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: Exhibits identical protein binding activity and protease binding activity. Involved in several processes, including cellular response to cytokine stimulus; cellular response to lipopolysaccharide; and response to herbicide. Localizes to cytosol and extracellular space. Biomarker of acute kidney failure; colon cancer; myocarditis; and obesity. 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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


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)
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)
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  (ISO)
aflatoxin B2  (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)
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)
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)
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)
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)
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)
silicon dioxide  (EXP,ISO)
sirolimus  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sodium dodecyl sulfate  (ISO)
Soman  (EXP)
streptozocin  (EXP)
succimer  (ISO)
tacrolimus hydrate  (EXP,ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (EXP,ISO)
trichloroethene  (ISO)
trimethyltin  (ISO)
troglitazone  (EXP)
tungsten  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vancomycin  (EXP)
vinclozolin  (EXP)
zoledronic acid  (ISO)
zomepirac  (ISO)

References

References - curated
1. Abassi Z, etal., J Urol. 2013 Apr;189(4):1559-66. doi: 10.1016/j.juro.2012.10.029. Epub 2012 Oct 22.
2. Alter ML, etal., Clin Lab. 2012;58(7-8):659-71.
3. Aoyama M, etal., Biochem Biophys Res Commun. 2012 Mar 9;419(2):244-9. doi: 10.1016/j.bbrc.2012.02.001. Epub 2012 Feb 8.
4. Bhavsar NA, etal., Am J Kidney Dis. 2012 Aug;60(2):233-40. doi: 10.1053/j.ajkd.2012.02.336. Epub 2012 Apr 28.
5. Bousserouel S, etal., Oncol Rep. 2010 Feb;23(2):511-7.
6. Bu DX, etal., Am J Pathol. 2006 Dec;169(6):2245-53.
7. Chan YL, etal., Nucleic Acids Res 1988 Dec 9;16(23):11368.
8. Ding L, etal., Circ J. 2010 Jan 7.
9. Eirin A, etal., Nephrol Dial Transplant. 2012 Nov;27(11):4153-61. doi: 10.1093/ndt/gfs370. Epub 2012 Aug 23.
10. Fraser DD, etal., Crit Care Explor. 2020 Jun 22;2(6):e0144. doi: 10.1097/CCE.0000000000000144. eCollection 2020 Jun.
11. Fu WJ, etal., Diabetes Res Clin Pract. 2012 Jan;95(1):105-9. doi: 10.1016/j.diabres.2011.09.031. Epub 2011 Oct 20.
12. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. Gerhardinger C, etal., Invest Ophthalmol Vis Sci. 2005 Jan;46(1):349-57.
14. GOA data from the GO Consortium
15. Guo H, etal., Diabetes. 2010 Jun;59(6):1376-85. doi: 10.2337/db09-1735. Epub 2010 Mar 23.
16. Ichino M, etal., J Urol. 2009 May;181(5):2326-31. Epub 2009 Mar 19.
17. Kamezaki K, etal., Eur J Haematol 2003 Dec;71(6):412-7.
18. Khalyfa A, etal., Mol Vis. 2007 Feb 28;13:293-308.
19. Lee S, etal., J Neurosci. 2009 Jan 7;29(1):234-49.
20. Lieberthal JG, etal., J Rheumatol. 2013 May;40(5):674-683. Epub 2013 Apr 1.
21. MGD data from the GO Consortium
22. NCBI rat LocusLink and RefSeq merged data July 26, 2002
23. Oh SW, etal., BMC Nephrol. 2013 May 17;14(1):105.
24. Peters HP, etal., Nephrol Dial Transplant. 2011 Nov;26(11):3581-8. doi: 10.1093/ndt/gfr135. Epub 2011 Apr 5.
25. Quiros Y, etal., Toxicol Sci. 2013 Apr;132(2):493-501. doi: 10.1093/toxsci/kft007. Epub 2013 Jan 18.
26. Rached E, etal., Toxicol Sci. 2008 Jun;103(2):371-81. Epub 2008 Feb 27.
27. RGD automated data pipeline
28. RGD automated import pipeline for gene-chemical interactions
29. Rouse RL, etal., Toxicol Pathol. 2013;41(4):662-80. doi: 10.1177/0192623312464122. Epub 2012 Oct 19.
30. Sohotnik R, etal., Am J Physiol Renal Physiol. 2013 Apr 15;304(8):F1099-104. doi: 10.1152/ajprenal.00649.2012. Epub 2013 Jan 30.
31. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
32. Tomczak J, etal., Pediatr Nephrol. 2013 May 15.
33. Torrens C, etal., Hypertension. 2009 Apr;53(4):661-7. Epub 2009 Feb 16.
34. Wang X, etal., Genomics. 2007 Aug;90(2):201-12. Epub 2007 Jun 5.
35. Wasilewska A, etal., Pediatr Nephrol. 2011 Apr;26(4):579-86. doi: 10.1007/s00467-011-1773-5. Epub 2011 Jan 31.
36. Yndestad A, etal., Eur Heart J. 2009 May;30(10):1229-36. Epub 2009 Mar 26.
37. Zhang J, etal., Mol Endocrinol. 2008 Jun;22(6):1416-26. Epub 2008 Feb 21.
38. 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:16446425   PMID:16502470   PMID:16546827   PMID:17490638   PMID:19056867   PMID:20550936   PMID:21457438   PMID:21551085   PMID:22117066  
PMID:22249220   PMID:22278021   PMID:22349381   PMID:22664934   PMID:22833177   PMID:22889806   PMID:23012479   PMID:23158800   PMID:23360846   PMID:23376485   PMID:23431168   PMID:23481292  
PMID:23533145   PMID:23940770   PMID:24006456   PMID:24374540   PMID:24587658   PMID:24816434   PMID:24916903   PMID:25062286   PMID:25087119   PMID:25148248   PMID:25645918   PMID:25782996  
PMID:26013918   PMID:26463963   PMID:27026710   PMID:27068509   PMID:27087673   PMID:27233602   PMID:27592368   PMID:27756197   PMID:27780864   PMID:27865916   PMID:29122651   PMID:29367586  
PMID:29378951   PMID:29402223   PMID:29704511   PMID:29845768   PMID:29980183   PMID:30087458   PMID:30367561   PMID:30404645   PMID:30574656   PMID:30871254   PMID:31269059   PMID:31327865  
PMID:31480394   PMID:31539545  


Genomics

Comparative Map Data
Lcn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - 130,915,734 (+)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_19131,062,719 - 131,066,744 (+)NCBICHM1_1
Lcn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39232,274,649 - 32,277,751 (-)NCBIGRCm39mm39
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
CanFam3.1 Ensembl955,328,133 - 55,332,038 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1955,328,118 - 55,342,535 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Lcn2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1129,976,278 - 9,981,087 (-)NCBI
ChlSab1.1 Ensembl129,976,614 - 9,980,870 (-)Ensembl

Position Markers
AA946503  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map3p11UniSTS
RH 3.4 Map360.1UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3125786001Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3128136884Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3128500807Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3132972944Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3137891710Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3139773425Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3195176874Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3263142133477544Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3263142148562146Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3328592928136884Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3328592928136884Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)3565463925105730Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)3600074851687917Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)3600074851687917Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)3600086634394121Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)3600086634394121Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)3600086634394121Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31009408193415837Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31011931879772001Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat

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
Rnor_6.0 Ensembl311,414,186 - 11,417,546 (-)Ensembl
RefSeq Acc Id: NM_130741   ⟹   NP_570097
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69408 AgrOrtholog
Ensembl Genes ENSRNOG00000013973 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000018776 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000018776 ENTREZGENE, 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
UniGene Rn.11303 ENTREZGENE
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