Format

Send to:

Choose Destination

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

Gene ID: 1524, updated on 3-Oct-2021

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
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See CX3CR1 in Genome Data Viewer
Location:
3p22.2
Exon count:
5
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (39263494..39281735, complement)
105.20201022 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 DSTN pseudogene 4 Neighboring gene uncharacterized LOC102724104 Neighboring gene adenosine deaminase domain containing 1 pseudogene 1 Neighboring gene C-C motif chemokine receptor 8

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables C-C chemokine binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables C-C chemokine receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables C-X3-C chemokine binding IDA
Inferred from Direct Assay
more info
PubMed 
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 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 ISS
Inferred from Sequence or Structural Similarity
more info
 
enables chemokine receptor activity TAS
Traceable Author Statement
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in G protein-coupled receptor signaling pathway TAS
Traceable Author Statement
more info
PubMed 
involved_in adaptive immune response ISS
Inferred from Sequence or Structural Similarity
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 ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in calcium-mediated signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell adhesion IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cell adhesion ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in cell chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 lipopolysaccharide ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in cellular response to transforming growth factor beta stimulus 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 IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in host-mediated regulation 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
PubMed 
involved_in immune response ISS
Inferred from Sequence or Structural Similarity
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 leukocyte chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in leukocyte tethering or rolling ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in memory 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 ISS
Inferred from Sequence or Structural Similarity
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 cell migration IEA
Inferred from Electronic Annotation
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 long-term synaptic potentiation 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 ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of I-kappaB phosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of NF-kappaB transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of angiogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of cytosolic calcium ion concentration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of microglial cell migration IEA
Inferred from Electronic Annotation
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 ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of protein kinase B signaling 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 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 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 social behavior ISS
Inferred from Sequence or Structural Similarity
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 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 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
PubMed 
is_active_in integral component of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
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
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

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)

NEW Try the new Transcript table

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_001171171.2NP_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_001171172.2NP_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_001337.4NP_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
    ENSP00000382166.3, ENST00000399220.3
    Conserved Domains (1) summary
    pfam00001
    Location:48293
    7tm_1; 7 transmembrane receptor (rhodopsin family)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

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