leiden Open Variation Database (LOVD)
CX3CR1

SNP Genotyping and Copy Number Assays for research

Disorders for CX3CR1 Gene

MalaCards: The human disease database

(34) MalaCards diseases for CX3CR1 Gene - From: OMI, CVR, GTR, COP, and GCD

Disorder Aliases PubMed IDs
macular degeneration, age-related, 12
  • armd12
human immunodeficiency virus type 1
  • human immunodeficiency virus type 1, susceptibility to
coronary heart disease 1
  • coronary heart disease, susceptibility to, 1
retinal vasculitis
cerebrovascular disease
  • cerebrovascular accident
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CX3C1_HUMAN
  • 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 variants affecting the gene represented in this entry.

Additional Disease Information for CX3CR1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CX3CR1: view

No data available for Genatlas for CX3CR1 Gene

Publications for CX3CR1 Gene

  1. The involvement of sequence variation and expression of CX3CR1 in the pathogenesis of age-related macular degeneration. (PMID: 15208270) Tuo J … Chan CC (FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2004) 3 4 22 72
  2. Polymorphism in the fractalkine receptor CX3CR1 as a genetic risk factor for coronary artery disease. (PMID: 11264153) Moatti D … Combadière C (Blood 2001) 3 4 40 72
  3. 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
  4. 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
  5. Relationship between CX3CR1 genetic polymorphism and carotid atherosclerosis. (PMID: 20047517) Zhao R … Sun Y (Artificial cells, blood substitutes, and immobilization biotechnology 2010) 3 22 40

ExternalLinks

View latest publications for CX3CR1 gene in Mastermind

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