Human Gene NR1I2 (ENST00000393716.8_5) from GENCODE V47lift37
  Description: nuclear receptor subfamily 1 group I member 2, transcript variant 1 (from RefSeq NM_003889.4)
Gencode Transcript: ENST00000393716.8_5
Gencode Gene: ENSG00000144852.20_13
Transcript (Including UTRs)
   Position: hg19 chr3:119,500,948-119,537,334 Size: 36,387 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr3:119,526,098-119,536,059 Size: 9,962 Coding Exon Count: 8 

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 (chr3:119,500,948-119,537,334)mRNA (may differ from genome)Protein (434 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NR1I2_HUMAN
DESCRIPTION: RecName: Full=Nuclear receptor subfamily 1 group I member 2; AltName: Full=Orphan nuclear receptor PAR1; AltName: Full=Orphan nuclear receptor PXR; AltName: Full=Pregnane X receptor; AltName: Full=Steroid and xenobiotic receptor; Short=SXR;
FUNCTION: Nuclear receptor that binds and is activated by variety of endogenous and xenobiotic compounds. Transcription factor that activates the transcription of multiple genes involved in the metabolism and secretion of potentially harmful xenobiotics, drugs and endogenous compounds. Activated by the antibiotic rifampicin and various plant metabolites, such as hyperforin, guggulipid, colupulone, and isoflavones. Response to specific ligands is species-specific. Activated by naturally occurring steroids, such as pregnenolone and progesterone. Binds to a response element in the promoters of the CYP3A4 and ABCB1/MDR1 genes.
SUBUNIT: Heterodimer with RXR. Interacts with NCOA1.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed in liver, colon and small intestine.
SIMILARITY: Belongs to the nuclear hormone receptor family. NR1 subfamily.
SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.
WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/nr1i2/";

-  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: NR1I2
Diseases sorted by gene-association score: cerebrotendinous xanthomatosis (22), biliary tract disease (17), xanthomatosis (9), intrahepatic cholestasis (9), cholestasis (9), osteomalacia (8), freemartinism (7), sclerosing cholangitis (7), cholangitis, primary sclerosing (5), bile duct disease (5), miles-carpenter syndrome (4), gastrointestinal system disease (2), leber congenital amaurosis (1)

-  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: 23.77 RPKM in Liver
Total median expression: 54.31 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 -64.90222-0.292 Picture PostScript Text
3' UTR -436.101275-0.342 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
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
1ILG - X-ray MuPIT 1ILH - X-ray MuPIT 1M13 - X-ray MuPIT 1NRL - X-ray MuPIT 1SKX - X-ray MuPIT 2O9I - X-ray MuPIT 2QNV - X-ray MuPIT 3CTB - X-ray 3HVL - X-ray 3R8D - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O75469
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:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific 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:0008144 drug binding
GO:0008270 zinc ion binding
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006367 transcription initiation from RNA polymerase II promoter
GO:0006805 xenobiotic metabolic process
GO:0007165 signal transduction
GO:0008202 steroid metabolic process
GO:0010628 positive regulation of gene expression
GO:0030522 intracellular receptor signaling pathway
GO:0042738 exogenous drug catabolic process
GO:0042908 xenobiotic transport
GO:0043401 steroid hormone mediated signaling pathway
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0046618 drug export

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016604 nuclear body
GO:0045111 intermediate filament cytoskeleton


-  Descriptions from all associated GenBank mRNAs
  AJ009936 - Homo sapiens mRNA for nuclear hormone receptor PRR1.
AJ009937 - Homo sapiens mRNA for nuclear hormone receptor PRR2.
AY091855 - Homo sapiens steroid and xenobiotic sensing nuclear receptor SXR (NR1I2) mRNA, complete cds.
AF061056 - Homo sapiens orphan nuclear receptor PXR mRNA, complete cds.
AK310789 - Homo sapiens cDNA, FLJ17831.
AK223456 - Homo sapiens mRNA, Splice isoform 1C of O75469 variant, clone: FCC115A09.
AF084645 - Homo sapiens orphan nuclear receptor (PAR1) mRNA, complete cds.
BC017304 - Homo sapiens nuclear receptor subfamily 1, group I, member 2, mRNA (cDNA clone MGC:29598 IMAGE:5087401), complete cds.
JD142446 - Sequence 123470 from Patent EP1572962.
JD256139 - Sequence 237163 from Patent EP1572962.
JD056332 - Sequence 37356 from Patent EP1572962.
JD080010 - Sequence 61034 from Patent EP1572962.
AF084644 - Homo sapiens orphan nuclear receptor (PAR2) mRNA, complete cds.
AB528010 - Synthetic construct DNA, clone: pF1KB7714, Homo sapiens NR1I2 gene for nuclear receptor subfamily 1, group I, member 2, without stop codon, in Flexi system.
HQ692837 - Homo sapiens pregnane X nuclear receptor variant 2 (NR1i2) mRNA, complete cds.
HQ709177 - Homo sapiens pregnane X nuclear receptor (NR1I2) mRNA, complete cds.
AB307701 - Homo sapiens NR1I2 mRNA for orphan nuclear receptor PXR, complete cds.
CU677901 - Synthetic construct Homo sapiens gateway clone IMAGE:100017628 5' read NR1I2 mRNA.
KJ901918 - Synthetic construct Homo sapiens clone ccsbBroadEn_11312 NR1I2 gene, encodes complete protein.
KR710565 - Synthetic construct Homo sapiens clone CCSBHm_00014073 NR1I2 (NR1I2) mRNA, encodes complete protein.
KR710566 - Synthetic construct Homo sapiens clone CCSBHm_00014074 NR1I2 (NR1I2) mRNA, encodes complete protein.
KR710567 - Synthetic construct Homo sapiens clone CCSBHm_00014076 NR1I2 (NR1I2) mRNA, encodes complete protein.
KR710568 - Synthetic construct Homo sapiens clone CCSBHm_00014078 NR1I2 (NR1I2) mRNA, encodes complete protein.
AK122990 - Homo sapiens cDNA FLJ16751 fis, clone BEAST2001444, highly similar to Orphan nuclear receptor PXR.
JD403439 - Sequence 384463 from Patent EP1572962.
JD125827 - Sequence 106851 from Patent EP1572962.
JD369530 - Sequence 350554 from Patent EP1572962.
JD159717 - Sequence 140741 from Patent EP1572962.
JD429258 - Sequence 410282 from Patent EP1572962.
JD347419 - Sequence 328443 from Patent EP1572962.
JD289228 - Sequence 270252 from Patent EP1572962.
JD325502 - Sequence 306526 from Patent EP1572962.
JD266795 - Sequence 247819 from Patent EP1572962.
JD176689 - Sequence 157713 from Patent EP1572962.
JD140719 - Sequence 121743 from Patent EP1572962.
JD204462 - Sequence 185486 from Patent EP1572962.
JD435256 - Sequence 416280 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_th1th2Pathway - Th1/Th2 Differentiation
h_nuclearRsPathway - Nuclear Receptors in Lipid Metabolism and Toxicity

Reactome (by CSHL, EBI, and GO)

Protein O75469 (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)
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)
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)
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: ENST00000393716.1, ENST00000393716.2, ENST00000393716.3, ENST00000393716.4, ENST00000393716.5, ENST00000393716.6, ENST00000393716.7, NM_003889, NR1I2_HUMAN, O75469, PXR, Q006P5, Q008C8, Q96AC7, Q9UJ22, Q9UJ23, Q9UJ24, Q9UJ25, Q9UJ26, Q9UJ27, Q9UNW4, uc318wbv.1, uc318wbv.2
UCSC ID: ENST00000393716.8_5
RefSeq Accession: NM_003889.4
Protein: O75469 (aka NR1I2_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.