Lcn2 (lipocalin 2) - Rat Genome Database

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Gene: Lcn2 (lipocalin 2) Rattus norvegicus
Analyze
Symbol: Lcn2
Name: lipocalin 2
RGD ID: 69408
Description: Enables enterobactin binding activity; identical protein binding activity; and protease binding activity. Involved in several processes, including cellular response to cytokine stimulus; memory; and regulation of neuron apoptotic process. Located in cytosol and extracellular space. Used to study intrahepatic cholangiocarcinoma and retinal degeneration. Biomarker of several diseases, including acute kidney failure; congenital diaphragmatic hernia; obesity; pulmonary hypertension; and transient cerebral ischemia. Human ortholog(s) of this gene implicated in urinary tract infection. Orthologous to human LCN2 (lipocalin 2); INTERACTS WITH (+)-schisandrin B; (-)-citrinin; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: alpha-2-microglobulin-related protein; alpha-2U globulin-related protein; lipocalin 2 (oncogene 24p3); lipocalin 24p3; lipocalin-2; neutrophil gelatinase-associated lipocalin; NGAL; p25; siderocalin LCN2; Sip24
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2315,680,688 - 15,684,033 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl315,680,687 - 15,684,095 (-)Ensembl
Rnor_6.0311,414,189 - 11,417,534 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl311,414,186 - 11,417,546 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0316,763,059 - 16,766,404 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4311,511,402 - 11,514,747 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1311,407,773 - 11,411,119 (-)NCBI
Celera310,423,569 - 10,426,914 (-)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Abscess  (IEP)
acute cystitis  (ISO)
acute kidney failure  (IEP,ISO)
adult respiratory distress syndrome  (ISO)
amyotrophic lateral sclerosis  (IEP)
Animal Hepatitis  (ISO)
autosomal dominant polycystic kidney disease  (ISO)
beta thalassemia  (ISO)
Brain Injuries, Traumatic  (IEP)
calcinosis  (ISO)
celiac disease  (ISO)
Cerebral Hemorrhage  (IEP)
Chemical and Drug Induced Liver Injury  (ISO)
Chlamydophila Infections  (ISO)
chronic kidney disease  (ISO)
colon cancer  (IEP)
congenital diaphragmatic hernia  (IEP,ISO)
congenital disorder of glycosylation Iu  (ISO)
contact dermatitis  (ISO)
Contrast-Induced Nephropathy  (IEP)
COVID-19  (ISO)
developmental and epileptic encephalopathy  (ISO)
developmental and epileptic encephalopathy 31  (ISO)
Diabetic Nephropathies  (IEP,ISO)
disease of cellular proliferation  (ISO)
Drug-Related Side Effects and Adverse Reactions  (ISO)
early infantile epileptic encephalopathy  (ISO)
end stage renal disease  (ISO)
Endotoxemia  (ISO)
Escherichia Coli Infections  (ISO)
essential hypertension  (ISO)
Experimental Diabetes Mellitus  (IEP)
Experimental Liver Cirrhosis  (ISO)
Haemophilus Infections  (ISO)
heart valve disease  (ISO)
Helicobacter Infections  (ISO)
hidradenitis suppurativa  (ISO)
hydronephrosis  (ISO)
hyperuricemia  (ISO)
IgA glomerulonephritis  (ISO)
Inflammation  (ISO)
intrahepatic cholangiocarcinoma  (IDA,ISO)
kidney disease  (ISO)
Kidney Reperfusion Injury  (IEP,ISO)
Klebsiella pneumonia  (ISO)
myocardial infarction  (ISO)
myocarditis  (IEP)
Neoplasm Metastasis  (ISO)
obesity  (IEP,ISO)
oral candidiasis  (ISO)
pneumonia  (ISO)
polycystic kidney disease  (ISO)
pre-eclampsia  (ISO)
primary coenzyme Q10 deficiency 7  (ISO)
pulmonary hypertension  (IEP,ISO)
pulmonary tuberculosis  (ISO)
Radiation Injuries, Experimental  (IEP)
renal fibrosis  (ISO)
Renal Ischemia  (ISO)
renovascular hypertension  (ISO)
retinal degeneration  (IDA,IMP)
rheumatoid arthritis  (ISO)
Sepsis  (ISO)
Streptococcal Infections  (ISO)
Stroke  (ISO)
Subarachnoid Hemorrhage  (ISO)
transient cerebral ischemia  (IEP)
type 2 diabetes mellitus  (ISO)
urinary tract infection  (ISO)
uveitis  (IEP)
West Nile encephalitis  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-citrinin  (EXP)
1,1-dichloroethene  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
11-deoxycorticosterone  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4,6-trinitrotoluene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-hydroxypropanoic acid  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-dichloroaniline  (EXP,ISO)
3-chloropropane-1,2-diol  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
8-anilinonaphthalene-1-sulfonic acid  (ISO)
9-cis-retinoic acid  (ISO)
acetylsalicylic acid  (EXP)
Actein  (EXP)
adefovir  (EXP)
adefovir pivoxil  (ISO)
aflatoxin B1  (EXP,ISO)
Aflatoxin B2 alpha  (ISO)
aldehydo-D-glucosamine  (ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-retinoic acid  (ISO)
aluminium oxide  (ISO)
ammonium chloride  (EXP)
amphotericin B methyl ester  (ISO)
anthocyanin  (EXP)
aristolochic acid  (EXP)
arsenous acid  (ISO)
atorvastatin calcium  (EXP,ISO)
bacitracin  (EXP)
benzo[a]pyrene  (ISO)
Benzo[ghi]perylene  (ISO)
beta-D-glucosamine  (ISO)
bicalutamide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
butanal  (ISO)
Butylbenzyl phthalate  (EXP)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
cannabidiol  (ISO)
carbon nanotube  (EXP,ISO)
carmustine  (EXP,ISO)
cerium trichloride  (ISO)
chlordecone  (ISO)
chloroquine  (EXP)
cholesterol  (ISO)
choline  (ISO)
ciprofibrate  (ISO)
ciprofloxacin  (ISO)
cisplatin  (EXP,ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
curcumin  (EXP,ISO)
cyanuric acid  (EXP)
cyclophosphamide  (EXP,ISO)
cyclosporin A  (EXP,ISO)
dapagliflozin  (EXP)
decabromodiphenyl ether  (EXP)
deferasirox  (EXP,ISO)
desferrioxamine B  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
diclofenac  (EXP,ISO)
dieldrin  (EXP)
diethyl phthalate  (EXP)
diethylstilbestrol  (EXP,ISO)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
dioxygen  (EXP,ISO)
diuron  (EXP)
doxorubicin  (EXP,ISO)
doxycycline  (ISO)
enilconazole  (ISO)
ethanol  (EXP,ISO)
etoposide  (EXP)
fenvalerate  (EXP)
ferric ammonium citrate  (ISO)
fluconazole  (EXP)
folic acid  (ISO)
fragrance  (ISO)
fructose  (EXP)
furan  (ISO)
gefitinib  (ISO)
gemfibrozil  (ISO)
genistein  (ISO)
gentamycin  (EXP,ISO)
glafenine  (EXP)
glycidol  (ISO)
graphene oxide  (ISO)
graphite  (EXP)
Hexachloro-1,3-butadiene  (EXP)
hexachlorobenzene  (EXP)
hydroquinone  (ISO)
iomeprol  (EXP)
iron atom  (ISO)
iron(0)  (ISO)
isocyanuric acid  (EXP)
isoniazide  (EXP)
isoprenaline  (ISO)
isotretinoin  (ISO)
ketamine  (ISO)
ketoconazole  (EXP)
lead diacetate  (EXP)
lipopolysaccharide  (ISO)
lovastatin  (ISO)
maleic acid  (EXP)
Mecamylamine  (ISO)
medroxyprogesterone acetate  (ISO)
melamine  (EXP)
mercury atom  (EXP)
mercury dichloride  (EXP,ISO)
mercury(0)  (EXP)
metformin  (EXP)
methimazole  (EXP)
methoxychlor  (EXP)
methylmercury chloride  (EXP,ISO)
morphine  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
natamycin  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP)
nickel sulfate  (ISO)
nitrofen  (EXP)
nystatin  (ISO)
ochratoxin A  (EXP)
Ondansetron  (ISO)
ozone  (ISO)
palmitoyl ethanolamide  (EXP)
paracetamol  (EXP,ISO)
paraquat  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
phenobarbital  (ISO)
PhIP  (EXP)
pirinixic acid  (ISO)
potassium bromate  (ISO)
prednisolone  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
propanal  (ISO)
propiconazole  (ISO)
protein kinase inhibitor  (ISO)
quartz  (EXP)
rac-lactic acid  (ISO)
raloxifene  (ISO)
resveratrol  (EXP,ISO)
ritodrine  (ISO)
rotenone  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP,ISO)
senecionine  (ISO)
serpentine asbestos  (ISO)
sevoflurane  (ISO)
silicon dioxide  (EXP,ISO)
sirolimus  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP)
sodium dodecyl sulfate  (ISO)
Soman  (EXP)
streptozocin  (EXP,ISO)
succimer  (ISO)
tacrolimus hydrate  (EXP,ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (EXP,ISO)
trichloroethene  (ISO)
trimethyltin  (ISO)
triptonide  (ISO)
troglitazone  (EXP)
tungsten  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vancomycin  (EXP)
vinclozolin  (EXP)
xylazine  (ISO)
zoledronic acid  (ISO)
zomepirac  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
acute-phase response  (IEP)
cellular response to amyloid-beta  (IEP)
cellular response to hydrogen peroxide  (IDA)
cellular response to increased oxygen levels  (IEP)
cellular response to interleukin-1  (IEP)
cellular response to interleukin-6  (IEP)
cellular response to lipopolysaccharide  (IEP)
cellular response to nerve growth factor stimulus  (IEP)
cellular response to nutrient levels  (IEP)
cellular response to oxygen-glucose deprivation  (IEP)
cellular response to tumor necrosis factor  (IEP)
cellular response to X-ray  (IEP)
defense response to bacterium  (ISO,ISS)
extrinsic apoptotic signaling pathway in absence of ligand  (ISO)
innate immune response  (ISO,ISS)
long-term memory  (IMP)
negative regulation of hippocampal neuron apoptotic process  (IMP)
positive regulation of apoptotic process  (IGI)
positive regulation of cell projection organization  (IDA)
positive regulation of cold-induced thermogenesis  (ISO,ISS)
positive regulation of endothelial cell migration  (IDA)
positive regulation of endothelial tube morphogenesis  (IDA)
positive regulation of gene expression  (IDA)
positive regulation of iron ion import across plasma membrane  (IDA)
positive regulation of neuron apoptotic process  (IMP)
positive regulation of neuron death  (IDA)
positive regulation of reactive oxygen species biosynthetic process  (IDA)
positive regulation of reactive oxygen species metabolic process  (IMP)
response to bacterium  (IEP,ISO)
response to blue light  (IEP)
response to fructose  (IEP)
response to herbicide  (IDA)
response to iron(II) ion  (IEP)
response to mycotoxin  (IEP)
response to nutrient levels  (IEP)
response to oxidative stress  (IEP)
response to toxic substance  (IEP)
response to virus  (ISO)
response to xenobiotic stimulus  (IEP,IMP)
sequestering of iron ion  (ISO,ISS)
short-term memory  (IMP)
siderophore transport  (ISO,ISS)

Cellular Component

Molecular Function

References

References - curated
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82. Xing C, etal., Stroke. 2014 Jul;45(7):2085-92. doi: 10.1161/STROKEAHA.114.005733. Epub 2014 Jun 10.
83. Xu MJ, etal., Hepatology. 2015 Feb;61(2):692-702. doi: 10.1002/hep.27447.
84. Yndestad A, etal., Eur Heart J. 2009 May;30(10):1229-36. Epub 2009 Mar 26.
85. Zhang J, etal., Mol Endocrinol. 2008 Jun;22(6):1416-26. Epub 2008 Feb 21.
86. Zheng LT, etal., J Neurochem. 2009 Dec;111(5):1238-51. Epub 2009 Oct 5.
Additional References at PubMed
PMID:2542864   PMID:12477932   PMID:16377569   PMID:16502470   PMID:16546827   PMID:17490638   PMID:19056867   PMID:20550936   PMID:21457438   PMID:21551085   PMID:22117066   PMID:22278021  
PMID:22349381   PMID:22664934   PMID:22833177   PMID:22889806   PMID:23012479   PMID:23158800   PMID:23360846   PMID:23376485   PMID:23481292   PMID:23533145   PMID:23940770   PMID:24006456  
PMID:24374540   PMID:24816434   PMID:25062286   PMID:25087119   PMID:25148248   PMID:25645918   PMID:25782996   PMID:26463963   PMID:27026710   PMID:27068509   PMID:27087673   PMID:27233602  
PMID:27756197   PMID:27780864   PMID:27865916   PMID:29367586   PMID:29378951   PMID:29402223   PMID:29704511   PMID:29845768   PMID:29980183   PMID:30087458   PMID:30367561   PMID:30404645  
PMID:30871254   PMID:31269059   PMID:31327865   PMID:31480394   PMID:32630021   PMID:32845875   PMID:33319934   PMID:33510115  


Genomics

Comparative Map Data
Lcn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2315,680,688 - 15,684,033 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl315,680,687 - 15,684,095 (-)Ensembl
Rnor_6.0311,414,189 - 11,417,534 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl311,414,186 - 11,417,546 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0316,763,059 - 16,766,404 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4311,511,402 - 11,514,747 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1311,407,773 - 11,411,119 (-)NCBI
Celera310,423,569 - 10,426,914 (-)NCBICelera
Cytogenetic Map3p12NCBI
LCN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9128,149,071 - 128,153,453 (+)EnsemblGRCh38hg38GRCh38
GRCh389128,149,453 - 128,153,453 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh379130,911,732 - 130,915,732 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369129,951,553 - 129,955,555 (+)NCBINCBI36hg18NCBI36
Build 349127,991,271 - 127,995,288NCBI
Celera9101,562,624 - 101,566,626 (+)NCBI
Cytogenetic Map9q34.11NCBI
HuRef9100,525,402 - 100,529,404 (+)NCBIHuRef
CHM1_19131,062,742 - 131,066,744 (+)NCBICHM1_1
Lcn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39232,274,649 - 32,277,751 (-)NCBIGRCm39mm39
GRCm39 Ensembl232,274,645 - 32,278,264 (-)Ensembl
GRCm38232,384,637 - 32,387,739 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl232,384,633 - 32,388,252 (-)EnsemblGRCm38mm10GRCm38
MGSCv37232,240,157 - 32,243,259 (-)NCBIGRCm37mm9NCBIm37
MGSCv36232,206,646 - 32,209,748 (-)NCBImm8
Celera232,090,046 - 32,093,150 (-)NCBICelera
Cytogenetic Map2BNCBI
cM Map222.09NCBI
LCN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19127,940,799 - 127,944,798 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9127,940,799 - 127,944,798 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0999,259,278 - 99,274,494 (+)NCBIMhudiblu_PPA_v0panPan3
LCN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1955,328,118 - 55,342,535 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl955,328,133 - 55,332,038 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha954,522,898 - 54,537,231 (-)NCBI
ROS_Cfam_1.0956,250,316 - 56,264,670 (-)NCBI
UMICH_Zoey_3.1955,010,191 - 55,024,522 (-)NCBI
UNSW_CanFamBas_1.0955,324,906 - 55,339,237 (-)NCBI
UU_Cfam_GSD_1.0955,416,588 - 55,430,934 (-)NCBI
Lcn2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947195,953,204 - 195,956,869 (+)NCBI
SpeTri2.0NW_00493648715,721,752 - 15,725,396 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LCN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11268,609,975 - 268,614,651 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21302,600,679 - 302,609,836 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LCN2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1129,976,278 - 9,981,087 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl129,976,614 - 9,980,870 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660796,251,600 - 6,256,754 (+)NCBIVero_WHO_p1.0

Position Markers
AA946503  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2315,681,562 - 15,681,921 (+)MAPPERmRatBN7.2
Rnor_6.0311,415,064 - 11,415,422NCBIRnor6.0
Rnor_5.0316,763,934 - 16,764,292UniSTSRnor5.0
RGSC_v3.4311,512,277 - 11,512,635UniSTSRGSC3.4
Celera310,424,444 - 10,424,802UniSTS
RH 3.4 Map360.1UniSTS
Cytogenetic Map3p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:139
Count of miRNA genes:98
Interacting mature miRNAs:103
Transcripts:ENSRNOT00000018776
Prediction methods:Microtar, 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 13 15 15 15 14 27 4
Low 2 25 26 18 10 18 2 3 51 15 12 7 2
Below cutoff 5 16 8 8 8 6 8 23 5 2 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018776   ⟹   ENSRNOP00000018776
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl315,680,689 - 15,684,095 (-)Ensembl
Rnor_6.0 Ensembl311,414,186 - 11,417,546 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000094191   ⟹   ENSRNOP00000078583
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl315,680,687 - 15,684,095 (-)Ensembl
RefSeq Acc Id: NM_130741   ⟹   NP_570097
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2315,680,688 - 15,684,033 (-)NCBI
Rnor_6.0311,414,189 - 11,417,534 (-)NCBI
Rnor_5.0316,763,059 - 16,766,404 (-)NCBI
RGSC_v3.4311,511,402 - 11,514,747 (-)RGD
Celera310,423,569 - 10,426,914 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_570097   ⟸   NM_130741
- Peptide Label: precursor
- UniProtKB: P30152 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018776   ⟸   ENSRNOT00000018776
RefSeq Acc Id: ENSRNOP00000078583   ⟸   ENSRNOT00000094191

Transcriptome

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

Promoters
RGD ID:13691985
Promoter ID:EPDNEW_R2510
Type:multiple initiation site
Name:Lcn2_1
Description:lipocalin 2
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_6.0311,417,542 - 11,417,602EPDNEW

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)
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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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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
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 (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
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)
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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
LEXF10A/StmMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (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
LEXF1C/Stm (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
LEXF2B/Stm (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
LEXF3/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
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
M520/NRrrcMcwi (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
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 (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)
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
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)
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)
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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)
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)
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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)
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 (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)
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)
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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)
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)
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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)
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 (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
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 (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)
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 (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
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:69408 AgrOrtholog
Ensembl Genes ENSRNOG00000013973 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000018776 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000018776 UniProtKB/Swiss-Prot
Gene3D-CATH 2.40.128.20 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7310185 IMAGE-MGC_LOAD
InterPro Calycin UniProtKB/Swiss-Prot
  LCN2/LCN12 UniProtKB/Swiss-Prot
  Lipocalin UniProtKB/Swiss-Prot
  Lipocln_cytosolic_FA-bd_dom UniProtKB/Swiss-Prot
KEGG Report rno:170496 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105339 IMAGE-MGC_LOAD
NCBI Gene 170496 ENTREZGENE
PANTHER PTHR11430 UniProtKB/Swiss-Prot
Pfam Lipocalin UniProtKB/Swiss-Prot
PharmGKB LCN2 RGD
PhenoGen Lcn2 PhenoGen
PRINTS NGELATINASE UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50814 UniProtKB/Swiss-Prot
TIGR TC207006
UniProt NGAL_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q5HZF1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Lcn2  lipocalin 2      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference