Nr1h4 nuclear receptor subfamily 1, group H, member 4 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Nr1h4provided by MGI
Official Full Name: nuclear receptor subfamily 1, group H, member 4provided by MGI
Primary source: MGI:MGI:1352464
See related: Ensembl:ENSMUSG00000047638 AllianceGenome:MGI:1352464
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: Fxr; HRR1; RIP14; Rxrip14
Summary: Enables DNA-binding transcription factor activity, RNA polymerase II-specific; bile acid binding activity; and nuclear retinoid X receptor binding activity. Involved in several processes, including intracellular receptor signaling pathway; negative regulation of cytokine production; and regulation of signal transduction. Acts upstream of or within several processes, including bile acid metabolic process; negative regulation of very-low-density lipoprotein particle remodeling; and positive regulation of transcription by RNA polymerase II. Predicted to be located in euchromatin. Predicted to be part of RNA polymerase II transcription regulator complex and receptor complex. Predicted to be active in nucleus. Is expressed in several structures, including branchial arch; central nervous system; genitourinary system; gut; and sensory organ. Used to study hepatocellular carcinoma. Human ortholog(s) of this gene implicated in extrahepatic cholestasis; hepatocellular carcinoma; and progressive familial intrahepatic cholestasis 5. Orthologous to human NR1H4 (nuclear receptor subfamily 1 group H member 4). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in large intestine adult (RPKM 22.6), liver adult (RPKM 18.8) and 10 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10 C2; 10 44.98 cM

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (89290096..89369484, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (89454234..89533645, complement)

Chromosome 10 - NC_000076.7 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?

Loss of the DNA-binding domain of the farnesoid X receptor gene causes severe liver and kidney injuries.
Title: Loss of the DNA-binding domain of the farnesoid X receptor gene causes severe liver and kidney injuries.
Farnesoid X Receptor Protects Murine Lung against IL-6-promoted Ferroptosis Induced by Polyriboinosinic-Polyribocytidylic Acid.
Title: Farnesoid X Receptor Protects Murine Lung against IL-6-promoted Ferroptosis Induced by Polyriboinosinic-Polyribocytidylic Acid.
Elevated expression of LCN13 through FXR activation ameliorates hepatocellular lipid accumulation and inflammation.
Title: Elevated expression of LCN13 through FXR activation ameliorates hepatocellular lipid accumulation and inflammation.
Nr1h4 and Thrb ameliorate ER stress and provide protection in the MPTP mouse model of Parkinson's.
Title: Nr1h4 and Thrb ameliorate ER stress and provide protection in the MPTP mouse model of Parkinson's.
FXR overexpression prevents hepatic steatosis through inhibiting AIM2 inflammasome activation in alcoholic liver disease.
Title: FXR overexpression prevents hepatic steatosis through inhibiting AIM2 inflammasome activation in alcoholic liver disease.
Farnesoid X receptor mediates macrophage-intrinsic responses to suppress colitis-induced colon cancer progression.
Title: Farnesoid X receptor mediates macrophage-intrinsic responses to suppress colitis-induced colon cancer progression.
Hepatic Zbtb18 (Zinc Finger and BTB Domain Containing 18) alleviates hepatic steatohepatitis via FXR (Farnesoid X Receptor).
Title: Hepatic Zbtb18 (Zinc Finger and BTB Domain Containing 18) alleviates hepatic steatohepatitis via FXR (Farnesoid X Receptor).
Farnesoid X receptor activation protects against renal fibrosis via modulation of beta-catenin signaling.
Title: Farnesoid X receptor activation protects against renal fibrosis via modulation of β-catenin signaling.
FXR controls insulin content by regulating Foxa2-mediated insulin transcription.
Title: FXR controls insulin content by regulating Foxa2-mediated insulin transcription.
Farnesoid X receptor overexpression prevents hepatic steatosis through inhibiting AIM2 inflammasome activation in nonalcoholic fatty liver disease.
Title: Farnesoid X receptor overexpression prevents hepatic steatosis through inhibiting AIM2 inflammasome activation in nonalcoholic fatty liver disease.

Submit: New GeneRIF Correction See all GeneRIFs (253)

Variation

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Alleles

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

Endonuclease-mediated (5) 1 citation
Targeted (10) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

U09416 (e-PCR)
- UniSTS:160018

AI646847 (e-PCR)
- UniSTS:178991

Nr1h4 (e-PCR), detects polymorphism
- UniSTS:527459

AI957360 (e-PCR)
- UniSTS:180099

NoName (e-PCR)
- UniSTS:236437

NoName (e-PCR)
- UniSTS:234914

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info	PubMed
enables DNA-binding transcription factor activity	IGI Inferred from Genetic Interaction more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables bile acid binding	IBA Inferred from Biological aspect of Ancestor more info
enables bile acid binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables bile acid binding	ISO Inferred from Sequence Orthology more info
enables bile acid nuclear receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables chenodeoxycholic acid binding	IEA Inferred from Electronic Annotation more info
enables chenodeoxycholic acid binding	ISO Inferred from Sequence Orthology more info
contributes_to double-stranded 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	PubMed
enables nuclear retinoid X receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables peptide 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 transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coregulator binding	IEA Inferred from Electronic Annotation more info
enables transcription coregulator 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 Notch signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in bile acid and bile salt transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within bile acid metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in bile acid metabolic process	ISO Inferred from Sequence Orthology more info
involved_in bile acid signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in bile acid signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell junction assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to bile acid	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to bile acid	ISO Inferred from Sequence Orthology more info
involved_in cellular response to fatty acid	IEA Inferred from Electronic Annotation more info
involved_in cellular response to fatty acid	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lipopolysaccharide	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to xenobiotic stimulus	ISO Inferred from Sequence Orthology more info
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 defense response to bacterium	IDA Inferred from Direct Assay more info	PubMed
involved_in fatty acid homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in glucose homeostasis	IDA Inferred from Direct Assay more info	PubMed
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in intracellular glucose homeostasis	IDA Inferred from Direct Assay more info	PubMed
involved_in intracellular triglyceride homeostasis	IEA Inferred from Electronic Annotation more info
involved_in intracellular triglyceride homeostasis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of NF-kappaB transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical NF-kappaB signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of collagen biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of inflammatory response	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of inflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of interleukin-1 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of interleukin-2 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of interleukin-6 production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of monocyte chemotactic protein-1 production	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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of triglyceride biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of tumor necrosis factor production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of tumor necrosis factor production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of tumor necrosis factor-mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of type II interferon production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of type II interferon production	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of very-low-density lipoprotein particle remodeling	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of very-low-density lipoprotein particle remodeling	ISO Inferred from Sequence Orthology more info	PubMed
involved_in nuclear receptor-mediated bile acid signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear receptor-mediated bile acid signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info	PubMed
involved_in positive regulation of adipose tissue development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of ammonia assimilation cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of glutamate metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of insulin receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of insulin secretion involved in cellular response to glucose stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of interleukin-17 production	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of interleukin-17 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of phosphatidic acid biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of phosphatidic acid biosynthetic process	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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	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 carbohydrate metabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of insulin secretion involved in cellular response to glucose stimulus	ISO Inferred from Sequence Orthology more info
involved_in regulation of low-density lipoprotein particle clearance	IEA Inferred from Electronic Annotation more info
involved_in regulation of low-density lipoprotein particle clearance	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 regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of urea metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to norepinephrine	ISO Inferred from Sequence Orthology more info
involved_in toll-like receptor 9 signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in triglyceride homeostasis	IDA Inferred from Direct Assay more info	PubMed
involved_in triglyceride homeostasis	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
located_in chromatin	IC Inferred by Curator more info	PubMed
located_in chromatin	ISO Inferred from Sequence Orthology more info	PubMed
located_in euchromatin	IEA Inferred from Electronic Annotation more info
located_in euchromatin	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation 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: bile acid receptor

Names: RXR-interacting protein 14; farnesoid X activated receptor; farnesol receptor HRR-1; retinoid X receptor-interacting protein 14

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_001163504.1 → NP_001156976.1 bile acid receptor isoform 2

See identical proteins and their annotated locations for NP_001156976.1

Status: VALIDATED

Description

Transcript Variant: This variant (2), alternatively referred to as alpha 1, differs in the 5' UTR and 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus compared to isoform 1.

Source sequence(s)

AC152417

Consensus CDS

CCDS48669.1

UniProtKB/Swiss-Prot

Q60641

Related

ENSMUSP00000100934.2, ENSMUST00000105297.2

Conserved Domains (2) summary

cd06936
Location:250 → 469

NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors

cd06962
Location:121 → 208

NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
NM_001163700.1 → NP_001157172.1 bile acid receptor isoform 1

See identical proteins and their annotated locations for NP_001157172.1

Status: VALIDATED

Description

Transcript Variant: This variant (1), alternatively referred to as beta 1 and alpha 3, encodes the longest isoform (1).

Source sequence(s)

AC152417, AK002513

Consensus CDS

CCDS48668.1

UniProtKB/Swiss-Prot

D3YTT2, E9QJW2, Q60641, Q60642, Q60643

Related

ENSMUSP00000100933.3, ENSMUST00000105296.9

Conserved Domains (2) summary

cd06936
Location:264 → 483

NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors

cd06962
Location:135 → 222

NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
NM_001385711.1 → NP_001372640.1 bile acid receptor isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (4), alternatively referred to as alpha 2, differs in the 5' UTR and 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (4) is shorter and has a distinct N-terminus compared to isoform 1.

Source sequence(s)

AC152417

Conserved Domains (2) summary

cd06936
Location:246 → 465

NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors

cd06962
Location:121 → 204

NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
NM_009108.2 → NP_033134.2 bile acid receptor isoform 3

See identical proteins and their annotated locations for NP_033134.2

Status: VALIDATED

Description

Transcript Variant: This variant (3), alternatively referred to as beta 2 and alpha 4, uses an alternate in-frame splice site in the coding region, compared to variant 1. This results in a shorter isoform (2), compared to isoform 1.

Source sequence(s)

AC152417, AK132255

Consensus CDS

CCDS24116.1

UniProtKB/TrEMBL

Q3V1T8

Related

ENSMUSP00000053092.9, ENSMUST00000058126.15

Conserved Domains (2) summary

cd06936
Location:260 → 479

NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors

cd06962
Location:135 → 218

NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) 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_000076.7 Reference GRCm39 C57BL/6J

Range

89290096..89369484 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006513391.4 → XP_006513454.1 bile acid receptor isoform X1

See identical proteins and their annotated locations for XP_006513454.1

UniProtKB/Swiss-Prot

Q60641

Conserved Domains (2) summary

cd06936
Location:250 → 469

NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors

cd06962
Location:121 → 208

NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
XM_030244963.2 → XP_030100823.1 bile acid receptor isoform X1

Conserved Domains (2) summary

cd06936
Location:250 → 469

NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors

cd06962
Location:121 → 208

NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers