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nr1h4 nuclear receptor subfamily 1, group H, member 4 [ Danio rerio (zebrafish) ]

Gene ID: 436847, updated on 11-Apr-2024

Summary

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Official Symbol
nr1h4provided by ZNC
Official Full Name
nuclear receptor subfamily 1, group H, member 4provided by ZNC
Primary source
ZFIN:ZDB-GENE-040718-313
See related
Ensembl:ENSDARG00000057741 AllianceGenome:ZFIN:ZDB-GENE-040718-313
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
fxr; zgc:92742; zgc:110190
Summary
Enables bile acid binding activity and nuclear receptor activity. Acts upstream of or within regulation of transcription, DNA-templated. Predicted to be located in nucleus. Is expressed in intestinal bulb and liver. 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]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 18
Exon count:
11
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 18 NC_007129.7 (15644559..15667016)
105 previous assembly GRCz10 (GCF_000002035.5) 18 NC_007129.6 (15676047..15698432)

Chromosome 18 - NC_007129.7Genomic Context describing neighboring genes Neighboring gene basic helix-loop-helix ARNT like 2 Neighboring gene solute carrier family 17 member 8 Neighboring gene si:ch211-264e16.2 Neighboring gene si:ch211-264e16.1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Evolution of the bile salt nuclear receptor FXR in vertebrates. Reschly EJ, et al. J Lipid Res, 2008 Jul. PMID 18362391, Free PMC Article
  2. Ligand specificity and evolution of liver X receptors. Reschly EJ, et al. J Steroid Biochem Mol Biol, 2008 May. PMID 18395439, Free PMC Article
  3. The evolution of farnesoid X, vitamin D, and pregnane X receptors: insights from the green-spotted pufferfish (Tetraodon nigriviridis) and other non-mammalian species. Krasowski MD, et al. BMC Biochem, 2011 Feb 3. PMID 21291553, Free PMC Article
  4. Disturbances in Microbial and Metabolic Communication across the Gut-Liver Axis Induced by a Dioxin-like Pollutant: An Integrated Metagenomics and Metabolomics Analysis. Hu C, et al. Environ Sci Technol, 2021 Jan 5. PMID 33356191
  5. Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine. Wen J, et al. Sci Adv, 2021 Jul. PMID 34301599, Free PMC Article

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Markers

Homology

Clone Names

  • MGC110190

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables bile acid binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables bile acid binding IEA
Inferred from Electronic Annotation
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
  
enables nuclear receptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables nuclear receptor activity IEA
Inferred from Electronic Annotation
more info
  
enables sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in bile acid signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within bile acid signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative 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 IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex IBA
Inferred from Biological aspect of Ancestor
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
  

General protein information

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Preferred Names
bile acid receptor
Names
FXRalpha

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)

  1. NM_001002574.1 → NP_001002574.1  bile acid receptor

    See identical proteins and their annotated locations for NP_001002574.1

    Status: PROVISIONAL

    Source sequence(s)
    BC076220
    UniProtKB/TrEMBL
    Q6DGW7
    Related
    ENSDARP00000061793.4, ENSDART00000061794.5
    Conserved Domains (2) summary
    cd06936
    Location:258 → 478
    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:134 → 217
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007129.7 Reference GRCz11 Primary Assembly

    Range
    15644559..15667016
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005169927.4 → XP_005169984.1  bile acid receptor isoform X1

    UniProtKB/TrEMBL
    A0A8M2BHM4
    Conserved Domains (2) summary
    cd06936
    Location:235 → 455
    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:111 → 194
    NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers

Reference GRCz11 ALT_DRER_TU_2

Genomic

  1. NW_018395336.1 Reference GRCz11 ALT_DRER_TU_2

    Range
    185700..212763
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

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