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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

NR1H4 Gene

protein-coding   GIFtS: 66
GCID: GC12P100867

Nuclear Receptor Subfamily 1, Group H, Member 4

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Nuclear Receptor Subfamily 1, Group H, Member 41 2     HRR12 3
FXR2 3 5     RXR-Interacting Protein 142 3
RIP142 3 5     HRR-12
Farnesoid X-Activated Receptor2 3     Bile Acid Receptor2
Farnesol Receptor HRR-12 3     Farnesoid X Nuclear Receptor2
Retinoid X Receptor-Interacting Protein 142 3     Nuclear Receptor Subfamily 1 Group H Member 43
BAR2 3     

External Ids:    HGNC: 79671   Entrez Gene: 99712   Ensembl: ENSG000000125047   OMIM: 6038265   UniProtKB: Q96RI13   

Export aliases for NR1H4 gene to outside databases

Previous GC identifers: GC12P100078 GC12P100850 GC12P099370 GC12P097928


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for NR1H4 Gene:
This gene encodes a ligand-activated transcription factor, which shares structural features in common with nuclear
hormone receptor family, such as a DNA-binding domain that targets the receptor to specific DNA sequences, and a
ligand-binding domain, which interacts directly with the ligand and contains a ligand-dependent transcriptional
activation domain. This protein functions as a receptor for bile acids, and when bound to bile acids, regulates
the expression of genes involved in bile acid synthesis and transport. Alternatively spliced transcript variants
encoding different isoforms have been described for this gene. (provided by RefSeq, Aug 2011)

GeneCards Summary for NR1H4 Gene: 
NR1H4 (nuclear receptor subfamily 1, group H, member 4) is a protein-coding gene. Diseases associated with NR1H4 include xanthomatosis, and biliary tract disease, and among its related super-pathways are Gene Expression and Nuclear Receptors. GO annotations related to this gene include transcription coactivator activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is VDR.

UniProtKB/Swiss-Prot: NR1H4_HUMAN, Q96RI1
Function: Ligand-activated transcription factor. Receptor for bile acids such as chenodeoxycholic acid,
lithocholic acid and deoxycholic acid. Represses the transcription of the cholesterol 7-alpha-hydroxylase gene
(CYP7A1) through the induction of NR0B2 or FGF19 expression, via two distinct mechanisms. Activates the
intestinal bile acid-binding protein (IBABP). Activates the transcription of bile salt export pump ABCB11 by
directly recruiting histone methyltransferase CARM1 to this locus

summary for NR1H4 Gene:
Liver X receptors (LXRs) and farnesoid X receptors (FXRs) are members of the steroid analog-activated
nuclear receptor subfamily, which form heterodimers with members of the retinoid X receptor family. There
are two closely related isoforms of each of these enzymes; LXRalpha and LXRbeta, and FXRalpha and FXRbeta
(pseudogene in man). LXRalpha and FXRalpha expression is restricted to the liver, small intestine, kidney
and adrenal gland, whilst LXRbeta and FXRbeta are ubiquitously expressed. Despite acting on some of the same
target genes, including cholesterol 7alpha-hydroxylase (CYP7A1) and SREBP-1c, LXRs and FXRs have different
physiological roles. LXRs are involved in cholesterol homeostasis, inhibition of proinflammatory gene
expression in atherosclerosis and activation of innate immunity, whilst FXRs have a vital function in bile
acid homeostasis.

Gene Wiki entry for NR1H4 (Farnesoid X receptor) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000012.11  NT_029419.12  NC_018923.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the NR1H4 gene promoter:
         NF-1   MEF-2   Evi-1   HNF-4alpha1   MEF-2A   PPAR-gamma1   Chx10   PPAR-gamma2   aMEF-2   RSRFC4   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): NR1H4 promoter sequence
   Search SABiosciences Chromatin IP Primers for NR1H4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NR1H4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 12q23.1   Ensembl cytogenetic band:  12q23.1   HGNC cytogenetic band: 12q23.1

NR1H4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NR1H4 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P100867:  view genomic region     (about GC identifiers)

Start:
100,867,486 bp from pter      End:
100,958,191 bp from pter
Size:
90,706 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: NR1H4_HUMAN, Q96RI1 (See protein sequence)
Recommended Name: Bile acid receptor  
Size: 486 amino acids; 55914 Da
Subunit: Heterodimer of NR1H4 and RXR. After activation by agonist binding, interacts with a coactivator, NCOA1 or
NCOA2 (By similarity). Interacts with CARM1 and SMARD1
Subcellular location: Nucleus (Probable)
Sequence caution: Sequence=BC144183; Type=Frameshift; Positions=156;
6/24 PDB 3D structures from and Proteopedia for NR1H4 (see all 24):
1OSH (3D)        1OSK (3D)        3BEJ (3D)        3DCT (3D)        3DCU (3D)        3FLI (3D)    
Secondary accessions: A1L4K5 B7Z412 B7ZM06 F8VYG8 Q8NFP5 Q8NFP6 Q92943
Alternative splicing: 5 isoforms:  Q96RI1-3   Q96RI1-4   Q96RI1-1   Q96RI1-2   Q96RI1-5   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for NR1H4: NX_Q96RI1

Explore proteomics data for NR1H4 at MOPED 

Post-translational modifications:

  • UniProtKB: Methylation may increase transactivation of target genes
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q96RI1

  • NR1H4 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    NR1H4 Protein Expression
    REFSEQ proteins (6 alternative transcripts): 
    NP_001193906.1  NP_001193907.1  NP_001193908.1  NP_001193921.1  NP_001193922.1  NP_005114.1  

    ENSEMBL proteins: 
     ENSP00000448506   ENSP00000376712   ENSP00000315442   ENSP00000448978   ENSP00000446760  
     ENSP00000446584   ENSP00000447149   ENSP00000188403   ENSP00000446861  
    Reactome Protein details: Q96RI1
    Human Recombinant Protein Products for NR1H4: 
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    Novus Biologicals NR1H4 Proteins
    Novus Biologicals NR1H4 Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ----
    GO:0005654nucleoplasm TAS--
    GO:0005719nuclear euchromatin IDA--

    NR1H4 for ontologies           About GeneDecksing



    NR1H4 Antibody Products: 
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    Browse CLIAs at Cloud-Clone Corp.


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    NR: Nuclear hormone receptors

    IUPHAR Guide to PHARMACOLOGY protein family classification: Farnesoid X receptor 
    1H. Liver X receptor-like receptors

    5/6 InterPro protein domains (see all 6):
     IPR008946 Nucl_hormone_rcpt_ligand-bd
     IPR001723 Str_hrmn_rcpt
     IPR001728 ThyrH_rcpt
     IPR013088 Znf_NHR/GATA
     IPR000536 Nucl_hrmn_rcpt_lig-bd_core

    Graphical View of Domain Structure for InterPro Entry Q96RI1

    ProtoNet protein and cluster: Q96RI1

    2 Blocks protein domains:
    IPB000324 Vitamin D receptor signature
    IPB001723 Steroid hormone receptor signature


    UniProtKB/Swiss-Prot: NR1H4_HUMAN, Q96RI1
    Similarity: Belongs to the nuclear hormone receptor family. NR1 subfamily
    Similarity: Contains 1 nuclear receptor DNA-binding domain


    NR1H4 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: NR1H4_HUMAN, Q96RI1
    Function: Ligand-activated transcription factor. Receptor for bile acids such as chenodeoxycholic acid,
    lithocholic acid and deoxycholic acid. Represses the transcription of the cholesterol 7-alpha-hydroxylase gene
    (CYP7A1) through the induction of NR0B2 or FGF19 expression, via two distinct mechanisms. Activates the
    intestinal bile acid-binding protein (IBABP). Activates the transcription of bile salt export pump ABCB11 by
    directly recruiting histone methyltransferase CARM1 to this locus

         Gene Ontology (GO): 5/20 molecular function terms (GO ID links to tree view) (see all 20):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000980RNA polymerase II distal enhancer sequence-specific DNA binding IDA--
    GO:0001190RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription IDA--
    GO:0003677DNA binding ----
    GO:0003700sequence-specific DNA binding transcription factor activity TAS10334992
    GO:0003705RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity IDA--
         
    NR1H4 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for NR1H4:
     Downregulation of NF-kappaB pa  Downregulation of NF-kappaB pa 

         8 MGI mutant phenotypes (inferred from 6 alleles(MGI details for Nr1h4):
     cellular  growth/size  homeostasis/metabolism  immune system  liver/biliary system 
     mortality/aging  no phenotypic analysis  tumorigenesis 

    NR1H4 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for NR1H4: Nr1h4tm1.2Auw Nr1h4tm1Kok Nr1h4tm1Gonz

       inGenious Targeting Laboratory - Custom generated mouse model solutions for NR1H4 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for NR1H4

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for NR1H4 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for NR1H4 

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat NR1H4
    1 QIAGEN miScript miRNA Assays for microRNA that regulate NR1H4:
    hsa-miR-582-5p
    SwitchGear 3'UTR luciferase reporter plasmidNR1H4 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector: NR1H4 (NM_005123)
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NR1H4


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for NR1H4 About   (see all 7)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Generic Transcription Pathway
    Gene Expression0.47
    Generic Transcription Pathway0.47
    2Nuclear Receptor transcription pathway
    Nuclear Receptor transcription pathway0.68
    3Selected targets of HNF1
    Selected targets of HNF1
    4RXR and RAR heterodimerization with other nuclear receptor
    RXR and RAR heterodimerization with other nuclear receptor
    5Nuclear receptors in lipid metabolism and toxicity
    Nuclear receptors in lipid metabolism and toxicity

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 EMD Millipore Pathway for NR1H4
        Selected targets of HNF1


    3 BioSystems Pathways for NR1H4
        Nuclear receptors in lipid metabolism and toxicity
    Drug Induction of Bile Acid Pathway
    RXR and RAR heterodimerization with other nuclear receptor

    3        Reactome Pathways for NR1H4
        Generic Transcription Pathway
    Nuclear Receptor transcription pathway
    Gene Expression


    1         Kegg Pathway  (Kegg details for NR1H4):
        Bile secretion


    NR1H4 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for NR1H4

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/52 Interacting proteins for NR1H4 (Q96RI13 ENSP000003154424) via UniProtKB, MINT, STRING, and/or I2D (see all 52)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053, ENSP000003529804I2D: score=1 STRING: ENSP00000352980
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

    Gene Ontology (GO): 5/25 biological process terms (GO ID links to tree view) (see all 25):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter ISS--
    GO:0001080nitrogen catabolite activation of transcription from RNA polymerase II promoter IC--
    GO:0006109regulation of carbohydrate metabolic process IEA--
    GO:0006351transcription, DNA-dependent ----
    GO:0006355regulation of transcription, DNA-dependent ----

    NR1H4 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    NR1H4 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Enzo Life Sciences drugs & compounds for NR1H4

    Compounds for NR1H4 available from Tocris Bioscience    About this table
    CompoundAction CAS #
    GW 3965 hydrochlorideOrally active liver X receptor (LXR) agonist[405911-09-3]
    GW 4064Selective farnesoid X receptor (FXR) agonist[278779-30-9]
    Fexaramine Potent, selective farnesoid X receptor (FXR) agonist [574013-66-4]
    T 0901317Potent liver X receptor (LXR) agonist; also CAR inverse agonist[293754-55-9]

    2 HMDB Compounds for NR1H4    About this table
    CompoundSynonyms CAS #PubMed Ids
    Deoxycholic acid5b-Cholanic acid-3a,12a-diol (see all 14)83-44-3--
    Lithocholic acid(3a,5b)-3-hydroxy-cholan-24-oate (see all 5)434-13-9--

    3 DrugBank Compounds for NR1H4    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Chenodeoxycholic acidChenocholic acid (see all 3)474-25-9targetother10334992 20104269
    Fexaramine-- 574013-66-4target--17139284 17016423
    (8alpha,10alpha,13alpha,17beta)-17-[(4-hydroxyphenyl)carbonyl]androsta-3,5-diene-3-carboxylic acid-- --target--10592235

    5 IUPHAR Ligands for NR1H4 (Farnesoid X receptor)    About this table 
    LigandTypeActionAffinityPubmed IDs
    GW4064
    AgonistAgonist7.8210956205
    ECDCA
    AgonistAgonist712166927
    fexaramine
    AgonistAgonist6.612718892
    guggulsterone
    AntagonistAntagonist5.7 - 612089353
    22R-hydroxycholesterol
    AgonistAgonist5.516371446

    10/43 Novoseek inferred chemical compound relationships for NR1H4 gene (see all 43)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    gw 4064 97.3 55 12052824 (3), 15882126 (2), 19228886 (2), 11607932 (2) (see all 33)
    chenodeoxycholic acid 94 111 19913492 (3), 17975826 (2), 16522742 (2), 19059462 (2) (see all 55)
    guggulsterone 92.3 38 17135343 (4), 12705905 (3), 17054793 (2), 18519703 (2) (see all 17)
    6-ethylchenodeoxycholic acid 89.6 12 15317466 (1), 18029909 (1), 19864602 (1), 19418582 (1) (see all 5)
    androstane 88.6 39 19300246 (2), 17132852 (1), 18037906 (1), 20048746 (1) (see all 24)
    guggul 85.5 3 16428513 (1), 19102680 (1)
    lithocholic acid 81.6 21 12052824 (5), 16178789 (2), 16946559 (1), 10334993 (1) (see all 7)
    cholesterol 75.2 199 19136377 (4), 12704471 (4), 15558057 (3), 15962294 (3) (see all 94)
    apomine 73.5 1 11350890 (1)
    farnesol 67.1 16 10753967 (1), 17333335 (1), 8625436 (1), 16540091 (1) (see all 9)

    Search CenterWatch for drugs/clinical trials and news about NR1H4

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
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    About This Section

    REFSEQ mRNAs for NR1H4 gene (6 alternative transcripts): 
    NM_001206977.1  NM_001206978.1  NM_001206979.1  NM_001206992.1  NM_001206993.1  NM_005123.3  

    Unigene Cluster for NR1H4:

    Nuclear receptor subfamily 1, group H, member 4
    Hs.282735  [show with all ESTs]
    Unigene Representative Sequence: NM_001206977
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000548884(uc001thq.2 uc001thp.2 uc001thr.2 uc010svk.2 uc010svj.2 uc001ths.2 uc001tht.2)
    ENST00000392986 ENST00000321046 ENST00000549996 ENST00000546380 ENST00000548621
    ENST00000551379 ENST00000188403 ENST00000551184
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    Additional mRNA sequence: 

    AB307699.1 AF384555.1 AF478445.1 AF478446.1 AK296612.1 AK296647.1 AK312959.1 BC035654.1 
    BC071778.1 BC130573.1 BC144183.1 BC144184.1 BC144187.1 BX571749.1 HQ709175.1 U68233.1 

    6 DOTS entries:

    DT.213616  DT.100021403  DT.100746912  DT.40229020  DT.444293  DT.402350 

    24/60 AceView cDNA sequences (see all 60):

    AI051958 BX571749 BX102734 BC035654 AA912967 AI075131 BC071778 AF478446 
    AF478445 AU104249 CB162215 AI628645 AI245366 AF384555 T89438 BM545805 
    CD619886 AI913526 CB111965 BX092610 AI023303 AA682292 U68233 AA862482 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for NR1H4 (see all 7)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b
    SP1:                          -           -                       -     -                 -                                             
    SP2:                                                              -     -                                                               
    SP3:                                                                    -                 -                                             
    SP4:                                                                    -                                                               
    SP5:                                                                                                                                    


    ECgene alternative splicing isoforms for NR1H4

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    NR1H4 expression in normal human tissues (normalized intensities)      NR1H4 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    NR1H4 Expression
    About this image


    NR1H4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/6 selected tissues (see all 6) fully expand
     
     Kidney (Urinary System)    fully expand to see all 4 entries
             Proximal Tubule Cells Proximal Tubule
             Proximal Tubule
             Human Renal Proximal Tubular Epithelial Cells (HRPTEpiC)   
     
     Liver (Hepatobiliary System)    fully expand to see all 3 entries
             Human Mesenchymal Stem Cell-hepatic (HMSC-he)   
     
     Ovary (Reproductive System)
             Granulosa Cells Primary Follicle
     
     Adipose (Muscoskeletal System)
             HyStem+BMP4-induced 7SMOO32 cells
     
     Mesenchymal Stem Cells
             Human Mesenchymal Stem Cell-hepatic (HMSC-he)   

    See NR1H4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for NR1H4

    SOURCE GeneReport for Unigene cluster: Hs.282735
        SABiosciences Expression via Pathway-Focused PCR Arrays including NR1H4: 
              Lipoprotein Signaling & Cholesterol Metabolism in human mouse rat
              Nuclear Receptors & Coregulators in human mouse rat
              Fatty Liver in human mouse rat
              Molecular Toxicology PathwayFinder 384HT in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for NR1H4 gene from 6/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Nr1h41 , 5 nuclear receptor subfamily 1, group H, member 41, 5 86.17(n)1
    92.74(a)1
      10 (44.98 cM)5
    201861  NM_009108.21  NP_033134.21 
     894542345 
    chicken
    (Gallus gallus)
    Aves NR1H41 nuclear receptor subfamily 1, group H, member 4 77.9(n)
    82.47(a)
      373902  NM_204113.1  NP_989444.1 
    lizard
    (Anolis carolinensis)
    Reptilia NR1H46
    Uncharacterized protein
    70(a)
    1 ↔ 1
    5(28594962-28632394)
    African clawed frog
    (Xenopus laevis)
    Amphibia MGC686932 hypothetical protein MGC68693 73.44(n)    AF456451.1 
    zebrafish
    (Danio rerio)
    Actinopterygii nr1h41 nuclear receptor subfamily 1, group H, member 4 66.59(n)
    68.02(a)
      436847  NM_001002574.1  NP_001002574.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta EcR3 imaginal disc eversion ecdysteroid
    hormone receptor
    36(a)     --


    ENSEMBL Gene Tree for NR1H4 (if available)
    TreeFam Gene Tree for NR1H4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for NR1H4 gene
    VDR2  NR4A32  RARG2  NR4A12  NR1I22  NR1I32  THRB2  RARA2  
    NR4A22  NR1H22  RARB2  THRA2  NR1H32  
    11 SIMAP similar genes for NR1H4 using alignment to 8 protein entries:     NR1H4_HUMAN (see all proteins):
    DKFZp686P04237    HNF4G    VDR    NR1H3    NR1I3    NR1H2
    NR1B2    NR1I2    DKFZp686D1580    NR1i1    RARB

    NR1H4 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for NR1H4
    PGOHUM00000261311


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1746 SNPs in NR1H4 are shown (see all 1746)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs725156951,2
    C--97950787(+) AATCA-/AT/TA 
            
    AAACA
    4 -- int10--------
    rs557448641,2
    C--97960603(+) ACACAG/CACAGA 6 -- int11Minor allele frequency- C:0.50WA 2
    rs357371,2
    C,F,A--98011027(-) TTTTTC/G/TTTTGA 6 -- int1 trp35NA WA CSA 10
    rs2013376121,2
    --98011027(+) TCAAA-/GAAAAA 6 -- int10--------
    rs2001872831,2
    --98011038(+) AAAAA-/CAAAAA 6 -- int10--------
    rs113277861,2
    C--98011826(+) TCACAT/-GGTGA 6 -- int12Minor allele frequency- -:0.25NA CSA 4
    rs1866414051,2
    C--100704898(+) AAATAA/GTAACA 4 -- us2k10--------
    rs1912920921,2
    C--100704930(+) TCTGTA/GTGTCA 4 -- us2k10--------
    rs1169893831,2
    C,F--100705070(+) GGTCAC/TACAGC 4 -- us2k11Minor allele frequency- T:0.03EA 120
    rs1436193971,2
    --100705109(+) CCAGCC/TGGTCC 4 -- us2k10--------

    HapMap Linkage Disequilibrium report for NR1H4 (100867486 - 100958191 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for NR1H4:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2673448CNV Deletion23128226
    nsv455700CNV Loss19166990
    dgv1484n71CNV Gain21882294
    nsv899470CNV Gain21882294
    nsv442285CNV CNV18776908


    Human Gene Mutation Database (HGMD): NR1H4
    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 603826    OMIM disorders: --

    20/48 diseases for NR1H4 (see all 48):    About MalaCards
    xanthomatosis    biliary tract disease    intrahepatic cholestasis of pregnancy    fragile x syndrome
    cerebrotendinous xanthomatosis    intrahepatic cholestasis    biliary atresia    cholestasis
    atherosclerosis    nonalcoholic steatohepatitis    hepatopulmonary syndrome    familial combined hyperlipidemia
    hepatoblastoma    cholelithiasis    metabolic disorders    hypertriglyceridemia
    liver disease    rickets    maturity-onset diabetes of the young    vascular disease

    4 diseases from the University of Copenhagen DISEASES database for NR1H4:
    Cholestasis     Liver disease     Atherosclerosis     Diabetes mellitus

    NR1H4 for disorders           About GeneDecksing

    10/28 Novoseek inferred disease relationships for NR1H4 gene (see all 28)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    byler disease 80.9 14 19381753 (4), 16628629 (2), 19027009 (1), 16819395 (1)
    cholestasis 76.7 29 19027009 (2), 19300246 (2), 15317749 (2), 16178789 (2) (see all 12)
    cholestasis intrahepatic 73.5 15 14988830 (2), 17681172 (1), 16819395 (1), 19490418 (1) (see all 8)
    dyslipidemia 54.8 10 19136377 (2), 15893927 (1), 18047847 (1), 18311660 (1)
    liver diseases 50.4 8 19187229 (1), 18668687 (1), 14992012 (1), 16706681 (1) (see all 6)
    biliary cirrhosis primary 48.6 2 15703646 (1), 19300246 (1)
    fragile x syndrome 45.9 2 8668200 (2)
    hypercholesterolemia 44 15 18948497 (2), 19136377 (1), 12704471 (1), 16905319 (1)
    atherosclerosis 39.6 8 20041971 (2), 17495603 (2), 17519356 (1), 18311660 (1) (see all 6)
    biliary atresia 39.4 2 16628629 (1), 15922475 (1)

    Genetic Association Database (GAD): NR1H4
    Human Genome Epidemiology (HuGE) Navigator: NR1H4 (13 documents)

    Export disorders for NR1H4 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for NR1H4 gene, integrated from 9 sources (see all 465):
    (articles sorted by number of sources associating them with NR1H4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of a nuclear receptor for bile acids. (PubMed id 10334992)1, 2, 7, 9 Makishima M.... Shan B. (1999)
    2. Functional variants of the central bile acid sensor FXR identified in intrahepatic cholestasis of pregnancy. (PubMed id 17681172)1, 4, 9 Van Mil S.W....Williamson C. (2007)
    3. Ligand-dependent activation of the farnesoid X-receptor directs arginine methylation of histone H3 by CARM1. (PubMed id 15471871)1, 2, 9 Ananthanarayanan M....Walsh M.J. (2004)
    4. High frequency of a retinoid X receptor gamma gene variant in familial combined hyperlipidemia that associates with atherogenic dyslipidemia. (PubMed id 17272748)1, 4, 9 Nohara A....Mabuchi H. (2007)
    5. Definition of a novel growth factor-dependent signal cascade for the suppression of bile acid biosynthesis. (PubMed id 12815072)1, 2, 9 Holt J.A....Jones S.A. (2003)
    6. Bile acids: natural ligands for an orphan nuclear receptor. (PubMed id 10334993)1, 2, 9 Parks D.J....Lehmann J.M. (1999)
    7. A common polymorphism in the ABCB11 gene is associate d with advanced fibrosis in hepatitis C but not in non-alcoholic fatty liver di sease. (PubMed id 20883210)1, 4 Iwata R....Geier A. (2010)
    8. Genetic susceptibility to distinct bladder cancer sub phenotypes. (PubMed id 19692168)1, 4 Guey L.T....Malats N. (2010)
    9. Genetic Risk Factors for Hepatopulmonary Syndrome in Patients With Advanced Liver Disease. (PubMed id 20346360)1, 4 Roberts K.E....Fallon M.B. (2010)
    10. Common genetic variation in multiple metabolic pathwa ys influences susceptibility to low HDL-cholesterol and coronary heart disease. (PubMed id 20855565)1, 4 Peloso G.M....Brousseau M.E. (2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 9971 HGNC: 7967 AceView: NR1H4 Ensembl:ENSG00000012504 euGenes: HUgn9971
    ECgene: NR1H4 Kegg: 9971 H-InvDB: NR1H4

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for NR1H4 Pharmacogenomics, SNPs, Pathways
    Wikipedia http://en.wikipedia.org/wiki/Farnesoid_X_receptor

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for NR1H4 gene:
    Search GeneIP for patents involving NR1H4

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    About This Section

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