RARG retinoic acid receptor, gamma [Homo sapiens (human)] - Gene

Summary

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Official Symbol: RARGprovided by HGNC
Official Full Name: retinoic acid receptor, gammaprovided by HGNC
Primary source: HGNC:9866
See related: Ensembl:ENSG00000172819; HPRD:01573; MIM:180190; Vega:OTTHUMG00000048077
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RARC; NR1B3
Summary: This gene encodes a retinoic acid receptor that belongs to the nuclear hormone receptor family. Retinoic acid receptors (RARs) act as ligand-dependent transcriptional regulators. When bound to ligands, RARs activate transcription by binding as heterodimers to the retinoic acid response elements (RARE) found in the promoter regions of the target genes. In their unbound form, RARs repress transcription of their target genes. RARs are involved in various biological processes, including limb bud development, skeletal growth, and matrix homeostasis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

Genomic context

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Location :: 12q13

Sequence :: Chromosome: 12; NC_000012.11 (53604350..53626040, complement)

See RARG in Epigenomics, MapViewer

Chromosome 12 - NC_000012.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence

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Bibliography

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GeneRIFs: Gene References Into Functions What's a GeneRIF?

Low RARgamma expression is associated with advanced gastric cancer.
Title: Retinoid receptors in gastric cancer: expression and influence on prognosis.
Evidence that the retinoic acid receptor gamma plays a major role in the regulation of the human prostatic transglutaminase gene.
Title: Retinoic acid and androgen receptors combine to achieve tissue specific control of human prostatic transglutaminase expression: a novel regulatory network with broader significance.
findings demonstrate that signaling through RARs has critical roles in molecular reprogramming and that the synergistic interaction between Rarg and Lrh1 directs reprogramming toward ground-state pluripotency
Title: Rapid and efficient reprogramming of somatic cells to induced pluripotent stem cells by retinoic acid receptor gamma and liver receptor homolog 1.
results suggest that a RARgamma-dependent functional crosstalk is present between the retinoic acid and BMP2 signaling to induce osteogenic transdifferentiation in myoblastic C2C12 cells
Title: Retinoic acid receptor γ-dependent signaling cooperates with BMP2 to induce osteoblastic differentiation of C2C12 cells.
One variant in the RARA gene (rs12051734), three variants in the RARB gene (rs6799734, rs12630816, rs17016462), and one variant in the RARG gene (rs3741434) were found to be statistically significant at p < 0.05 as risk factors for meningomyelocele.
Title: Association of retinoic acid receptor genes with meningomyelocele.
Microbiota are required for the generation of both IL-17-positive and Foxp3-positive, retinoic acid-related orphan receptor gamma-positive transgenic T cell subsets in the intestinal lamina propria.
Title: Restricted microbiota and absence of cognate TCR antigen leads to an unbalanced generation of Th17 cells.
PARgamma expressions are decreased in PBMC and SWAT of obese subjects in weight gain.
Title: RARgamma and TRbeta expressions are decreased in PBMC and SWAT of obese subjects in weight gain.
Retinoic acid receptor gamma 2 could specifically interact with vitamin D response elements, either in the presence or absence of the vitamin D receptor.
Title: Retinoic acid receptor gamma 2 interactions with vitamin D response elements.
Data show significant associations between SNPs in RARA, RARB, TOP2B and RARG, RXRA, TLR3, TRIM5 and RIG-I genes and rubella virus-specific cytokine immune responses.
Title: Rubella vaccine-induced cellular immunity: evidence of associations with polymorphisms in the Toll-like, vitamin A and D receptors, and innate immune response genes.
TNIP1 interacts with liganded RARalpha and RARgamma but acts as a corepressor of their activity.
Title: Liganded RARalpha and RARgamma interact with but are repressed by TNIP1.

Submit: New GeneRIF Correction See all (28)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

HIV-1 protein interactions

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Protein	Gene	Interaction	Pubs
Nef, p27	nef	HIV-1 Nef induces loss of F-actin assembly and inhibits retinoid receptor-mediated transcription	PubMed

Go to the HIV-1, Human Protein Interaction Database

Interactions

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Products	Interactant	Other Gene	Source	Pubs	Description
NP_000957.1	NM_004409.2	DMPK	BIND	PubMed	Mutant DMPK mRNA interacts with RAR-gamma.
P13631	P17096	HMGA1	HPRD	PubMed
P13631	Q9UKP3	ITGB1BP2	HPRD	PubMed
P13631	Q6P3T0	MAP6	HPRD	PubMed
P13631	Q15788	NCOA1	HPRD	PubMed
P13631	Q9Y6Q9	NCOA3	HPRD	PubMed
P13631	Q9Y618	NCOR2	HPRD	PubMed
P13631	Q15466	NR0B2	HPRD	PubMed
P13631	Q12796	PNRC1	HPRD	PubMed
P13631	Q9NPJ4	PNRC2	HPRD	PubMed
P13631	P19793	RXRA	HPRD	PubMed
P13631	P28702	RXRB	HPRD	PubMed
P13631	P48443	RXRG	HPRD	PubMed
P13631	P84022	SMAD3	HPRD	PubMed
BioGRID:111851	BioGRID:124869	ACY3	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:124393	AJUBA	BioGRID	PubMed	Affinity Capture-Western
BioGRID:111851	BioGRID:114217	EIF3I	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:109269	H2AFZ	BioGRID	PubMed	Affinity Capture-Western
BioGRID:111851	BioGRID:121590	HACE1	BioGRID	PubMed	Affinity Capture-Western
BioGRID:111851	BioGRID:116199	IL24	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:117742	ITGB1BP2	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:119629	LSR	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:110307	MAP6	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:112097	MRPL12	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:114558	MTMR6	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:114200	NCOA1	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:113841	NCOA3	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:114973	NCOR1	BioGRID	PubMed	Reconstituted Complex; Two-hybrid
BioGRID:111851	BioGRID:114974	NCOR2	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:110888	NKX3-1	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:114012	NR0B2	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:108375	NR2F6	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:116467	OIP5	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:116157	PNRC1	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:120768	PNRC2	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:124521	RHPN2	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:112168	RXRA	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:112169	RXRB	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:112170	RXRG	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:114396	SPHK1	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:112592	SRC	BioGRID	PubMed	Reconstituted Complex
BioGRID:111851	BioGRID:112600	SRF	BioGRID	PubMed	Reconstituted Complex
BioGRID:111851	BioGRID:117059	SUZ12	BioGRID	PubMed	Affinity Capture-Western
BioGRID:111851	BioGRID:115602	TNIP1	BioGRID	PubMed	Two-hybrid
BioGRID:111851	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111851	BioGRID:122594	ZNF576	BioGRID	PubMed	Two-hybrid

Pathways from BioSystems

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Gene Expression, organism-specific biosystem (from REACTOME)
Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
Nuclear Receptor transcription pathway, organism-specific biosystem (from REACTOME)
Nuclear Receptor transcription pathway, organism-specific biosystemA classic example of bifunctional transcription factors is the family of Nuclear Receptor (NR) proteins. These are DNA-binding transcription factors that bind certain hormones, vitamins, and other s...
Nuclear Receptors, organism-specific biosystem (from WikiPathways)
Nuclear Receptors, organism-specific biosystemNuclear receptors are a class of proteins found within the interior of cells that are responsible for sensing the presence of steroid and thyroid hormones and certain other molecules. In response, th...
Nuclear receptors in lipid metabolism and toxicity, organism-specific biosystem (from WikiPathways)
Nuclear receptors in lipid metabolism and toxicity, organism-specific biosystemNuclear receptors are transcription factors that are activated upon binding to its ligands. Initially, they had been classified as classic endocrine nuclear hormone receptors and orphan receptors. Ho...
Vitamin A and carotenoid metabolism, organism-specific biosystem (from WikiPathways)
Vitamin A and carotenoid metabolism, organism-specific biosystemThis pathway is about carotenoid and vitamin A metabolism. The initial version was created by the NuGO focusteam on Carotenoid metabolism. It was used to test a text mining workflow which added some ...

General gene information

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Markers

GDB:677651 (e-PCR)
- UniSTS:32015

NoName (e-PCR)
- UniSTS:483356

WI-18980 (e-PCR)
- UniSTS:71750

AFM310yh9 (e-PCR)
- UniSTS:35171

GDB:376723 (e-PCR)
- UniSTS:157062

RARG_247 (e-PCR)
- UniSTS:468118

Rarg (e-PCR), detects polymorphism
- UniSTS:186533

GDB:384836 (e-PCR)
- UniSTS:157104

STS-M38258 (e-PCR)
- UniSTS:1997

Homology

Homologs of the RARG gene: The RARG gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, and zebrafish.
Map Viewer (Mouse, Rat)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
DNA binding	ISS Inferred from Sequence or Structural Similarity more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed
retinoic acid receptor activity	IEA Inferred from Electronic Annotation more info
retinoid X receptor binding	ISS Inferred from Sequence or Structural Similarity more info
sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
sequence-specific DNA binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
steroid hormone receptor activity	IEA Inferred from Electronic Annotation more info
zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
Harderian gland development	IEA Inferred from Electronic Annotation more info
anterior/posterior pattern specification	IEA Inferred from Electronic Annotation more info
canonical Wnt receptor signaling pathway	TAS Traceable Author Statement more info	PubMed
cellular response to retinoic acid	IEA Inferred from Electronic Annotation more info
embryonic eye morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
embryonic hindlimb morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
gene expression	TAS Traceable Author Statement more info
growth plate cartilage chondrocyte growth	IEA Inferred from Electronic Annotation more info
multicellular organism growth	IEA Inferred from Electronic Annotation more info
negative regulation of cartilage development	IEA Inferred from Electronic Annotation more info
negative regulation of cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
negative regulation of chondrocyte differentiation	IEA Inferred from Electronic Annotation more info
negative regulation of transcription from RNA polymerase II promoter	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of cell proliferation	IEA Inferred from Electronic Annotation more info
positive regulation of programmed cell death	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of transcription from RNA polymerase II promoter	ISS Inferred from Sequence or Structural Similarity more info
prostate gland epithelium morphogenesis	IEA Inferred from Electronic Annotation more info
regulation of cell size	TAS Traceable Author Statement more info	PubMed
regulation of myelination	IEA Inferred from Electronic Annotation more info
response to retinoic acid	IDA Inferred from Direct Assay more info	PubMed
retinoic acid receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
trachea cartilage development	IEA Inferred from Electronic Annotation more info
transcription initiation from RNA polymerase II promoter	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
integral to membrane	NAS Non-traceable Author Statement more info	PubMed
nucleoplasm	TAS Traceable Author Statement more info
nucleus	IDA Inferred from Direct Assay more info	PubMed
nucleus	ISS Inferred from Sequence or Structural Similarity more info
transcription factor complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: retinoic acid receptor gamma

Names: retinoic acid receptor gamma; RAR-gamma; nuclear receptor subfamily 1 group B member 3; retinoic acid nuclear receptor gamma variant 1; retinoic acid nuclear receptor gamma variant 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_029822.1 RefSeqGene

Range

5001..26691

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000966.5 → NP_000957.1 retinoic acid receptor gamma isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AW002722, BC072462, DA436501

Consensus CDS

CCDS8850.1

UniProtKB/TrEMBL

A8K3H3

UniProtKB/Swiss-Prot

P13631

Related

ENSP00000388510, OTTHUMP00000045736, ENST00000425354, OTTHUMT00000109404

Conserved Domains (2) summary

cd06937
Location:188 – 418
Blast Score: 1090

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cd06964
Location:85 – 168
Blast Score: 471

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
NM_001042728.2 → NP_001036193.1 retinoic acid receptor gamma isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate 5' terminal exon compared to variant 1. This results in translation initiation from an alternate start codon, and a shorter isoform (2) with a distinct N-terminus compared to isoform 1.

Source sequence(s)

AK297277, AK316259, AW002722, BC072462, DC294855

Consensus CDS

CCDS41790.1

UniProtKB/TrEMBL

F1D8P1

UniProtKB/Swiss-Prot

P13631

Conserved Domains (2) summary

cd06937
Location:177 – 407
Blast Score: 1099

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cd06964
Location:74 – 157
Blast Score: 463

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
NM_001243730.1 → NP_001230659.1 retinoic acid receptor gamma isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an exon containing the start codon used in variant 1. This results in translation initiation from an in-frame downstream AUG, and an isoform (4) with a shorter N-terminus compared to isoform 1.

Source sequence(s)

AK297023, AW002722, BC072462, DA436501

Consensus CDS

CCDS58236.1

UniProtKB/Swiss-Prot

P13631

Conserved Domains (2) summary

cd06937
Location:116 – 346
Blast Score: 1096

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cd06964
Location:13 – 96
Blast Score: 463

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
NM_001243731.1 → NP_001230660.1 retinoic acid receptor gamma isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks two consecutive exons compared to variant 1. This results in translation initiation from an in-frame downstream AUG, and an isoform (5) with a shorter N-terminus compared to isoform 1.

Source sequence(s)

AK297110, AW002722, BC072462, DA436501

UniProtKB/TrEMBL

B7Z4B4

Conserved Domains (2) summary

cd06937
Location:67 – 297
Blast Score: 1080

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cl02596
Location:1 – 47
Blast Score: 262

NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
NM_001243732.1 → NP_001230661.1 retinoic acid receptor gamma isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate 5' terminal exon, and lacks another coding exon compared to variant 1. This results in translation initiation from an alternate start codon, and a shorter isoform (3) with a distinct N-terminus compared to isoform 1.

Source sequence(s)

AK297277, AW002722, BC072462, DC294855

Consensus CDS

CCDS58237.1

UniProtKB/Swiss-Prot

P13631

Conserved Domains (2) summary

cd06937
Location:166 – 396
Blast Score: 1094

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cl02596
Location:88 – 146
Blast Score: 329

NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh37.p10 Primary Assembly

Genomic

NC_000012.11 Reference GRCh37.p10 Primary Assembly

Range

53604350..53626040, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000144.1 Alternate HuRef

Range

50646458..50668146, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.0

Genomic

NC_018923.1 Alternate CHM1_1.0

Range

53438349..53460016, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	ABBA01008318.1 (8153..29841)	None
genomic	AC021072.27 (44046..53030)	None
genomic	AC073573.27 (145166..157807)	None
genomic	AJ250835.1	CAB60726.1
genomic	AMYH01004477.1 (206631..228298)	None
genomic	AY013703.2	AAG41594.2
genomic	AY013704.1	AAG41595.1
genomic	CH471054.1	EAW96676.1
		EAW96677.1
		EAW96678.1
genomic	CS542443.1	CAM91171.1
genomic	X57280.1	CAA40548.1
mRNA	AB307689.1	BAH02280.1
mRNA	AK290588.1	BAF83277.1
mRNA	AK297023.1	BAH12478.1
mRNA	AK297110.1	BAH12500.1
mRNA	AK297277.1	BAH12537.1
mRNA	AK297801.1	BAH12670.1
mRNA	AK301057.1	BAH13399.1
mRNA	AK316259.1	BAH14630.1
mRNA	AL701206.1	None
mRNA	AW002722.1	None
mRNA	BC019098.2	None
mRNA	BC064524.1	None
mRNA	BC072462.1	None
mRNA	BC093727.1	AAH93727.1
mRNA	BC093729.1	AAH93729.1
mRNA	BC098421.1	None
mRNA	CO394652.1	None
mRNA	DA436501.1	None
mRNA	DA552724.1	None
mRNA	DC294855.1	None
mRNA	HQ692828.1	ADZ17339.1
mRNA	HQ692829.1	ADZ17340.1
mRNA	L12060.1	None
mRNA	M24857.1	AAA52692.1
mRNA	M32074.1	AAA60253.1
mRNA	M38258.1	AAA60254.1
mRNA	M57707.1	AAA63254.1