Rarg retinoic acid receptor, gamma [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Rargprovided by RGD
Official Full Name: retinoic acid receptor, gammaprovided by RGD
Primary source: RGD:1583230
See related: Ensembl:ENSRNOG00000012499 AllianceGenome:RGD:1583230
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables nuclear receptor activity. Involved in several processes, including cellular response to retinoic acid; regulation of myelination; and retinoic acid receptor signaling pathway. Predicted to be located in chromatin and nucleoplasm. Predicted to be part of transcription regulator complex. Orthologous to human RARG (retinoic acid receptor gamma). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 58.4), Thymus (RPKM 34.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q36

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (135246427..135268889, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (133367833..133390301, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (143840739..143863206, complement)

Chromosome 7 - NC_086025.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

We showed that the embryo hearts from vitamin A insufficient groups exhibited ultrastructural changes and significantly lowe expression of GATA-4, RARalpha and gamma, and higher expression of RXRalpha and beta.
Title: Ectopic expression of retinoic acid receptors and change of myocardial structure in the offspring heart with vitamin A deficiency.
Retinoic acid receptor gamma expression is decreased in cerebellar granule cells in an animal model of fetal alcohol syndrome.
Title: Ethanol impairs activation of retinoic acid receptors in cerebellar granule cells in a rodent model of fetal alcohol spectrum disorders.

Submit: New GeneRIF Correction

General gene information

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Markers

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

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

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:144328

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

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables nuclear retinoid X receptor binding	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within bone development	ISO Inferred from Sequence Orthology more info
involved_in bone development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within bone morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within camera-type eye development	ISO Inferred from Sequence Orthology more info
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of cell population proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	ISO Inferred from Sequence Orthology more info
involved_in cellular response to retinoic acid	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within cellular response to retinoic acid	ISO Inferred from Sequence Orthology more info
involved_in chondrocyte development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic camera-type eye development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic eye morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic hindlimb morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within epithelium development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within face development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within gland development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within glandular epithelial cell development	ISO Inferred from Sequence Orthology more info
involved_in growth plate cartilage chondrocyte growth	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within growth plate cartilage development	ISO Inferred from Sequence Orthology more info
involved_in hormone-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within limb development	ISO Inferred from Sequence Orthology more info
involved_in limb development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within multicellular organism growth	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of cartilage development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of chondrocyte differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of stem cell proliferation	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neural tube closure	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of programmed cell death	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of programmed cell death	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within prostate gland epithelium morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in regulation of myelination	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of myeloid cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within reproductive structure development	ISO Inferred from Sequence Orthology more info
involved_in response to retinoic acid	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within retina development in camera-type eye	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within retinal pigment epithelium development	ISO Inferred from Sequence Orthology more info
involved_in retinoic acid receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in retinoic acid receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retinoic acid receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in retinoic acid receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of stem cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within trachea cartilage development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of chromatin	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: retinoic acid receptor gamma

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_001135249.1 → NP_001128721.1 retinoic acid receptor gamma isoform 1

See identical proteins and their annotated locations for NP_001128721.1

Status: PROVISIONAL

Description

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

Source sequence(s)

JAXUCZ010000007

UniProtKB/TrEMBL

A6KCU0, D3ZF61

Related

ENSRNOP00000017096.5, ENSRNOT00000017096.8

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
NM_001135250.1 → NP_001128722.1 retinoic acid receptor gamma isoform 2

Status: PROVISIONAL

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is longer than isoform 1.

Source sequence(s)

JAXUCZ010000007

UniProtKB/TrEMBL

D3ZWV0

Related

ENSRNOP00000016801.4, ENSRNOT00000016801.6

Conserved Domains (2) summary

cd06937
Location:215 → 445

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

cd06964
Location:112 → 192

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

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086025.1 Reference GRCr8

Range

135246427..135268889 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039079887.2 → XP_038935815.1 retinoic acid receptor gamma isoform X2

UniProtKB/TrEMBL

A6KCU0, D3ZF61

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
XM_008765785.4 → XP_008764007.1 retinoic acid receptor gamma isoform X2

See identical proteins and their annotated locations for XP_008764007.1

UniProtKB/TrEMBL

A6KCU0, D3ZF61

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
XM_008765784.4 → XP_008764006.1 retinoic acid receptor gamma isoform X1

Conserved Domains (2) summary

cd06937
Location:201 → 431

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

cd06964
Location:98 → 178

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
XM_039079888.2 → XP_038935816.1 retinoic acid receptor gamma isoform X3

Conserved Domains (2) summary

cd06964
Location:112 → 192

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

cl11397
Location:215 → 304

NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators