Rxra (retinoid X receptor alpha) - Rat Genome Database

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Gene: Rxra (retinoid X receptor alpha) Rattus norvegicus
Analyze
Symbol: Rxra
Name: retinoid X receptor alpha
RGD ID: 3610
Description: Enables nuclear retinoic acid receptor binding activity; nuclear thyroid hormone receptor binding activity; and protein domain specific binding activity. Contributes to double-stranded DNA binding activity. Involved in several processes, including cellular response to insulin stimulus; response to vitamin A; and response to vitamin D. Located in axon. Biomarker of alcoholic cardiomyopathy and prostate carcinoma in situ. Human ortholog(s) of this gene implicated in pancreatic cancer. Orthologous to human RXRA (retinoid X receptor alpha); PARTICIPATES IN retinoic acid signaling pathway; bile acid transport pathway; eicosanoid signaling pathway via peroxisome proliferator-activated receptor gamma; INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: nuclear receptor subfamily 2 group B member 1; retinoic acid receptor RXR-alpha
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8331,387,892 - 31,474,415 (+)NCBIGRCr8
mRatBN7.2310,989,832 - 11,076,366 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl310,989,832 - 11,073,712 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx314,057,333 - 14,141,119 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0322,642,768 - 22,726,554 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0320,896,722 - 20,980,500 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.036,272,560 - 6,295,354 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl36,211,789 - 6,295,908 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0311,631,209 - 11,653,959 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.436,605,782 - 6,689,224 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.136,606,054 - 6,690,078 (+)NCBI
Celera35,843,675 - 5,866,536 (+)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-anisomycin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(1->4)-beta-D-glucan  (ISO)
(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoic acid  (ISO)
(R,R,R)-alpha-tocopherol  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (ISO)
13-cis-retinal  (ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
17beta-estradiol  (EXP)
2,2-(2-Chlorophenyl-4'-chlorophenyl)-1,1-dichloroethene  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-[(2,4-dichlorophenyl)methyl]-4-(2,4,4-trimethylpentan-2-yl)phenol  (EXP)
2-bromohexadecanoic acid  (ISO)
2-hydroxyphytanic acid  (ISO)
2-hydroxypropanoic acid  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,3',5,5'-tetraiodothyroacetic acid  (ISO)
3-[3-(tert-butylsulfanyl)-1-(4-chlorobenzyl)-5-(propan-2-yl)-1H-indol-2-yl]-2,2-dimethylpropanoic acid  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-nonylphenol  (ISO)
5-(2-chloroethyl)-4-methylthiazole  (ISO)
6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime  (ISO)
6-propyl-2-thiouracil  (EXP)
9-cis-retinal  (ISO)
9-cis-retinoic acid  (EXP,ISO)
acetamide  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
alfacalcidol  (ISO)
all-cis-docosa-7,10,13,16-tetraenoic acid  (ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-acitretin  (ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (EXP,ISO)
allyl isothiocyanate  (ISO)
alpha-linolenic acid  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
aphidicolin  (ISO)
arachidonic acid  (ISO)
aristolochic acid A  (ISO)
arotinoid acid  (ISO)
arsenous acid  (ISO)
beauvericin  (ISO)
benzene  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-carotene  (ISO)
beta-lapachone  (ISO)
bexarotene  (ISO)
bezafibrate  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
Butylbenzyl phthalate  (ISO)
cadmium dichloride  (ISO)
caesium atom  (EXP)
caffeine  (ISO)
calciol  (ISO)
calcitriol  (ISO)
Calphostin C  (ISO)
capsaicin  (ISO)
carnosic acid  (ISO)
cerivastatin  (ISO)
chloroacetaldehyde  (ISO)
chlorogenic acid  (ISO)
cholesterol  (ISO)
choline  (EXP,ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
Clofop  (ISO)
conjugated linoleic acid  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
cyclosporin A  (ISO)
DDE  (EXP,ISO)
decabromodiphenyl ether  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
Di-n-hexyl phthalate  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
dibutylstannane  (ISO)
dicrotophos  (ISO)
dieldrin  (EXP,ISO)
diethyl phthalate  (ISO)
diethylstilbestrol  (EXP)
diheptyl phthalate  (ISO)
Diisodecyl phthalate  (ISO)
diisononyl phthalate  (ISO)
Dimethyl phthalate  (ISO)
dimethyl sulfoxide  (ISO)
dimethylarsinous acid  (ISO)
diosgenin  (ISO)
dioxygen  (ISO)
dipentyl phthalate  (ISO)
dipropyl phthalate  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
enniatin  (ISO)
epoxiconazole  (EXP)
equilin  (ISO)
ethanol  (EXP,ISO)
etodolac  (ISO)
etoposide  (ISO)
farnesol  (ISO)
fenofibrate  (EXP,ISO)
fentin chloride  (EXP,ISO)
fentin hydroxide  (ISO)
fenvalerate  (ISO)
fipronil  (ISO)
flurbiprofen  (ISO)
flutamide  (EXP)
fluvastatin  (ISO)
folic acid  (ISO)
fructose  (ISO)
gamma-hexachlorocyclohexane  (EXP)
genistein  (ISO)
gentamycin  (EXP)
geranylgeraniol  (ISO)
glutathione  (ISO)
glycidol  (EXP)
griseofulvin  (ISO)
GW 1929  (ISO)
hydrogen peroxide  (ISO)
ibuprofen  (ISO)
indometacin  (EXP,ISO)
inulin  (ISO)
isotretinoin  (EXP,ISO)
ketoconazole  (EXP)
L-methionine  (EXP,ISO)
leptomycin B  (ISO)
levofloxacin  (EXP)
linoleic acid  (ISO)
linuron  (EXP)
lipopolysaccharide  (ISO)
lithocholic acid  (EXP,ISO)
menadione  (ISO)
menaquinone  (ISO)
metformin  (EXP)
methapyrilene  (EXP)
methimazole  (EXP)
methoprene  (EXP,ISO)
methoxychlor  (EXP)
methyltestosterone  (ISO)
mevalonic acid  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N,N-dimethylformamide  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nitrofen  (EXP)
obeticholic acid  (ISO)
okadaic acid  (ISO)
oleic acid  (ISO)
orotic acid  (EXP)
Osajin  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP,ISO)
penconazole  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP,ISO)
phorbol 13-acetate 12-myristate  (ISO)
phthalic acid  (ISO)
pioglitazone  (ISO)
pirinixic acid  (EXP,ISO)
pitavastatin  (ISO)
pitavastatin(1-)  (ISO)
PK-11195  (ISO)
poly(propylene imine) macromolecule  (ISO)
pravastatin  (EXP)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
prochloraz  (EXP)
procymidone  (EXP)
progesterone  (ISO)
prostaglandin J2  (EXP)
rac-lactic acid  (ISO)
resveratrol  (ISO)
retinyl acetate  (ISO)
rifampicin  (EXP,ISO)
Ro 41-5253  (ISO)
Rosavin  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
selenium atom  (ISO)
senecionine  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sincalide  (EXP)
sodium arsenite  (ISO)
Soman  (EXP)
Sorbitan monooleate  (ISO)
sucrose  (EXP)
Sudan III  (ISO)
sulindac  (EXP)
tamibarotene  (ISO)
teniposide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
thyroxine  (ISO)
tiratricol  (ISO)
titanium dioxide  (ISO)
tomelukast  (ISO)
tributylstannane  (EXP,ISO)
trichloroethene  (ISO)
triphenyl phosphate  (ISO)
triphenylphosphane oxide  (ISO)
triphenylstannane  (ISO)
troglitazone  (ISO)
uranium atom  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin D  (ISO)
zinc acetate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
axon regeneration  (IEP)
camera-type eye development  (ISO)
cardiac muscle cell proliferation  (ISO)
cell differentiation  (IBA)
cellular response to insulin stimulus  (IEP)
embryo implantation  (ISO)
female pregnancy  (IEP)
gene expression  (ISO)
heart development  (ISO)
hormone-mediated signaling pathway  (ISO)
in utero embryonic development  (ISO)
liver development  (IEP)
maternal placenta development  (ISO)
midgut development  (IEP)
mRNA transcription by RNA polymerase II  (IEA,ISO)
negative regulation of cell population proliferation  (IMP)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
nervous system development  (IBA)
peroxisome proliferator activated receptor signaling pathway  (IEA,ISO)
placenta development  (IEP,ISO)
positive regulation of apoptotic process  (IMP)
positive regulation of DNA-templated transcription  (ISO)
positive regulation of thyroid hormone receptor signaling pathway  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IBA,IEA,ISO)
positive regulation of translational initiation by iron  (ISO)
positive regulation of vitamin D receptor signaling pathway  (IEA,ISO)
regulation of branching involved in prostate gland morphogenesis  (ISO)
regulation of DNA-templated transcription  (IDA,IEA,ISO)
regulation of myelination  (IDA)
regulation of transcription by RNA polymerase II  (ISO)
response to ethanol  (IEP)
response to glucocorticoid  (IEP,IMP)
response to nutrient  (IEP)
response to organic cyclic compound  (IEP)
response to retinoic acid  (IEA,IEP,ISO)
response to selenium ion  (IEP)
response to vitamin A  (IEP)
response to vitamin D  (IEP)
retinoic acid receptor signaling pathway  (IBA,IEA,ISO)
secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development  (ISO)
steroid hormone receptor signaling pathway  (IEA)
ventricular cardiac muscle cell differentiation  (ISO)
ventricular cardiac muscle tissue morphogenesis  (ISO)

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Expression of retinoid X receptor alpha is decreased in 3'-methyl-4-dimethylaminoazobenzene-induced hepatocellular carcinoma in rats. Ando N, etal., Oncol Rep. 2007 Oct;18(4):879-84.
2. Effect of vitamin A content in cafeteria diet on the expression of nuclear receptors in rat subcutaneous adipose tissue. Bairras C, etal., J Physiol Biochem. 2005 Jun;61(2):353-61.
3. Senescence-associated decline in hepatic peroxisomal enzyme activities corresponds with diminished levels of retinoid X receptor alpha, but not peroxisome proliferator-activated receptor alpha. Chao C, etal., Mech Ageing Dev. 2002 Sep;123(11):1469-76.
4. Retinoid X receptor alpha participation in dexamethasone-induced rat bile acid coenzyme A-amino acid N-acyltransferase expression in septic liver. Chen BC, etal., Shock. 2009 Aug;32(2):164-71.
5. Hydrodynamic-based in vivo transfection of retinoic X receptor-alpha gene can enhance vitamin A-induced attenuation of liver fibrosis in mice. Chen C, etal., Liver Int. 2004 Dec;24(6):679-86.
6. Role of retinoid-X receptor-alpha in the suppression of rat bile acid coenzyme A-amino acid N-acyltransferase in liver during sepsis. Chen YH, etal., Shock. 2007 Jul;28(1):65-70.
7. Retinoid X receptor alpha represses GATA-4-mediated transcription via a retinoid-dependent interaction with the cardiac-enriched repressor FOG-2. Clabby ML, etal., J Biol Chem 2003 Feb 21;278(8):5760-7.
8. Suppression of pancreatic carcinoma growth by activating peroxisome proliferator-activated receptor gamma involves angiogenesis inhibition. Dong YW, etal., World J Gastroenterol. 2009 Jan 28;15(4):441-8.
9. Role of MAP kinases in the 1,25-dihydroxyvitamin D3-induced transactivation of the rat cytochrome P450C24 (CYP24) promoter. Specific functions for ERK1/ERK2 and ERK5. Dwivedi PP, etal., J Biol Chem 2002 Aug 16;277(33):29643-53.
10. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Interaction of the peroxisome-proliferator-activated receptor and retinoid X receptor. Gearing KL, etal., Proc Natl Acad Sci U S A 1993 Feb 15;90(4):1440-4.
12. International Union of Pharmacology. LXIII. Retinoid X receptors. Germain P, etal., Pharmacol Rev. 2006 Dec;58(4):760-72.
13. Peroxisome proliferator-activated receptor-gamma and retinoid X receptor-alpha expression in pancreatic ductal adenocarcinoma: association with clinicopathological parameters, tumor proliferative capacity, and patients' survival. Giaginis C, etal., Med Sci Monit. 2009 May;15(5):BR148-56.
14. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
15. Hyperlipidic diets induce early alterations of the vitamin A signalling pathway in rat colonic mucosa. Groubet R, etal., Endocr Regul. 2003 Sep;37(3):137-44.
16. Efficacy of new retinoids in the prevention of mammary cancers and correlations with short-term biomarkers. Grubbs CJ, etal., Carcinogenesis. 2006 Jun;27(6):1232-9. Epub 2005 Dec 12.
17. Placental expression of peroxisome proliferator-activated receptors in rat pregnancy and the effect of increased glucocorticoid exposure. Hewitt DP, etal., Biol Reprod. 2006 Jan;74(1):23-8. Epub 2005 Aug 31.
18. [Peroxisome proliferator-activated receptor alpha and retinoid X receptor alpha expressions and intervention in alcoholic cardiomyopathy rats] Jing L, etal., Zhonghua Xin Xue Guan Bing Za Zhi. 2009 Apr;37(4):324-9.
19. Identification and characterization of a tissue-specific coactivator, GT198, that interacts with the DNA-binding domains of nuclear receptors. Ko L, etal., Mol Cell Biol 2002 Jan;22(1):357-69.
20. Retinoic acid regulates myelin formation in the peripheral nervous system. Latasa MJ, etal., Glia. 2010 Sep;58(12):1451-64.
21. Mechanistic principles in NR box-dependent interaction between nuclear hormone receptors and the coactivator TIF2. Leers J, etal., Mol Cell Biol 1998 Oct;18(10):6001-13.
22. Interleukin-1beta -mediated Suppression of RXR:RAR Transactivation of the Ntcp Promoter Is JNK-dependent. Li D, etal., J Biol Chem 2002 Aug 30;277(35):31416-22.
23. Modification of RXRalpha expression according to the duration of a cafeteria diet. Margareto J, etal., J Physiol Biochem 2001 Dec;57(4):347-8.
24. Vitamin A regulation of gene expression: molecular mechanism of a prototype gene. McGrane MM J Nutr Biochem. 2007 Aug;18(8):497-508. Epub 2007 Feb 22.
25. Functional role of RXRs and PPARgamma in mature adipocytes. Metzger D, etal., Prostaglandins Leukot Essent Fatty Acids. 2005 Jul;73(1):51-8.
26. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
27. Disturbance of retinol transportation causes nitrofen-induced hypoplastic lung. Nakazawa N, etal., J Pediatr Surg. 2007 Feb;42(2):345-9.
28. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
29. Postnatal changes in gene expression of retinal dehydrogenase and retinoid receptors in liver of rats. Ogura Y, etal., Life Sci. 2004 Feb 6;74(12):1519-28.
30. Developmental changes of the expression of the genes regulated by retinoic acid in the small intestine of rats. Ogura Y, etal., Life Sci. 2005 Oct 14;77(22):2804-13.
31. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
32. GOA pipeline RGD automated data pipeline
33. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
34. Cross-species global and subset gene expression profiling identifies genes involved in prostate cancer response to selenium. Schlicht M, etal., BMC Genomics. 2004 Aug 20;5(1):58.
35. Concomitant pancreatic activation of Kras(G12D) and Tgfa results in cystic papillary neoplasms reminiscent of human IPMN. Siveke JT, etal., Cancer Cell. 2007 Sep;12(3):266-79.
36. Ubiquitous receptor: a receptor that modulates gene activation by retinoic acid and thyroid hormone receptors. Song C, etal., Proc Natl Acad Sci U S A 1994 Nov 8;91(23):10809-13.
37. Gene transcription of the retinoid X receptor alpha (RXRalpha) is regulated by fatty acids and hormones in rat hepatic cells. Steineger HH, etal., J Lipid Res. 1998 Apr;39(4):744-54.
38. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
39. Competition between thyroid hormone receptor-associated protein (TRAP) 220 and transcriptional intermediary factor (TIF) 2 for binding to nuclear receptors. Implications for the recruitment of TRAP and p160 coactivator complexes. Treuter E, etal., J Biol Chem. 1999 Mar 5;274(10):6667-77.
40. Regulation of alpha 2(I) collagen expression in stellate cells by retinoic acid and retinoid X receptors through interactions with their cofactors. Wang L, etal., Arch Biochem Biophys. 2004 Aug 1;428(1):92-8.
41. Heterodimeric interaction between retinoid X receptor alpha and orphan nuclear receptor OR1 reveals dimerization-induced activation as a novel mechanism of nuclear receptor activation. Wiebel FF and Gustafsson JA, Mol Cell Biol. 1997 Jul;17(7):3977-86.
42. Regulation of retinoic acid receptors alpha, beta and retinoid X receptor alpha after sciatic nerve injury. Zhelyaznik N and Mey J, Neuroscience. 2006 Sep 15;141(4):1761-74. Epub 2006 Jun 19.
Additional References at PubMed
PMID:1312497   PMID:7744009   PMID:7760852   PMID:7823919   PMID:7831303   PMID:7990953   PMID:8954108   PMID:9356169   PMID:9376317   PMID:9428411   PMID:9550726   PMID:9892670  
PMID:10195690   PMID:10385625   PMID:11915042   PMID:12015306   PMID:12037571   PMID:12039952   PMID:12183441   PMID:12477932   PMID:12593720   PMID:14622989   PMID:15319426   PMID:15322135  
PMID:15340084   PMID:15601870   PMID:15681609   PMID:15766748   PMID:16428452   PMID:16584836   PMID:17107947   PMID:17195188   PMID:17426122   PMID:17538076   PMID:17641689   PMID:17952069  
PMID:18502116   PMID:18511497   PMID:19043829   PMID:19917671   PMID:20219900   PMID:20945395   PMID:21882190   PMID:22001906   PMID:22230368   PMID:23017197   PMID:23327965   PMID:23499423  
PMID:23723389   PMID:23775127   PMID:26875149   PMID:28267642   PMID:29445990   PMID:32125053   PMID:33628383  


Genomics

Comparative Map Data
Rxra
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8331,387,892 - 31,474,415 (+)NCBIGRCr8
mRatBN7.2310,989,832 - 11,076,366 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl310,989,832 - 11,073,712 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx314,057,333 - 14,141,119 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0322,642,768 - 22,726,554 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0320,896,722 - 20,980,500 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.036,272,560 - 6,295,354 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl36,211,789 - 6,295,908 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0311,631,209 - 11,653,959 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.436,605,782 - 6,689,224 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.136,606,054 - 6,690,078 (+)NCBI
Celera35,843,675 - 5,866,536 (+)NCBICelera
Cytogenetic Map3p12NCBI
RXRA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389134,326,455 - 134,440,585 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9134,317,098 - 134,440,585 (+)EnsemblGRCh38hg38GRCh38
GRCh379137,218,301 - 137,332,431 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369136,358,231 - 136,472,252 (+)NCBINCBI36Build 36hg18NCBI36
Build 349134,519,421 - 134,558,376NCBI
Celera9107,734,128 - 107,848,213 (+)NCBICelera
Cytogenetic Map9q34.2NCBI
HuRef9106,757,493 - 106,796,351 (+)NCBIHuRef
CHM1_19137,442,044 - 137,480,968 (+)NCBICHM1_1
T2T-CHM13v2.09146,541,633 - 146,657,063 (+)NCBIT2T-CHM13v2.0
Rxra
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39227,566,457 - 27,653,331 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl227,566,452 - 27,652,969 (+)EnsemblGRCm39 Ensembl
GRCm38227,676,445 - 27,763,319 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl227,676,440 - 27,762,957 (+)EnsemblGRCm38mm10GRCm38
MGSCv37227,532,721 - 27,618,839 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36227,499,210 - 27,585,328 (+)NCBIMGSCv36mm8
Celera227,439,778 - 27,465,824 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map219.38NCBI
Rxra
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555133,335,897 - 3,386,994 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555133,313,544 - 3,386,544 (+)NCBIChiLan1.0ChiLan1.0
RXRA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2114,937,570 - 5,052,654 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan194,939,903 - 5,054,985 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09105,424,046 - 105,539,241 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19134,082,865 - 134,144,704 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9134,082,865 - 134,144,704 (+)Ensemblpanpan1.1panPan2
RXRA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1950,525,195 - 50,575,720 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl950,484,567 - 50,573,119 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha949,766,609 - 49,860,130 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0951,360,100 - 51,453,773 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl951,359,634 - 51,453,363 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1950,120,766 - 50,214,385 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0950,464,001 - 50,557,538 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0950,541,613 - 50,635,257 (+)NCBIUU_Cfam_GSD_1.0
Rxra
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947200,612,017 - 200,639,947 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366692,738,448 - 2,763,070 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366692,735,111 - 2,763,060 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RXRA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1273,705,505 - 273,797,620 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11273,698,842 - 273,797,622 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
RXRA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1123,704,129 - 3,814,707 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl123,699,923 - 3,814,678 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660581,284,770 - 1,401,711 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rxra
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247602,380,708 - 2,456,928 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247602,379,809 - 2,455,749 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rxra
174 total Variants
miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir27arno-miR-27a-3pMirtarbaseexternal_infoLuciferase reporter assay//qRT-PCR//Western blotFunctional MTI19185571
Mir27brno-miR-27b-3pMirtarbaseexternal_infoLuciferase reporter assay//qRT-PCR//Western blotFunctional MTI19185571

Predicted Target Of
Summary Value
Count of predictions:62
Count of miRNA genes:48
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000012892
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
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
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)31043430624512004Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat

Markers in Region
D3Arb4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2311,051,600 - 11,051,742 (+)MAPPERmRatBN7.2
Rnor_6.036,273,816 - 6,273,957NCBIRnor6.0
Rnor_5.0311,632,465 - 11,632,606UniSTSRnor5.0
RGSC_v3.436,667,553 - 6,667,695RGDRGSC3.4
RGSC_v3.436,667,554 - 6,667,695UniSTSRGSC3.4
RGSC_v3.136,667,853 - 6,667,995RGD
Celera35,844,931 - 5,845,072UniSTS
Cytogenetic Map3p12UniSTS
AU047320  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2311,027,373 - 11,027,613 (+)MAPPERmRatBN7.2
Rnor_6.036,249,348 - 6,249,587NCBIRnor6.0
Rnor_5.0311,608,169 - 11,608,408UniSTSRnor5.0
RGSC_v3.436,643,237 - 6,643,476UniSTSRGSC3.4
Celera35,820,736 - 5,820,975UniSTS
Cytogenetic Map3p12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000012892   ⟹   ENSRNOP00000012892
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl310,989,832 - 11,073,712 (+)Ensembl
Rnor_6.0 Ensembl36,211,789 - 6,295,908 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000099288   ⟹   ENSRNOP00000087257
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl311,037,450 - 11,073,712 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000100573   ⟹   ENSRNOP00000091257
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl310,990,065 - 11,073,712 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000107435   ⟹   ENSRNOP00000087600
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl311,049,509 - 11,073,712 (+)Ensembl
RefSeq Acc Id: NM_012805   ⟹   NP_036937
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8331,387,892 - 31,471,765 (+)NCBI
mRatBN7.2310,989,832 - 11,073,712 (+)NCBI
Rnor_6.036,272,560 - 6,295,354 (+)NCBI
Rnor_5.0311,631,209 - 11,653,959 (+)NCBI
RGSC_v3.436,605,782 - 6,689,224 (+)RGD
Celera35,843,675 - 5,866,536 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039104342   ⟹   XP_038960270
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8331,388,108 - 31,474,415 (+)NCBI
mRatBN7.2310,990,047 - 11,076,366 (+)NCBI
RefSeq Acc Id: XM_063283140   ⟹   XP_063139210
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8331,431,825 - 31,474,415 (+)NCBI
RefSeq Acc Id: NP_036937   ⟸   NM_012805
- UniProtKB: Q0VJ96 (UniProtKB/TrEMBL),   F6T454 (UniProtKB/TrEMBL),   A0A8I6GFA6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000012892   ⟸   ENSRNOT00000012892
RefSeq Acc Id: XP_038960270   ⟸   XM_039104342
- Peptide Label: isoform X2
- UniProtKB: A0A8I6AQ23 (UniProtKB/TrEMBL),   A0A8I6GFA6 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000087600   ⟸   ENSRNOT00000107435
Ensembl Acc Id: ENSRNOP00000087257   ⟸   ENSRNOT00000099288
Ensembl Acc Id: ENSRNOP00000091257   ⟸   ENSRNOT00000100573
RefSeq Acc Id: XP_063139210   ⟸   XM_063283140
- Peptide Label: isoform X1
Protein Domains
NR LBD   Nuclear receptor

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q05343-F1-model_v2 AlphaFold Q05343 1-467 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3610 AgrOrtholog
BioCyc Gene G2FUF-50288 BioCyc
Ensembl Genes ENSRNOG00000009446 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012892.5 UniProtKB/TrEMBL
  ENSRNOT00000099288.1 UniProtKB/TrEMBL
  ENSRNOT00000100573.1 UniProtKB/TrEMBL
  ENSRNOT00000107435.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro NHR-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuc_recep-AF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuclear_hormone_rcpt_NR2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuclear_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Retinoid-X_rcpt/HNF4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25271 UniProtKB/TrEMBL
NCBI Gene 25271 ENTREZGENE
PANTHER NUCLEAR HORMONE RECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RETINOIC ACID RECEPTOR RXR-ALPHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Hormone_recep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuc_recep-AF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rxra PhenoGen
PRINTS RETINOIDXR 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
RatGTEx ENSRNOG00000009446 RatGTEx
SMART HOLI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF48508 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC217090
UniProt A0A8I6A846_RAT UniProtKB/TrEMBL
  A0A8I6AQ23 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GFA6 ENTREZGENE, UniProtKB/TrEMBL
  A6JTL8_RAT UniProtKB/TrEMBL
  F6T454 ENTREZGENE, UniProtKB/TrEMBL
  Q05343 ENTREZGENE
  Q0VJ96 ENTREZGENE, UniProtKB/TrEMBL
  RXRA_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Rxra  Retinoid X receptor alpha      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process facilitates binding of the peroxisome-proliferator-activated receptor to the acyl-CoA oxidase gene PPAR response element 729726