Nr1h3 nuclear receptor subfamily 1, group H, member 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Nr1h3provided by MGI
Official Full Name: nuclear receptor subfamily 1, group H, member 3provided by MGI
Primary source: MGI:MGI:1352462
See related: Ensembl:ENSMUSG00000002108 AllianceGenome:MGI:1352462
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: LXR; RLD1; Unr1
Summary: Enables DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin DNA binding activity. Contributes to nuclear receptor activity and transcription cis-regulatory region binding activity. Involved in several processes, including cholesterol homeostasis; negative regulation of secretion; and regulation of transcription by RNA polymerase II. Acts upstream of or within cellular lipid metabolic process and negative regulation of DNA-templated transcription. Located in cytoplasm and nucleus. Part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including 1st branchial arch; genitourinary system; gut; hemolymphoid system gland; and nervous system. Used to study ovarian hyperstimulation syndrome. Human ortholog(s) of this gene implicated in cerebral infarction; cerebrovascular disease; myocardial infarction; and obesity. Orthologous to human NR1H3 (nuclear receptor subfamily 1 group H member 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in liver adult (RPKM 58.9), subcutaneous fat pad adult (RPKM 41.9) and 21 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 E1; 2 50.52 cM

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (91014406..91033189, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (91184061..91202829, complement)

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 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?

LXR-dependent enhancer activation regulates the temporal organization of the liver's response to refeeding leading to lipogenic gene overshoot.
Title: LXR-dependent enhancer activation regulates the temporal organization of the liver's response to refeeding leading to lipogenic gene overshoot.
Adipose tissue peroxisomal lipid synthesis orchestrates obesity and insulin resistance through LXR-dependent lipogenesis.
Title: Adipose tissue peroxisomal lipid synthesis orchestrates obesity and insulin resistance through LXR-dependent lipogenesis.
Enhanced liver X receptor signalling reduces brain injury and promotes tissue regeneration following experimental intracerebral haemorrhage: roles of microglia/macrophages.
Title: Enhanced liver X receptor signalling reduces brain injury and promotes tissue regeneration following experimental intracerebral haemorrhage: roles of microglia/macrophages.
Activation of NR1H3 signaling pathways by psoralidin attenuates septic myocardial injury.
Title: Activation of NR1H3 signaling pathways by psoralidin attenuates septic myocardial injury.
Sterol-regulated transmembrane protein TMEM86a couples LXR signaling to regulation of lysoplasmalogens in macrophages.
Title: Sterol-regulated transmembrane protein TMEM86a couples LXR signaling to regulation of lysoplasmalogens in macrophages.
Liver X receptor controls follicular helper T cell differentiation via repression of TCF-1.
Title: Liver X receptor controls follicular helper T cell differentiation via repression of TCF-1.
Pioneer factor Foxa2 enables ligand-dependent activation of type II nuclear receptors FXR and LXRalpha.
Title: Pioneer factor Foxa2 enables ligand-dependent activation of type II nuclear receptors FXR and LXRα.
Liver X receptors regulate natural killer T cell population and antitumor activity in the liver of mice.
Title: Liver X receptors regulate natural killer T cell population and antitumor activity in the liver of mice.
Liver X receptor beta deficiency attenuates autoimmune-associated neuroinflammation in a T cell-dependent manner.
Title: Liver X receptor beta deficiency attenuates autoimmune-associated neuroinflammation in a T cell-dependent manner.
Hepatic lysosomal acid lipase drives the autophagy-lysosomal response and alleviates cholesterol metabolic disorder in ApoE deficient mice.
Title: Hepatic lysosomal acid lipase drives the autophagy-lysosomal response and alleviates cholesterol metabolic disorder in ApoE deficient mice.

Submit: New GeneRIF Correction See all GeneRIFs (277)

Variation

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Alleles

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

Endonuclease-mediated (2)
Targeted (14) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC33205P3 (e-PCR)
- UniSTS:273158

RH136462 (e-PCR)
- UniSTS:210448

ksks34 (e-PCR)
- UniSTS:514386

STS-U22662 (e-PCR)
- UniSTS:66401

Nr1h3 (e-PCR), detects polymorphism
- UniSTS:547277

Nr1h3 (e-PCR), detects polymorphism
- UniSTS:536536

MARC_26635-26636:1034090477:1 (e-PCR)
- UniSTS:269047

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
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 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor 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	ISS Inferred from Sequence or Structural Similarity 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	ISO Inferred from Sequence Orthology more info
enables sterol response element binding	IEA Inferred from Electronic Annotation more info
enables sterol response element binding	ISO Inferred from Sequence Orthology more info
contributes_to transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to transcription cis-regulatory region 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
involved_in apoptotic cell clearance	IEA Inferred from Electronic Annotation more info
involved_in apoptotic cell clearance	ISO Inferred from Sequence Orthology more info
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cellular lipid metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to lipopolysaccharide	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in cholesterol homeostasis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cholesterol homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cholesterol homeostasis	ISO Inferred from Sequence Orthology more info
involved_in fatty acid biosynthetic process	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
involved_in intracellular receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in lipid homeostasis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in lipid homeostasis	IMP Inferred from Mutant Phenotype 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
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cholesterol storage	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of cholesterol storage	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cold-induced thermogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of inflammatory response	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of inflammatory response	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of lipid transport	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of lipid transport	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of macrophage activation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of pancreatic juice secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of pinocytosis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of pinocytosis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of proteolysis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of response to endoplasmic reticulum stress	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of secretion of lysosomal enzymes	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in phosphatidylcholine acyl-chain remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cholesterol efflux	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cholesterol efflux	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of fatty acid biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of fatty acid biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of lipid biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of lipoprotein lipase activity	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of lipoprotein lipase activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein metabolic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein metabolic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of toll-like receptor 4 signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of toll-like receptor 4 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
involved_in 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	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 triglyceride biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of triglyceride biosynthetic process	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 fatty acid metabolic process	ISO Inferred from Sequence Orthology more info
involved_in response to progesterone	IEA Inferred from Electronic Annotation more info
involved_in response to progesterone	ISO Inferred from Sequence Orthology more info
involved_in sterol homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in triglyceride homeostasis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in triglyceride homeostasis	IMP Inferred from Mutant Phenotype 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
located_in chromatin	IEA Inferred from Electronic Annotation more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology 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
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of receptor complex	IEA Inferred from Electronic Annotation more info
part_of receptor complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: oxysterols receptor LXR-alpha

Names: LXR alpha; liver X receptor alpha; ubiquitously-expressed nuclear receptor 1

NP_001171201.1

EC 3.4.13.9

NP_001342208.1

EC 3.4.13.9

NP_038867.2

EC 3.4.13.9

XP_006499230.1

EC 3.4.13.9

XP_006499231.1

EC 3.4.13.9

XP_030105325.1

EC 3.4.13.9

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_001177730.1 → NP_001171201.1 oxysterols receptor LXR-alpha

See identical proteins and their annotated locations for NP_001171201.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) contains a different segment for its 5' UTR, compared to variant 1. Variants 1, 2, and 3 all encode the same protein.

Source sequence(s)

AK143904, AL691450

Consensus CDS

CCDS16426.1

UniProtKB/Swiss-Prot

Q9QUH7, Q9Z0Y9

UniProtKB/TrEMBL

A2AGR4, Q91X41

Related

ENSMUSP00000002177.3, ENSMUST00000002177.9

Conserved Domains (2) summary

cd06954
Location:208 → 443

NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors

cd07160
Location:76 → 176

NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
NM_001355279.1 → NP_001342208.1 oxysterols receptor LXR-alpha

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 all encode the same protein.

Source sequence(s)

AL691450

Consensus CDS

CCDS16426.1

UniProtKB/Swiss-Prot

Q9QUH7, Q9Z0Y9

UniProtKB/TrEMBL

A2AGR4, Q91X41

Related

ENSMUSP00000106986.2, ENSMUST00000111354.2

Conserved Domains (2) summary

cd06954
Location:208 → 443

NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors

cd07160
Location:76 → 176

NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
NM_013839.4 → NP_038867.2 oxysterols receptor LXR-alpha

See identical proteins and their annotated locations for NP_038867.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript. Variants 1, 2, and 3 all encode the same protein.

Source sequence(s)

AK159250, AL691450

Consensus CDS

CCDS16426.1

UniProtKB/Swiss-Prot

Q9QUH7, Q9Z0Y9

UniProtKB/TrEMBL

A2AGR4, Q91X41

Related

ENSMUSP00000106988.2, ENSMUST00000111356.8

Conserved Domains (2) summary

cd06954
Location:208 → 443

NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors

cd07160
Location:76 → 176

NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers

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

91014406..91033189 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006499168.4 → XP_006499231.1 oxysterols receptor LXR-alpha isoform X1

See identical proteins and their annotated locations for XP_006499231.1

UniProtKB/Swiss-Prot

Q9QUH7, Q9Z0Y9

UniProtKB/TrEMBL

A2AGR4, Q91X41

Conserved Domains (2) summary

cd06954
Location:208 → 443

NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors

cd07160
Location:76 → 176

NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
XM_030249465.2 → XP_030105325.1 oxysterols receptor LXR-alpha isoform X1

UniProtKB/Swiss-Prot

Q9QUH7, Q9Z0Y9

UniProtKB/TrEMBL

A2AGR4, Q91X41

Conserved Domains (2) summary

cd06954
Location:208 → 443

NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors

cd07160
Location:76 → 176

NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers
XM_006499167.4 → XP_006499230.1 oxysterols receptor LXR-alpha isoform X1

See identical proteins and their annotated locations for XP_006499230.1

UniProtKB/Swiss-Prot

Q9QUH7, Q9Z0Y9

UniProtKB/TrEMBL

A2AGR4, Q91X41

Conserved Domains (2) summary

cd06954
Location:208 → 443

NR_LBD_LXR; The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors

cd07160
Location:76 → 176

NR_DBD_LXR; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers