Rarg retinoic acid receptor, gamma [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rargprovided by MGI
Official Full Name: retinoic acid receptor, gammaprovided by MGI
Primary source: MGI:MGI:97858
See related: Ensembl:ENSMUSG00000001288 AllianceGenome:MGI:97858
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: RARD; Nr1b3; RAR-gamma; RARgamma2
Summary: Enables several functions, including DNA-binding transcription factor activity; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and retinoid X receptor binding activity. Involved in growth plate cartilage chondrocyte growth and limb development. Acts upstream of or within several processes, including animal organ development; regulation of apoptotic process; and regulation of transcription by RNA polymerase II. Located in nucleus. Part of transcription regulator complex. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; genitourinary system; and limb. Orthologous to human RARG (retinoic acid receptor gamma). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in limb E14.5 (RPKM 41.8), lung adult (RPKM 29.3) and 22 other tissues See more
Orthologs: human all
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Genomic context

Location:: 15 F2; 15 57.4 cM

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	15	NC_000081.7 (102143373..102165891, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	15	NC_000081.6 (102234938..102257522, complement)

Chromosome 15 - NC_000081.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Synergistic activation of RARbeta and RARgamma nuclear receptors restores cell specialization during stem cell differentiation by hijacking RARalpha-controlled programs.
Title: Synergistic activation of RARβ and RARγ nuclear receptors restores cell specialization during stem cell differentiation by hijacking RARα-controlled programs.
RARgamma expression by Prrx1-Cre-targeted cells extrinsically regulates osteoclastogenesis and B lymphopoiesis in male mice.
Title: Retinoic Acid Receptor γ Activity in Mesenchymal Stem Cells Regulates Endochondral Bone, Angiogenesis, and B Lymphopoiesis.
EtOH stimulates stem cell differentiation by increasing the influx and metabolism of ROL for downstream RARgamma-dependent transcription. In stem cells, EtOH may shift cell fate decisions to alter developmental outcomes by increasing endogenous ROL/RA signaling via increased Stra6 expression and ROL oxidation.
Title: Ethanol promotes differentiation of embryonic stem cells through retinoic acid receptor-γ.
RARgamma signaling is required for the differentiation of hypertrophic chondrocytes, with differential cooperation with p38 MAPK.
Title: Retinoic Receptor Signaling Regulates Hypertrophic Chondrocyte-specific Gene Expression.
the RAR:RXR and LXR:RXR-mediated transcriptional program in embryonic stem cells, neural progenitors and terminally differentiated neurons, is reported.
Title: RXR heterodimers orchestrate transcriptional control of neurogenesis and cell fate specification.
This study used CRISPR technology to introduce biallelic frameshift mutations in RAR alpaha, RAR beta, and RAR gamma, thereby abrogating all RAR functions in murine embryonic stem cells. RAR-null cells display no changes in transcripts in response to All-trans-retinoic acid (RA), demonstrating that the RARs are essential for the regulation of all transcripts in murine embryonic stem cells in response to RA.
Title: Combinatorial knockout of RARα, RARβ, and RARγ completely abrogates transcriptional responses to retinoic acid in murine embryonic stem cells.
RARalpha and RARgamma reciprocally control K5(+) progenitor cell proliferation and distribution in the developing submandibular salivary epithelium in a cell cycle-dependent manner while regulating lumenization independently of keratinizing differentiation
Title: RARα and RARγ reciprocally control K5(+) progenitor cell expansion in developing salivary glands.
these studies show that RARgamma is a regulator of B and T lymphopoiesis
Title: Retinoic Acid Receptor γ Regulates B and T Lymphopoiesis via Nestin-Expressing Cells in the Bone Marrow and Thymic Microenvironments.
the reprogramming of epiblast stem cells into embryonic stem cell-like cells also requires low levels of retinoic acid (RA), which can modulate Wnt signalling through physical interactions of RARs with beta-catenin.
Title: Signalling Through Retinoic Acid Receptors is Required for Reprogramming of Both Mouse Embryonic Fibroblast Cells and Epiblast Stem Cells to Induced Pluripotent Stem Cells.
Data show that retinoic acid receptor gamma (RARgamma)-proto-oncogene protein c-fos (c-Fos)-PPARgamma2 (PPARgamma2) signaling rather than reactive oxygen species generation is critical for all-trans retinoic acid (ATRA)-inhibited adipocyte differentiation.
Title: RARγ-C-Fos-PPARγ2 signaling rather than ROS generation is critical for all-trans retinoic acid-inhibited adipocyte differentiation.

Submit: New GeneRIF Correction See all GeneRIFs (41)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1)
Targeted (7) 1 citation
Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

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

AI385767 (e-PCR)
- UniSTS:180840

Rarg (e-PCR), detects polymorphism
- UniSTS:243346

Rarg (e-PCR), detects polymorphism
- UniSTS:243347

Rarg (e-PCR), detects polymorphism
- UniSTS:243348

Rarg (e-PCR), detects polymorphism
- UniSTS:527515

Rarg (e-PCR), detects polymorphism
- UniSTS:265628

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

Rarg (e-PCR), detects polymorphism
- UniSTS:496807

Rarg (e-PCR), detects polymorphism
- UniSTS:144328

NoName (e-PCR)
- UniSTS:548563

Rarg (e-PCR), detects polymorphism
- UniSTS:519411

M34476 (e-PCR)
- UniSTS:160509

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear receptor activity	ISO Inferred from Sequence Orthology more info
enables nuclear retinoid X receptor binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within Harderian gland development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within anterior/posterior pattern specification	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within anterior/posterior pattern specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of apoptotic process	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within bone development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in bone development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within bone morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within bone morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of cell population proliferation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	IEP Inferred from Expression Pattern more info	PubMed
involved_in chondrocyte development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic camera-type eye development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic eye morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic hindlimb morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within epithelium development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within face development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within gland development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within glandular epithelial cell development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in growth plate cartilage chondrocyte growth	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within growth plate cartilage development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in hormone-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within limb development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in limb development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within multicellular organism growth	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of chondrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of stem cell proliferation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within neural tube closure	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of apoptotic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of programmed cell death	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IC Inferred by Curator more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of programmed cell death	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within prostate gland epithelium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of myelination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of myeloid cell differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within reproductive structure development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to retinoic acid	ISO Inferred from Sequence Orthology more info
involved_in retinoic acid receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within retinoic acid receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retinoic acid receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of stem cell proliferation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within trachea cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: retinoic acid receptor gamma

Names: RAR gamma 2; nuclear receptor subfamily 1 group B member 3; retinoic acid receptor gamma 4

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.

mRNA and Protein(s)

NM_001042727.3 → NP_001036192.1 retinoic acid receptor gamma isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate 5'-terminal exon, lacks part of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AC123791

Consensus CDS

CCDS37226.1

UniProtKB/Swiss-Prot

P18911

Related

ENSMUSP00000067266.8, ENSMUST00000063339.14

Conserved Domains (2) summary

cd06937
Location:177 → 407

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

cd06964
Location:74 → 154

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
NM_001411714.1 → NP_001398643.1 retinoic acid receptor gamma isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR, compared to variant 1, and encodes isoform (1).

Source sequence(s)

AC123791, AC163291

UniProtKB/Swiss-Prot

P18911, P20787, Q3UG86, Q62149, Q91VK5, Q91YX2
NM_011244.5 → NP_035374.3 retinoic acid receptor gamma isoform 1

See identical proteins and their annotated locations for NP_035374.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC123791, AC163291

Consensus CDS

CCDS27875.1

UniProtKB/Swiss-Prot

P18911, P20787, Q3UG86, Q62149, Q91VK5, Q91YX2

Related

ENSMUSP00000048838.9, ENSMUST00000043172.15

Conserved Domains (2) summary

cd06937
Location:188 → 418

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

cd06964
Location:85 → 165

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers