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Aliases for NR1H3 Gene

Aliases for NR1H3 Gene

  • Nuclear Receptor Subfamily 1 Group H Member 3 2 3 4 5
  • LXRA 3 4
  • Nuclear Receptor Subfamily 1, Group H, Member 3 2
  • Liver X Nuclear Receptor Alpha Variant 1 3
  • Oxysterols Receptor LXR-Alpha 3
  • Liver X Receptor-Alpha 2
  • Liver X Receptor Alpha 4
  • LXR-A 3
  • RLD-1 3

External Ids for NR1H3 Gene

Previous GeneCards Identifiers for NR1H3 Gene

  • GC11P049220
  • GC11P048157
  • GC11P047302
  • GC11P047245
  • GC11P047243
  • GC11P047236
  • GC11P046969

Summaries for NR1H3 Gene

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 Multiple Sclerosis and Cerebrotendinous Xanthomatosis. Among its related pathways are Gene Expression and Lipoprotein metabolism. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and transcription coactivator activity. An important paralog of this gene is NR1H2.

UniProtKB/Swiss-Prot for NR1H3 Gene

  • Nuclear 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. Interplays functionally with RORA for the regulation of genes involved in liver metabolism (By similarity). Exhibits a ligand-dependent transcriptional activation activity (PubMed:25661920).

Tocris 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; alpha and beta.

Gene Wiki entry for NR1H3 Gene

Additional gene information for NR1H3 Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NR1H3 Gene

Genomics for NR1H3 Gene

GeneHancer (GH) Regulatory Elements for NR1H3 Gene

Promoters and enhancers for NR1H3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I047256 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 550.4 +10.5 10513 3.9 MLX ARID4B DMAP1 BRCA1 ZNF48 YY1 ZNF121 GLIS2 ELK1 ARID2 NR1H3 PACSIN3 ACP2 ARFGAP2 MADD C1QTNF4
GH11I047247 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +0.5 485 2.2 ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 MEF2D ACP2 NR1H3 DDB2 NUP160 ENSG00000270060 FNBP4 RPS10P19 PACSIN3 ZNF408 ENSG00000200090
GH11I047267 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 12.1 +22.0 22044 5.4 HDGF PKNOX1 CLOCK FOXA2 ARNT ZFP64 ARID4B SIN3A FEZF1 YY1 MADD LOC101928943 FNBP4 NUP160 ENSG00000270060 ENSG00000200090 DDB2 ACP2 RPS10P19 PACSIN3
GH11I047277 Enhancer 1.1 ENCODE dbSUPER 12 +29.5 29531 1.3 HDAC1 ATF1 PKNOX1 ARNT NFRKB BRCA1 RFX5 TCF12 FOS ATF7 NR1H3 ACP2 SLC39A13 PACSIN3 ARFGAP2 FNBP4 MADD LOC101928943 ENSG00000283338
GH11I047336 Enhancer 1 ENCODE dbSUPER 11.2 +89.2 89206 1.1 HDAC1 ATF1 EGR1 ATF7 CREM ZEB2 ZNF148 MTA1 GMEB1 SMARCA4 LOC101928943 MADD NR1H3 MTCH2 MYBPC3 GC11P047345 ENSG00000283338
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NR1H3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NR1H3 gene promoter:

Genomic Locations for NR1H3 Gene

Genomic Locations for NR1H3 Gene
chr11:47,248,300-47,269,033
(GRCh38/hg38)
Size:
20,734 bases
Orientation:
Plus strand
chr11:47,269,851-47,290,401
(GRCh37/hg19)

Genomic View for NR1H3 Gene

Genes around NR1H3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NR1H3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NR1H3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NR1H3 Gene

Proteins for NR1H3 Gene

  • Protein details for NR1H3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13133-NR1H3_HUMAN
    Recommended name:
    Oxysterols receptor LXR-alpha
    Protein Accession:
    Q13133
    Secondary Accessions:
    • A8K3J9
    • D3DQR1
    • Q8IW13
    • Q96H87

    Protein attributes for NR1H3 Gene

    Size:
    447 amino acids
    Molecular mass:
    50396 Da
    Quaternary structure:
    • Heterodimer of LXRA and RXR. Interacts with CCAR2 (via N-terminus) in a ligand-independent manner. Interacts with SIRT1 and this interaction is inhibited by CCAR2.

    Three dimensional structures from OCA and Proteopedia for NR1H3 Gene

    Alternative splice isoforms for NR1H3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NR1H3 Gene

Post-translational modifications for NR1H3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NR1H3 Gene

Domains & Families for NR1H3 Gene

Gene Families for NR1H3 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Nuclear receptors
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Graphical View of Domain Structure for InterPro Entry

Q13133

UniProtKB/Swiss-Prot:

NR1H3_HUMAN :
  • Belongs to the nuclear hormone receptor family. NR1 subfamily.
Family:
  • Belongs to the nuclear hormone receptor family. NR1 subfamily.
genes like me logo Genes that share domains with NR1H3: view

Function for NR1H3 Gene

Molecular function for NR1H3 Gene

UniProtKB/Swiss-Prot Function:
Nuclear 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. Interplays functionally with RORA for the regulation of genes involved in liver metabolism (By similarity). Exhibits a ligand-dependent transcriptional activation activity (PubMed:25661920).
UniProtKB/Swiss-Prot Induction:
By 9-cis retinoic acid (9CRA).

Phenotypes From GWAS Catalog for NR1H3 Gene

Gene Ontology (GO) - Molecular Function for NR1H3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0003677 DNA binding TAS,IEA 7744246
GO:0003700 DNA binding transcription factor activity IEA --
GO:0003707 steroid hormone receptor activity IEA --
genes like me logo Genes that share ontologies with NR1H3: view
genes like me logo Genes that share phenotypes with NR1H3: view

Animal Models for NR1H3 Gene

MGI Knock Outs for NR1H3:

Animal Model Products

  • Taconic Biosciences Mouse Models for NR1H3

CRISPR Products

miRNA for NR1H3 Gene

miRTarBase miRNAs that target NR1H3

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NR1H3 Gene

Localization for NR1H3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NR1H3 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NR1H3 gene
Compartment Confidence
nucleus 5
cytosol 3
extracellular 2
peroxisome 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for NR1H3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IDA 18511497
GO:0005634 nucleus IDA,IEA 25661920
GO:0005654 nucleoplasm TAS --
GO:0043235 receptor complex IDA 18511497
GO:0090575 RNA polymerase II transcription factor complex IDA,IEA 18511497
genes like me logo Genes that share ontologies with NR1H3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NR1H3 Gene

Pathways & Interactions for NR1H3 Gene

genes like me logo Genes that share pathways with NR1H3: view

SIGNOR curated interactions for NR1H3 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for NR1H3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II ISS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II IEA --
GO:0006367 transcription initiation from RNA polymerase II promoter TAS --
genes like me logo Genes that share ontologies with NR1H3: view

Drugs & Compounds for NR1H3 Gene

(30) Drugs for NR1H3 Gene - From: DrugBank, PharmGKB, ApexBio, DGIdb, IUPHAR, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Diacerein Approved, Investigational Pharma Target, inhibitor 0
Atenolol Approved Pharma Antagonist 108
Verapamil Approved Pharma Channel blocker 135
(2E,4E)-11-METHOXY-3,7,11-TRIMETHYLDODECA-2,4-DIENOIC ACID Experimental Pharma Target 0
1-BENZYL-3-(4-METHOXYPHENYLAMINO)-4-PHENYLPYRROLE-2,5-DIONE Experimental Pharma Target 0

(9) Additional Compounds for NR1H3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs

(3) Tocris Compounds for NR1H3 Gene

Compound Action Cas Number
27-Hydroxycholesterol LXR agonist; also ER partial agonist 20380-11-4
GW 4064 Selective farnesoid X receptor (FXR) agonist 278779-30-9
T 0901317 Potent liver X receptor (LXR) agonist; also CAR inverse agonist 293754-55-9

(6) ApexBio Compounds for NR1H3 Gene

Compound Action Cas Number
Fexaramine 574013-66-4
GW3965 HLXRα/hLXRβ agonist,potent and selective 405911-09-3
GW3965 HCl 405911-17-3
LXR-623 Liver X-receptor agonist 875787-07-8
SR-9243 inverse agonist of LXR 1613028-81-1
T0901317 Liver X receptor agonist,potent and selective 293754-55-9
genes like me logo Genes that share compounds with NR1H3: view

Drug Products

Transcripts for NR1H3 Gene

Unigene Clusters for NR1H3 Gene

Nuclear receptor subfamily 1, group H, member 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NR1H3 Gene

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: - - - -
SP6: - - - - -
SP7: - - - - - - - - -
SP8: - - - - - - - - - - - - - - -
SP9: - - - - -
SP10: - - - - -
SP11: - - - - - - - -
SP12: -
SP13: - - - - - -
SP14: - - - -
SP15: - - - -
SP16:
SP17:
SP18: - - - -
SP19: - - -
SP20:
SP21:

ExUns: 9c · 9d · 9e · 9f ^ 10a · 10b · 10c · 10d · 10e · 10f ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15a · 15b
SP1: -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11: - - - -
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:

Relevant External Links for NR1H3 Gene

GeneLoc Exon Structure for
NR1H3
ECgene alternative splicing isoforms for
NR1H3

Expression for NR1H3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NR1H3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NR1H3 Gene

This gene is overexpressed in Liver (x4.2).

Protein differential expression in normal tissues from HIPED for NR1H3 Gene

This gene is overexpressed in Stomach (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for NR1H3 Gene



Protein tissue co-expression partners for NR1H3 Gene

NURSA nuclear receptor signaling pathways regulating expression of NR1H3 Gene:

NR1H3

SOURCE GeneReport for Unigene cluster for NR1H3 Gene:

Hs.438863

mRNA Expression by UniProt/SwissProt for NR1H3 Gene:

Q13133-NR1H3_HUMAN
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.

Evidence on tissue expression from TISSUES for NR1H3 Gene

  • Liver(4.6)
  • Nervous system(4.3)
  • Heart(4.2)
  • Gall bladder(2.2)
  • Intestine(2.1)
genes like me logo Genes that share expression patterns with NR1H3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for NR1H3 Gene

Orthologs for NR1H3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NR1H3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NR1H3 33 34
  • 99.63 (n)
dog
(Canis familiaris)
Mammalia NR1H3 33 34
  • 91.5 (n)
cow
(Bos Taurus)
Mammalia NR1H3 33 34
  • 90.31 (n)
rat
(Rattus norvegicus)
Mammalia Nr1h3 33
  • 88.76 (n)
mouse
(Mus musculus)
Mammalia Nr1h3 33 16 34
  • 88.39 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NR1H3 34
  • 82 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NR1H3 34
  • 73 (a)
OneToOne
chicken
(Gallus gallus)
Aves LXR 34
  • 77 (a)
OneToOne
NR1H3 33
  • 75.04 (n)
lizard
(Anolis carolinensis)
Reptilia NR1H3 34
  • 76 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii nr1h3 33 34
  • 74 (n)
fruit fly
(Drosophila melanogaster)
Insecta EcR 35 34
  • 40 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5106 33
Species where no ortholog for NR1H3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for NR1H3 Gene

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

Paralogs for NR1H3 Gene

Variants for NR1H3 Gene

Sequence variations from dbSNP and Humsavar for NR1H3 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs61731956 pathogenic, Multiple sclerosis 47,268,596(+) G/A coding_sequence_variant, downstream_transcript_variant, genic_downstream_transcript_variant, missense_variant
rs1000022350 -- 47,257,992(+) C/G 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000196549 -- 47,257,014(+) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000214685 -- 47,250,638(+) A/C genic_upstream_transcript_variant, intron_variant
rs1000233100 -- 47,256,869(+) T/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for NR1H3 Gene

Variant ID Type Subtype PubMed ID
esv3626200 CNV loss 21293372

Variation tolerance for NR1H3 Gene

Residual Variation Intolerance Score: 24.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.12; 22.74% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NR1H3 Gene

Human Gene Mutation Database (HGMD)
NR1H3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NR1H3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NR1H3 Gene

Disorders for NR1H3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for NR1H3 Gene - From: HGMD, ClinVar, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
multiple sclerosis
  • multiple sclerosis, susceptibility to
cerebrotendinous xanthomatosis
  • ctx
- elite association - COSMIC cancer census association via MalaCards
Search NR1H3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NR1H3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NR1H3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NR1H3 Gene

Publications for NR1H3 Gene

  1. Functional and genetic analysis in type 2 diabetes of liver X receptor alleles--a cohort study. (PMID: 19292929) Dahlman I … Steffensen KR (BMC medical genetics 2009) 3 22 44 58
  2. Association between liver X receptor alpha gene polymorphisms and risk of metabolic syndrome in French populations. (PMID: 18209740) Legry V … Meirhaeghe A (International journal of obesity (2005) 2008) 3 22 44 58
  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. (PMID: 17217555) Robitaille J … Vohl MC (The British journal of nutrition 2007) 3 22 44 58
  4. LXR, a nuclear receptor that defines a distinct retinoid response pathway. (PMID: 7744246) Willy PJ … Mangelsdorf DJ (Genes & development 1995) 2 3 4 58
  5. CCAR2 negatively regulates nuclear receptor LXRα by competing with SIRT1 deacetylase. (PMID: 25661920) Sakurabashi A … Fujii T (The Journal of steroid biochemistry and molecular biology 2015) 3 4 58

Products for NR1H3 Gene

Sources for NR1H3 Gene

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