Cxcl3 (C-X-C motif chemokine ligand 3) - Rat Genome Database

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Gene: Cxcl3 (C-X-C motif chemokine ligand 3) Rattus norvegicus
Analyze
Symbol: Cxcl3
Name: C-X-C motif chemokine ligand 3
RGD ID: 621812
Description: Exhibits chemokine activity. Involved in several processes, including cellular response to lipopolysaccharide; neutrophil chemotaxis; and positive regulation of cytosolic calcium ion concentration. Localizes to extracellular space. Biomarker of Coronavirus infectious disease and bacterial pneumonia. Orthologous to human CXCL1 (C-X-C motif chemokine ligand 1); CXCL2 (C-X-C motif chemokine ligand 2); and CXCL3 (C-X-C motif chemokine ligand 3); PARTICIPATES IN interleukin-23 signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: C-X-C motif chemokine 3; chemokine (C-X-C motif) ligand 3; Cinc-2; Cinc2; cytokine-induced neutrophil chemoattractant 2; cytokine-induced neutrophil chemoattractant-2; gene model 1960, (NCBI); Gm1960; macrophage inflammatory protein 2-alpha/beta; MIP2-alpha/beta
RGD Orthologs
Human
Mouse
Bonobo
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21417,270,146 - 17,289,458 (-)NCBI
Rnor_6.0 Ensembl1418,820,168 - 18,839,595 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01418,820,168 - 18,839,659 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01418,729,345 - 18,748,734 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41418,767,306 - 18,787,340 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11418,767,305 - 18,787,340 (-)NCBI
Celera1416,646,603 - 16,666,030 (-)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-anisomycin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(4Z,7Z,10Z,13Z,15E,19Z)-17-hydroxydocosahexaenoic acid  (ISO)
(S)-nicotine  (ISO)
1,1,1-trichloroethane  (ISO)
1,3-benzothiazole-2-thiol  (ISO)
1,4-phenylenediamine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-fluoro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
1-nitropyrene  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-dinitrobenzenesulfonic acid  (ISO)
2-amino-2-deoxy-D-galactopyranose  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-nitrofluorene  (EXP)
2-tert-butylhydroquinone  (ISO)
22-Hydroxycholesterol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-chloropropane-1,2-diol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methyladenine  (ISO)
3-Nitrofluoranthene  (ISO)
3-phenylprop-2-enal  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-hydroxynon-2-enal  (ISO)
4-nitroquinoline N-oxide  (ISO)
5-fluorouracil  (ISO)
6alpha-methylprednisolone  (ISO)
7,12-dimethyltetraphene  (ISO)
9-cis-retinoic acid  (ISO)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
Aflatoxin G1  (ISO)
aldehydo-D-glucosamine  (EXP)
aldehydo-D-glucose  (ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-retinoic acid  (ISO)
alpha-hexylcinnamaldehyde  (ISO)
AM-251  (ISO)
amlexanox  (ISO)
ammonium chloride  (EXP)
amphibole asbestos  (EXP)
antimycin A  (ISO)
antirheumatic drug  (ISO)
apocynin  (ISO)
aripiprazole  (ISO)
arsane  (ISO)
arsenic acid  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
asbestos  (ISO)
asperentin  (ISO)
astemizole  (EXP)
astressin 2B  (ISO)
atrazine  (ISO)
atropine  (ISO)
benzalkonium chloride  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
beryllium sulfate  (ISO)
beta-D-glucosamine  (EXP)
beta-naphthoflavone  (ISO)
bexarotene  (EXP)
bifenthrin  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
bortezomib  (ISO)
budesonide  (EXP)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
cadmium sulfate  (ISO)
Calcimycin  (ISO)
calcitriol  (ISO)
carbon nanotube  (EXP,ISO)
carmustine  (ISO)
carrageenan  (ISO)
carvacrol  (ISO)
ceruletide  (ISO)
cetirizine  (ISO)
chenodeoxycholic acid  (ISO)
chlorogenic acid  (ISO)
chloropicrin  (ISO)
chloroprene  (EXP,ISO)
choline  (ISO)
chondroitin sulfate  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clozapine  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
cobalt(2+) sulfate  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
corosolic acid  (ISO)
crocidolite asbestos  (ISO)
crotonaldehyde  (ISO)
curcumin  (ISO)
cyanuric chloride  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
decabromodiphenyl ether  (EXP)
deoxycholic acid  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dichlorine  (ISO)
dichloroacetic acid  (ISO)
diclofenac  (ISO)
dicloxacillin  (ISO)
diethyl malate  (ISO)
diisopropyl fluorophosphate  (ISO)
dimercaprol  (ISO)
dinitrogen  (ISO)
dioxygen  (ISO)
domperidone  (ISO)
doramapimod  (ISO)
doxorubicin  (ISO)
edaravone  (EXP)
elemental selenium  (ISO)
enniatin  (ISO)
Erionite  (ISO)
ethanol  (ISO)
eugenol  (ISO)
flavonoids  (EXP)
flucloxacillin  (ISO)
fluoranthene  (ISO)
fluticasone  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
gadolinium trichloride  (ISO)
gemcitabine  (ISO)
glucose  (ISO)
glutathione  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
gossypol  (ISO)
graphene oxide  (ISO)
halothane  (ISO)
heparan sulfate  (ISO)
hesperidin  (ISO)
hydrogen peroxide  (ISO)
hydroxychloroquine  (ISO)
imiquimod  (ISO)
indometacin  (ISO)
irinotecan  (ISO)
isoflurane  (ISO)
isotretinoin  (ISO)
ketamine  (ISO)
L-methionine  (ISO)
leukotriene B4  (ISO)
leukotriene C4  (ISO)
lipopolysaccharide  (ISO)
manganese(II) chloride  (EXP)
maslinic acid  (ISO)
mesalamine  (ISO)
methotrexate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
metoclopramide  (ISO)
mifepristone  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
monocrotaline  (ISO)
muramyl dipeptide  (ISO)
mycophenolic acid  (ISO)
mycotoxin  (ISO)
N,N-diethyl-m-toluamide  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (ISO)
naphthalene  (ISO)
neocuproine  (ISO)
neoechinulin A  (ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
nickel sulfate  (ISO)
nicotine  (ISO)
nonivamide  (ISO)
o-anisidine  (ISO)
obeticholic acid  (ISO)
oleanolic acid  (ISO)
ozone  (EXP,ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
parthenolide  (ISO)
PD 0325901  (ISO)
pentanal  (ISO)
pentane-2,3-dione  (EXP)
perfluorooctanoic acid  (ISO)
phalloidin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
poly(I:C)  (ISO)
polymyxin B2  (ISO)
potassium bromate  (ISO)
potassium chromate  (ISO)
prednisolone  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
propanal  (ISO)
propofol  (ISO)
Pyridostigmine bromide  (ISO)
quercetin  (ISO)
resolvin D1  (ISO)
resolvin D2  (ISO)
resveratrol  (EXP,ISO)
rimonabant  (ISO)
ritonavir  (ISO)
rofecoxib  (ISO)
rosmarinic acid  (ISO)
rotenone  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
SB 203580  (ISO)
selenium atom  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
silver atom  (EXP,ISO)
silver(0)  (EXP,ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sodium aurothiomalate  (ISO)
sodium dodecyl sulfate  (ISO)
Soman  (ISO)
sterigmatocystin  (ISO)
succimer  (ISO)
sulfapyridine  (ISO)
sulfasalazine  (ISO)
sulforaphane  (ISO)
tamoxifen  (ISO)
tauro-beta-muricholic acid  (ISO)
taurocholic acid  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
thioacetamide  (ISO)
Tiron  (ISO)
titanium dioxide  (EXP,ISO)
toluene 2,4-diisocyanate  (ISO)
tremolite asbestos  (ISO)
tributylstannane  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
Triptolide  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate  (ISO)
trovafloxacin  (ISO)
tunicamycin  (ISO)
ursodeoxycholic acid  (ISO)
valproic acid  (ISO)
vanadyl sulfate  (ISO)
vancomycin  (ISO)
vitamin D  (ISO)
XL147  (ISO)
zaragozic acid A  (ISO)
zileuton  (ISO)
zinc acetate  (ISO)
zinc atom  (ISO)
zinc dichloride  (ISO)
zinc oxide  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
extracellular space  (IBA,IDA,ISS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8471066   PMID:8607872   PMID:12829448   PMID:12949249   PMID:14764687   PMID:16055671   PMID:18323732   PMID:19497959   PMID:20226088   PMID:20602290   PMID:27967265   PMID:31616413  


Genomics

Comparative Map Data
Cxcl3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21417,270,146 - 17,289,458 (-)NCBI
Rnor_6.0 Ensembl1418,820,168 - 18,839,595 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01418,820,168 - 18,839,659 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01418,729,345 - 18,748,734 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41418,767,306 - 18,787,340 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11418,767,305 - 18,787,340 (-)NCBI
Celera1416,646,603 - 16,666,030 (-)NCBICelera
Cytogenetic Map14p22NCBI
CXCL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl473,869,393 - 73,871,308 (+)EnsemblGRCh38hg38GRCh38
GRCh38473,869,393 - 73,871,308 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37474,735,110 - 74,737,025 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36474,953,973 - 74,955,817 (+)NCBINCBI36hg18NCBI36
Build 34475,100,143 - 75,101,988NCBI
Celera472,095,237 - 72,097,087 (+)NCBI
Cytogenetic Map4q13.3NCBI
HuRef470,546,248 - 70,548,158 (+)NCBIHuRef
CHM1_1474,771,032 - 74,772,942 (+)NCBICHM1_1
Cxcl3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39590,933,960 - 90,935,952 (+)NCBIGRCm39mm39
GRCm39 Ensembl590,933,962 - 90,937,459 (+)Ensembl
GRCm38590,786,101 - 90,788,093 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl590,786,103 - 90,789,600 (+)EnsemblGRCm38mm10GRCm38
MGSCv37591,215,129 - 91,217,116 (+)NCBIGRCm37mm9NCBIm37
MGSCv36591,861,303 - 91,863,290 (+)NCBImm8
Celera588,937,720 - 88,939,708 (+)NCBICelera
Cytogenetic Map5E1NCBI
CXCL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1456,157,626 - 56,159,522 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl456,153,899 - 56,159,474 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0450,325,248 - 50,327,165 (-)NCBIMhudiblu_PPA_v0panPan3

Position Markers
D14Rat77  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01418,833,818 - 18,834,102NCBIRnor6.0
Rnor_5.01418,742,995 - 18,743,279UniSTSRnor5.0
RGSC_v3.41418,781,071 - 18,782,022UniSTSRGSC3.4
Celera1416,660,252 - 16,660,493UniSTS
RH 3.4 Map14216.4RGD
RH 3.4 Map14216.4UniSTS
RH 2.0 Map14215.5RGD
SHRSP x BN Map146.92RGD
Cytogenetic Map14p22UniSTS
AI045017  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21417,270,396 - 17,270,567 (+)MAPPER
Rnor_6.01418,820,419 - 18,820,589NCBIRnor6.0
Rnor_5.01418,729,596 - 18,729,766UniSTSRnor5.0
RGSC_v3.41418,767,557 - 18,767,727UniSTSRGSC3.4
Celera1416,646,854 - 16,647,024UniSTS
RH 3.4 Map14213.6UniSTS
Cytogenetic Map14p22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14134403399Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14141333960Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14141333960Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14142766285Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14222782519230541Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14483323319909932Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14483323319909932Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14483323323004027Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14483323326466248Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14483323333040042Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14975643572854397Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin141053997755539977Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)141053997755539977Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)141072926861873323Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141268042430155192Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141268061332593926Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141633698833163485Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:53
Count of miRNA genes:43
Interacting mature miRNAs:50
Transcripts:ENSRNOT00000034090
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 11
Low 4 7 5 2 5 3 3 13 3 3
Below cutoff 2 13 33 21 15 21 5 5 34 15 21 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000034090   ⟹   ENSRNOP00000038520
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1418,820,168 - 18,839,420 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078746   ⟹   ENSRNOP00000070985
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1418,837,821 - 18,839,595 (-)Ensembl
RefSeq Acc Id: NM_138522   ⟹   NP_612531
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21417,270,146 - 17,289,380 (-)NCBI
Rnor_6.01418,820,168 - 18,839,420 (-)NCBI
Rnor_5.01418,729,345 - 18,748,734 (-)NCBI
RGSC_v3.41418,767,306 - 18,787,340 (-)RGD
Celera1416,646,603 - 16,666,030 (-)RGD
Sequence:
RefSeq Acc Id: XM_006250721   ⟹   XP_006250783
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21417,287,727 - 17,289,458 (-)NCBI
Rnor_6.01418,837,767 - 18,839,659 (-)NCBI
Rnor_5.01418,729,345 - 18,748,734 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_612531   ⟸   NM_138522
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_006250783   ⟸   XM_006250721
- Peptide Label: isoform X1
- UniProtKB: Q10746 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000038520   ⟸   ENSRNOT00000034090
RefSeq Acc Id: ENSRNOP00000070985   ⟸   ENSRNOT00000078746

Transcriptome

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

Promoters
RGD ID:13699227
Promoter ID:EPDNEW_R9751
Type:single initiation site
Name:Cxcl3_1
Description:chemokine (C-X-C motif) ligand 3
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_6.01418,839,486 - 18,839,546EPDNEW

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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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:621812 AgrOrtholog
Ensembl Genes ENSRNOG00000028043 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000038520 UniProtKB/Swiss-Prot
  ENSRNOP00000070985 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000034090 UniProtKB/Swiss-Prot
  ENSRNOT00000078746 UniProtKB/Swiss-Prot
InterPro Chemokine_CXC UniProtKB/Swiss-Prot
  Chemokine_CXC_CS UniProtKB/Swiss-Prot
  Chemokine_IL8-like_dom UniProtKB/Swiss-Prot
  CXC_Chemokine_domain UniProtKB/Swiss-Prot
  Interleukin_8-like_sf UniProtKB/Swiss-Prot
KEGG Report rno:171551 UniProtKB/Swiss-Prot
NCBI Gene 171551 ENTREZGENE
PANTHER PTHR10179 UniProtKB/Swiss-Prot
Pfam IL8 UniProtKB/Swiss-Prot
PhenoGen Cxcl3 PhenoGen
PRINTS SMALLCYTKCXC UniProtKB/Swiss-Prot
PROSITE SMALL_CYTOKINES_CXC UniProtKB/Swiss-Prot
SMART SCY UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54117 UniProtKB/Swiss-Prot
UniProt CXCL3_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q10747 UniProtKB/Swiss-Prot
  Q5CZ55 UniProtKB/Swiss-Prot
  Q9EP62 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-12-12 Cxcl3  C-X-C motif chemokine ligand 3  Cxcl3  chemokine (C-X-C motif) ligand 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-25 Cxcl3  chemokine (C-X-C motif) ligand 3  Gm1960  gene model 1960, (NCBI)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Gm1960  gene model 1960, (NCBI)  Cinc2  cytokine-induced neutrophil chemoattractant-2  Symbol and Name updated 1299863 APPROVED
2002-08-07 Cinc2  cytokine-induced neutrophil chemoattractant-2      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_product member of the CXC chemokine family 632410
gene_transcript has two splicing isoforms, CINC-2 alpha and CINC-2 beta 632410