RXRG (retinoid X receptor gamma) - Rat Genome Database

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Pathways
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Gene: RXRG (retinoid X receptor gamma) Homo sapiens
Analyze
Symbol: RXRG
Name: retinoid X receptor gamma
RGD ID: 733408
HGNC Page HGNC:10479
Description: Enables molecular condensate scaffold activity and sequence-specific double-stranded DNA binding activity. Predicted to be involved in several processes, including positive regulation of transcription by RNA polymerase II; response to retinoic acid; and retinoic acid receptor signaling pathway. Predicted to be located in nucleoplasm. Predicted to be part of RNA polymerase II transcription regulator complex and chromatin. Implicated in lung non-small cell carcinoma. Biomarker of thyroid gland papillary carcinoma.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: NR2B3; nuclear receptor subfamily 2 group B member 3; retinoic acid receptor RXR-gamma; retinoid X nuclear receptor gamma variant 1; retinoid X receptor, gamma; retinoid X receptor-gamma; RXR-gamma; RXRC; RXRgamma
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Candidate Gene For: GLUCO121_H GLUCO118_H GLUCO149_H GLUCO177_H
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381165,400,922 - 165,445,126 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1165,400,922 - 165,445,355 (-)EnsemblGRCh38hg38GRCh38
GRCh371165,370,159 - 165,414,363 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361163,636,974 - 163,681,054 (-)NCBINCBI36Build 36hg18NCBI36
Build 341162,102,008 - 162,146,088NCBI
Celera1138,475,332 - 138,519,756 (-)NCBICelera
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 (-)NCBIT2T-CHM13v2.0
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  (ISO)
(1->4)-beta-D-glucan  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-estradiol 3-benzoate  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4-dinitrotoluene  (ISO)
2-hydroxyphytanic acid  (EXP)
3,3',5-triiodo-L-thyronine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-phenoxybenzoic acid  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-hydroxyphenyl retinamide  (EXP,ISO)
6-propyl-2-thiouracil  (ISO)
8-Br-cAMP  (EXP)
9-cis-retinoic acid  (EXP,ISO)
acrylamide  (ISO)
aldrin  (ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (EXP,ISO)
amiodarone  (ISO)
ammonium chloride  (ISO)
benzo[a]pyrene  (EXP,ISO)
beta-naphthoflavone  (ISO)
bexarotene  (EXP,ISO)
bezafibrate  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Butylbenzyl phthalate  (EXP)
cadmium sulfate  (EXP,ISO)
carbon nanotube  (ISO)
cefaloridine  (ISO)
CGP 52608  (EXP)
chlorpromazine  (ISO)
clofibrate  (ISO)
clozapine  (ISO)
Cuprizon  (ISO)
D-gluconic acid  (ISO)
deoxycholic acid  (ISO)
dexamethasone  (ISO)
Di-n-hexyl phthalate  (EXP)
dibutyl phthalate  (EXP)
diethyl phthalate  (EXP)
diethylstilbestrol  (ISO)
diheptyl phthalate  (EXP)
diisobutyl phthalate  (ISO)
Dimethyl phthalate  (EXP)
dimethyl sulfoxide  (ISO)
dioxygen  (ISO)
dipentyl phthalate  (EXP)
dipropyl phthalate  (EXP)
doxorubicin  (EXP)
endosulfan  (ISO)
epoxiconazole  (ISO)
ethanol  (EXP,ISO)
fentin hydroxide  (EXP)
fenvalerate  (EXP)
fulvestrant  (EXP)
gamma-hexachlorocyclohexane  (ISO)
genistein  (ISO)
glafenine  (ISO)
griseofulvin  (ISO)
haloperidol  (ISO)
hydralazine  (EXP)
indometacin  (ISO)
ketamine  (ISO)
ketoconazole  (ISO)
lead diacetate  (ISO)
lipopolysaccharide  (EXP,ISO)
mercury dichloride  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
mono(2-ethylhexyl) phthalate  (EXP)
Muraglitazar  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (ISO)
nimesulide  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phthalic acid  (EXP)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
quercetin  (EXP)
rotenone  (EXP)
S-(1,2-dichlorovinyl)-L-cysteine  (EXP)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sunitinib  (EXP)
Tesaglitazar  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
tetracycline  (ISO)
thioacetamide  (ISO)
titanium dioxide  (ISO)
tributylstannane  (ISO)
trichloroethene  (ISO)
triclosan  (EXP)
trimellitic anhydride  (ISO)
triticonazole  (ISO)
valproic acid  (EXP)
vinyl carbamate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. 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.
2. International Union of Pharmacology. LXIII. Retinoid X receptors. Germain P, etal., Pharmacol Rev. 2006 Dec;58(4):760-72.
3. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
4. 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.
5. 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.
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:1310259   PMID:1312497   PMID:7806300   PMID:8034312   PMID:8127707   PMID:8391126   PMID:8616895   PMID:8650544   PMID:8889548   PMID:9006910   PMID:9143002   PMID:9147069  
PMID:9150186   PMID:9794455   PMID:11158331   PMID:11397877   PMID:11641790   PMID:11713274   PMID:11839661   PMID:12082103   PMID:12361685   PMID:12444914   PMID:12477932   PMID:12514092  
PMID:12615696   PMID:15186611   PMID:15299084   PMID:15489334   PMID:15604093   PMID:15608692   PMID:15635645   PMID:15919723   PMID:16169070   PMID:16189514   PMID:16197915   PMID:16344560  
PMID:16710414   PMID:17195188   PMID:17272748   PMID:17643375   PMID:18269685   PMID:18398047   PMID:18660489   PMID:19064610   PMID:19106195   PMID:19274049   PMID:19453261   PMID:19536175  
PMID:19754311   PMID:20019805   PMID:20133701   PMID:20211142   PMID:20379614   PMID:20510503   PMID:20602615   PMID:20634891   PMID:20855565   PMID:21102462   PMID:21131950   PMID:21145461  
PMID:21187846   PMID:21355951   PMID:21368711   PMID:21516116   PMID:21697133   PMID:21843636   PMID:21873635   PMID:21900206   PMID:21923909   PMID:21988832   PMID:22020178   PMID:22100394  
PMID:22180072   PMID:22193333   PMID:22205725   PMID:23759678   PMID:23936423   PMID:23969901   PMID:25231870   PMID:25303530   PMID:25416956   PMID:25910212   PMID:26148973   PMID:26355550  
PMID:27245436   PMID:27636996   PMID:27721113   PMID:28473536   PMID:28514442   PMID:29892012   PMID:31359385   PMID:31515488   PMID:31808386   PMID:31881311   PMID:32296183   PMID:32814053  
PMID:33961781   PMID:34633445   PMID:35914814   PMID:36215168  


Genomics

Comparative Map Data
RXRG
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381165,400,922 - 165,445,126 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1165,400,922 - 165,445,355 (-)EnsemblGRCh38hg38GRCh38
GRCh371165,370,159 - 165,414,363 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361163,636,974 - 163,681,054 (-)NCBINCBI36Build 36hg18NCBI36
Build 341162,102,008 - 162,146,088NCBI
Celera1138,475,332 - 138,519,756 (-)NCBICelera
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 (-)NCBIT2T-CHM13v2.0
Rxrg
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391167,425,902 - 167,467,191 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1167,425,953 - 167,467,192 (+)EnsemblGRCm39 Ensembl
GRCm381167,598,362 - 167,639,623 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1167,598,384 - 167,639,623 (+)EnsemblGRCm38mm10GRCm38
MGSCv371169,528,493 - 169,569,754 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361169,435,059 - 169,476,298 (+)NCBIMGSCv36mm8
Celera1170,022,008 - 170,069,461 (+)NCBICelera
Cytogenetic Map1H2.3NCBI
cM Map174.99NCBI
Rxrg
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81382,276,330 - 82,318,097 (+)NCBIGRCr8
mRatBN7.21379,743,430 - 79,785,173 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1379,743,563 - 79,785,167 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1382,373,401 - 82,414,881 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01383,680,439 - 83,722,040 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01380,918,510 - 80,960,010 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11383,287,103 - 83,307,114 (+)NCBI
Celera1379,448,171 - 79,489,515 (+)NCBICelera
Cytogenetic Map13q24NCBI
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
NHGRI_mPanPan1-v2184,320,687 - 84,365,083 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1183,989,216 - 84,033,594 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01140,832,717 - 140,877,046 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11144,623,133 - 144,667,503 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1144,623,133 - 144,723,494 (-)Ensemblpanpan1.1panPan2
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03817,947,065 - 17,992,337 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3817,947,141 - 18,000,604 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13817,919,625 - 17,964,835 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03818,271,342 - 18,316,575 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03818,565,728 - 18,610,954 (+)NCBIUU_Cfam_GSD_1.0
Rxrg
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344101,933,905 - 101,979,926 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648119,789,641 - 19,826,698 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648119,789,753 - 19,826,665 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RXRG
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl485,308,508 - 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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2563,443,944 - 63,490,635 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605565,204,356 - 65,250,988 (+)NCBIVero_WHO_p1.0Vero_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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248263,723,056 - 3,969,597 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in RXRG
22 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_006917.4(RXRG):c.1139-113C>G single nucleotide variant Lung cancer [RCV000089885] Chr1:165407030 [GRCh38]
Chr1:165376267 [GRCh37]
Chr1:1q23.3		 uncertain significance
NM_006917.4(RXRG):c.50-2747A>G single nucleotide variant Lung cancer [RCV000089886] Chr1:165431713 [GRCh38]
Chr1:165400950 [GRCh37]
Chr1:1q23.3		 uncertain significance
GRCh38/hg38 1q23.2-24.1(chr1:159479887-166895086)x1 copy number loss See cases [RCV000051172] Chr1:159479887..166895086 [GRCh38]
Chr1:159449677..166864323 [GRCh37]
Chr1:157716301..165130947 [NCBI36]
Chr1:1q23.2-24.1		 pathogenic
GRCh38/hg38 1q23.1-25.1(chr1:157747246-176021247)x3 copy number gain See cases [RCV000051854] Chr1:157747246..176021247 [GRCh38]
Chr1:157717036..175990383 [GRCh37]
Chr1:155983660..174257006 [NCBI36]
Chr1:1q23.1-25.1		 pathogenic
GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3 copy number gain See cases [RCV000051856] Chr1:164922655..180061589 [GRCh38]
Chr1:164891892..180030724 [GRCh37]
Chr1:163158516..178297347 [NCBI36]
Chr1:1q23.3-25.2		 pathogenic
GRCh38/hg38 1q23.3-24.1(chr1:164547546-165689403)x1 copy number loss See cases [RCV000053213] Chr1:164547546..165689403 [GRCh38]
Chr1:164516783..165658640 [GRCh37]
Chr1:162783407..163925264 [NCBI36]
Chr1:1q23.3-24.1		 uncertain significance
GRCh38/hg38 1q23.3-24.2(chr1:160789732-168617494)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053913]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053913]|See cases [RCV000053913] Chr1:160789732..168617494 [GRCh38]
Chr1:160759522..168586732 [GRCh37]
Chr1:159026146..166853356 [NCBI36]
Chr1:1q23.3-24.2		 pathogenic
GRCh38/hg38 1q23.3-25.1(chr1:161740907-173965154)x1 copy number loss See cases [RCV000053914] Chr1:161740907..173965154 [GRCh38]
Chr1:161710697..173934292 [GRCh37]
Chr1:159977321..172200915 [NCBI36]
Chr1:1q23.3-25.1		 pathogenic
GRCh38/hg38 1q23.3-24.2(chr1:162040050-167480663)x1 copy number loss See cases [RCV000053915] Chr1:162040050..167480663 [GRCh38]
Chr1:162009840..167449900 [GRCh37]
Chr1:160276464..165716524 [NCBI36]
Chr1:1q23.3-24.2		 pathogenic
GRCh38/hg38 1q23.3-24.3(chr1:164036599-171252077)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053916]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053916]|See cases [RCV000053916] Chr1:164036599..171252077 [GRCh38]
Chr1:164005836..171221216 [GRCh37]
Chr1:162272460..169487840 [NCBI36]
Chr1:1q23.3-24.3		 pathogenic
GRCh38/hg38 1q23.3-25.1(chr1:163382523-175877022)x1 copy number loss See cases [RCV000143292] Chr1:163382523..175877022 [GRCh38]
Chr1:163352313..175846158 [GRCh37]
Chr1:161618937..174112781 [NCBI36]
Chr1:1q23.3-25.1		 pathogenic
GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3 copy number gain See cases [RCV000143515] Chr1:149854269..180267197 [GRCh38]
Chr1:149825831..180236332 [GRCh37]
Chr1:148092455..178502955 [NCBI36]
Chr1:1q21.2-25.2		 pathogenic
GRCh37/hg19 1q23.2-25.1(chr1:160369890-175796325) copy number loss not provided [RCV000767779] Chr1:160369890..175796325 [GRCh37]
Chr1:1q23.2-25.1		 pathogenic
GRCh37/hg19 1q23.3-25.3(chr1:161676893-184071723)x1 copy number loss See cases [RCV000447098] Chr1:161676893..184071723 [GRCh37]
Chr1:1q23.3-25.3		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
NM_006917.5(RXRG):c.394G>A (p.Gly132Arg) single nucleotide variant Inborn genetic diseases [RCV003300843] Chr1:165419918 [GRCh38]
Chr1:165389155 [GRCh37]
Chr1:1q23.3		 uncertain significance
NM_006917.5(RXRG):c.702G>A (p.Met234Ile) single nucleotide variant Inborn genetic diseases [RCV003285154] Chr1:165411030 [GRCh38]
Chr1:165380267 [GRCh37]
Chr1:1q23.3		 uncertain significance
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1q23.2-25.2(chr1:159815642-177026983)x1 copy number loss not provided [RCV000736717] Chr1:159815642..177026983 [GRCh37]
Chr1:1q23.2-25.2		 pathogenic
GRCh37/hg19 1q23.3-24.2(chr1:163093021-168991239)x1 copy number loss not provided [RCV000849156] Chr1:163093021..168991239 [GRCh37]
Chr1:1q23.3-24.2		 pathogenic
GRCh37/hg19 1q23.1-24.2(chr1:157321299-167391423)x1 copy number loss not provided [RCV000848773] Chr1:157321299..167391423 [GRCh37]
Chr1:1q23.1-24.2		 pathogenic
GRCh37/hg19 1q23.3-24.2(chr1:164608682-169216098)x1 copy number loss not provided [RCV001258478] Chr1:164608682..169216098 [GRCh37]
Chr1:1q23.3-24.2		 likely pathogenic
NC_000001.10:g.(?_130980840)_(248900000_?)dup duplication Gastrointestinal stromal tumor [RCV001300221]|Parathyroid carcinoma [RCV001341077] Chr1:130980840..248900000 [GRCh37]
Chr1:1q12-44		 uncertain significance
NM_006917.5(RXRG):c.1135C>A (p.Pro379Thr) single nucleotide variant Inborn genetic diseases [RCV003253740] Chr1:165408230 [GRCh38]
Chr1:165377467 [GRCh37]
Chr1:1q23.3		 uncertain significance
GRCh37/hg19 1q23.2-24.1(chr1:160417296-166197042) copy number loss not specified [RCV002053658] Chr1:160417296..166197042 [GRCh37]
Chr1:1q23.2-24.1		 pathogenic
GRCh37/hg19 1q23.3-24.3(chr1:162330810-171532331) copy number loss not specified [RCV002053680] Chr1:162330810..171532331 [GRCh37]
Chr1:1q23.3-24.3		 pathogenic
NM_006917.5(RXRG):c.355C>A (p.Pro119Thr) single nucleotide variant Inborn genetic diseases [RCV002728847] Chr1:165419957 [GRCh38]
Chr1:165389194 [GRCh37]
Chr1:1q23.3		 uncertain significance
NM_006917.5(RXRG):c.349G>C (p.Gly117Arg) single nucleotide variant Inborn genetic diseases [RCV002822558] Chr1:165419963 [GRCh38]
Chr1:165389200 [GRCh37]
Chr1:1q23.3		 uncertain significance
NM_006917.5(RXRG):c.170G>A (p.Ser57Asn) single nucleotide variant Inborn genetic diseases [RCV002783135] Chr1:165428846 [GRCh38]
Chr1:165398083 [GRCh37]
Chr1:1q23.3		 uncertain significance
NM_006917.5(RXRG):c.683C>G (p.Thr228Ser) single nucleotide variant Inborn genetic diseases [RCV002784120] Chr1:165411049 [GRCh38]
Chr1:165380286 [GRCh37]
Chr1:1q23.3		 likely benign
NM_006917.5(RXRG):c.1184A>G (p.Glu395Gly) single nucleotide variant Inborn genetic diseases [RCV002709727] Chr1:165406872 [GRCh38]
Chr1:165376109 [GRCh37]
Chr1:1q23.3		 uncertain significance
NM_006917.5(RXRG):c.346C>A (p.Pro116Thr) single nucleotide variant Inborn genetic diseases [RCV002769023] Chr1:165419966 [GRCh38]
Chr1:165389203 [GRCh37]
Chr1:1q23.3		 uncertain significance
NM_006917.5(RXRG):c.650G>A (p.Arg217Gln) single nucleotide variant Inborn genetic diseases [RCV002674816] Chr1:165411082 [GRCh38]
Chr1:165380319 [GRCh37]
Chr1:1q23.3		 uncertain significance
NM_006917.5(RXRG):c.841G>A (p.Val281Ile) single nucleotide variant Inborn genetic diseases [RCV003212236] Chr1:165410774 [GRCh38]
Chr1:165380011 [GRCh37]
Chr1:1q23.3		 uncertain significance
NM_006917.5(RXRG):c.211C>G (p.Arg71Gly) single nucleotide variant Inborn genetic diseases [RCV003204268] Chr1:165428805 [GRCh38]
Chr1:165398042 [GRCh37]
Chr1:1q23.3		 uncertain significance
NM_006917.5(RXRG):c.1358T>C (p.Met453Thr) single nucleotide variant Inborn genetic diseases [RCV003362352] Chr1:165401297 [GRCh38]
Chr1:165370534 [GRCh37]
Chr1:1q23.3		 uncertain significance
NM_006917.5(RXRG):c.182C>A (p.Thr61Asn) single nucleotide variant Inborn genetic diseases [RCV003347475] Chr1:165428834 [GRCh38]
Chr1:165398071 [GRCh37]
Chr1:1q23.3		 uncertain significance
NM_006917.5(RXRG):c.1229C>A (p.Pro410Gln) single nucleotide variant Inborn genetic diseases [RCV003386551] Chr1:165406827 [GRCh38]
Chr1:165376064 [GRCh37]
Chr1:1q23.3		 uncertain significance
GRCh37/hg19 1q23.3-25.1(chr1:164571371-175708060)x1 copy number loss not provided [RCV003483966] Chr1:164571371..175708060 [GRCh37]
Chr1:1q23.3-25.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:735
Count of miRNA genes:472
Interacting mature miRNAs:522
Transcripts:ENST00000359842, ENST00000465764, ENST00000470566
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.

Markers in Region
D1S2878  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371165,403,477 - 165,403,655UniSTSGRCh37
Build 361163,670,101 - 163,670,279RGDNCBI36
Celera1138,508,662 - 138,508,837RGD
Cytogenetic Map1q22-q23UniSTS
HuRef1136,650,251 - 136,650,423UniSTS
Marshfield Genetic Map1177.86RGD
Marshfield Genetic Map1177.86UniSTS
Genethon Genetic Map1181.7UniSTS
TNG Radiation Hybrid Map174899.0UniSTS
deCODE Assembly Map1165.78UniSTS
Stanford-G3 RH Map16310.0UniSTS
NCBI RH Map11447.2UniSTS
GeneMap99-G3 RH Map16266.0UniSTS
SHGC-89236  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371165,380,823 - 165,381,135UniSTSGRCh37
Build 361163,647,447 - 163,647,759RGDNCBI36
Celera1138,486,014 - 138,486,326RGD
Cytogenetic Map1q22-q23UniSTS
HuRef1136,627,604 - 136,627,916UniSTS
TNG Radiation Hybrid Map174885.0UniSTS
WI-15938  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371165,370,382 - 165,370,482UniSTSGRCh37
Build 361163,637,006 - 163,637,106RGDNCBI36
Celera1138,475,555 - 138,475,655RGD
Cytogenetic Map1q22-q23UniSTS
HuRef1136,617,145 - 136,617,245UniSTS
GeneMap99-GB4 RH Map1594.41UniSTS
GeneMap99-GB4 RH Map1596.32UniSTS
Whitehead-RH Map1732.4UniSTS


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 sensory system visual system adipose tissue appendage entire extraembryonic component
High
Medium 259 26 310 8 5 8 1130 703 1526 1 40 70 51 1048
Low 1756 1588 805 195 304 73 2659 1406 1981 90 1079 1242 125 1 1070 1450 1
Below cutoff 291 986 534 357 658 318 495 59 157 202 233 142 45 83 285 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_029517 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001256570 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001256571 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_006917 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_033824 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB307706 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB593015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB593016 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK125497 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK312922 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL160058 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL538345 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC012063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BE349162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BI768747 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BM684530 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BM728015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX118484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR456705 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA251671 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA893476 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HQ692845 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF455045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF455048 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U38480 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000359842   ⟹   ENSP00000352900
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,400,922 - 165,445,126 (-)Ensembl
RefSeq Acc Id: ENST00000465764
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,436,928 - 165,445,172 (-)Ensembl
RefSeq Acc Id: ENST00000470566
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,410,750 - 165,424,972 (-)Ensembl
RefSeq Acc Id: ENST00000619224   ⟹   ENSP00000482458
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,400,923 - 165,445,355 (-)Ensembl
RefSeq Acc Id: NM_001256570   ⟹   NP_001243499
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381165,400,922 - 165,445,126 (-)NCBI
GRCh371165,370,159 - 165,414,592 (-)NCBI
HuRef1136,616,922 - 136,661,341 (-)NCBI
CHM1_11166,792,871 - 166,837,301 (-)NCBI
T2T-CHM13v2.01164,747,271 - 164,791,474 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001256571   ⟹   NP_001243500
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381165,400,922 - 165,424,984 (-)NCBI
GRCh371165,370,159 - 165,414,592 (-)NCBI
HuRef1136,616,922 - 136,661,341 (-)NCBI
CHM1_11166,792,871 - 166,816,930 (-)NCBI
T2T-CHM13v2.01164,747,271 - 164,771,334 (-)NCBI
Sequence:
RefSeq Acc Id: NM_006917   ⟹   NP_008848
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381165,400,922 - 165,445,126 (-)NCBI
GRCh371165,370,159 - 165,414,592 (-)ENTREZGENE
Build 361163,636,974 - 163,681,054 (-)NCBI Archive
HuRef1136,616,922 - 136,661,341 (-)ENTREZGENE
CHM1_11166,792,871 - 166,837,301 (-)NCBI
T2T-CHM13v2.01164,747,271 - 164,791,474 (-)NCBI
Sequence:
RefSeq Acc Id: NR_033824
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381165,436,931 - 165,445,126 (-)NCBI
GRCh371165,370,159 - 165,414,592 (-)ENTREZGENE
HuRef1136,616,922 - 136,661,341 (-)ENTREZGENE
CHM1_11166,828,874 - 166,837,301 (-)NCBI
T2T-CHM13v2.01164,783,279 - 164,791,474 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_008848   ⟸   NM_006917
- Peptide Label: isoform a
- UniProtKB: A6NIP1 (UniProtKB/Swiss-Prot),   Q6IBU7 (UniProtKB/Swiss-Prot),   P48443 (UniProtKB/Swiss-Prot),   F1D8Q7 (UniProtKB/TrEMBL),   B2R7C0 (UniProtKB/TrEMBL),   B6ZGT6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001243499   ⟸   NM_001256570
- Peptide Label: isoform c
- UniProtKB: A0A087WZ88 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001243500   ⟸   NM_001256571
- Peptide Label: isoform c
- UniProtKB: A0A087WZ88 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000352900   ⟸   ENST00000359842
RefSeq Acc Id: ENSP00000482458   ⟸   ENST00000619224
Protein Domains
NR LBD   Nuclear receptor   Nuclear/hormone receptor activator site AF-1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P48443-F1-model_v2 AlphaFold P48443 1-463 view protein structure

Promoters
RGD ID:6857964
Promoter ID:EPDNEW_H2147
Type:initiation region
Name:RXRG_1
Description:retinoid X receptor gamma
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H2148  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381165,445,126 - 165,445,186EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:10479 AgrOrtholog
COSMIC RXRG COSMIC
Ensembl Genes ENSG00000143171 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000359842 ENTREZGENE
  ENST00000359842.10 UniProtKB/Swiss-Prot
  ENST00000465764 ENTREZGENE
  ENST00000619224 ENTREZGENE
  ENST00000619224.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000143171 GTEx
HGNC ID HGNC:10479 ENTREZGENE
Human Proteome Map RXRG Human Proteome Map
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 hsa:6258 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 6258 ENTREZGENE
OMIM 180247 OMIM
PANTHER NUCLEAR HORMONE RECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RETINOIC ACID RECEPTOR RXR-GAMMA 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
PharmGKB PA34892 PharmGKB
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 Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF48508 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A087WZ88 ENTREZGENE, UniProtKB/TrEMBL
  A6NIP1 ENTREZGENE
  B2R7C0 ENTREZGENE, UniProtKB/TrEMBL
  B6ZGT6 ENTREZGENE, UniProtKB/TrEMBL
  F1D8Q7 ENTREZGENE, UniProtKB/TrEMBL
  F1T097_HUMAN UniProtKB/TrEMBL
  P48443 ENTREZGENE
  Q6IBU7 ENTREZGENE
  RXRG_HUMAN UniProtKB/Swiss-Prot
UniProt Secondary A6NIP1 UniProtKB/Swiss-Prot
  Q6IBU7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-17 RXRG  retinoid X receptor gamma    retinoid X receptor, gamma  Symbol and/or name change 5135510 APPROVED