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Cx3cl1 C-X3-C motif chemokine ligand 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 89808, updated on 22-May-2022

Summary

Official Symbol
Cx3cl1provided by RGD
Official Full Name
C-X3-C motif chemokine ligand 1provided by RGD
Primary source
RGD:620458
See related
Ensembl:ENSRNOG00000016326 AllianceGenome:RGD:620458
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Cx3c; Scyd1
Summary
Enables chemokine activity. Involved in several processes, including positive regulation of cell population proliferation; regulation of gene expression; and regulation of signal transduction. Located in several cellular components, including neuron projection; neuronal cell body; and perinuclear region of cytoplasm. Used to study acute pancreatitis; ischemia; and status epilepticus. Biomarker of several diseases, including borna disease; brain disease (multiple); liver disease (multiple); lung disease (multiple); and pulmonary hypertension. Human ortholog(s) of this gene implicated in Cor pulmonale and common cold. Orthologous to human CX3CL1 (C-X3-C motif chemokine ligand 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Brain (RPKM 207.2), Kidney (RPKM 160.2) and 6 other tissues See more
Orthologs
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Genomic context

See Cx3cl1 in Genome Data Viewer
Location:
19p13
Exon count:
4
Annotation release Status Assembly Chr Location
108 current mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (10227337..10237826, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (10644267..10654861, complement)

Chromosome 19 - NC_051354.1Genomic Context describing neighboring genes Neighboring gene C-C motif chemokine ligand 17 Neighboring gene aldo-keto reductase family 1 member B, pseudogene 4 Neighboring gene G protein subunit beta 1, pseudogene 1 Neighboring gene proteasome assembly chaperone 4, pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables CCR chemokine receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables CX3C chemokine receptor binding IEA
Inferred from Electronic Annotation
more info
 
enables CX3C chemokine receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables CX3C chemokine receptor binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables CXCR1 chemokine receptor binding IEA
Inferred from Electronic Annotation
more info
 
enables CXCR1 chemokine receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables chemoattractant activity IEA
Inferred from Electronic Annotation
more info
 
enables chemoattractant activity ISO
Inferred from Sequence Orthology
more info
 
enables chemokine activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables chemokine activity IDA
Inferred from Direct Assay
more info
PubMed 
enables chemokine activity IEA
Inferred from Electronic Annotation
more info
 
enables chemokine activity ISO
Inferred from Sequence Orthology
more info
 
enables integrin binding IEA
Inferred from Electronic Annotation
more info
 
enables integrin binding ISO
Inferred from Sequence Orthology
more info
 
enables integrin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
involved_in G protein-coupled receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in G protein-coupled receptor signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in aging IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in angiogenesis involved in wound healing IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within angiogenesis involved in wound healing ISO
Inferred from Sequence Orthology
more info
 
involved_in autocrine signaling IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in cell adhesion IEA
Inferred from Electronic Annotation
more info
 
involved_in cell adhesion ISO
Inferred from Sequence Orthology
more info
 
involved_in cell chemotaxis ISO
Inferred from Sequence Orthology
more info
 
involved_in cell-cell adhesion IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to interferon-gamma IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cellular response to interleukin-1 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cellular response to tumor necrosis factor IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in chemokine-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in chemokine-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in chemokine-mediated signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in chemotaxis IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in chemotaxis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within cytokine-mediated signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in eosinophil chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in extrinsic apoptotic signaling pathway in absence of ligand IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of extrinsic apoptotic signaling pathway in absence of ligand ISO
Inferred from Sequence Orthology
more info
 
involved_in immune response IEA
Inferred from Electronic Annotation
more info
 
involved_in inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in inhibitory postsynaptic potential IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in integrin activation IEA
Inferred from Electronic Annotation
more info
 
involved_in integrin activation ISO
Inferred from Sequence Orthology
more info
 
involved_in integrin activation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in leukocyte adhesive activation IEA
Inferred from Electronic Annotation
more info
 
involved_in leukocyte migration involved in inflammatory response IEA
Inferred from Electronic Annotation
more info
 
involved_in leukocyte migration involved in inflammatory response ISO
Inferred from Sequence Orthology
more info
 
involved_in leukocyte migration involved in inflammatory response ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in lymphocyte chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in lymphocyte chemotaxis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within lymphocyte chemotaxis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within macrophage chemotaxis ISO
Inferred from Sequence Orthology
more info
 
involved_in microglial cell activation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in microglial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in microglial cell proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in monocyte chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of apoptotic process ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of apoptotic signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of cell migration IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of cell migration ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of extrinsic apoptotic signaling pathway in absence of ligand IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of extrinsic apoptotic signaling pathway in absence of ligand ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of glutamate receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of hippocampal neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of hippocampal neuron apoptotic process ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of interleukin-1 alpha production IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of microglial cell activation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of tumor necrosis factor production IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of tumor necrosis factor production ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of vasoconstriction IDA
Inferred from Direct Assay
more info
PubMed 
involved_in neuron cellular homeostasis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in neutrophil chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in neutrophil chemotaxis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within neutrophil chemotaxis ISO
Inferred from Sequence Orthology
more info
 
involved_in platelet activation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive chemotaxis IEA
Inferred from Electronic Annotation
more info
 
involved_in positive chemotaxis ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of ERK1 and ERK2 cascade IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of I-kappaB kinase/NF-kappaB signaling IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of I-kappaB phosphorylation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of I-kappaB phosphorylation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of MAPK cascade IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of MAPK cascade ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of NF-kappaB transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of NF-kappaB transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of actin filament bundle assembly IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of actin filament bundle assembly ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of angiogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of calcium-independent cell-cell adhesion IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of calcium-independent cell-cell adhesion ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of cell adhesion IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of cell migration IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of cell population proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of inflammatory response IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of inflammatory response ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of macrophage chemotaxis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of microglial cell migration IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of microglial cell migration ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of neuroblast proliferation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of neuron projection development IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of protein kinase B signaling IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of protein kinase B signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of protein kinase B signaling ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of release of sequestered calcium ion into cytosol IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of release of sequestered calcium ion into cytosol ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of smooth muscle cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transforming growth factor beta1 production IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of transforming growth factor beta1 production ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of lipopolysaccharide-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of lipopolysaccharide-mediated signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in response to hypoxia IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to ischemia IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within wound healing ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in cell body ISO
Inferred from Sequence Orthology
more info
 
located_in cell projection IDA
Inferred from Direct Assay
more info
PubMed 
located_in cell surface IEA
Inferred from Electronic Annotation
more info
 
located_in cell surface ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular region IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular region ISO
Inferred from Sequence Orthology
more info
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in extracellular space IEA
Inferred from Electronic Annotation
more info
 
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
located_in integral component of membrane ISO
Inferred from Sequence Orthology
more info
 
is_active_in integral component of plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in membrane ISO
Inferred from Sequence Orthology
more info
 
located_in neuron projection IDA
Inferred from Direct Assay
more info
PubMed 
located_in neuron projection IEA
Inferred from Electronic Annotation
more info
 
located_in neuron projection ISO
Inferred from Sequence Orthology
more info
 
located_in neuronal cell body IDA
Inferred from Direct Assay
more info
PubMed 
located_in neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
located_in neuronal cell body ISO
Inferred from Sequence Orthology
more info
 
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
 
located_in postsynapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
fractalkine
Names
C-X3-C motif chemokine 1
CX3C membrane-anchored chemokine
chemokine (C-X3-C motif) ligand 1
neurotactin
small inducible cytokine subfamily D, 1
small-inducible cytokine D1

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.

mRNA and Protein(s)

  1. NM_134455.2NP_604450.2  fractalkine precursor

    Status: PROVISIONAL

    Source sequence(s)
    JACYVU010000303
    Related
    ENSRNOP00000022128.3, ENSRNOT00000022128.6
    Conserved Domains (2) summary
    cd00274
    Location:25100
    Chemokine_CX3C; 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteines; differ structurally from the other subgroups in that they are attached to a membrane-spanning domain via a mucin-like stalk and can be proteolytically cleaved to a ...
    pfam05109
    Location:109334
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051354.1 Reference mRatBN7.2 Primary Assembly

    Range
    10227337..10237826 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_008772329.3XP_008770551.1  fractalkine isoform X1

    See identical proteins and their annotated locations for XP_008770551.1

    UniProtKB/TrEMBL
    Q6IRF7
    Conserved Domains (2) summary
    cd00274
    Location:25100
    Chemokine_CX3C; 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteines; differ structurally from the other subgroups in that they are attached to a membrane-spanning domain via a mucin-like stalk and can be proteolytically cleaved to a ...
    pfam05109
    Location:109334
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)