Rxrb retinoid X receptor beta [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Rxrbprovided by RGD
Official Full Name: retinoid X receptor betaprovided by RGD
Primary source: RGD:3611
See related: EnsemblRapid:ENSRNOG00000000464 AllianceGenome:RGD:3611
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
Also known as: RXR-beta
Summary: Enables nuclear receptor activity; nuclear receptor binding activity; and nuclear receptor coactivator activity. Involved in regulation of myelination. Predicted to be located in cytosol; nucleolus; and nucleoplasm. Predicted to be part of RNA polymerase II transcription regulator complex. Orthologous to human RXRB (retinoid X receptor beta). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Heart (RPKM 93.4), Adrenal (RPKM 86.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20p12

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (4818707..4824968, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (4816813..4823267, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (3822673..3829138)

Chromosome 20 - NC_086038.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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?

Data suggest cells of the adrenal gland that contain RXRalpha are primarily localized in zona fasciculata and adrenal medulla with RXRalpha almost exclusively localized in cell nucleus; cells that contain RXRbeta are primarily localized in zona fasciculata. RXR ligands, such as all-trans-retinoic acid and long-chain polyunsaturated fatty acids, are also present in the adrenal gland.
Title: Fundamental studies of adrenal retinoid-X-receptor: Protein isoform, tissue expression, subcellular distribution, and ligand availability.
RARalpha and beta isotypes were detected in practically all the male rat brain areas whereas immunostaining was weak or absent in the female brain except RARalpha.
Title: Expression of retinoic acid receptors and retinoid X receptors in normal and vitamin A deficient adult rat brain.
all-trans retinoic acid pre-induction facilitates the neuronal differentiation of mesenchymal stem cells
Title: Retinoic acid receptor beta mediates all-trans retinoic acid facilitation of mesenchymal stem cells neuronal differentiation.
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.
Data describe the role of retinoic acid receptor beta and alpha signalling in adult forebrain neural progenitor cells, and show that RARbeta activation stimulates Sonic hedgehog signalling and induces the cell proliferation.
Title: Sequential RARbeta and alpha signalling in vivo can induce adult forebrain neural progenitor cells to differentiate into neurons through Shh and FGF signalling pathways.
dietary soy proteins affect hepatic RARbeta2 protein content and RARbeta DNA binding activity.
Title: Dietary soy protein isolate modifies hepatic retinoic acid receptor-beta proteins and inhibits their DNA binding activity in rats.

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General gene information

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Markers

BM385817 (e-PCR)
- UniSTS:261386

MARC_5897-5898:997299407:1 (e-PCR)
- UniSTS:269602

UniSTS:237626 (e-PCR)
- UniSTS:237626

MARC_6301-6302:997299518:1 (e-PCR)
- UniSTS:269632

Rxrb (e-PCR), detects polymorphism
- UniSTS:526981

Rxrb (e-PCR), detects polymorphism
- UniSTS:186541

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin DNA 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	IDA Inferred from Direct Assay more info	PubMed
enables nuclear receptor activity	ISO Inferred from Sequence Orthology more info
enables nuclear receptor coactivator activity	IDA Inferred from Direct Assay more info	PubMed
enables nuclear retinoic acid receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables nuclear steroid receptor activity	IEA Inferred from Electronic Annotation more info
enables nuclear thyroid hormone receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables nuclear vitamin D receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
enables retinoic acid-responsive element binding	IBA Inferred from Biological aspect of Ancestor more info
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
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 transcription cis-regulatory region 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 cardiac muscle cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to retinoic acid	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
involved_in intracellular receptor signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within maternal placenta development	ISO Inferred from Sequence Orthology more info
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of DNA-templated transcription	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
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of myelination	IDA Inferred from Direct Assay more info	PubMed
involved_in retinoic acid receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in steroid hormone receptor signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within ventricular cardiac muscle cell differentiation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	IBA Inferred from Biological aspect of Ancestor more info
part_of RNA polymerase II transcription regulator complex	IEA Inferred from Electronic Annotation more info
part_of RNA polymerase II transcription regulator complex	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	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
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: retinoic acid receptor RXR-beta

Names: nuclear receptor co-regulator 1; nuclear receptor coregulator 1; nuclear receptor subfamily 2 group B member 2; 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_206849.3 → NP_996731.2 retinoic acid receptor RXR-beta

See identical proteins and their annotated locations for NP_996731.2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000020

UniProtKB/TrEMBL

A6JJF7, Q499T0

Conserved Domains (3) summary

cd06943
Location:283 → 496

NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

cd06956
Location:189 → 264

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

pfam11825
Location:120 → 174

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

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_086038.1 Reference GRCr8

Range

4818707..4824968 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006255960.5 → XP_006256022.2 retinoic acid receptor RXR-beta isoform X1

Related

ENSRNOP00000109374.1, ENSRNOT00000171523.1
XM_006255961.5 → XP_006256023.1 retinoic acid receptor RXR-beta isoform X2

UniProtKB/TrEMBL

F1M9P1, Q6MGB3

Conserved Domains (3) summary

cd06943
Location:175 → 392

NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

cd06956
Location:81 → 156

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

pfam11825
Location:12 → 66

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1