Rxra retinoid X receptor alpha [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rxraprovided by MGI
Official Full Name: retinoid X receptor alphaprovided by MGI
Primary source: MGI:MGI:98214
See related: Ensembl:ENSMUSG00000015846 AllianceGenome:MGI:98214
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: Nr2b1; RXRalpha1; 9530071D11Rik
Summary: Enables DNA binding activity; DNA-binding transcription factor activity; and transcription coactivator binding activity. Contributes to nuclear receptor activity and transcription cis-regulatory region binding activity. Involved in several processes, including mRNA transcription by RNA polymerase II; positive regulation of thyroid hormone receptor signaling pathway; and retinoic acid receptor signaling pathway. Acts upstream of or within several processes, including cardiac muscle tissue development; regulation of branching involved in prostate gland morphogenesis; and regulation of gene expression. Located in nucleus. Part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; liver; and sensory organ. Used to study congenital heart disease; dilated cardiomyopathy; and systemic lupus erythematosus. Human ortholog(s) of this gene implicated in pancreatic cancer. Orthologous to human RXRA (retinoid X receptor alpha). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in liver adult (RPKM 80.9), mammary gland adult (RPKM 32.7) and 23 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 A3; 2 19.38 cM

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (27566457..27653331)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (27676445..27763319)

Chromosome 2 - NC_000068.8 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?

Activation of RXRalpha exerts cardioprotection through transcriptional upregulation of Ndufs4 in heart failure.
Title: Activation of RXRα exerts cardioprotection through transcriptional upregulation of Ndufs4 in heart failure.
Inhibition of RXRA-mediated PLA2G2A improves delirium in COPD mice by regulating endoplasmic reticulum stress pathway and inhibiting cell apoptosis.
Title: Inhibition of RXRA-mediated PLA2G2A improves delirium in COPD mice by regulating endoplasmic reticulum stress pathway and inhibiting cell apoptosis.
The Transcription Factor RXRalpha in CD11c+ APCs Regulates Intestinal Immune Homeostasis and Inflammation.
Title: The Transcription Factor RXRα in CD11c+ APCs Regulates Intestinal Immune Homeostasis and Inflammation.
Transcriptional control of nucleus accumbens neuronal excitability by retinoid X receptor alpha tunes sensitivity to drug rewards.
Title: Transcriptional control of nucleus accumbens neuronal excitability by retinoid X receptor alpha tunes sensitivity to drug rewards.
Addiction neuroscience goes nuclear: A role for the transcription factor RXRalpha.
Title: Addiction neuroscience goes nuclear: A role for the transcription factor RXRα.
Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of Egr1, Rxra and Max in kidney stone disease.
Title: Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of Egr1, Rxra and Max in kidney stone disease.
Phosphorylation of RXRalpha mediates the effect of JNK to suppress hepatic FGF21 expression and promote metabolic syndrome.
Title: Phosphorylation of RXRα mediates the effect of JNK to suppress hepatic FGF21 expression and promote metabolic syndrome.
RXRA DT448/9PP generates a dominant active variant capable of inducing maturation in acute myeloid leukemia cells.
Title: RXRA DT448/9PP generates a dominant active variant capable of inducing maturation in acute myeloid leukemia cells.
T-Cell Death Associated Gene 51 Is a Novel Negative Regulator of PPARgamma That Inhibits PPARgamma-RXRalpha Heterodimer Formation in Adipogenesis
Title: T-Cell Death Associated Gene 51 Is a Novel Negative Regulator of PPARγ That Inhibits PPARγ-RXRα Heterodimer Formation in Adipogenesis.
Structural Insights into the Interaction of the Intrinsically Disordered Co-activator TIF2 with Retinoic Acid Receptor Heterodimer (RXR/RAR).
Title: Structural Insights into the Interaction of the Intrinsically Disordered Co-activator TIF2 with Retinoic Acid Receptor Heterodimer (RXR/RAR).

Submit: New GeneRIF Correction See all GeneRIFs (108)

Variation

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Alleles

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

Chemically induced (ENU) (1) 1 citation
Endonuclease-mediated (2)
Gene trapped (1)
Targeted (11) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Rxra (e-PCR), detects polymorphism
- UniSTS:527530

Rxra (e-PCR), detects polymorphism
- UniSTS:186540

D2Mit120 (e-PCR), detects polymorphism
- UniSTS:128979

NoName (e-PCR)
- UniSTS:548564

Rxra (e-PCR), detects polymorphism
- UniSTS:536547

Rxra (e-PCR), detects polymorphism
- UniSTS:519412

Rxra (e-PCR), detects polymorphism
- UniSTS:465406

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding domain binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IGI Inferred from Genetic Interaction more info	PubMed
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables LBD domain binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin DNA binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
contributes_to nuclear receptor activity	IDA Inferred from Direct Assay more info	PubMed
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 retinoic acid receptor binding	ISO Inferred from Sequence Orthology more info
enables nuclear steroid receptor activity	IEA Inferred from Electronic Annotation more info
enables nuclear thyroid hormone receptor binding	ISO Inferred from Sequence Orthology more info
enables nuclear vitamin D receptor binding	ISO Inferred from Sequence Orthology more info
enables peptide binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables retinoic acid binding	ISO Inferred from Sequence Orthology more info
enables retinoic acid-responsive element binding	IBA Inferred from Biological aspect of Ancestor more info
enables retinoic acid-responsive element binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	IGI Inferred from Genetic 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
contributes_to transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coregulator binding	ISO Inferred from Sequence Orthology more info
contributes_to vitamin D response element binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in angiogenesis involved in coronary vascular morphogenesis	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within camera-type eye development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cardiac muscle cell differentiation	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within cardiac muscle cell proliferation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cardiac muscle cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cardiac muscle cell proliferation	TAS Traceable Author Statement more info	PubMed
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within embryo implantation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart development	TAS Traceable Author Statement more info	PubMed
involved_in heart morphogenesis	TAS Traceable Author Statement more info	PubMed
involved_in hormone-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in hormone-mediated signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within in utero embryonic development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in mRNA transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in mRNA transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within maternal placenta development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in mesenchyme development	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in peroxisome proliferator activated receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within placenta development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of DNA-templated transcription	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of bone mineralization	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of thyroid hormone receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of thyroid hormone receptor signaling pathway	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	IDA Inferred from Direct Assay more info	PubMed
involved_in 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_or_within positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
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 positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within positive regulation of translational initiation by iron	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of vitamin D receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of branching involved in prostate gland morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of myelination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in response to glucocorticoid	ISO Inferred from Sequence Orthology more info
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	IDA Inferred from Direct Assay more info	PubMed
involved_in retinoic acid receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
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_or_within secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in steroid hormone receptor signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within ventricular cardiac muscle cell differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within ventricular cardiac muscle cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within ventricular cardiac muscle tissue morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in visceral serous pericardium development	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	EXP Inferred from Experiment more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
part_of RNA polymerase II transcription regulator complex	ISO Inferred from Sequence Orthology more info
part_of RNA polymerase II transcription regulator complex	ISS Inferred from Sequence or Structural Similarity more info
part_of RNA polymerase II transcription regulator complex	NAS Non-traceable Author Statement more info	PubMed
located_in axon	ISO Inferred from Sequence Orthology more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of receptor complex	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	EXP Inferred from Experiment more info	PubMed
part_of transcription regulator complex	IPI Inferred from Physical Interaction more info	PubMed
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: retinoic acid receptor RXR-alpha

Names: RXR alpha 1; nuclear receptor subfamily 2 group B member 1

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_001290481.1 → NP_001277410.1 retinoic acid receptor RXR-alpha isoform 2

See identical proteins and their annotated locations for NP_001277410.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) contains an alternate 5' terminal exon and it thus differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1. Both variants 2 and 3 encode isoform 2.

Source sequence(s)

AI647710, AK029121, BC138800

Consensus CDS

CCDS71011.1

UniProtKB/TrEMBL

Q3UMU4, Q6LC96

Related

ENSMUSP00000097822.3, ENSMUST00000100251.9

Conserved Domains (3) summary

cd06943
Location:206 → 417

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

cd06956
Location:110 → 186

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

pfam11825
Location:1 → 103

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
NM_001290482.1 → NP_001277411.1 retinoic acid receptor RXR-alpha isoform 2

See identical proteins and their annotated locations for NP_001277411.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) contains an alternate 5' terminal exon and it thus differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1. Both variants 2 and 3 encode isoform 2.

Source sequence(s)

AK029121, AL772166, BC138800

Consensus CDS

CCDS71011.1

UniProtKB/TrEMBL

Q3UMU4, Q6LC96

Related

ENSMUSP00000109567.2, ENSMUST00000113934.2

Conserved Domains (3) summary

cd06943
Location:206 → 417

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

cd06956
Location:110 → 186

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

pfam11825
Location:1 → 103

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
NM_011305.3 → NP_035435.1 retinoic acid receptor RXR-alpha isoform 1

See identical proteins and their annotated locations for NP_035435.1

Status: VALIDATED

Description

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

Source sequence(s)

AK029121, AK144675, X66223

Consensus CDS

CCDS15830.1

UniProtKB/Swiss-Prot

P28700

UniProtKB/TrEMBL

A2AJP1, Q3UMU4

Related

ENSMUSP00000076491.6, ENSMUST00000077257.12

Conserved Domains (3) summary

cd06943
Location:234 → 445

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

cd06956
Location:138 → 214

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

pfam11825
Location:18 → 131

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

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

NC_000068.8 Reference GRCm39 C57BL/6J

Range

27566457..27653331

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006497805.2 → XP_006497868.1 retinoic acid receptor RXR-alpha isoform X1

See identical proteins and their annotated locations for XP_006497868.1

UniProtKB/TrEMBL

Q3UMU4, Q6LC96

Related

ENSMUSP00000159198.2, ENSMUST00000238913.2

Conserved Domains (3) summary

cd06943
Location:206 → 417

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

cd06956
Location:110 → 186

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

pfam11825
Location:1 → 103

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
XM_030248867.2 → XP_030104727.1 retinoic acid receptor RXR-alpha isoform X1

UniProtKB/TrEMBL

Q3UMU4, Q6LC96

Conserved Domains (3) summary

cd06943
Location:206 → 417

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

cd06956
Location:110 → 186

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

pfam11825
Location:1 → 103

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