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

Gene ID: 19411, updated on 12-May-2024

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
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Genomic context

See Rarg in Genome Data Viewer
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_000081.7Genomic Context describing neighboring genes Neighboring gene cysteine sulfinic acid decarboxylase Neighboring gene STARR-positive B cell enhancer ABC_E5519 Neighboring gene STARR-seq mESC enhancer starr_39822 Neighboring gene zinc finger protein 740 Neighboring gene STARR-positive B cell enhancer mm9_chr15:102055434-102055734 Neighboring gene STARR-positive B cell enhancer mm9_chr15:102055789-102056089 Neighboring gene integrin beta 7 Neighboring gene STARR-seq mESC enhancer starr_39826 Neighboring gene STARR-seq mESC enhancer starr_39827 Neighboring gene STARR-seq mESC enhancer starr_39828 Neighboring gene STARR-seq mESC enhancer starr_39829 Neighboring gene predicted gene 9918 Neighboring gene major facilitator superfamily domain containing 5

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 
  • Gene trapped (1) 
  • Targeted (7)  1 citation

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC11555, MGC18523

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

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)

  1. NM_001042727.3NP_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:177407
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:74154
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  2. NM_001411714.1NP_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
  3. NM_011244.5NP_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:188418
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:85165
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000081.7 Reference GRCm39 C57BL/6J

    Range
    102143373..102165891 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)