CX3CR1 C-X3-C motif chemokine receptor 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CX3CR1provided by HGNC
Official Full Name: C-X3-C motif chemokine receptor 1provided by HGNC
Primary source: HGNC:HGNC:2558
See related: Ensembl:ENSG00000168329 MIM:601470; AllianceGenome:HGNC:2558
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: V28; CCRL1; GPR13; CMKDR1; GPRV28; CMKBRL1
Summary: 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]
Expression: Biased expression in brain (RPKM 21.4), lung (RPKM 6.4) and 12 other tissues See more
Orthologs: all
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Genomic context

Location:: 3p22.2

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2025_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (39263494..39292966, complement)
RS_2025_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (39276418..39305868, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (39304985..39323226, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Microglia undergo disease-associated transcriptional activation and CX3C motif chemokine receptor 1 expression regulates neurogenesis in the aged brain.
Title: Microglia undergo disease-associated transcriptional activation and CX3C motif chemokine receptor 1 expression regulates neurogenesis in the aged brain.
m[6]A Reader YTHDC1 Impairs Respiratory Syncytial Virus Infection by Downregulating Membrane CX3CR1 Expression.
Title: m(6)A Reader YTHDC1 Impairs Respiratory Syncytial Virus Infection by Downregulating Membrane CX3CR1 Expression.
Relationship between aggressive features of oral squamous cell carcinoma and the immunoexpression of CX3CR1, CX3CL1 and ITGAV.
Title: Relationship between aggressive features of oral squamous cell carcinoma and the immunoexpression of CX3CR1, CX3CL1 and ITGAV.
Deciphering the role of CX3CL1-CX3CR1 in aortic aneurysm pathogenesis: insights from Mendelian randomization and transcriptomic analyses.
Title: Deciphering the role of CX3CL1-CX3CR1 in aortic aneurysm pathogenesis: insights from Mendelian randomization and transcriptomic analyses.
Mild Hypoxia Accelerates Cerebral Cavernous Malformation Disease Through CX3CR1-CX3CL1 Signaling.
Title: Mild Hypoxia Accelerates Cerebral Cavernous Malformation Disease Through CX3CR1-CX3CL1 Signaling.
CX3CR1 is a potential biomarker of immune microenvironment and prognosis in epithelial ovarian cancer.
Title: CX3CR1 is a potential biomarker of immune microenvironment and prognosis in epithelial ovarian cancer.
Validating Fractalkine receptor as a target and identifying candidates for drug discovery against type 2 diabetes.
Title: Validating Fractalkine receptor as a target and identifying candidates for drug discovery against type 2 diabetes.
Obesity-related Plasma CXCL10 Drives CX3CR1-dependent Monocytic Secretion of Macrophage Migration Inhibitory Factor.
Title: Obesity-related Plasma CXCL10 Drives CX3CR1-dependent Monocytic Secretion of Macrophage Migration Inhibitory Factor.
Significant association of CX3CR1+CD8 T cells with aging and distinct clinical features in Sjogren's syndrome and IgG4-related disease.
Title: Significant association of CX3CR1+CD8 T cells with aging and distinct clinical features in Sjögren's syndrome and IgG4-related disease.
Upregulation of CX3CR1 expression in circulating T cells of systemic lupus erythematosus patients as a reflection of autoimmune status through characterization of cytotoxic capacity.
Title: Upregulation of CX3CR1 expression in circulating T cells of systemic lupus erythematosus patients as a reflection of autoimmune status through characterization of cytotoxic capacity.

Submit: New GeneRIF Correction See all GeneRIFs (275)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Age related macular degeneration 12 MedGen: C3151079 OMIM: 613784 GeneReviews: Not available	Compare labs
Coronary heart disease, susceptibility to, 1 MedGen: C1846418 OMIM: 607339 GeneReviews: Not available	Compare labs
Susceptibility to HIV infection MedGen: C1836230 OMIM: 609423 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	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
	env	HIV-1 gp120 from CXCR4-tropic subtype E viruses isolated in Thailand associates with and uses at least one of the following coreceptors for virus entry: CCR8, CCR1, CCR2b, or CX3CR1	PubMed
Tat	tat	Inhibition of NF-kappaB and YY1 reverses HIV-1 Tat-mediated downregulation of CX3CR1 in microglia	PubMed
	tat	HIV-1 Tat-mediated downregulation of CX3CR1 inhibits CX3CL1-induced migration of microglia	PubMed
	tat	HIV-1 Tat upregulates chemokine (C-X3-C motif) receptor 1 (CX3CR1) in HEK 293 cells	PubMed
	tat	Fractalkine-CX3CR1 signaling contributes to the inhibition of the synergistic neurotoxic effects by opioids and HIV-1 Tat	PubMed

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D8S2279 (e-PCR)
- UniSTS:473907

SGC44481 (e-PCR)
- UniSTS:23375

D3S2899E (e-PCR)
- UniSTS:150887

SHGC-44481 (e-PCR)
- UniSTS:58757

D3S2853E (e-PCR)
- UniSTS:73874

CX3CR1_554 (e-PCR)
- UniSTS:277142

RH91803 (e-PCR)
- UniSTS:85934

PMC135988P14 (e-PCR)
- UniSTS:270786

RH18026 (e-PCR)
- UniSTS:51442

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables C-C chemokine binding	IBA Inferred from Biological aspect of Ancestor more info
enables C-C chemokine receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables C-X3-C chemokine binding	IDA Inferred from Direct Assay more info	PubMed
enables C-X3-C chemokine binding	IEA Inferred from Electronic Annotation more info
enables C-X3-C chemokine binding	ISS Inferred from Sequence or Structural Similarity more info
enables C-X3-C chemokine receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables C-X3-C chemokine receptor activity	IEA Inferred from Electronic Annotation more info
enables CX3C chemokine receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables G protein-coupled peptide receptor activity	TAS Traceable Author Statement more info	PubMed
enables G protein-coupled receptor activity	IEA Inferred from Electronic Annotation more info
enables G protein-coupled receptor activity	ISS Inferred from Sequence or Structural Similarity more info
enables chemokine receptor activity	TAS Traceable Author Statement more info	PubMed
enables cytokine receptor activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in G protein-coupled receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in G protein-coupled receptor signaling pathway	TAS Traceable Author Statement more info	PubMed
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
involved_in adaptive immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in antifungal innate immune response	IEA Inferred from Electronic Annotation more info
involved_in antifungal innate immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in antifungal innate immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in autocrine signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in brain development	IEA Inferred from Electronic Annotation more info
involved_in brain development	ISS Inferred from Sequence or Structural Similarity more info
involved_in calcium-mediated signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell adhesion	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell adhesion	TAS Traceable Author Statement more info	PubMed
involved_in cell chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell surface receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in cell-cell signaling	TAS Traceable Author Statement more info	PubMed
involved_in cellular defense response	TAS Traceable Author Statement more info	PubMed
involved_in cellular response to cytokine stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
involved_in cellular response to lipopolysaccharide	ISS Inferred from Sequence or Structural Similarity more info
involved_in central nervous system maturation	IEA Inferred from Electronic Annotation more info
involved_in central nervous system maturation	ISS Inferred from Sequence or Structural Similarity more info
involved_in chemokine-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in chemotaxis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in chemotaxis	TAS Traceable Author Statement more info	PubMed
involved_in cytokine-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in host-mediated modulation of intestinal microbiota composition	IEA Inferred from Electronic Annotation more info
involved_in host-mediated modulation of intestinal microbiota composition	ISS Inferred from Sequence or Structural Similarity more info
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in immune response	IEA Inferred from Electronic Annotation more info
involved_in immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in immune system process	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IC Inferred by Curator more info	PubMed
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in leukocyte chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in leukocyte chemotaxis	ISS Inferred from Sequence or Structural Similarity more info
involved_in leukocyte tethering or rolling	IEA Inferred from Electronic Annotation more info
involved_in leukocyte tethering or rolling	ISS Inferred from Sequence or Structural Similarity more info
involved_in microglial cell activation involved in immune response	IEA Inferred from Electronic Annotation more info
involved_in microglial cell activation involved in immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in modulation of chemical synaptic transmission	IEA Inferred from Electronic Annotation more info
involved_in modulation of chemical synaptic transmission	ISS Inferred from Sequence or Structural Similarity more info
involved_in multiple spine synapse organization, single dendrite	IEA Inferred from Electronic Annotation more info
involved_in multiple spine synapse organization, single dendrite	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of apoptotic signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of hippocampal neuron apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of interleukin-1 beta production	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of microglial cell mediated cytotoxicity	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of microglial cell mediated cytotoxicity	ISS Inferred from Sequence or Structural Similarity more info
involved_in phospholipase C-activating G protein-coupled receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in phospholipase C-activating G protein-coupled receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of canonical NF-kappaB signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cytosolic calcium ion concentration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of monocyte chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of neuroblast proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of neurogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of neurogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of microglial cell migration	TAS Traceable Author Statement more info	PubMed
involved_in regulation of neurogenesis	TAS Traceable Author Statement more info	PubMed
involved_in regulation of nitric oxide biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in regulation of nitric oxide biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of synaptic plasticity	TAS Traceable Author Statement more info	PubMed
involved_in regulation of tumor necrosis factor production	IEA Inferred from Electronic Annotation more info
involved_in regulation of tumor necrosis factor production	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to ischemia	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to wounding	TAS Traceable Author Statement more info	PubMed
involved_in signal transduction	IEA Inferred from Electronic Annotation more info
involved_in social behavior	IEA Inferred from Electronic Annotation more info
involved_in social behavior	ISS Inferred from Sequence or Structural Similarity more info
involved_in synapse maturation	IEA Inferred from Electronic Annotation more info
involved_in synapse maturation	ISS Inferred from Sequence or Structural Similarity more info
involved_in synapse pruning	IC Inferred by Curator more info
involved_in synapse pruning	IEA Inferred from Electronic Annotation more info
involved_in synapse pruning	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	IEA Inferred from Electronic Annotation more info
located_in cell surface	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in cell surface	TAS Traceable Author Statement more info	PubMed
located_in dendritic tree	ISS Inferred from Sequence or Structural Similarity more info
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in macropinosome membrane	TAS Traceable Author Statement more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in neuron projection	ISS Inferred from Sequence or Structural Similarity more info
located_in neuronal cell body membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in perinuclear region of cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: CX3C chemokine receptor 1

Names: C-X3-C CKR-1; CMK-BRL-1; CMK-BRL1; G-protein coupled receptor 13; beta chemokine receptor-like 1; chemokine (C-C) receptor-like 1; chemokine (C-X3-C motif) receptor 1; chemokine (C-X3-C) receptor 1; fractalkine receptor

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.

Genomic

NG_016362.2 RefSeqGene

Range

17930..34470

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001171171.2 → NP_001164642.1 CX3C chemokine receptor 1 isoform b

See identical proteins and their annotated locations for NP_001164642.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2, 3, and 4 all encode the same isoform.

Source sequence(s)

AC092053, AI400350, BC028078, DA406242

Consensus CDS

CCDS43069.1

UniProtKB/Swiss-Prot

A0N0N6, B2R5Z4, J3KP17, P49238

Related

ENSP00000439140.1, ENST00000541347.5

Conserved Domains (1) summary

pfam00001
Location:48 → 293

7tm_1; 7 transmembrane receptor (rhodopsin family)
NM_001171172.2 → NP_001164643.1 CX3C chemokine receptor 1 isoform b

See identical proteins and their annotated locations for NP_001164643.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2, 3, and 4 all encode the same isoform.

Source sequence(s)

AC092053, AI400350, BC028078, DA396634, DB274136

Consensus CDS

CCDS43069.1

UniProtKB/Swiss-Prot

A0N0N6, B2R5Z4, J3KP17, P49238

Related

ENSP00000444928.1, ENST00000542107.5

Conserved Domains (1) summary

pfam00001
Location:48 → 293

7tm_1; 7 transmembrane receptor (rhodopsin family)
NM_001171174.1 → NP_001164645.1 CX3C chemokine receptor 1 isoform a

See identical proteins and their annotated locations for NP_001164645.1

Status: REVIEWED

Description

Transcript Variant: This variant (1, also known as clone 10) encodes the longer isoform (a).

Source sequence(s)

AC092053, AI400350, BC028078

Consensus CDS

CCDS54571.1

UniProtKB/Swiss-Prot

P49238

Related

ENSP00000351059.3, ENST00000358309.3

Conserved Domains (1) summary

pfam00001
Location:80 → 325

7tm_1; 7 transmembrane receptor (rhodopsin family)
NM_001337.4 → NP_001328.1 CX3C chemokine receptor 1 isoform b

See identical proteins and their annotated locations for NP_001328.1

Status: REVIEWED

Description

Transcript Variant: This variant (4, also known as V28) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2, 3, and 4 all encode the same isoform.

Source sequence(s)

AC092053, BG541473, U20350

Consensus CDS

CCDS43069.1

UniProtKB/Swiss-Prot

A0N0N6, B2R5Z4, J3KP17, P49238

Related

ENSP00000382166.3, ENST00000399220.3

Conserved Domains (1) summary

pfam00001
Location:48 → 293

7tm_1; 7 transmembrane receptor (rhodopsin family)