Cx3cl1 (C-X3-C motif chemokine ligand 1) - Rat Genome Database
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Gene: Cx3cl1 (C-X3-C motif chemokine ligand 1) Rattus norvegicus
Analyze
Symbol: Cx3cl1
Name: C-X3-C motif chemokine ligand 1
RGD ID: 620458
Description: Exhibits chemokine activity. Involved in several processes, including positive regulation of cell population proliferation; regulation of gene expression; and regulation of signal transduction. Localizes to 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; liver disease (multiple); lung disease (multiple); pulmonary hypertension; and transient cerebral ischemia. Human ortholog(s) of this gene implicated in Cor pulmonale and common cold. Orthologous to human CX3CL1 (C-X3-C motif chemokine ligand 1); PARTICIPATES IN chemokine mediated signaling pathway; cytokine mediated signaling pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2-acetamidofluorene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: C-X3-C motif chemokine 1; chemokine (C-X3-C motif) ligand 1; Cx3c; CX3C membrane-anchored chemokine; fractalkine; neurotactin; Scyd1; small inducible cytokine subfamily D 1; small inducible cytokine subfamily D, 1; small-inducible cytokine D1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21910,227,337 - 10,237,826 (-)NCBI
Rnor_6.0 Ensembl1910,644,244 - 10,653,800 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01910,644,267 - 10,654,861 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01910,638,466 - 10,647,951 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41910,666,940 - 10,676,424 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11910,671,765 - 10,681,250 (-)NCBI
Celera1910,113,300 - 10,122,786 (-)NCBICelera
Cytogenetic Map19p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3-dimethoxynaphthalene-1,4-dione  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-diaminotoluene  (ISO)
2-acetamidofluorene  (EXP)
2-methylcholine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,4-dichloroaniline  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-hydroxyphenyl retinamide  (ISO)
8-Br-cAMP  (ISO)
acetylsalicylic acid  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (EXP)
aripiprazole  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
asperentin  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
beta-naphthoflavone  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
capsaicin  (EXP)
carbon nanotube  (ISO)
ceric oxide  (EXP)
chloroprene  (EXP)
choline  (ISO)
chromium atom  (ISO)
ciguatoxin CTX1B  (ISO)
clofibrate  (ISO)
cobalt atom  (ISO)
cocaine  (EXP)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (ISO)
D-glucose  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP,ISO)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
enzacamene  (ISO)
ethanol  (EXP,ISO)
fenofibrate  (ISO)
fenvalerate  (EXP)
fipronil  (EXP)
folic acid  (ISO)
fructose  (ISO)
furan  (EXP)
gamma-aminobutyric acid  (EXP)
glucose  (ISO)
hydrogen peroxide  (EXP)
ibuprofen  (ISO)
ketamine  (EXP)
lead diacetate  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
manganese(II) chloride  (EXP)
mechlorethamine  (EXP)
methadone  (EXP)
methylmercury chloride  (ISO)
mifepristone  (ISO)
morphine  (EXP)
mycophenolic acid  (ISO)
mycotoxin  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (ISO)
naproxen  (EXP)
neoechinulin A  (ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
ozone  (EXP,ISO)
p-cresol  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
phenobarbital  (ISO)
phenytoin  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
quercetin  (ISO)
resveratrol  (EXP,ISO)
rofecoxib  (ISO)
rutin  (EXP)
SB 203580  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP)
silver atom  (EXP)
silver(0)  (EXP)
sodium arsenite  (ISO)
sterigmatocystin  (ISO)
sumatriptan  (EXP)
sunitinib  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
titanium dioxide  (EXP,ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aging  (IEP)
angiogenesis involved in wound healing  (IEA,ISO)
autocrine signaling  (IGI)
cell adhesion  (ISO)
cell chemotaxis  (ISO)
cell-cell adhesion  (IDA)
cellular response to interferon-gamma  (IBA)
cellular response to interleukin-1  (IBA)
cellular response to tumor necrosis factor  (IBA)
chemokine-mediated signaling pathway  (IBA,ISO)
chemotaxis  (IDA,IGI,ISO)
cytokine-mediated signaling pathway  (IEA,ISO)
eosinophil chemotaxis  (IBA)
G protein-coupled receptor signaling pathway  (IBA,IGI)
immune response  (IEA)
inflammatory response  (IBA)
inhibitory postsynaptic potential  (IMP)
integrin activation  (ISO,ISS)
leukocyte adhesive activation  (IEA)
leukocyte migration involved in inflammatory response  (ISO,ISS)
lymphocyte chemotaxis  (IBA,IEA,ISO)
macrophage chemotaxis  (IEA,ISO)
microglial cell activation  (IDA)
microglial cell proliferation  (ISO)
monocyte chemotaxis  (IBA)
negative regulation of apoptotic process  (ISO)
negative regulation of apoptotic signaling pathway  (ISO)
negative regulation of cell migration  (ISO)
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand  (IEA,ISO)
negative regulation of glutamate receptor signaling pathway  (IDA)
negative regulation of hippocampal neuron apoptotic process  (ISO)
negative regulation of interleukin-1 alpha production  (IDA)
negative regulation of microglial cell activation  (IDA)
negative regulation of tumor necrosis factor production  (ISO)
negative regulation of vasoconstriction  (IDA)
neuron cellular homeostasis  (IDA)
neutrophil chemotaxis  (IBA,IEA,ISO)
platelet activation  (IMP)
positive chemotaxis  (ISO)
positive regulation of actin filament bundle assembly  (ISO)
positive regulation of angiogenesis  (IEA,ISO)
positive regulation of calcium-independent cell-cell adhesion  (ISO)
positive regulation of cell adhesion  (IDA)
positive regulation of cell migration  (IDA)
positive regulation of cell population proliferation  (ISO)
positive regulation of ERK1 and ERK2 cascade  (IBA)
positive regulation of GTPase activity  (IBA)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (IGI)
positive regulation of I-kappaB phosphorylation  (ISO)
positive regulation of inflammatory response  (ISO)
positive regulation of macrophage chemotaxis  (IMP)
positive regulation of MAPK cascade  (ISO)
positive regulation of microglial cell migration  (ISO)
positive regulation of neuroblast proliferation  (IDA)
positive regulation of neuron projection development  (IDA)
positive regulation of NF-kappaB transcription factor activity  (ISO)
positive regulation of protein kinase B signaling  (IMP,ISO)
positive regulation of release of sequestered calcium ion into cytosol  (ISO)
positive regulation of smooth muscle cell proliferation  (IDA)
positive regulation of transcription by RNA polymerase II  (IDA)
positive regulation of transforming growth factor beta1 production  (IEA,ISO)
regulation of lipopolysaccharide-mediated signaling pathway  (ISO)
response to hypoxia  (IEP)
response to ischemia  (IGI)
wound healing  (ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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36. NCBI rat LocusLink and RefSeq merged data July 26, 2002
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39. Pipeline to import KEGG annotations from KEGG into RGD
40. Rauer M, etal., J Neurovirol. 2002 Jan;8(3):168-79.
41. RGD automated data pipeline
42. RGD automated import pipeline for gene-chemical interactions
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Additional References at PubMed
PMID:9177350   PMID:10187784   PMID:10415068   PMID:10869418   PMID:10899174   PMID:11777952   PMID:12125082   PMID:12631113   PMID:12714508   PMID:12815711   PMID:12837921   PMID:15111313  
PMID:15321787   PMID:15525271   PMID:15993821   PMID:16234287   PMID:16272359   PMID:16413026   PMID:16980051   PMID:17174525   PMID:17430890   PMID:17953351   PMID:17971299   PMID:18097059  
PMID:18292196   PMID:18322241   PMID:18971423   PMID:19422292   PMID:19474321   PMID:21829356   PMID:21840883   PMID:22387113   PMID:22435508   PMID:22536384   PMID:22871113   PMID:23125415  
PMID:23147224   PMID:23361876   PMID:23400803   PMID:23718544   PMID:23776243   PMID:23897050   PMID:23953563   PMID:23968561   PMID:24036597   PMID:24175290   PMID:24294368   PMID:24603149  
PMID:24731444   PMID:25195598   PMID:25435433   PMID:25494456   PMID:25559502   PMID:25768734   PMID:27209190   PMID:27923568   PMID:28612258   PMID:28849713   PMID:29313211   PMID:30248434  
PMID:32152663  


Genomics

Comparative Map Data
Cx3cl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21910,227,337 - 10,237,826 (-)NCBI
Rnor_6.0 Ensembl1910,644,244 - 10,653,800 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01910,644,267 - 10,654,861 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01910,638,466 - 10,647,951 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41910,666,940 - 10,676,424 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11910,671,765 - 10,681,250 (-)NCBI
Celera1910,113,300 - 10,122,786 (-)NCBICelera
Cytogenetic Map19p13NCBI
CX3CL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1657,372,477 - 57,385,044 (+)EnsemblGRCh38hg38GRCh38
GRCh381657,372,490 - 57,385,044 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371657,406,402 - 57,418,956 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361655,963,915 - 55,976,457 (+)NCBINCBI36hg18NCBI36
Build 341655,963,914 - 55,976,455NCBI
Celera1641,906,410 - 41,918,956 (+)NCBI
Cytogenetic Map16q21NCBI
HuRef1643,274,294 - 43,286,836 (+)NCBIHuRef
CHM1_11658,814,588 - 58,827,172 (+)NCBICHM1_1
Cx3cl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39895,498,808 - 95,509,055 (+)NCBIGRCm39mm39
GRCm39 Ensembl895,498,637 - 95,509,055 (+)Ensembl
GRCm38894,772,180 - 94,782,427 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl894,772,009 - 94,782,427 (+)EnsemblGRCm38mm10GRCm38
MGSCv37897,296,080 - 97,306,327 (+)NCBIGRCm37mm9NCBIm37
MGSCv36897,661,355 - 97,671,556 (+)NCBImm8
Celera899,100,414 - 99,110,655 (+)NCBICelera
Cytogenetic Map8C5NCBI
cM Map846.79NCBI
Cx3cl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543315,023,050 - 15,034,711 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543315,023,272 - 15,034,650 (+)NCBIChiLan1.0ChiLan1.0
CX3CL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11656,779,065 - 56,791,760 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1656,779,065 - 56,791,760 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01637,646,447 - 37,659,078 (+)NCBIMhudiblu_PPA_v0panPan3
CX3CL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl259,022,794 - 59,032,095 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1259,022,794 - 59,032,095 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cx3cl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364759,443,851 - 9,454,715 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CX3CL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1619,312,351 - 19,324,439 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2617,304,118 - 17,315,820 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103233058
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1543,310,711 - 43,323,533 (+)NCBI
ChlSab1.1 Ensembl543,310,753 - 43,323,529 (+)Ensembl
Cx3cl1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474628,677,956 - 28,688,638 (-)NCBI

Position Markers
U92565  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01910,644,839 - 10,644,991NCBIRnor6.0
Rnor_5.01910,639,030 - 10,639,182UniSTSRnor5.0
RGSC_v3.41910,667,504 - 10,667,656UniSTSRGSC3.4
Celera1910,113,864 - 10,114,016UniSTS
Cytogenetic Map19p12UniSTS
BF390094  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01910,652,182 - 10,652,339NCBIRnor6.0
Rnor_5.01910,646,373 - 10,646,530UniSTSRnor5.0
RGSC_v3.41910,674,845 - 10,675,002UniSTSRGSC3.4
Celera1910,121,207 - 10,121,364UniSTS
RH 3.4 Map1997.1UniSTS
Cytogenetic Map19p12UniSTS
PMC86945P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01910,646,893 - 10,647,103NCBIRnor6.0
Rnor_5.01910,641,084 - 10,641,294UniSTSRnor5.0
RGSC_v3.41910,669,558 - 10,669,768UniSTSRGSC3.4
Celera1910,115,918 - 10,116,128UniSTS
Cytogenetic Map19p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19195770746957707Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19807254547318201Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19500757143907843Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19129558305Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19129558305Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19132379055Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19104464846044648Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)19370183548701835Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19243296347217667Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19138221845Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)19370183548701835Rat
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124933090Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19138221845Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19138221845Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19138221845Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127635288Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:330
Count of miRNA genes:195
Interacting mature miRNAs:250
Transcripts:ENSRNOT00000022128
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 11 6 54 27 15 6
Low 32 25 15 19 15 7 10 20 8 26 5 7
Below cutoff 26 26 26 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022128   ⟹   ENSRNOP00000022128
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1910,644,244 - 10,653,800 (-)Ensembl
RefSeq Acc Id: NM_134455   ⟹   NP_604450
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21910,227,345 - 10,236,832 (-)NCBI
Rnor_6.01910,644,275 - 10,653,761 (-)NCBI
Rnor_5.01910,638,466 - 10,647,951 (-)NCBI
RGSC_v3.41910,666,940 - 10,676,424 (-)RGD
Celera1910,113,300 - 10,122,786 (-)RGD
Sequence:
RefSeq Acc Id: XM_008772329   ⟹   XP_008770551
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21910,227,337 - 10,237,826 (-)NCBI
Rnor_6.01910,644,267 - 10,654,861 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_604450   ⟸   NM_134455
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_008770551   ⟸   XM_008772329
- Peptide Label: isoform X1
- UniProtKB: Q6IRF7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022128   ⟸   ENSRNOT00000022128
Protein Domains
SCY

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13700942
Promoter ID:EPDNEW_R11466
Type:single initiation site
Name:Cx3cl1_1
Description:C-X3-C motif chemokine ligand 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01910,653,810 - 10,653,870EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620458 AgrOrtholog
Ensembl Genes ENSRNOG00000016326 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022128 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022128 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7099250 IMAGE-MGC_LOAD
InterPro Chemokine_b/g/d UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chemokine_CX3C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chemokine_IL8-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CX3CL1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Interleukin_8-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:89808 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91495 IMAGE-MGC_LOAD
NCBI Gene 89808 ENTREZGENE
PANTHER PTHR12015 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12015:SF92 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam IL8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cx3cl1 PhenoGen
SMART SCY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54117 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt O55145 ENTREZGENE
  Q6IRF7 ENTREZGENE, UniProtKB/TrEMBL
  X3CL1_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-08 Cx3cl1  C-X3-C motif chemokine ligand 1  Cx3cl1  chemokine (C-X3-C motif) ligand 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Cx3cl1  chemokine (C-X3-C motif) ligand 1      Symbol and Name status set to approved 625702 APPROVED
2003-03-04 Cx3cl1  chemokine (C-X3-C motif) ligand 1  Scyd1  small inducible cytokine subfamily D, 1  Symbol and Name updated to reflect Human and Mouse nomenclature 61478 PROVISIONAL
2002-08-07 Scyd1  small inducible cytokine subfamily D, 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains a Cys-X-X-X-Cys motif 728291