Rarb retinoic acid receptor, beta [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Rarbprovided by RGD
Full Name: retinoic acid receptor, betaprovided by RGD
Primary source: RGD:3535
See related: EnsemblRapid:ENSRNOG00000024061 AllianceGenome:RGD:3535
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables heterocyclic compound binding activity and nuclear retinoid X receptor binding activity. Involved in neural precursor cell proliferation and regulation of myelination. Predicted to be located in nucleoplasm. 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, Dec 2024]
Expression: Biased expression in Liver (RPKM 117.5), Heart (RPKM 68.7) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 15p16

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	15	NC_086033.1 (10837252..11482037)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	15	NC_051350.1 (8700533..9051288)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	15	NC_005114.4 (9915223..10262599)

Chromosome 15 - NC_086033.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Maternal vitamin A deficiency impairs cholinergic and nitrergic neurons, leading to gastrointestinal dysfunction in rat offspring via RARbeta.
Title: Maternal vitamin A deficiency impairs cholinergic and nitrergic neurons, leading to gastrointestinal dysfunction in rat offspring via RARβ.
RARbeta in the kidney, which was induced in a retinoic acid-dependent manner, was downregulated by 90% in nonobese Goto-Kakizaki rats.
Title: High dietary fat-induced obesity in Wistar rats and type 2 diabetes in nonobese Goto-Kakizaki rats differentially affect retinol binding protein 4 expression and vitamin A metabolism.
Activation of RARBeta in the neuron induces its transfer into astrocytes where it prevents scar formation.
Title: Neuronal RARβ Signaling Modulates PTEN Activity Directly in Neurons and via Exosome Transfer in Astrocytes to Prevent Glial Scar Formation and Induce Spinal Cord Regeneration.
Its expression is involved in axonal regeneration in CNS neurons.
Title: Neuritogenic activity of trichostatin A in adult rat retinal ganglion cells through acetylation of histone H3 lysine 9 and RARβ induction.
There was no significant difference in RARbeta between the groups
Title: Effect of marginal vitamin A deficiency during pregnancy on retinoic acid receptors and N-methyl-D-aspartate receptor expression in the offspring of rats.
Immunohistochemical analysis of normal vocal folds revealed expression of retinoic acid receptor a in vocal fold stellate cells.
Title: Roles of vitamin A and macula flava in maintaining vocal folds.

Submit: New GeneRIF Correction

General gene information

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Markers

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

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

AW531034 (e-PCR)
- UniSTS:245066

RARB-707F (e-PCR)
- UniSTS:20814

D15Got21 (e-PCR)
- UniSTS:113763

BE119548 (e-PCR)
- UniSTS:249215

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

RH133722 (e-PCR)
- UniSTS:217005

AW529852 (e-PCR)
- UniSTS:261294

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

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables heterocyclic compound binding	IDA Inferred from Direct Assay more info	PubMed
enables nuclear receptor activity	ISO Inferred from Sequence Orthology more info
enables nuclear receptor activity	NAS Non-traceable Author Statement more info	PubMed
enables nuclear retinoid X receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA 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 apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within bone development	ISO Inferred from Sequence Orthology more info
acts_upstream_of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in embryonic digestive tract 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 glandular epithelial cell development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within growth plate cartilage development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within multicellular organism growth	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation 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 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
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in neural precursor cell proliferation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within neurogenesis	ISO Inferred from Sequence Orthology more info
involved_in outflow tract septum morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of apoptotic process	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
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
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of myelination	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of stem cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within striatum development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ureteric bud development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ventricular cardiac muscle cell differentiation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology 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

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_031529.1 → NP_113717.1 retinoic acid receptor beta

See identical proteins and their annotated locations for NP_113717.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000015

UniProtKB/TrEMBL

A0A8I6AIB6, A6K045, D3ZFD9

Related

ENSRNOP00000036692.5, ENSRNOT00000033048.8

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

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_086033.1 Reference GRCr8

Range

10837252..11482037

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017599578.3 → XP_017455067.1 retinoic acid receptor beta isoform X1

UniProtKB/TrEMBL

A0A8I6A7Z0, A0A8I6AIB6

Related

ENSRNOP00000098454.2, ENSRNOT00000120842.2

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
XM_017599579.3 → XP_017455068.1 retinoic acid receptor beta isoform X2

UniProtKB/TrEMBL

A0A8I6AIB6

Conserved Domains (2) summary

cd06937
Location:67 → 297

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

cl02596
Location:1 → 47

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