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

Gene ID: 1524, updated on 3-Jun-2018
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; Vega:OTTHUMG00000156249
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
See CX3CR1 in Genome Data Viewer
Location:
3p22.2
Exon count:
5
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (39263494..39281735, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (39304985..39323226, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene destrin, actin depolymerizing factor pseudogene 4 Neighboring gene uncharacterized LOC102724104 Neighboring gene adenosine deaminase domain containing 1 pseudogene 1 Neighboring gene C-C motif chemokine receptor 8

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Protein interactions

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

Go to the HIV-1, Human Interaction Database

  • Chemokine receptors bind chemokines, organism-specific biosystem (from REACTOME)
    Chemokine receptors bind chemokines, organism-specific biosystemChemokine receptors are cytokine receptors found on the surface of certain cells, which interact with a type of cytokine called a chemokine. Following interaction, these receptors trigger a flux of i...
  • Chemokine signaling pathway, organism-specific biosystem (from KEGG)
    Chemokine signaling pathway, organism-specific biosystemInflammatory immune response requires the recruitment of leukocytes to the site of inflammation upon foreign insult. Chemokines are small chemoattractant peptides that provide directional cues for th...
  • Chemokine signaling pathway, conserved biosystem (from KEGG)
    Chemokine signaling pathway, conserved biosystemInflammatory immune response requires the recruitment of leukocytes to the site of inflammation upon foreign insult. Chemokines are small chemoattractant peptides that provide directional cues for th...
  • Class A/1 (Rhodopsin-like receptors), organism-specific biosystem (from REACTOME)
    Class A/1 (Rhodopsin-like receptors), organism-specific biosystemRhodopsin-like receptors (class A/1) are the largest group of GPCRs and are the best studied group from a functional and structural point of view. They show great diversity at the sequence level and ...
  • Cytokine-cytokine receptor interaction, organism-specific biosystem (from KEGG)
    Cytokine-cytokine receptor interaction, organism-specific biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
  • Cytokine-cytokine receptor interaction, conserved biosystem (from KEGG)
    Cytokine-cytokine receptor interaction, conserved biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
  • GPCR ligand binding, organism-specific biosystem (from REACTOME)
    GPCR ligand binding, organism-specific biosystemThere are more than 800 G-protein coupled receptor (GPCRs) in the human genome, making it the largest receptor superfamily. GPCRs are also the largest class of drug targets, involved in virtually all...
  • GPCRs, Class A Rhodopsin-like, organism-specific biosystem (from WikiPathways)
    GPCRs, Class A Rhodopsin-like, organism-specific biosystemThis pathway was created using the GPCRDB (Horn et al., 1998), http://www.gpcr.org/7tm/ (originally at http://www.cmbi.kun.nl/7tm/). The groupings are based on the GPCR phylogenetic tree available fr...
  • Peptide GPCRs, organism-specific biosystem (from WikiPathways)
    Peptide GPCRs, organism-specific biosystem
    Peptide GPCRs
  • Peptide ligand-binding receptors, organism-specific biosystem (from REACTOME)
    Peptide ligand-binding receptors, organism-specific biosystemThese receptors, a subset of the Class A/1 (Rhodopsin-like) family, all bind peptide ligands which include the chemokines, opioids and somatostatins.
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by GPCR, organism-specific biosystem (from REACTOME)
    Signaling by GPCR, organism-specific biosystemG protein-coupled receptors (GPCRs; 7TM receptors; seven transmembrane domain receptors; heptahelical receptors; G protein-linked receptors [GPLR]) are the largest family of transmembrane receptors i...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
C-C chemokine binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
C-C chemokine receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
C-X3-C chemokine binding IDA
Inferred from Direct Assay
more info
PubMed 
C-X3-C chemokine receptor activity IEA
Inferred from Electronic Annotation
more info
 
chemokine binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemokine receptor activity TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
G-protein coupled receptor signaling pathway TAS
Traceable Author Statement
more info
 
calcium-mediated signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
cell chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular defense response TAS
Traceable Author Statement
more info
PubMed 
cellular response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
 
cellular response to transforming growth factor beta stimulus IEA
Inferred from Electronic Annotation
more info
 
cerebral cortex cell migration IEA
Inferred from Electronic Annotation
more info
 
chemokine-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemotaxis TAS
Traceable Author Statement
more info
PubMed 
immune response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
macrophage chemotaxis IEA
Inferred from Electronic Annotation
more info
 
memory IEA
Inferred from Electronic Annotation
more info
 
microglial cell activation involved in immune response IEA
Inferred from Electronic Annotation
more info
 
negative regulation of angiogenesis IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cell migration IEA
Inferred from Electronic Annotation
more info
 
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand IEA
Inferred from Electronic Annotation
more info
 
negative regulation of long-term synaptic potentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of angiogenesis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cytosolic calcium ion concentration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of neuroblast proliferation IEA
Inferred from Electronic Annotation
more info
 
response to wounding TAS
Traceable Author Statement
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
neuron projection IEA
Inferred from Electronic Annotation
more info
 
neuronal cell body membrane IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
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

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

  1. NG_016362.1 RefSeqGene

    Range
    5001..23242
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001171171.1NP_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
    P49238
    Related
    ENSP00000439140.1, ENST00000541347.5
    Conserved Domains (1) summary
    pfam00001
    Location:48293
    7tm_1; 7 transmembrane receptor (rhodopsin family)
  2. NM_001171172.1NP_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
    P49238
    Related
    ENSP00000444928.1, ENST00000542107.5
    Conserved Domains (1) summary
    pfam00001
    Location:48293
    7tm_1; 7 transmembrane receptor (rhodopsin family)
  3. NM_001171174.1NP_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:80325
    7tm_1; 7 transmembrane receptor (rhodopsin family)
  4. NM_001337.3NP_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
    P49238
    Related
    ENSP00000382166.2, OTTHUMP00000209587, ENST00000399220.2, OTTHUMT00000343613
    Conserved Domains (1) summary
    pfam00001
    Location:48293
    7tm_1; 7 transmembrane receptor (rhodopsin family)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    39263494..39281735 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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