Human Gene NR1H3 (ENST00000441012.7_4) from GENCODE V47lift37
  Description: nuclear receptor subfamily 1 group H member 3, transcript variant 1 (from RefSeq NM_005693.4)
Gencode Transcript: ENST00000441012.7_4
Gencode Gene: ENSG00000025434.19_13
Transcript (Including UTRs)
   Position: hg19 chr11:47,279,547-47,290,584 Size: 11,038 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr11:47,280,768-47,290,247 Size: 9,480 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:47,279,547-47,290,584)mRNA (may differ from genome)Protein (447 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NR1H3_HUMAN
DESCRIPTION: RecName: Full=Oxysterols receptor LXR-alpha; AltName: Full=Liver X receptor alpha; AltName: Full=Nuclear receptor subfamily 1 group H member 3;
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).
SUBUNIT: Heterodimer of LXRA and RXR.
INTERACTION: O60869:EDF1; NbExp=4; IntAct=EBI-781356, EBI-781301;
SUBCELLULAR LOCATION: Nucleus (Potential).
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.
INDUCTION: By 9-cis retinoic acid (9CRA).
SIMILARITY: Belongs to the nuclear hormone receptor family. NR1 subfamily.
SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: NR1H3
Diseases sorted by gene-association score: multiple sclerosis, disease progression, modifier of* (202), cerebrotendinous xanthomatosis (8), fatty liver disease (8)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 31.14 RPKM in Spleen
Total median expression: 420.87 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -66.90171-0.391 Picture PostScript Text
3' UTR -108.60337-0.322 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR023257 - Liver_X_rcpt
IPR008946 - Nucl_hormone_rcpt_ligand-bd
IPR000536 - Nucl_hrmn_rcpt_lig-bd_core
IPR001723 - Str_hrmn_rcpt
IPR001628 - Znf_hrmn_rcpt
IPR013088 - Znf_NHR/GATA

Pfam Domains:
PF00104 - Ligand-binding domain of nuclear hormone receptor
PF00105 - Zinc finger, C4 type (two domains)

SCOP Domains:
48508 - Nuclear receptor ligand-binding domain
57716 - Glucocorticoid receptor-like (DNA-binding domain)

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1UHL - X-ray MuPIT 3IPQ - X-ray MuPIT 3IPS - X-ray MuPIT 3IPU - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q13133
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003707 steroid hormone receptor activity
GO:0003713 transcription coactivator activity
GO:0004879 RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0015485 cholesterol binding
GO:0032810 sterol response element binding
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006367 transcription initiation from RNA polymerase II promoter
GO:0010745 negative regulation of macrophage derived foam cell differentiation
GO:0010867 positive regulation of triglyceride biosynthetic process
GO:0010870 positive regulation of receptor biosynthetic process
GO:0010875 positive regulation of cholesterol efflux
GO:0010887 negative regulation of cholesterol storage
GO:0030522 intracellular receptor signaling pathway
GO:0032270 positive regulation of cellular protein metabolic process
GO:0032369 negative regulation of lipid transport
GO:0032376 positive regulation of cholesterol transport
GO:0032570 response to progesterone
GO:0034145 positive regulation of toll-like receptor 4 signaling pathway
GO:0042632 cholesterol homeostasis
GO:0042752 regulation of circadian rhythm
GO:0043031 negative regulation of macrophage activation
GO:0043277 apoptotic cell clearance
GO:0043401 steroid hormone mediated signaling pathway
GO:0045723 positive regulation of fatty acid biosynthetic process
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048550 negative regulation of pinocytosis
GO:0050728 negative regulation of inflammatory response
GO:0051006 positive regulation of lipoprotein lipase activity
GO:0055088 lipid homeostasis
GO:0055092 sterol homeostasis
GO:0060336 negative regulation of interferon-gamma-mediated signaling pathway
GO:0070328 triglyceride homeostasis
GO:0071222 cellular response to lipopolysaccharide
GO:0090188 negative regulation of pancreatic juice secretion
GO:0090341 negative regulation of secretion of lysosomal enzymes
GO:2000325 regulation of ligand-dependent nuclear receptor transcription coactivator activity

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0043235 receptor complex
GO:0090575 RNA polymerase II transcription factor complex


-  Descriptions from all associated GenBank mRNAs
  AK311590 - Homo sapiens cDNA, FLJ18632.
HZ466390 - JP 2015532642-A/14: MicroRNAs that Suppress Human Melanoma.
LP722514 - Sequence 27 from Patent EP2882496.
AK302132 - Homo sapiens cDNA FLJ56172 complete cds, highly similar to Oxysterols receptor LXR-alpha.
HZ466389 - JP 2015532642-A/13: MicroRNAs that Suppress Human Melanoma.
LP722512 - Sequence 25 from Patent EP2882496.
BC041172 - Homo sapiens nuclear receptor subfamily 1, group H, member 3, mRNA (cDNA clone MGC:48988 IMAGE:5744574), complete cds.
HZ466387 - JP 2015532642-A/11: MicroRNAs that Suppress Human Melanoma.
HZ466388 - JP 2015532642-A/12: MicroRNAs that Suppress Human Melanoma.
LP722508 - Sequence 21 from Patent EP2882496.
LP722510 - Sequence 23 from Patent EP2882496.
AK290614 - Homo sapiens cDNA FLJ78537 complete cds.
AK313311 - Homo sapiens cDNA, FLJ93824, highly similar to Homo sapiens nuclear receptor subfamily 1, group H, member 3 (NR1H3), mRNA.
AK309027 - Homo sapiens cDNA, FLJ99068.
AK122661 - Homo sapiens cDNA FLJ16096 fis, clone SPLEN2006232, highly similar to OXYSTEROLS RECEPTOR LXR-ALPHA.
BC008819 - Homo sapiens nuclear receptor subfamily 1, group H, member 3, mRNA (cDNA clone MGC:10474 IMAGE:3957848), complete cds.
U22662 - Human nuclear orphan receptor LXR-alpha mRNA, complete cds.
JD381948 - Sequence 362972 from Patent EP1572962.
CU679127 - Synthetic construct Homo sapiens gateway clone IMAGE:100019197 5' read NR1H3 mRNA.
AB463942 - Synthetic construct DNA, clone: pF1KB7759, Homo sapiens NR1H3 gene for nuclear receptor subfamily 1, group H, member 3, without stop codon, in Flexi system.
BT019411 - Homo sapiens nuclear receptor subfamily 1, group H, member 3 mRNA, complete cds.
EU832060 - Synthetic construct Homo sapiens clone HAIB:100067089; DKFZo004F0824 nuclear receptor subfamily 1, group H, member 3 protein (NR1H3) gene, encodes complete protein.
KJ892905 - Synthetic construct Homo sapiens clone ccsbBroadEn_02299 NR1H3 gene, encodes complete protein.
KR710035 - Synthetic construct Homo sapiens clone CCSBHm_00009168 NR1H3 (NR1H3) mRNA, encodes complete protein.
AB307698 - Homo sapiens NR1H3 mRNA for liver X receptor alpha, complete cds.
EU831967 - Synthetic construct Homo sapiens clone HAIB:100066996; DKFZo008F0823 nuclear receptor subfamily 1, group H, member 3 protein (NR1H3) gene, encodes complete protein.
HQ692819 - Homo sapiens liver X nuclear receptor alpha variant 1 (NR1H3) mRNA, complete cds.
CU691980 - Synthetic construct Homo sapiens gateway clone IMAGE:100021159 5' read NR1H3 mRNA.
KJ892906 - Synthetic construct Homo sapiens clone ccsbBroadEn_02300 NR1H3 gene, encodes complete protein.
JD420927 - Sequence 401951 from Patent EP1572962.
JD425024 - Sequence 406048 from Patent EP1572962.
JD023727 - Sequence 4751 from Patent EP1572962.
JD019067 - Sequence 91 from Patent EP1572962.
JD029804 - Sequence 10828 from Patent EP1572962.
JD029787 - Sequence 10811 from Patent EP1572962.
MA622455 - JP 2018140982-A/14: MicroRNAs that Suppress Human Melanoma.
MA622454 - JP 2018140982-A/13: MicroRNAs that Suppress Human Melanoma.
MA622452 - JP 2018140982-A/11: MicroRNAs that Suppress Human Melanoma.
MA622453 - JP 2018140982-A/12: MicroRNAs that Suppress Human Melanoma.
MP557078 - Sequence 27 from Patent EP3626309.
MP557076 - Sequence 25 from Patent EP3626309.
MP557072 - Sequence 21 from Patent EP3626309.
MP557074 - Sequence 23 from Patent EP3626309.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_pparaPathway - Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa(alpha)
h_nuclearRsPathway - Nuclear Receptors in Lipid Metabolism and Toxicity
h_fxrPathway - FXR and LXR Regulation of Cholesterol Metabolism

Reactome (by CSHL, EBI, and GO)

Protein Q13133 (Reactome details) participates in the following event(s):

R-HSA-376419 Formation of NR-MED1 Coactivator Complex
R-HSA-383280 Nuclear Receptor transcription pathway
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)
R-HSA-376419 Formation of NR-MED1 Coactivator Complex
R-HSA-383280 Nuclear Receptor transcription pathway
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: A8K3J9, D3DQR1, ENST00000441012.1, ENST00000441012.2, ENST00000441012.3, ENST00000441012.4, ENST00000441012.5, ENST00000441012.6, LXRA, NM_005693, NR1H3_HUMAN, Q13133, Q8IW13, Q96H87, uc320jdg.1, uc320jdg.2
UCSC ID: ENST00000441012.7_4
RefSeq Accession: NM_005693.4
Protein: Q13133 (aka NR1H3_HUMAN or NRH3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.