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

Summary

Official Symbol: Cx3cl1provided by RGD
Official Full Name: C-X3-C motif chemokine ligand 1provided by RGD
Primary source: RGD:620458
See related: EnsemblRapid: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 cellular response to cytokine stimulus; positive regulation of cell population proliferation; 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, Dec 2024]
Expression: Biased expression in Brain (RPKM 207.2), Kidney (RPKM 160.2) and 6 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 19p13

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (10233326..10244856, complement)
RS_2023_06	previous assembly	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_086037.1 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Expression and significance of Fractalkine/CX3CL1 in MPO-AAV-associated glomerulonephritis rats.
Title: Expression and significance of Fractalkine/CX3CL1 in MPO-AAV-associated glomerulonephritis rats.
Spinal Cord Stimulation Increases Chemoefficacy and Prevents Paclitaxel-Induced Pain via CX3CL1.
Title: Spinal Cord Stimulation Increases Chemoefficacy and Prevents Paclitaxel-Induced Pain via CX3CL1.
Dapagliflozin Protects H9c2 Cells Against Injury Induced by Lipopolysaccharide via Suppression of CX3CL1/CX3CR1 Axis and NF-kappaB Activity.
Title: Dapagliflozin Protects H9c2 Cells Against Injury Induced by Lipopolysaccharide via Suppression of CX3CL1/CX3CR1 Axis and NF-κB Activity.
FKN/CX3CR1 axis facilitates migraine-Like behaviour by activating thalamic-cortical network microglia in status epilepticus model rats.
Title: FKN/CX3CR1 axis facilitates migraine-Like behaviour by activating thalamic-cortical network microglia in status epilepticus model rats.
Bone marrow stromal cells reverse the microglia type from pro-inflammatory tumour necrosis factor a microglia to anti-inflammatory CD206 microglia of middle cerebral artery occlusion rats through triggering secretion of CX3CL1.
Title: Bone marrow stromal cells reverse the microglia type from pro-inflammatory tumour necrosis factor a microglia to anti-inflammatory CD206 microglia of middle cerebral artery occlusion rats through triggering secretion of CX3CL1.
MicroRNA-195 prevents hippocampal microglial/macrophage polarization towards the M1 phenotype induced by chronic brain hypoperfusion through regulating CX3CL1/CX3CR1 signaling.
Title: MicroRNA-195 prevents hippocampal microglial/macrophage polarization towards the M1 phenotype induced by chronic brain hypoperfusion through regulating CX3CL1/CX3CR1 signaling.
Leptin and fractalkine: novel subcutaneous cytokines in burn injury.
Title: Leptin and fractalkine: novel subcutaneous cytokines in burn injury.
CX3CL1/CX3CR1 axis attenuates early brain injury via promoting the delivery of exosomal microRNA-124 from neuron to microglia after subarachnoid hemorrhage.
Title: CX3CL1/CX3CR1 axis attenuates early brain injury via promoting the delivery of exosomal microRNA-124 from neuron to microglia after subarachnoid hemorrhage.
Maternal Immune Activation Sensitizes Male Offspring Rats to Lipopolysaccharide-Induced Microglial Deficits Involving the Dysfunction of CD200-CD200R and CX3CL1-CX3CR1 Systems.
Title: Maternal Immune Activation Sensitizes Male Offspring Rats to Lipopolysaccharide-Induced Microglial Deficits Involving the Dysfunction of CD200-CD200R and CX3CL1-CX3CR1 Systems.
MMP-9 regulates CX3CL1/CX3CR1 in the early phase of neuropathic pain in chronic sciatic nerve constriction injury (CCI) rats.
Title: MMP-9 regulates CX3CL1/CX3CR1 in the early phase of neuropathic pain in chronic sciatic nerve constriction injury (CCI) rats.

Submit: New GeneRIF Correction See all GeneRIFs (64)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BF390094 (e-PCR)
- UniSTS:249380

U92565 (e-PCR)
- UniSTS:159796

AF010586 (e-PCR)
- UniSTS:179784

PMC86945P1 (e-PCR)
- UniSTS:273566

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables CCR chemokine receptor binding	IBA Inferred from Biological aspect of Ancestor more info
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
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	IGI Inferred from Genetic Interaction 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 antimicrobial humoral immune response mediated by antimicrobial peptide	IBA Inferred from Biological aspect of Ancestor 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	IEA Inferred from Electronic Annotation 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 tumor necrosis factor	IDA Inferred from Direct Assay more info	PubMed
involved_in chemokine-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in chemokine-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in chemokine-mediated signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
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
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
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 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	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lymphocyte chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in macrophage chemotaxis	IEA Inferred from Electronic Annotation 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 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	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neutrophil chemotaxis	ISO Inferred from Sequence Orthology more info
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 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 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
involved_in positive regulation of angiogenesis	IEA Inferred from Electronic Annotation 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 canonical NF-kappaB signal transduction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of canonical NF-kappaB signal transduction	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of canonical NF-kappaB signal transduction	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	IBA Inferred from Biological aspect of Ancestor more info
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 phosphatidylinositol 3-kinase/protein kinase B signal transduction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	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
involved_in signal transduction	IEA Inferred from Electronic Annotation more info
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 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
located_in extracellular space	IEA Inferred from Electronic Annotation more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
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
is_active_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in postsynapse	IEA Inferred from Electronic Annotation more info

General protein information

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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)

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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.

mRNA and Protein(s)

NM_134455.2 → NP_604450.2 fractalkine precursor

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000019

UniProtKB/Swiss-Prot

O55145

UniProtKB/TrEMBL

A6JY48, F7EX30, Q6IRF7

Related

ENSRNOP00000022128.4, ENSRNOT00000022128.7

Conserved Domains (2) summary

cd00274
Location:25 → 100

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:109 → 334

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086037.1 Reference GRCr8

Range

10233326..10244856 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_008772329.4 → XP_008770551.1 fractalkine isoform X1

See identical proteins and their annotated locations for XP_008770551.1

UniProtKB/Swiss-Prot

O55145

UniProtKB/TrEMBL

A6JY48, F7EX30, Q6IRF7

Conserved Domains (2) summary

cd00274
Location:25 → 100

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:109 → 334

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)