Rxrg (retinoid X receptor gamma) - Rat Genome Database

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Gene: Rxrg (retinoid X receptor gamma) Rattus norvegicus
Analyze
Symbol: Rxrg
Name: retinoid X receptor gamma
RGD ID: 620046
Description: Predicted to enable identical protein binding activity; nuclear receptor activity; and retinoic acid-responsive element binding activity. Involved in several processes, including nervous system development; regulation of myelination; and response to retinoic acid. Located in nucleus. Human ortholog(s) of this gene implicated in lung non-small cell carcinoma. Orthologous to human RXRG (retinoid X receptor gamma); PARTICIPATES IN retinoic acid signaling pathway; eicosanoid signaling pathway via peroxisome proliferator-activated receptor gamma; non-small cell lung carcinoma pathway; INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC102553986; MGC109416; nuclear receptor subfamily 2 group B member 3; retinoic acid receptor RXR-gamma; retinoic acid receptor RXR-gamma-like; retinoic X receptor gamma-1; RXR gamma-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21379,743,430 - 79,785,173 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1379,743,563 - 79,785,167 (+)Ensembl
Rnor_6.01385,818,473 - 85,868,555 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1385,818,427 - 85,868,552 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01390,460,380 - 90,511,048 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41383,256,823 - 83,298,724 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11383,287,103 - 83,307,114 (+)NCBI
Celera1379,448,171 - 79,489,515 (+)NCBICelera
Cytogenetic Map13q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2-hydroxyphytanic acid  (ISO)
3,3',5-triiodo-L-thyronine  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-phenoxybenzoic acid  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
9-cis-retinoic acid  (ISO)
acrylamide  (EXP)
aldrin  (ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (EXP,ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
benzo[a]pyrene  (EXP,ISO)
beta-naphthoflavone  (EXP)
bexarotene  (ISO)
bezafibrate  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Butylbenzyl phthalate  (ISO)
cadmium sulfate  (ISO)
carbon nanotube  (ISO)
cefaloridine  (EXP)
CGP 52608  (ISO)
chlorpromazine  (ISO)
clofibrate  (EXP)
clozapine  (EXP)
Cuprizon  (EXP)
D-gluconic acid  (EXP)
deoxycholic acid  (EXP)
dexamethasone  (ISO)
Di-n-hexyl phthalate  (ISO)
dibutyl phthalate  (ISO)
diethyl phthalate  (ISO)
diheptyl phthalate  (ISO)
diisobutyl phthalate  (EXP)
Dimethyl phthalate  (ISO)
dimethyl sulfoxide  (ISO)
dioxygen  (EXP)
dipentyl phthalate  (ISO)
dipropyl phthalate  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fentin hydroxide  (ISO)
fenvalerate  (ISO)
fulvestrant  (ISO)
gamma-hexachlorocyclohexane  (EXP)
genistein  (EXP)
glafenine  (EXP)
griseofulvin  (ISO)
haloperidol  (EXP,ISO)
hydralazine  (ISO)
ketamine  (EXP)
lead diacetate  (EXP)
lipopolysaccharide  (ISO)
mercury dichloride  (EXP)
methapyrilene  (EXP)
methotrexate  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
Muraglitazar  (EXP)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (EXP)
nimesulide  (EXP)
paracetamol  (ISO)
paraquat  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
phthalic acid  (ISO)
pirinixic acid  (EXP,ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
quercetin  (ISO)
rotenone  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
Tesaglitazar  (EXP)
testosterone  (EXP)
tetrachloromethane  (EXP)
tetracycline  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
tributylstannane  (EXP,ISO)
trichloroethene  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
valproic acid  (ISO)
vinyl carbamate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Expression of peroxisome proliferator-activated receptors (PPARs) and retinoic acid receptors (RXRs) in rat cortical neurons. Cimini A, etal., Neuroscience. 2005;130(2):325-37.
2. WNT10A/ß-catenin pathway in tumorigenesis of papillary thyroid carcinoma. Dong T, etal., Oncol Rep. 2017 Aug;38(2):1287-1294. doi: 10.3892/or.2017.5777. Epub 2017 Jul 3.
3. 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.
4. Regulation of retinoid X receptor-gamma gene transcript levels in rat heart cells. Georgiades P and Brickell PM, Cell Biol Int. 1998;22(6):457-63.
5. Differential expression of the rat retinoid X receptor gamma gene during skeletal muscle differentiation suggests a role in myogenesis. Georgiades P and Brickell PM, Dev Dyn 1997 Nov;210(3):227-35.
6. Retinoid X receptor-gamma gene expression is developmentally regulated in the embryonic rodent peripheral nervous system. Georgiades P, etal., Anat Embryol (Berl). 1998 Jun;197(6):477-84.
7. International Union of Pharmacology. LXIII. Retinoid X receptors. Germain P, etal., Pharmacol Rev. 2006 Dec;58(4):760-72.
8. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
9. Antiestrogenic activity of vitamin A in in vivo uterotrophic assay. Koda T, etal., Life Sci. 2007 Feb 13;80(10):945-9. Epub 2006 Nov 22.
10. Retinoic acid regulates myelin formation in the peripheral nervous system. Latasa MJ, etal., Glia. 2010 Sep;58(12):1451-64.
11. Epigenetic inactivation of retinoid X receptor genes in non-small cell lung cancer and the relationship with clinicopathologic features. Lee SM, etal., Cancer Genet Cytogenet. 2010 Feb;197(1):39-45. doi: 10.1016/j.cancergencyto.2009.10.008.
12. 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.
13. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
14. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
16. GOA pipeline RGD automated data pipeline
17. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
19. Time-response effects of testicular gene expression profiles in Sprague-Dawley male rats treated with di(n-butyl) phthalate. Ryu JY, etal., J Toxicol Environ Health A. 2008;71(23):1542-9.
Additional References at PubMed
PMID:1312497   PMID:7823919   PMID:7831303   PMID:8391126   PMID:12477932   PMID:15878969   PMID:17195188   PMID:17963722   PMID:23017197   PMID:30015907  


Genomics

Comparative Map Data
Rxrg
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21379,743,430 - 79,785,173 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1379,743,563 - 79,785,167 (+)Ensembl
Rnor_6.01385,818,473 - 85,868,555 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1385,818,427 - 85,868,552 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01390,460,380 - 90,511,048 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41383,256,823 - 83,298,724 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11383,287,103 - 83,307,114 (+)NCBI
Celera1379,448,171 - 79,489,515 (+)NCBICelera
Cytogenetic Map13q24NCBI
RXRG
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381165,400,922 - 165,445,126 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1165,400,922 - 165,445,355 (-)EnsemblGRCh38hg38GRCh38
GRCh371165,370,159 - 165,414,363 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361163,636,974 - 163,681,054 (-)NCBINCBI36hg18NCBI36
Build 341162,102,008 - 162,146,088NCBI
Celera1138,475,332 - 138,519,756 (-)NCBI
Cytogenetic Map1q23.3NCBI
HuRef1136,616,922 - 136,661,341 (-)NCBIHuRef
CHM1_11166,792,871 - 166,837,301 (-)NCBICHM1_1
T2T-CHM13v2.01164,747,271 - 164,791,474 (-)NCBI
Rxrg
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391167,425,931 - 167,467,192 (+)NCBIGRCm39mm39
GRCm39 Ensembl1167,425,953 - 167,467,192 (+)Ensembl
GRCm381167,598,362 - 167,639,623 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1167,598,384 - 167,639,623 (+)EnsemblGRCm38mm10GRCm38
MGSCv371169,528,493 - 169,569,754 (+)NCBIGRCm37mm9NCBIm37
MGSCv361169,435,059 - 169,476,298 (+)NCBImm8
Celera1170,022,008 - 170,069,461 (+)NCBICelera
Cytogenetic Map1H2.3NCBI
cM Map174.99NCBI
Rxrg
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546211,238,794 - 11,281,956 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495546211,238,963 - 11,281,905 (+)NCBIChiLan1.0ChiLan1.0
RXRG
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11144,623,133 - 144,667,503 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1144,623,133 - 144,723,494 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01140,832,717 - 140,877,046 (-)NCBIMhudiblu_PPA_v0panPan3
RXRG
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13817,867,123 - 17,912,328 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3817,867,182 - 17,920,085 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3817,922,970 - 17,968,200 (+)NCBI
ROS_Cfam_1.03817,947,065 - 17,992,337 (+)NCBI
ROS_Cfam_1.0 Ensembl3817,947,141 - 18,000,604 (+)Ensembl
UMICH_Zoey_3.13817,919,625 - 17,964,835 (+)NCBI
UNSW_CanFamBas_1.03818,271,342 - 18,316,575 (+)NCBI
UU_Cfam_GSD_1.03818,565,728 - 18,610,954 (+)NCBI
Rxrg
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344101,933,905 - 101,979,926 (+)NCBI
SpeTri2.0NW_00493648119,789,753 - 19,826,665 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RXRG
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl485,158,276 - 85,357,137 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1485,158,313 - 85,357,116 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2492,982,235 - 93,063,524 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RXRG
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12563,444,128 - 63,490,594 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2563,443,944 - 63,490,635 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605565,204,356 - 65,250,988 (+)NCBIVero_WHO_p1.0
Rxrg
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248263,736,290 - 3,780,338 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046248263,723,056 - 3,969,597 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH129058  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21379,785,001 - 79,785,172 (+)MAPPERmRatBN7.2
Rnor_6.01385,868,378 - 85,868,548NCBIRnor6.0
Rnor_5.01390,510,875 - 90,511,045UniSTSRnor5.0
RGSC_v3.41383,298,558 - 83,298,728UniSTSRGSC3.4
Celera1379,489,349 - 79,489,519UniSTS
RH 3.4 Map13525.1UniSTS
Cytogenetic Map13q24UniSTS
RH135186  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21379,779,475 - 79,779,660 (+)MAPPERmRatBN7.2
Rnor_6.01385,862,852 - 85,863,036NCBIRnor6.0
Rnor_5.01390,505,349 - 90,505,533UniSTSRnor5.0
RGSC_v3.41383,293,032 - 83,293,216UniSTSRGSC3.4
Celera1379,483,823 - 79,484,007UniSTS
RH 3.4 Map13525.7UniSTS
Cytogenetic Map13q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
12879477Bp401Blood pressure QTL 401arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133726209282262092Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
4889861Pur29Proteinuria QTL 2913.80.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)133741558480753406Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133741558482415584Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)133843340883433408Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat
12879444Bp397Blood pressure QTL 397arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134504940490049404Rat
12879471Bp398Blood pressure QTL 398arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134551471990514719Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134619797684753113Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)135987440885581182Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)136906051986800898Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)136906051986800898Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)136906051986800898Rat
11530006Niddm72Non-insulin dependent diabetes mellitus QTL 720.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)137402391880753406Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137402391897213863Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)137486211785581182Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:100
Count of miRNA genes:68
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000006117
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 33 18 17 17 8 11 22 1 8
Low 2 10 37 22 19 22 52 35 29 11
Below cutoff 1 2 2 2 11

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006117   ⟹   ENSRNOP00000006117
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1379,743,563 - 79,785,167 (+)Ensembl
Rnor_6.0 Ensembl1385,818,473 - 85,868,543 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077227   ⟹   ENSRNOP00000070882
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1379,758,315 - 79,785,167 (+)Ensembl
Rnor_6.0 Ensembl1385,818,427 - 85,868,552 (+)Ensembl
RefSeq Acc Id: NM_031765   ⟹   NP_113953
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21379,743,563 - 79,785,168 (+)NCBI
Rnor_6.01385,818,473 - 85,868,544 (+)NCBI
Rnor_5.01390,460,380 - 90,511,048 (+)NCBI
RGSC_v3.41383,256,823 - 83,298,724 (+)RGD
Celera1379,448,171 - 79,489,515 (+)RGD
Sequence:
RefSeq Acc Id: XM_039091122   ⟹   XP_038947050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21379,743,430 - 79,785,173 (+)NCBI
RefSeq Acc Id: XM_039091123   ⟹   XP_038947051
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21379,763,444 - 79,785,173 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_113953   ⟸   NM_031765
- UniProtKB: Q5BJR8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006117   ⟸   ENSRNOT00000006117
RefSeq Acc Id: ENSRNOP00000070882   ⟸   ENSRNOT00000077227
RefSeq Acc Id: XP_038947050   ⟸   XM_039091122
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947051   ⟸   XM_039091123
- Peptide Label: isoform X2
Protein Domains
NR LBD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5BJR8-F1-model_v2 AlphaFold Q5BJR8 1-463 view protein structure

Transcriptome

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

Promoters
RGD ID:13698991
Promoter ID:EPDNEW_R9501
Type:multiple initiation site
Name:Rxrg_1
Description:retinoid X receptor gamma
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_6.01385,818,358 - 85,818,418EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 85835798 85835799 G A snv CDS


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620046 AgrOrtholog
BioCyc Gene G2FUF-17505 BioCyc
Ensembl Genes ENSRNOG00000004537 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006117 ENTREZGENE
  ENSRNOP00000070882 ENTREZGENE
  ENSRNOP00000070882.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006117 ENTREZGENE
  ENSRNOT00000077227 ENTREZGENE
  ENSRNOT00000077227.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7319081 IMAGE-MGC_LOAD
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_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:83574 UniProtKB/Swiss-Prot
MGC_CLONE MGC:109416 IMAGE-MGC_LOAD
NCBI Gene 83574 ENTREZGENE
Pfam Hormone_recep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuc_recep-AF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rxrg 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
SMART HOLI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48508 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JZ22_RAT UniProtKB/TrEMBL
  Q5BJR8 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Rxrg  retinoid X receptor gamma  LOC102553986  retinoic acid receptor RXR-gamma-like  Data Merged 737654 PROVISIONAL
2013-12-18 LOC102553986  retinoic acid receptor RXR-gamma-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-20 Rxrg  retinoid X receptor gamma      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Rxrg  retinoid X receptor gamma      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in differentiating myoblasts, but not in proliferating myoblasts 633976