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

NR1H3 Gene

protein-coding   GIFtS: 64
GCID: GC11P047269

Nuclear Receptor Subfamily 1, Group H, Member 3

  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 31 2     Liver X Nuclear Receptor Alpha Variant 12
LXRA2 3     Oxysterols Receptor LXR-Alpha2
Liver X Receptor-Alpha1     Liver X Receptor Alpha3
LXR-a2     Nuclear Receptor Subfamily 1 Group H Member 33
RLD-12     

External Ids:    HGNC: 79661   Entrez Gene: 100622   Ensembl: ENSG000000254347   OMIM: 6024235   UniProtKB: Q131333   

Export aliases for NR1H3 gene to outside databases

Previous GC identifers: GC11P049220 GC11P048157 GC11P047302 GC11P047245 GC11P047243 GC11P047236 GC11P046969


(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 NR1H3 Gene:
The protein encoded by this gene belongs to the NR1 subfamily of the nuclear receptor superfamily. The NR1 family
members are key regulators of macrophage function, controlling transcriptional programs involved in lipid
homeostasis and inflammation. This protein is highly expressed in visceral organs, including liver, kidney and
intestine. It forms a heterodimer with retinoid X receptor (RXR), and regulates expression of target genes
containing retinoid response elements. Studies in mice lacking this gene suggest that it may play an important
role in the regulation of cholesterol homeostasis. Alternatively spliced transcript variants encoding different
isoforms have been found for this gene. (provided by RefSeq, Oct 2011)

GeneCards Summary for NR1H3 Gene: 
NR1H3 (nuclear receptor subfamily 1, group H, member 3) is a protein-coding gene. Diseases associated with NR1H3 include acth-secreting pituitary adenoma, and myxoid liposarcoma, and among its related super-pathways are Nuclear Receptors and Gene Expression. GO annotations related to this gene include sequence-specific DNA binding and transcription regulatory region DNA binding. An important paralog of this gene is VDR.

UniProtKB/Swiss-Prot: NR1H3_HUMAN, Q13133
Function: Orphan receptor. Interaction with RXR shifts RXR from its role as a silent DNA-binding partner to an
active ligand-binding subunit in mediating retinoid responses through target genes defined by LXRES. LXRES are
DR4-type response elements characterized by direct repeats of two similar hexanuclotide half-sites spaced by four
nucleotides. Plays an important role in the regulation of cholesterol homeostasis, regulating cholesterol uptake
through MYLIP-dependent ubiquitination of LDLR, VLDLR and LRP8 (By similarity)

summary for NR1H3 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 NR1H3 (Liver X receptor alpha) 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_000011.9  NT_009237.18  NC_018922.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the NR1H3 gene promoter:
         COUP-TF1   COUP-TF   COUP   HNF-4alpha2   HNF-4alpha1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 4): NR1H3 promoter sequence
   Search SABiosciences Chromatin IP Primers for NR1H3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NR1H3


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

Entrez Gene cytogenetic band: 11p11.2   Ensembl cytogenetic band:  11p11.2   HGNC cytogenetic band: 11p11.2

NR1H3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NR1H3 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P047269:  view genomic region     (about GC identifiers)

Start:
47,269,851 bp from pter      End:
47,290,401 bp from pter
Size:
20,551 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: NR1H3_HUMAN, Q13133 (See protein sequence)
Recommended Name: Oxysterols receptor LXR-alpha  
Size: 447 amino acids; 50396 Da
Subunit: Heterodimer of LXRA and RXR
Subcellular location: Nucleus (Potential)
4 PDB 3D structures from and Proteopedia for NR1H3:
1UHL (3D)        3IPQ (3D)        3IPS (3D)        3IPU (3D)    
Secondary accessions: A8K3J9 D3DQR1 Q8IW13 Q96H87
Alternative splicing: 3 isoforms:  Q13133-1   Q13133-2   Q13133-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for NR1H3: NX_Q13133

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q13133

  • NR1H3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --
    REFSEQ proteins (5 alternative transcripts): 
    NP_001123573.1  NP_001123574.1  NP_001238863.1  NP_001238864.1  NP_005684.2  

    ENSEMBL proteins: 
     ENSP00000378793   ENSP00000385073   ENSP00000433271   ENSP00000403798   ENSP00000434650  
     ENSP00000385801   ENSP00000391005   ENSP00000413095   ENSP00000412636   ENSP00000415591  
     ENSP00000407716   ENSP00000387946   ENSP00000396132   ENSP00000403696   ENSP00000420656  
     ENSP00000406692   ENSP00000384745   ENSP00000432073  
    Reactome Protein details: Q13133
    Human Recombinant Protein Products for NR1H3: 
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    Novus Biologicals NR1H3 Lysates
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    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:0000790nuclear chromatin IDA18511497
    GO:0005634nucleus TAS7744246
    GO:0005654nucleoplasm TAS--

    NR1H3 for ontologies           About GeneDecksing



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    (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: Liver X receptor-&alpha 
    1H. Liver X receptor-like receptors

    5/6 InterPro protein domains (see all 6):
     IPR008946 Nucl_hormone_rcpt_ligand-bd
     IPR023257 Liver_X_rcpt
     IPR001723 Str_hrmn_rcpt
     IPR013088 Znf_NHR/GATA
     IPR000536 Nucl_hrmn_rcpt_lig-bd_core

    Graphical View of Domain Structure for InterPro Entry Q13133

    ProtoNet protein and cluster: Q13133

    1 Blocks protein domain: IPB001723 Steroid hormone receptor signature

    UniProtKB/Swiss-Prot: NR1H3_HUMAN, Q13133
    Similarity: Belongs to the nuclear hormone receptor family. NR1 subfamily
    Similarity: Contains 1 nuclear receptor DNA-binding domain


    NR1H3 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: NR1H3_HUMAN, Q13133
    Function: Orphan receptor. Interaction with RXR shifts RXR from its role as a silent DNA-binding partner to an
    active ligand-binding subunit in mediating retinoid responses through target genes defined by LXRES. LXRES are
    DR4-type response elements characterized by direct repeats of two similar hexanuclotide half-sites spaced by four
    nucleotides. Plays an important role in the regulation of cholesterol homeostasis, regulating cholesterol uptake
    through MYLIP-dependent ubiquitination of LDLR, VLDLR and LRP8 (By similarity)
    Induction: By 9-cis retinoic acid (9CRA)

         Gene Ontology (GO): 5/11 molecular function terms (GO ID links to tree view) (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding TAS7744246
    GO:0003700sequence-specific DNA binding transcription factor activity ----
    GO:0003707steroid hormone receptor activity IEA--
    GO:0003713transcription coactivator activity TAS7744246
    GO:0004879ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity IEA--
         
    NR1H3 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for NR1H3:
     Increased cell death HMECs cel 

         14 MGI mutant phenotypes (inferred from 7 alleles(MGI details for Nr1h3):
     behavior/neurological  cardiovascular system  cellular  endocrine/exocrine gland  hematopoietic system 
     homeostasis/metabolism  immune system  liver/biliary system  mortality/aging  muscle 
     nervous system  normal  other  reproductive system 

    NR1H3 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for NR1H3: Nr1h3tm1Dgen Nr1h3tm1.1Gstr Nr1h3tm1.1Nph Nr1h3tm1Djm

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    hsa-miR-4264 hsa-miR-206 hsa-miR-155 hsa-miR-622 hsa-miR-613 hsa-miR-1
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NR1H3


    (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 NR1H3 About   (see all 8)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Nuclear Receptor transcription pathway
    Nuclear Receptor transcription pathway0.68
    Nuclear Receptors0.68
    2Generic Transcription Pathway
    Gene Expression0.47
    Generic Transcription Pathway0.47
    3Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.
    Non-alcoholic fatty liver disease (NAFLD)0.41
    4SREBF and miR33 in cholesterol and lipid homeostasis
    SREBF and miR33 in cholesterol and lipid homeostasis
    5PPAR signaling pathway
    PPAR signaling pathway

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    4 BioSystems Pathways for NR1H3
        Adipogenesis
    Nuclear Receptors
    SREBF and miR33 in cholesterol and lipid homeostasis
    Nuclear receptors in lipid metabolism and toxicity

    3        Reactome Pathways for NR1H3
        Generic Transcription Pathway
    Nuclear Receptor transcription pathway
    Gene Expression


    3         Kegg Pathways  (Kegg details for NR1H3):
        PPAR signaling pathway
    Non-alcoholic fatty liver disease (NAFLD)
    Hepatitis C


    NR1H3 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for NR1H3

    5/38 Interacting proteins for NR1H3 (Q131331, 2, 3) via UniProtKB, MINT, STRING, and/or I2D (see all 38)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NCOA1Q157882, 3MINT-7986700 MINT-7986907 MINT-7986678 MINT-7986760 MINT-7986890 MINT-7986720 MINT-7986621 MINT-7986736 MINT-7986787 MINT-7986596 MINT-7986639 MINT-7986575 MINT-7986555 MINT-7986808 I2D: score=2 
    RXRAP197932, 3MINT-7986700 MINT-7986678 MINT-7986760 MINT-7986720 MINT-7986736 MINT-7986787 MINT-7986639 I2D: score=5 
    EDF1O608691, 3EBI-781356,EBI-781301 I2D: score=3 
    ENSG00000206289P287023I2D: score=3 
    ENSG00000227322P287023I2D: score=3 
    About this table

    Gene Ontology (GO): 5/38 biological process terms (GO ID links to tree view) (see all 38):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter ISS--
    GO:0006351transcription, DNA-dependent ----
    GO:0006355regulation of transcription, DNA-dependent ----
    GO:0006367transcription initiation from RNA polymerase II promoter TAS--
    GO:0010467gene expression TAS--

    NR1H3 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

    NR1H3 for compounds           About GeneDecksing

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

    Compounds for NR1H3 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]

    4 DrugBank Compounds for NR1H3    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    (2E,4E)-11-METHOXY-3,7,11-TRIMETHYLDODECA-2,4-DIENOIC ACID-- --target--10592235
    1-BENZYL-3-(4-METHOXYPHENYLAMINO)-4-PHENYLPYRROLE-2,5-DIONE-- --target--10592235
    N-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE-- --target--10592235
    N-(TERT-BUTYL)-3,5-DIMETHYL-N'-[(5-METHYL-2,3-DIHYDRO-1,4-BENZODIOXIN-6-YL)CARBONYL]BENZOHYDRAZIDE-- --target--10592235

    9 IUPHAR Ligands for NR1H3 (Liver X receptor-&alpha)    About this table 
    LigandTypeActionAffinityPubmed IDs
    acetyl-podocarpic dimer
    Agonist911790770
    L-783483
    AgonistAgonist7.912072387
    T0901317
    AgonistAgonist7.311090131
    27-hydroxycholesterol
    AgonistAgonist7.111504730
    GW3965
    AgonistAgonist6.711985463
    24(S)-hydroxycholesterol
    AgonistAgonist5.49013544
    24(S), 25-epoxycholesterol
    AgonistAgonist5.49874807 9013544
    paxilline
    AgonistAgonist5.412893846
    22R-hydroxycholesterol
    AgonistAgonist5.38878485

    10/14 Novoseek inferred chemical compound relationships for NR1H3 gene (see all 14)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    sterol 82.3 18 19962449 (1), 20032471 (1), 12230796 (1), 12617469 (1) (see all 16)
    cholesterol 76 56 15280160 (2), 10936612 (1), 15539633 (1), 17845217 (1) (see all 46)
    cholesterol ester 65.4 1 18270459 (1)
    lipid 63.8 31 17217555 (2), 12700342 (1), 14703507 (1), 17154100 (1) (see all 25)
    lanosterol 60.4 2 18676367 (1), 20037138 (1)
    fatty acid 52.8 8 12917410 (1), 19885625 (1), 20032471 (1), 12617469 (1) (see all 7)
    atorvastatin 36.8 2 18427282 (1), 17644777 (1)
    atp 29.5 6 17767055 (1), 12632092 (1), 15769938 (1), 16311343 (1) (see all 6)
    retinoic acid 28.1 2 12632092 (1), 15615782 (1)
    glucose 27.9 5 12970362 (1), 16973760 (1), 19292929 (1), 15708349 (1) (see all 5)

    Search CenterWatch for drugs/clinical trials and news about NR1H3

    (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,
    RNAi Products from EMD Millipore,
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    About This Section

    REFSEQ mRNAs for NR1H3 gene (5 alternative transcripts): 
    NM_001130101.2  NM_001130102.2  NM_001251934.1  NM_001251935.1  NM_005693.3  

    Unigene Cluster for NR1H3:

    Nuclear receptor subfamily 1, group H, member 3
    Hs.438863  [show with all ESTs]
    Unigene Representative Sequence: AK122661
    18/34 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 34):
    ENST00000495866 ENST00000527464 ENST00000529540(uc010rhk.2 uc009yll.2)
    ENST00000395397 ENST00000405576 ENST00000481020 ENST00000481889(uc001nek.3)
    ENST00000436778 ENST00000487913 ENST00000531660 ENST00000532630 ENST00000407404
    ENST00000444396 ENST00000457932 ENST00000412937 ENST00000449369 ENST00000486991
    ENST00000419652
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    Additional mRNA sequence: 

    AB307698.1 AK122661.1 AK290614.1 AK302132.1 AK309027.1 AK311590.1 AK313311.1 BC008819.2 
    BC041172.1 BT019411.1 HQ692819.1 U22662.1 

    24/34 DOTS entries (see all 34):

    DT.120730649  DT.414781  DT.100026354  DT.99967362  DT.414782  DT.120730684  DT.120730568  DT.100787250 
    DT.99982968  DT.100787248  DT.92324908  DT.120730673  DT.75172113  DT.92036313  DT.95129136  DT.120730569 
    DT.120730654  DT.120730662  DT.95129127  DT.100787249  DT.100787254  DT.120730603  DT.120730646  DT.120730701 

    24/196 AceView cDNA sequences (see all 196):

    AI206938 AI985346 BM560055 BE542999 CR607859 AA884852 AW770753 BP338102 
    CR615123 CA445177 CR607396 CR596655 BC008819 BM855407 AI288682 CR606496 
    AI703008 AW590068 BP381781 AI927058 BC041172 CB529591 AI521157 BI521046 

    GeneLoc Exon Structure

    5/21 Alternative Splicing Database (ASD) splice patterns (SP) for NR1H3 (see all 21)    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b · 3c · 3d · 3e · 3f · 3g · 3h · 3i · 3j ^ 4a · 4b ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ·
    SP1:                                                                                                  -     -     -                                             
    SP2:                                                                                -     -           -     -     -                                             
    SP3:              -     -     -     -     -     -     -                             -     -           -     -     -                                             
    SP4:                          -     -     -     -     -                             -     -           -     -     -                                             
    SP5:                                                                                      -           -     -     -                                             

    ExUns: 9c · 9d · 9e · 9f ^ 10a · 10b · 10c · 10d · 10e · 10f ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15a · 15b
    SP1:                                                                    -                                 
    SP2:                                                              -     -                                 
    SP3:                                                                                                      
    SP4:                                                                                                      
    SP5:                                                                                                      


    ECgene alternative splicing isoforms for NR1H3

    (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

    NR1H3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACCGACTGAT
    NR1H3 Expression
    About this image


    Genevestigator expression for NR1H3

    SOURCE GeneReport for Unigene cluster: Hs.438863

    UniProtKB/Swiss-Prot: NR1H3_HUMAN, Q13133
    Tissue specificity: Visceral organs specific expression. Strong expression was found in liver, kidney and
    intestine followed by spleen and to a lesser extent the adrenals

        SABiosciences Expression via Pathway-Focused PCR Arrays including NR1H3 (see all 6): 
              Atherosclerosis in human mouse rat
              Lipoprotein Signaling & Cholesterol Metabolism in human mouse rat
              Nuclear Receptors & Coregulators in human mouse rat
              Fatty Liver in human mouse rat
              PPAR Targets in human mouse rat

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NR1H3

    (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 NR1H3 gene from 5/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Nr1h31 , 5 nuclear receptor subfamily 1, group H, member 31, 5 88.39(n)1
    91.91(a)1
      2 (50.52 cM)5
    222591  NM_001177730.11  NP_001171201.11 
     911840615 
    chicken
    (Gallus gallus)
    Aves NR1H31 nuclear receptor subfamily 1, group H, member 3 75.04(n)
    80.31(a)
      395221  NM_204542.2  NP_989873.1 
    lizard
    (Anolis carolinensis)
    Reptilia NR1H36
    Uncharacterized protein
    77(a)
    1 ↔ 1
    1(43772914-43800240)
    zebrafish
    (Danio rerio)
    Actinopterygii nr1h31 nuclear receptor subfamily 1, group H, member 3 74(n)
    78.53(a)
      548341  NM_001017545.1  NP_001017545.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta EcR1 , 3 imaginal disc eversion ecdysteroid
    hormone receptor3
    Ecdysone receptor1
    40(a)3
    51.82(n)1
    42.69(a)1
      355401  NM_165461.21  NP_724456.11 


    ENSEMBL Gene Tree for NR1H3 (if available)
    TreeFam Gene Tree for NR1H3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for NR1H3 gene
    VDR2  NR4A32  RARG2  NR4A12  NR1I22  NR1I32  THRB2  RARA2  
    NR4A22  NR1H42  NR1H22  RARB2  THRA2  
    18/39 SIMAP similar genes for NR1H3 using alignment to 16 protein entries:     NR1H3_HUMAN (see all proteins) (see all similar genes):
    NR3C2    VDR    NR2C2    HNF4G    NR5A2    NR1H2
    HNF4alpha    ESRRG    ESR1    RXRB    DKFZp686D1580    THRB
    NR1F1    RORC    ESR2    NR1I3    NR6A1    THRA

    NR1H3 for paralogs           About GeneDecksing



    (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

    10/494 SNPs in NR1H3 are shown (see all 494)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1442616111,2
    C--46976057(+) GACTC-/TCTT  
            
    TCTTT
    3 -- int10--------
    rs2014565241,2
    --46976068(+) TTTCT-/TTCTTTTT 3 -- int10--------
    rs787077041,2
    C--46976072(+) TTTCTC/TTTTCT 3 -- int10--------
    rs43209171,2
    C,F--46976074(+) TCTTTC/TTCTTT 3 -- int1 trp34Minor allele frequency- T:0.29NA WA CSA 7
    rs1996207911,2
    --46976084(+) CTTTC-/TTTTTCT 3 -- int10--------
    rs609845871,2
    C--46976088(+) TCTTT-/TC/TTCT
    TTCTTTCTTT
    CTTTC
    3 -- int10--------
    rs2012833701,2
    C--46976114(+) TTTCTC/TTCTTT 3 -- int10--------
    rs1392347251,2
    --47193643(+) GGATCA/GCTTGA 2 -- us2k10--------
    rs1440490111,2
    C--47193929(+) AGGCCA/GAGGCA 2 -- us2k10--------
    rs356776031,2
    C,F--47194046(+) TAATCC/TCAGCT 2 -- us2k14Minor allele frequency- T:0.50NA 8

    HapMap Linkage Disequilibrium report for NR1H3 (47269851 - 47290401 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for NR1H3:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv897323CNV Loss21882294


    Human Gene Mutation Database (HGMD): NR1H3
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing NR1H3
    DNA2.0 Custom Variant and Variant Library Synthesis for NR1H3

    (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: 602423    OMIM disorders: --

    20/37 diseases for NR1H3 (see all 37):    About MalaCards
    acth-secreting pituitary adenoma    myxoid liposarcoma    hypobetalipoproteinemia    pulmonary alveolar proteinosis
    familial combined hyperlipidemia    atherosclerosis    liposarcoma    coronary heart disease
    rickets    maturity-onset diabetes of the young    fatty liver disease    vitiligo
    pituitary adenoma    vascular disease    liver disease    adenoma
    cytochrome p450    psoriasis    chronic lymphocytic leukemia    hepatitis b

    1 disease from the University of Copenhagen DISEASES database for NR1H3:
    Atherosclerosis

    NR1H3 for disorders           About GeneDecksing

    5 Novoseek inferred disease relationships for NR1H3 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    inflammation 32.8 11 18752326 (1), 16461908 (1), 18372238 (1), 19211025 (1) (see all 10)
    cardiovascular diseases 11.8 2 16973760 (1), 17626048 (1)
    coronary heart disease 7.52 1 16252156 (1)
    necrosis 0 2 17224343 (1), 18302511 (1)
    tumors 0 2 17224343 (1), 18302511 (1)

    Genetic Association Database (GAD): NR1H3
    Human Genome Epidemiology (HuGE) Navigator: NR1H3 (18 documents)

    Export disorders for NR1H3 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 NR1H3 gene, integrated from 9 sources (see all 313):
    (articles sorted by number of sources associating them with NR1H3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. LXR, a nuclear receptor that defines a distinct retinoid response pathway. (PubMed id 7744246)1, 2, 3 Willy P.J....Mangelsdorf D.J. (1995)
    2. Association between liver X receptor alpha gene polymorphisms and risk of metabolic syndrome in French populations. (PubMed id 18209740)1, 4, 9 Legry V....Meirhaeghe A. (2008)
    3. The lipoprotein/lipid profile is modulated by a gene-diet interaction effect between polymorphisms in the liver X receptor-alpha and dietary cholesterol intake in French-Canadians. (PubMed id 17217555)1, 4, 9 Robitaille J....Vohl M.C. (2007)
    4. Functional and genetic analysis in type 2 diabetes of liver X receptor alleles--a cohort study. (PubMed id 19292929)1, 4, 9 Dahlman I....Steffensen K.R. (2009)
    5. Genome-wide screen for metabolic syndrome susceptibili ty Loci reveals strong lipid gene contribution but no evidence for common geneti c basis for clustering of metabolic syndrome traits. (PubMed id 22399527)1, 4 Kristiansson K....Salomaa V. (2012)
    6. Polymorphisms in NFkB, PXR, LXR and risk of colorecta l cancer in a prospective study of Danes. (PubMed id 20836841)1, 4 Andersen V....Vogel U. (2010)
    7. Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (2010)
    8. 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)
    9. Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. (PubMed id 19060910)1, 4 Sabatti C....Peltonen L. (2009)
    10. Polymorphisms in the estrogen receptor 1 and vitamin C and matrix metalloproteinase gene families are associated with susceptibility to lymphoma. (PubMed id 18636124)1, 4 Skibola C.F....Smith M.T. (2008)

    (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: 10062 HGNC: 7966 AceView: NR1H3 Ensembl:ENSG00000025434 euGenes: HUgn10062
    ECgene: NR1H3 Kegg: 10062 H-InvDB: NR1H3

    (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 NR1H3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for NR1H3 gene:
    Search GeneIP for patents involving NR1H3

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



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    About This Section

     
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