Cxcl1 (C-X-C motif chemokine ligand 1) - Rat Genome Database

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Gene: Cxcl1 (C-X-C motif chemokine ligand 1) Rattus norvegicus
Analyze
Symbol: Cxcl1
Name: C-X-C motif chemokine ligand 1
RGD ID: 619869
Description: Enables chemokine activity. Involved in several processes, including neutrophil chemotaxis; positive regulation of ion transport; and response to amphetamine. Located in extracellular space. Biomarker of several diseases, including esophageal cancer; pneumonia (multiple); prostatitis; severe acute respiratory syndrome; and status epilepticus. 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; chemokine mediated signaling pathway; NOD-like receptor signaling pathway; INTERACTS WITH (+)-alpha-tocopherol; (+)-schisandrin B; (-)-epigallocatechin 3-gallate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: C-X-C motif chemokine 1; chemokine (C-X-C motif) ligand 1; chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha); CINC-1; cytokine-induced neutrophil chemoattractant 1; Gro; Gro1; growth-regulated alpha protein; platelet-derived growth factor-inducible protein KC
RGD Orthologs
Human
Mouse
Bonobo
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21417,193,364 - 17,195,143 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl1418,743,685 - 18,745,457 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01418,743,678 - 18,745,457 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01418,653,032 - 18,654,811 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41418,690,339 - 18,692,118 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11418,690,338 - 18,692,118 (-)NCBI
Celera1416,570,160 - 16,571,939 (-)NCBICelera
RH 3.4 Map14215.0RGD
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acute kidney failure  (ISO)
Acute Lung Injury  (ISO)
acute necrotizing pancreatitis  (IEP)
Alcoholic Liver Diseases  (IEP)
allergic disease  (ISO)
Animal Hepatitis  (IEP)
aspiration pneumonia  (IEP)
asthma  (ISO)
autoimmune hepatitis  (ISO)
bacterial pneumonia  (IEP,ISO)
Brain Injuries  (IEP)
Bronchial Hyperreactivity  (ISO)
Bronchopulmonary Dysplasia  (IEP)
Burns  (IEP)
Chemical and Drug Induced Liver Injury  (ISO)
chronic obstructive pulmonary disease  (ISO)
common cold  (ISO)
COVID-19  (ISO)
cystic fibrosis  (ISO)
dilated cardiomyopathy  (IEP)
Endotoxemia  (ISO)
Enteritis  (IEP)
esophageal cancer  (IEP)
Experimental Arthritis  (IEP)
Experimental Liver Cirrhosis  (ISO)
Femoral Fractures  (IEP)
Hemorrhage  (IEP)
Hemorrhagic Shock  (IEP,ISO)
Human Influenza  (ISO)
hyperhomocysteinemia  (ISO)
Inflammation  (IDA,IEP)
juvenile rheumatoid arthritis  (ISO)
Legionnaires' disease  (ISO)
Liver Neoplasms  (ISO)
Liver Reperfusion Injury  (IDA)
lung disease  (IEP,ISO)
Myocardial Reperfusion Injury  (IMP)
Nasal Polyps  (ISO)
plague  (ISO)
pleurisy  (ISO)
Pneumococcal Meningitis  (IEP)
Pneumococcal Pneumonia  (ISO)
pneumonia  (IEP,ISO)
prostatitis  (IEP)
pulmonary emphysema  (ISO)
Reperfusion Injury  (IEP,ISO)
respiratory allergy  (ISO)
respiratory syncytial virus infectious disease  (ISO)
severe acute respiratory syndrome  (IEP)
Spinal Cord Injuries  (IEP)
status epilepticus  (IEP)
Stroke  (IEP)
Subarachnoid Hemorrhage  (IEP)
Ventricular Dysfunction, Right  (IEP)
viral pneumonia  (IEP)
Wounds and Injuries  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-alpha-tocopherol  (EXP)
(+)-schisandrin B  (EXP)
(-)-anisomycin  (ISO)
(-)-epigallocatechin 3-gallate  (EXP,ISO)
(S)-colchicine  (EXP)
1,2,4-trimethylbenzene  (EXP)
1,2-dichlorobenzene  (EXP)
1,3-benzothiazole-2-thiol  (ISO)
1,4-phenylenediamine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (EXP)
1-nitropyrene  (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-dinitrotoluene  (EXP)
2-acetamidofluorene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-tert-butylhydroquinone  (ISO)
22-Hydroxycholesterol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3-Nitrofluoranthene  (ISO)
3-phenylprop-2-enal  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
6alpha-methylprednisolone  (ISO)
9-cis-retinoic acid  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
acrolein  (EXP)
Actein  (EXP)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucosamine  (EXP)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amosite asbestos  (EXP)
amphibole asbestos  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP)
antirheumatic drug  (ISO)
apocynin  (ISO)
aripiprazole  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
asbestos  (ISO)
atrazine  (ISO)
benazepril  (EXP)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beryllium sulfate  (ISO)
beta-D-glucosamine  (EXP)
beta-naphthoflavone  (ISO)
bexarotene  (EXP)
bis(2-chloroethyl) sulfide  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
budesonide  (EXP)
butanal  (ISO)
butane-2,3-dione  (EXP)
C60 fullerene  (EXP)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
candesartan  (EXP)
carbon nanotube  (EXP,ISO)
carmustine  (ISO)
cefaloridine  (EXP)
chloropicrin  (ISO)
chondroitin sulfate  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clozapine  (ISO)
cobalt atom  (EXP)
cobalt dichloride  (ISO)
cobalt(2+) sulfate  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
crotonaldehyde  (ISO)
curcumin  (ISO)
cyanuric chloride  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
deoxynivalenol  (ISO)
dexamethasone  (EXP)
dibutyl phthalate  (EXP)
diclofenac  (EXP)
diisopropyl fluorophosphate  (EXP)
dinitrogen  (ISO)
diuron  (EXP)
divanadium pentaoxide  (EXP)
doramapimod  (ISO)
doxorubicin  (ISO)
edaravone  (EXP)
elemental selenium  (ISO)
emodin  (EXP)
endosulfan  (EXP)
ethanol  (EXP)
eugenol  (ISO)
famotidine  (EXP)
fluticasone  (ISO)
formaldehyde  (ISO)
fulvestrant  (EXP)
fumonisin B1  (ISO)
furan  (EXP)
gadolinium trichloride  (EXP)
gemcitabine  (ISO)
gentamycin  (EXP)
glafenine  (EXP)
glutathione  (EXP)
gossypol  (ISO)
graphite  (EXP)
halothane  (EXP)
heparan sulfate  (ISO)
hexachlorobenzene  (EXP)
Hexadimethrine bromide  (EXP)
hydrogen chloride  (EXP)
hydrogen peroxide  (ISO)
hydroxychloroquine  (ISO)
idelalisib  (ISO)
indometacin  (EXP)
iron atom  (EXP)
iron(0)  (EXP)
isoflurane  (EXP)
isotretinoin  (ISO)
ketorolac  (EXP)
L-ascorbic acid  (EXP)
lansoprazole  (EXP)
lipopolysaccharide  (EXP,ISO)
losartan  (EXP)
manganese(II) chloride  (EXP)
mesalamine  (ISO)
metformin  (EXP)
methadone  (EXP)
methapyrilene  (EXP)
methimazole  (EXP)
methotrexate  (ISO)
methylisothiazolinone  (ISO)
metyrapone  (EXP)
mifepristone  (ISO)
mono(2-ethylhexyl) phthalate  (EXP)
morphine  (EXP)
muramyl dipeptide  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodimethylamine  (EXP)
N1'-[2-[[5-[(dimethylamino)methyl]-2-furanyl]methylthio]ethyl]-N1-methyl-2-nitroethene-1,1-diamine  (EXP)
naphthalenes  (EXP)
nickel atom  (EXP,ISO)
nickel dichloride  (ISO)
nickel sulfate  (ISO)
o-anisidine  (ISO)
oxaliplatin  (EXP)
ozone  (EXP,ISO)
paclitaxel  (EXP)
paracetamol  (EXP,ISO)
PD 0325901  (ISO)
pentanal  (ISO)
pentane-2,3-dione  (EXP)
perfluorooctanoic acid  (EXP)
phenformin  (EXP)
phenobarbital  (EXP)
phenylephrine  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (EXP)
piroxicam  (ISO)
poly(I:C)  (EXP)
potassium chromate  (ISO)
prednisolone  (ISO)
progesterone  (ISO)
propanal  (ISO)
pyrrolidine dithiocarbamate  (EXP)
quartz  (EXP)
ranitidine  (EXP)
resveratrol  (EXP,ISO)
rifampicin  (EXP)
ritonavir  (ISO)
rofecoxib  (ISO)
rotenone  (EXP)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP)
SB 203580  (EXP,ISO)
SCH-351591  (EXP)
SCH772984  (EXP)
selenium atom  (ISO)
serpentine asbestos  (ISO)
sevoflurane  (EXP)
silicon dioxide  (EXP,ISO)
sodium arsenite  (EXP,ISO)
sodium aurothiomalate  (ISO)
sodium dichromate  (EXP)
sodium dodecyl sulfate  (ISO)
Soman  (EXP)
spironolactone  (EXP)
sulfapyridine  (ISO)
sulfasalazine  (ISO)
sulforaphane  (ISO)
sulfur dioxide  (EXP)
tamoxifen  (EXP)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
Tesaglitazar  (EXP)
testosterone  (EXP)
tetrachloromethane  (EXP)
tetradecane  (EXP)
thioacetamide  (EXP)
Tiron  (ISO)
titanium dioxide  (EXP,ISO)
topotecan  (EXP)
trichostatin A  (ISO)
trimethyltin  (EXP)
troglitazone  (ISO)
tropisetron  (EXP)
tungsten  (EXP)
tunicamycin  (ISO)
undecane  (EXP)
ursodeoxycholic acid  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vanadyl sulfate  (ISO)
vitamin E  (EXP)
wortmannin  (EXP)
zaragozic acid A  (EXP)
zinc acetate  (ISO)
zinc atom  (EXP)
zinc dichloride  (ISO)
zinc protoporphyrin  (EXP)
zinc(0)  (EXP)
zoledronic acid  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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35. MGD data from the GO Consortium
36. Nanji AA, etal., Hepatology. 1999 Oct;30(4):934-43.
37. NCBI rat LocusLink and RefSeq merged data July 26, 2002
38. Neumann B, etal., Int Immunol. 1999 Feb;11(2):217-27.
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41. Payne SC, etal., Am J Rhinol. 2008 Nov-Dec;22(6):568-81.
42. Pipeline to import KEGG annotations from KEGG into RGD
43. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
44. Raghavendran K, etal., J Surg Res. 2009 Aug;155(2):273-82. Epub 2008 Sep 16.
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46. RGD automated data pipeline
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Additional References at PubMed
PMID:1415488   PMID:2684956   PMID:7957925   PMID:8607872   PMID:9192722   PMID:9504410   PMID:10725737   PMID:10915734   PMID:12055258   PMID:12517731   PMID:12824006   PMID:12829448  
PMID:12949249   PMID:14617513   PMID:15942680   PMID:16271365   PMID:16522746   PMID:16618742   PMID:16637227   PMID:16818791   PMID:16942465   PMID:17164575   PMID:17166735   PMID:17632282  
PMID:17666044   PMID:17702850   PMID:17959522   PMID:18559975   PMID:18683011   PMID:18694739   PMID:20003523   PMID:20180411   PMID:20226088   PMID:20602290   PMID:21030786   PMID:21418993  
PMID:21905265   PMID:22466126   PMID:22554866   PMID:23460747   PMID:23892723   PMID:24006456   PMID:24280128   PMID:24464584   PMID:25084278   PMID:25383568   PMID:26724371   PMID:27672274  
PMID:28300348   PMID:28820395   PMID:29117499   PMID:30349936   PMID:30397790   PMID:31422522   PMID:31665717   PMID:31722447   PMID:31887360   PMID:32119843   PMID:32802846   PMID:33109545  


Genomics

Comparative Map Data
Cxcl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21417,193,364 - 17,195,143 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl1418,743,685 - 18,745,457 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01418,743,678 - 18,745,457 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01418,653,032 - 18,654,811 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41418,690,339 - 18,692,118 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11418,690,338 - 18,692,118 (-)NCBI
Celera1416,570,160 - 16,571,939 (-)NCBICelera
RH 3.4 Map14215.0RGD
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
Cxcl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39591,039,104 - 91,040,980 (+)NCBIGRCm39mm39
GRCm39 Ensembl591,039,100 - 91,040,974 (+)Ensembl
GRCm38590,891,245 - 90,893,121 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl590,891,241 - 90,893,115 (+)EnsemblGRCm38mm10GRCm38
MGSCv37591,320,271 - 91,322,147 (+)NCBIGRCm37mm9NCBIm37
MGSCv36591,966,510 - 91,968,315 (+)NCBImm8
Celera589,035,565 - 89,037,441 (+)NCBICelera
Cytogenetic Map5E1NCBI
cM Map544.78NCBI
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
CXCL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1722,327,041 - 22,329,405 (+)NCBI
ChlSab1.1 Ensembl722,569,355 - 22,569,900 (-)Ensembl
ChlSab1.1 Ensembl722,327,508 - 22,328,959 (+)Ensembl
Vero_WHO_p1.0NW_023666084462,274 - 464,225 (-)NCBI

Position Markers
RH142406  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21417,193,616 - 17,193,797 (+)MAPPERmRatBN7.2
Rnor_6.01418,743,931 - 18,744,111NCBIRnor6.0
Rnor_5.01418,653,285 - 18,653,465UniSTSRnor5.0
RGSC_v3.41418,690,592 - 18,690,772UniSTSRGSC3.4
Celera1416,570,413 - 16,570,593UniSTS
RH 3.4 Map14215.0UniSTS
Cytogenetic Map14p22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14381307418274691Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14381307418274691Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:81
Count of miRNA genes:60
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000003778
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 10
Low 23 45 37 18 37 1 2 15 26 1 1
Below cutoff 3 14 12 4 1 4 7 8 35 19 14 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003778   ⟹   ENSRNOP00000003778
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1418,743,685 - 18,745,457 (-)Ensembl
RefSeq Acc Id: NM_030845   ⟹   NP_110472
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21417,193,364 - 17,195,143 (-)NCBI
Rnor_6.01418,743,678 - 18,745,457 (-)NCBI
Rnor_5.01418,653,032 - 18,654,811 (-)NCBI
RGSC_v3.41418,690,339 - 18,692,118 (-)RGD
Celera1416,570,160 - 16,571,939 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_110472 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA42053 (Get FASTA)   NCBI Sequence Viewer  
  BAA02008 (Get FASTA)   NCBI Sequence Viewer  
  BAA02009 (Get FASTA)   NCBI Sequence Viewer  
  EDL88575 (Get FASTA)   NCBI Sequence Viewer  
  P14095 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_110472   ⟸   NM_030845
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000003778   ⟸   ENSRNOT00000003778
Protein Domains
SCY

Transcriptome

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

Promoters
RGD ID:13699226
Promoter ID:EPDNEW_R9750
Type:single initiation site
Name:Cxcl1_1
Description:C-X-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_6.01418,745,473 - 18,745,533EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:619869 AgrOrtholog
Ensembl Genes ENSRNOG00000002802 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003778 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003778 ENTREZGENE, UniProtKB/TrEMBL
InterPro Chemokine_CXC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chemokine_CXC_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chemokine_IL8-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CXC_Chemokine_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Interleukin_8-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:81503 UniProtKB/Swiss-Prot
NCBI Gene 81503 ENTREZGENE
PANTHER PTHR10179 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam IL8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cxcl1 PhenoGen
PRINTS SMALLCYTKCXC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE SMALL_CYTOKINES_CXC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SCY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54117 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V6C6_RAT UniProtKB/TrEMBL
  GROA_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-21 Cxcl1  C-X-C motif chemokine ligand 1  Cxcl1  chemokine (C-X-C motif) ligand 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-07-09 Cxcl1  chemokine (C-X-C motif) ligand 1  Cxcl1  chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-26 Cxcl1  chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha)  Cxcl1  chemokine (C-X-C motif) ligand 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Cxcl1  chemokine (C-X-C motif) ligand 1  Gro1  gro  Symbol and Name updated 1299863 APPROVED
2002-08-07 Gro1  gro      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expression is induced in response to injury 632968