Rarb retinoic acid receptor, beta [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rarbprovided by MGI
Official Full Name: retinoic acid receptor, betaprovided by MGI
Primary source: MGI:MGI:97857
See related: Ensembl:ENSMUSG00000017491 AllianceGenome:MGI:97857
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: Hap; Nr1b2; A830025K23
Summary: Enables DNA-binding transcription factor activity and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Acts upstream of or within several processes, including animal organ development; regulation of apoptotic process; and regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; genitourinary system; and sensory organ. Human ortholog(s) of this gene implicated in asbestos-related lung carcinoma; lung adenocarcinoma; lung non-small cell carcinoma; lung small cell carcinoma; and syndromic microphthalmia 12. Orthologous to human RARB (retinoic acid receptor beta). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in CNS E18 (RPKM 5.2), limb E14.5 (RPKM 4.2) and 24 other tissues See more
Orthologs: human all
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Genomic context

Location:: 14 A1; 14 7.08 cM

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	14	NC_000080.7 (5387365..6038924)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	14	NC_000080.6 (16430839..17082331, complement)

Chromosome 14 - NC_000080.7 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: 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?

Retinoic Acid Receptor beta Loss in Hepatocytes Increases Steatosis and Elevates the Integrated Stress Response in Alcohol-Associated Liver Disease.
Title: Retinoic Acid Receptor β Loss in Hepatocytes Increases Steatosis and Elevates the Integrated Stress Response in Alcohol-Associated Liver Disease.
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.
Retinoic acid receptor beta protects striatopallidal medium spiny neurons from mitochondrial dysfunction and neurodegeneration.
Title: Retinoic acid receptor beta protects striatopallidal medium spiny neurons from mitochondrial dysfunction and neurodegeneration.
Transgene integration causes RARB downregulation in homozygous Tg4-42 mice.
Title: Transgene integration causes RARB downregulation in homozygous Tg4-42 mice.
significant reduction in expression in fibrotic liver
Title: Retinoic Acid Receptor-β Is Downregulated in Hepatocellular Carcinoma and Cirrhosis and Its Expression Inhibits Myosin-Driven Activation and Durotaxis in Hepatic Stellate Cells.
RAR-beta signaling promotes the binding of the mitochondria to the anchoring protein, glucose-related protein 75, at the growing tip of neurite, thus allowing them to provide energy and metabolic roles required for neurite outgrowth.
Title: The regulation of mitochondrial dynamics in neurite outgrowth by retinoic acid receptor β signaling.
Studied role of dietary vitamin A, intestinal immunity and amyloid A expression regulation through retinoic acid receptor beta (Rarb.)
Title: Epithelial retinoic acid receptor β regulates serum amyloid A expression and vitamin A-dependent intestinal immunity.
AC261066 (AC261), a highly selective agonist for RARbeta2, exhibited therapeutic effects in a HFD model of DN in C57BL/6 mice.
Title: Amelioration of Diabetic Nephropathy Using a Retinoic Acid Receptor β2 Agonist.
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.
The RARbeta transcriptional targets were particularly enriched for transcripts affected in Huntington's disease.
Title: Genome-wide Analysis of RARβ Transcriptional Targets in Mouse Striatum Links Retinoic Acid Signaling with Huntington's Disease and Other Neurodegenerative Disorders.

Submit: New GeneRIF Correction See all GeneRIFs (52)

Variation

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Alleles

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

Targeted (6) 1 citation
Endonuclease-mediated (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Rarb (e-PCR), detects polymorphism
- UniSTS:526094

Rarb (e-PCR), detects polymorphism
- UniSTS:470565

PMC316377P10 (e-PCR)
- UniSTS:272968

PMC134698P2 (e-PCR)
- UniSTS:270736

PMC134698P3 (e-PCR)
- UniSTS:270737

Rarb (e-PCR), detects polymorphism
- UniSTS:265627

Rarb (e-PCR), detects polymorphism
- UniSTS:186532

PMC113761P1 (e-PCR)
- UniSTS:270252

Rarb (e-PCR), detects polymorphism
- UniSTS:516537

Rarb (e-PCR), detects polymorphism
- UniSTS:516538

Rarb (e-PCR), detects polymorphism
- UniSTS:144325

Rarb (e-PCR), detects polymorphism
- UniSTS:144326

Rarb (e-PCR), detects polymorphism
- UniSTS:144327

D14Mit78 (e-PCR), detects polymorphism
- UniSTS:127434

NoName (e-PCR)
- UniSTS:548562

D14Mit98 (e-PCR), detects polymorphism
- UniSTS:127455

D14Mit98.1 (e-PCR), detects polymorphism
- UniSTS:127456

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
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 heterocyclic compound binding	ISO Inferred from Sequence Orthology more info
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 retinoid X receptor binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	IGI Inferred from Genetic Interaction more info	PubMed
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 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 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
involved_in embryonic digestive tract development	ISO Inferred from Sequence Orthology more info
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 glandular epithelial cell development	IGI Inferred from Genetic Interaction 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 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 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
involved_in neural precursor cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neurogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of apoptotic process	IGI Inferred from Genetic Interaction 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
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
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of myelination	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 stem cell proliferation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within striatum development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within ureteric bud development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within ventricular cardiac muscle cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
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	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: retinoic acid receptor beta

Names: RAR-beta; nuclear receptor subfamily 1 group B member 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.

mRNA and Protein(s)

NM_001289760.1 → NP_001276689.1 retinoic acid receptor beta isoform beta3

See identical proteins and their annotated locations for NP_001276689.1

Status: VALIDATED

Description

Transcript Variant: This variant (beta3) encodes the longest isoform (beta3).

Source sequence(s)

AC137681, AC138667, AC167564, BC076597, X56574

UniProtKB/Swiss-Prot

P11417, P22604, P22605

Conserved Domains (2) summary

cd06937
Location:213 → 443

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

cd06964
Location:109 → 193

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
NM_001289761.1 → NP_001276690.1 retinoic acid receptor beta isoform beta1

Status: VALIDATED

Description

Transcript Variant: This variant (beta1) lacks an in-frame exon in the 5' coding region, compared to variant beta3. The resulting isoform (beta1) lacks an internal segment, compared to isoform beta3.

Source sequence(s)

AC138667, AC167564, BC076597, X56569

UniProtKB/Swiss-Prot

P22605

UniProtKB/TrEMBL

Q6DFX0

Conserved Domains (2) summary

cd06937
Location:186 → 416

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

cd06964
Location:82 → 166

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
NM_001289762.1 → NP_001276691.1 retinoic acid receptor beta isoform beta4

Status: VALIDATED

Description

Transcript Variant: This variant (beta4) has an alternate 5' UTR and 5' coding region which is initiated by a non-AUG (CUG) codon, compared to variant beta3. The resulting isoform (beta4) is shorter and has a distinct N-terminus, compared to isoform beta3.

Source sequence(s)

BC076597, S92180, X56573

UniProtKB/TrEMBL

A0A286YCH1

Conserved Domains (2) summary

cd06937
Location:130 → 360

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

cd06964
Location:26 → 110

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
NM_011243.2 → NP_035373.1 retinoic acid receptor beta isoform beta2

See identical proteins and their annotated locations for NP_035373.1

Status: VALIDATED

Description

Transcript Variant: This variant (beta2, also known as beta0) has an alternate 5' UTR and 5' coding region, compared to variant beta3. The resulting isoform (beta2) is shorter and has a distinct N-terminus, compared to isoform beta3.

Source sequence(s)

BC076597, S56660, X56573

Consensus CDS

CCDS26834.1

UniProtKB/TrEMBL

A0A286YCH1, Q6DFX0

Related

ENSMUSP00000067694.7, ENSMUST00000063750.8

Conserved Domains (2) summary

cd06937
Location:179 → 409

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

cd06964
Location:75 → 159

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