Nr1h2 (nuclear receptor subfamily 1, group H, member 2) - Rat Genome Database

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Gene: Nr1h2 (nuclear receptor subfamily 1, group H, member 2) Rattus norvegicus
Analyze
Symbol: Nr1h2
Name: nuclear receptor subfamily 1, group H, member 2
RGD ID: 61906
Description: Exhibits DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and retinoid X receptor binding activity. Contributes to sequence-specific DNA binding activity. Involved in regulation of gene expression; response to nutrient levels; and retinoic acid receptor signaling pathway. Predicted to localize to cytoplasm and nucleus. Biomarker of obesity. Human ortholog(s) of this gene implicated in obesity and type 2 diabetes mellitus. Orthologous to human NR1H2 (nuclear receptor subfamily 1 group H member 2); INTERACTS WITH (S)-nicotine; 2,4-dinitrotoluene; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: liver X receptor beta; LXR beta; LXRB; LXRbeta; nuclear orphan receptor LXR-beta; nuclear receptor subfamily 1 group H member 2; OR-1; orphan nuclear receptor OR-1; oxysterols receptor LXR-beta; ubiquitous receptor; ubiquitously-expressed nuclear receptor; UR
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2195,041,967 - 95,047,377 (-)NCBI
Rnor_6.0 Ensembl1100,554,544 - 100,559,942 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01100,554,577 - 100,559,896 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01101,619,964 - 101,625,283 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4195,027,197 - 95,032,516 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1195,105,321 - 95,110,627 (-)NCBI
Celera189,304,444 - 89,309,763 (-)NCBICelera
Cytogenetic Map1q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2-hydroxypropanoic acid  (ISO)
22-Hydroxycholesterol  (ISO)
8-(4-chlorophenylthio)-cAMP  (ISO)
8-Br-cAMP  (ISO)
9-cis-retinoic acid  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
alpha-linolenic acid  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (EXP,ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bezafibrate  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bosentan  (ISO)
bucladesine  (ISO)
cholesterol  (ISO)
choline  (ISO)
clofibrate  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (EXP,ISO)
etoposide  (ISO)
ezetimibe  (ISO)
fenofibrate  (ISO)
finasteride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fumonisin B1  (ISO)
gemfibrozil  (ISO)
guggulsterone  (ISO)
GW 3965  (ISO)
GW 501516  (ISO)
hexadecanoic acid  (ISO)
ketoconazole  (ISO)
L-methionine  (ISO)
lansoprazole  (ISO)
lipopolysaccharide  (EXP,ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
nefazodone  (EXP)
nicotine  (EXP,ISO)
octanoic acid  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
perfluorohexanesulfonic acid  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pioglitazone  (ISO)
piperonyl butoxide  (ISO)
pitavastatin  (ISO)
pitavastatin(1-)  (ISO)
rac-lactic acid  (ISO)
sodium arsenite  (ISO)
streptozocin  (EXP)
teniposide  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
triptonide  (ISO)
uranium atom  (EXP)
valproic acid  (ISO)
vecuronium bromide  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cell differentiation  (IBA)
cellular lipid metabolic process  (ISO)
cholesterol homeostasis  (ISO,ISS)
lipid homeostasis  (ISO)
negative regulation of cholesterol storage  (ISO)
negative regulation of cold-induced thermogenesis  (ISO,ISS)
negative regulation of gene expression  (IDA)
negative regulation of lipid transport  (ISO)
negative regulation of pinocytosis  (ISO)
negative regulation of proteolysis  (ISO)
negative regulation of response to endoplasmic reticulum stress  (ISO,ISS)
negative regulation of transcription by RNA polymerase II  (IBA,ISO)
negative regulation of transcription, DNA-templated  (ISO)
phosphatidylcholine acyl-chain remodeling  (ISO,ISS)
positive regulation of cellular protein metabolic process  (ISO)
positive regulation of cholesterol efflux  (ISO)
positive regulation of cholesterol transport  (ISO)
positive regulation of fatty acid biosynthetic process  (ISO)
positive regulation of gene expression  (IDA)
positive regulation of high-density lipoprotein particle assembly  (ISO)
positive regulation of lipid storage  (ISO)
positive regulation of lipoprotein lipase activity  (ISO)
positive regulation of pancreatic juice secretion  (ISO)
positive regulation of secretion of lysosomal enzymes  (ISO)
positive regulation of transcription by RNA polymerase II  (IBA,IDA,ISO)
positive regulation of transcription, DNA-templated  (ISO)
positive regulation of triglyceride biosynthetic process  (ISO)
regulation of transcription by RNA polymerase II  (ISO)
regulation of transcription, DNA-templated  (ISO)
response to nutrient levels  (IEP)
retinoic acid receptor signaling pathway  (IDA)

Cellular Component
cytoplasm  (ISO)
nucleus  (ISO)

References

References - curated
1. Asquith DL, etal., Ann Rheum Dis. 2011 Dec;70(12):2225-8. Epub 2011 Aug 22.
2. Bigini P, etal., J Neuropathol Exp Neurol. 2010 Jun;69(6):593-605.
3. Cui G, etal., J Clin Invest. 2011 Feb;121(2):658-70. doi: 10.1172/JCI42974. Epub 2011 Jan 25.
4. Dahlman I, etal., Pharmacogenet Genomics. 2006 Dec;16(12):881-9.
5. Feltkamp D, etal., J Biol Chem. 1999 Apr 9;274(15):10421-9.
6. Gabbi C, etal., Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14763-8. Epub 2010 Aug 2.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Ghoneim RH, etal., Br J Nutr. 2015 Feb 14;113(3):507-16. doi: 10.1017/S0007114514003717. Epub 2015 Jan 23.
9. Korach-André M, etal., Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):403-8. doi: 10.1073/pnas.1017884108. Epub 2010 Dec 20.
10. MGD data from the GO Consortium
11. NCBI rat LocusLink and RefSeq merged data July 26, 2002
12. RGD automated data pipeline
13. RGD automated import pipeline for gene-chemical interactions
14. Solaas K, etal., BMC Med Genet. 2010 Oct 12;11:144. doi: 10.1186/1471-2350-11-144.
15. Song C, etal., Proc Natl Acad Sci U S A 1994 Nov 8;91(23):10809-13.
16. Teboul M, etal., Proc Natl Acad Sci U S A 1995 Mar 14;92(6):2096-100.
17. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
18. Wang YY, etal., Surg Infect (Larchmt). 2011 Aug;12(4):283-9. Epub 2011 Aug 4.
19. Wiebel FF and Gustafsson JA, Mol Cell Biol. 1997 Jul;17(7):3977-86.
Additional References at PubMed
PMID:7760852   PMID:9013544   PMID:12393874   PMID:12477932   PMID:14739254   PMID:16141411   PMID:16354191   PMID:16524875   PMID:16825483   PMID:17186944   PMID:17657314   PMID:17693624  
PMID:17766241   PMID:18055760   PMID:18806227   PMID:19228891   PMID:19351492   PMID:19782030   PMID:20219900   PMID:20388921   PMID:22729460   PMID:22836489   PMID:22984598   PMID:23931754  
PMID:24398515   PMID:25661920   PMID:27352290   PMID:27485016   PMID:29654801   PMID:30471864   PMID:31161476  


Genomics

Comparative Map Data
Nr1h2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2195,041,967 - 95,047,377 (-)NCBI
Rnor_6.0 Ensembl1100,554,544 - 100,559,942 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01100,554,577 - 100,559,896 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01101,619,964 - 101,625,283 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4195,027,197 - 95,032,516 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1195,105,321 - 95,110,627 (-)NCBI
Celera189,304,444 - 89,309,763 (-)NCBICelera
Cytogenetic Map1q22NCBI
NR1H2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1950,329,653 - 50,383,388 (+)EnsemblGRCh38hg38GRCh38
GRCh381950,376,457 - 50,383,388 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371950,879,714 - 50,886,645 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361955,571,497 - 55,578,079 (+)NCBINCBI36hg18NCBI36
Build 341955,571,514 - 55,578,048NCBI
Celera1947,929,924 - 47,936,510 (+)NCBI
Cytogenetic Map19q13.33NCBI
HuRef1947,217,814 - 47,224,423 (+)NCBIHuRef
CHM1_11950,881,453 - 50,888,062 (+)NCBICHM1_1
Nr1h2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39744,199,040 - 44,204,928 (-)NCBIGRCm39mm39
GRCm39 Ensembl744,199,040 - 44,203,375 (-)Ensembl
GRCm38744,549,616 - 44,553,968 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl744,549,616 - 44,553,951 (-)EnsemblGRCm38mm10GRCm38
MGSCv37751,805,002 - 51,809,293 (-)NCBIGRCm37mm9NCBIm37
MGSCv36744,417,674 - 44,421,965 (-)NCBImm8
Celera739,999,761 - 40,004,052 (-)NCBICelera
Cytogenetic Map7B3NCBI
Nr1h2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955559730,670 - 737,505 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955559731,630 - 736,973 (-)NCBIChiLan1.0ChiLan1.0
NR1H2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11956,243,124 - 56,250,024 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1956,243,124 - 56,250,024 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01947,340,077 - 47,346,737 (+)NCBIMhudiblu_PPA_v0panPan3
NR1H2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11106,332,691 - 106,339,168 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1106,332,798 - 106,339,135 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1105,905,786 - 105,912,261 (-)NCBI
ROS_Cfam_1.01106,843,783 - 106,850,258 (-)NCBI
UMICH_Zoey_3.11106,515,887 - 106,522,355 (-)NCBI
UNSW_CanFamBas_1.01106,157,420 - 106,163,895 (-)NCBI
UU_Cfam_GSD_1.01106,998,070 - 107,004,546 (-)NCBI
Nr1h2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934922,347,505 - 22,353,794 (+)NCBI
SpeTri2.0NW_004936889223,137 - 229,968 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NR1H2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl655,237,953 - 55,245,456 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1655,238,536 - 55,245,457 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2651,087,383 - 51,094,318 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NR1H2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1643,438,428 - 43,445,190 (+)NCBI
ChlSab1.1 Ensembl643,437,950 - 43,446,063 (+)Ensembl
Nr1h2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248324,136,052 - 4,141,648 (-)NCBI

Position Markers
AJ132602  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01100,554,604 - 100,554,711NCBIRnor6.0
Rnor_5.01101,619,991 - 101,620,098UniSTSRnor5.0
RGSC_v3.4195,027,224 - 95,027,331UniSTSRGSC3.4
Celera189,304,471 - 89,304,578UniSTS
Cytogenetic Map1q22UniSTS
AA891955  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01100,554,656 - 100,554,809NCBIRnor6.0
Rnor_5.01101,620,043 - 101,620,196UniSTSRnor5.0
RGSC_v3.4195,027,276 - 95,027,429UniSTSRGSC3.4
Celera189,304,523 - 89,304,676UniSTS
RH 3.4 Map1886.8UniSTS
Cytogenetic Map1q22UniSTS
RH140629  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01100,555,403 - 100,556,815NCBIRnor6.0
Rnor_5.01101,620,790 - 101,622,202UniSTSRnor5.0
RGSC_v3.4195,028,023 - 95,029,435UniSTSRGSC3.4
Celera189,305,270 - 89,306,682UniSTS
RH 3.4 Map1906.5UniSTS
Cytogenetic Map1q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143579208126240667Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143579208126240667Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143579208126240667Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143579208126240667Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143579208126240667Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)157761301104391981Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)158209327103209327Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)164588516125875986Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)166113339122614963Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)179134941113593716Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)179689548124689548Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)183502376128502376Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)183656882126240667Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)185779320130779320Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)185917265130917265Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)186776571131776571Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)188634585106002500Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)190804143161321256Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)191093646136093646Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)194201400184846632Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)194201400197187904Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)194225372130917265Rat
1300153Bp171Blood pressure QTL 1713.37arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)194364073153076991Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)195304961156446783Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)199983293127203999Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)199983293188289386Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)199983293198656062Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)199983293216213510Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)199983293216325819Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100131562236763528Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100354344145354344Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:197
Count of miRNA genes:136
Interacting mature miRNAs:151
Transcripts:ENSRNOT00000026862
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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026862   ⟹   ENSRNOP00000026862
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1100,554,544 - 100,559,942 (-)Ensembl
RefSeq Acc Id: NM_031626   ⟹   NP_113814
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,041,967 - 95,047,377 (-)NCBI
Rnor_6.01100,554,577 - 100,559,896 (-)NCBI
Rnor_5.01101,619,964 - 101,625,283 (-)NCBI
RGSC_v3.4195,027,197 - 95,032,516 (-)RGD
Celera189,304,444 - 89,309,763 (-)RGD
Sequence:
RefSeq Acc Id: XM_039088756   ⟹   XP_038944684
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,041,983 - 95,047,361 (-)NCBI
RefSeq Acc Id: XM_039088759   ⟹   XP_038944687
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,041,983 - 95,047,361 (-)NCBI
RefSeq Acc Id: XM_039088762   ⟹   XP_038944690
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,041,983 - 95,047,359 (-)NCBI
RefSeq Acc Id: XM_039088764   ⟹   XP_038944692
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,041,983 - 95,047,358 (-)NCBI
RefSeq Acc Id: XM_039088765   ⟹   XP_038944693
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,041,983 - 95,045,990 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_113814   ⟸   NM_031626
- Sequence:
RefSeq Acc Id: ENSRNOP00000026862   ⟸   ENSRNOT00000026862
RefSeq Acc Id: XP_038944684   ⟸   XM_039088756
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944687   ⟸   XM_039088759
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944690   ⟸   XM_039088762
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944692   ⟸   XM_039088764
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944693   ⟸   XM_039088765
- Peptide Label: isoform X3
Protein Domains
NR LBD   Nuclear receptor

Transcriptome

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

Promoters
RGD ID:13690001
Promoter ID:EPDNEW_R526
Type:initiation region
Name:Nr1h2_1
Description:nuclear receptor subfamily 1, group H, member 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_6.01100,559,912 - 100,559,972EPDNEW

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:61906 AgrOrtholog
Ensembl Genes ENSRNOG00000019812 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000026862 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000026862 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.565.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9089489 IMAGE-MGC_LOAD
InterPro Liver_X_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NHR-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuclear_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:58851 UniProtKB/Swiss-Prot
MGC_CLONE MGC:187363 IMAGE-MGC_LOAD
NCBI Gene 58851 ENTREZGENE
Pfam Hormone_recep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nr1h2 PhenoGen
PRINTS LIVERXRECPTR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  STRDHORMONER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  STROIDFINGER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NR_LBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOLI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48508 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC204017
UniProt A9UMV6_RAT UniProtKB/TrEMBL
  NR1H2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q62694 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Nr1h2  nuclear receptor subfamily 1, group H, member 2      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function OR-1/RXR complex to bind to a DNA direct repeat (DR4) 729016
gene_physical_interaction interacts with the 9-cis-retinoic acid receptor 729016