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Cx3cr1 Gene Detail
Summary
  • Symbol
    Cx3cr1
  • Name
    C-X3-C motif chemokine receptor 1
  • Feature Type
    protein coding gene
  • IDs
    MGI:1333815
    NCBI Gene: 13051
  • Alliance
    genome feature page
  • Transcription Start Sites
    3 TSS
Location &
Maps
more
  • Sequence Map
    Chr9:119877749-119897362 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 9, 71.37 cM
  • Mapping Data
    1 experiment
Strain
Comparison
more
  • SNPs within 2kb
    693 from dbSNP Build 142
  • Strain Annotations
    19
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1333815
 protein coding gene Chr9:119877749-119898945 (-)
129S1/SvImJ ENSMUSG00200025417
 protein coding gene Chr9:116998731-117019922 (-)
A/J ENSMUSG00195027566
 protein coding gene Chr9:116180551-116201624 (-)
AKR/J ENSMUSG00220017970
 protein coding gene Chr9:116635721-116656734 (-)
BALB/cJ ENSMUSG00180028488
 protein coding gene Chr9:116717846-116738907 (-)
C3H/HeJ ENSMUSG00175018952
 protein coding gene Chr9:116961162-116982231 (-)
C57BL/6NJ ENSMUSG00215019094
 protein coding gene Chr9:116830015-116851209 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0032807
 protein coding gene Chr9:115319102-115487836 (-)
CAST/EiJ ENSTCUG00005015766
 protein coding gene Chr9:116588663-116609766 (-)
CBA/J ENSMUSG00210031827
 protein coding gene Chr9:116674571-116695584 (-)
DBA/2J ENSMUSG00185016401
 protein coding gene Chr9:117008818-117029831 (-)
FVB/NJ ENSMUSG00205016297
 protein coding gene Chr9:116849366-116870433 (-)
JF1/MsJ ENSUMUG00000028913
 protein coding gene Chr9:116862854-116884375 (-)
LP/J ENSMUSG00230037611
 protein coding gene Chr9:117127064-117148249 (-)
NOD/ShiLtJ ENSMUSG00190013343
 protein coding gene Chr9:116608448-116629645 (-)
NZO/HlLtJ ENSMUSG00225023238
 protein coding gene Chr9:117391630-117412821 (-)
PWK/PhJ ENSLUMG00010032821
 protein coding gene Chr9:116758255-116779765 (-)
SPRET/EiJ ENSMSPG00010023442
 protein coding gene Chr9:118458228-118478131 (-)
WSB/EiJ ENSIUOG00005021154
 protein coding gene Chr9:116063622-116084660 (-)



Homology
more
  • Human Ortholog
    CX3CR1, C-X3-C motif chemokine receptor 1
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    CX3CR1, C-X3-C motif chemokine receptor 1
  • Synonyms
    CCRL1, CMKBRL1, CMKDR1, GPR13, GPRV28, V28
  • Links
    NCBI Gene ID: 1524
    UniProt: P49238

  • Chr Location
    3p22.2; chr3:39263494-39292966 (-)  GRCh38
Human Diseases
more
  • Diseases
    1 with Cx3cr1 mouse models; 10 with human CX3CR1 associations

Human Disease Mouse Models
      
IDs
 View 2 models
      
IDs
IDs
IDs
IDs
IDs
IDs
IDs
IDs
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    2 with disease annotations
  • References
    3 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    48 phenotypes from 4 alleles in 8 genetic backgrounds
    52 phenotypes from multigenic genotypes
    4 images
    2394 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Age related retinal degeneration with abnormal subretinal microglial cell accumulation in one homozygous null mice. Other null mice shows impaired monocyte recruitment after vascular injury, kidney ischemia and reperfusion, and bacterial infection of the instestine.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    90
  • GO References
    19
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    769
  • Tissues
    70
  • cDNA Data
    9
  • Literature Summary
    67
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 13051 NCBI Gene Model | MGI Sequence Detail 19614 C57BL/6J ±  kb
    transcript NM_009987 RefSeq | MGI Sequence Detail 3753 C57BL/6  
    polypeptide Q9Z0D9 UniProt | EBI | MGI Sequence Detail 354 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 12
      Genomic 1
      cDNA 9
      Primer pair 2
      Antibodies 3

      Microarray probesets 5
    References
    more
    • Summaries
      All 2552
      Developmental Gene Expression 67
      Diseases 3
      Gene Ontology 19
      Phenotypes 2394
    • Earliest
      J:51793 Combadiere C, et al., Gene cloning, RNA distribution, and functional expression of mCX3CR1, a mouse chemotactic receptor for the CX3C chemokine fractalkine. Biochem Biophys Res Commun. 1998 Dec 30;253(3):728-32
    • Latest
      J:392461 Huang Y, et al., cGAS-mediated type I IFN signaling contributes to disease progression in drug-refractory epilepsy. Nat Neurosci. 2026 Sep;29(9):2124-2138
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Funding Information
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    Send questions and comments to User Support.     		last database update
    09/15/2026
    MGI 6.29     		The Jackson Laboratory