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

Gene ID: 20186, updated on 5-Jan-2023

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 retinoid X receptor binding activity. Involved in several processes, including lipid homeostasis; negative regulation of cytokine production; and regulation of signal transduction. Acts upstream of or within several processes, including Notch signaling pathway; bile acid metabolic process; and negative regulation of very-low-density lipoprotein particle remodeling. Predicted to be located in euchromatin and nucleus. Predicted to be part of receptor complex. Is expressed in several structures, including 1st branchial arch; central nervous system; liver; sensory organ; and urinary system. 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, Apr 2022]
Expression
Biased expression in large intestine adult (RPKM 22.6), liver adult (RPKM 18.8) and 10 other tissues See more
Orthologs
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Genomic context

See Nr1h4 in Genome Data Viewer
Location:
10 C2; 10 44.98 cM
Exon count:
12
Annotation release Status Assembly Chr Location
109 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_000076.7Genomic Context describing neighboring genes Neighboring gene anoctamin 4 Neighboring gene predicted gene, 30769 Neighboring gene growth arrest-specific 2 like 3 Neighboring gene solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8 Neighboring gene SCY1-like 2 (S. cerevisiae)

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

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
PubMed 
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
PubMed 
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 receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables bile acid receptor activity IC
Inferred by Curator
more info
PubMed 
enables bile acid receptor activity ISO
Inferred from Sequence Orthology
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 metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables nuclear receptor activity IMP
Inferred from Mutant Phenotype
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 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
PubMed 
involved_in bile acid signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
PubMed 
involved_in cell-cell junction assembly 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 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 organonitrogen compound 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 
acts_upstream_of_or_within immune system process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within inflammatory response IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within innate immune response IEA
Inferred from Electronic Annotation
more info
 
involved_in intracellular bile acid receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in intracellular glucose homeostasis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in intracellular receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in intracellular triglyceride homeostasis ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of I-kappaB kinase/NF-kappaB signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of I-kappaB kinase/NF-kappaB signaling 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 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
PubMed 
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
PubMed 
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 nitrogen catabolite activation of transcription from RNA polymerase II promoter IC
Inferred by Curator
more info
PubMed 
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 ISO
Inferred from Sequence Orthology
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
PubMed 
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 gene expression 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 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 4 signaling pathway 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
located_in chromatin IC
Inferred by Curator
more info
PubMed 
located_in chromatin ISO
Inferred from Sequence Orthology
more info
PubMed 
located_in euchromatin ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
part_of receptor complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

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)

NEW Try the new Transcript table

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)

  1. NM_001163504.1NP_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:250469
    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:121208
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  2. NM_001163700.1NP_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
    Q60641, Q60643
    Related
    ENSMUSP00000100933.3, ENSMUST00000105296.9
    Conserved Domains (2) summary
    cd06936
    Location:264483
    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:135222
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  3. NM_001385711.1NP_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:246465
    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:121204
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  4. NM_009108.2NP_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:260479
    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:135218
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000076.7 Reference GRCm39 C57BL/6J

    Range
    89290096..89369484 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006513391.4XP_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:250469
    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:121208
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
  2. XM_030244963.2XP_030100823.1  bile acid receptor isoform X1

    Conserved Domains (2) summary
    cd06936
    Location:250469
    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:121208
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers

RNA

  1. XR_001779493.2 RNA Sequence