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NR1I2 nuclear receptor subfamily 1 group I member 2 [ Homo sapiens (human) ]

Gene ID: 8856, updated on 2-Nov-2024

Summary

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Official Symbol
NR1I2provided by HGNC
Official Full Name
nuclear receptor subfamily 1 group I member 2provided by HGNC
Primary source
HGNC:HGNC:7968
See related
Ensembl:ENSG00000144852 MIM:603065; AllianceGenome:HGNC:7968
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BXR; PAR; PRR; PXR; SAR; SXR; ONR1; PAR1; PAR2; PARq
Summary
This gene product belongs to the nuclear receptor superfamily, members of which are transcription factors characterized by a ligand-binding domain and a DNA-binding domain. The encoded protein is a transcriptional regulator of the cytochrome P450 gene CYP3A4, binding to the response element of the CYP3A4 promoter as a heterodimer with the 9-cis retinoic acid receptor RXR. It is activated by a range of compounds that induce CYP3A4, including dexamethasone and rifampicin. Several alternatively spliced transcripts encoding different isoforms, some of which use non-AUG (CUG) translation initiation codon, have been described for this gene. Additional transcript variants exist, however, they have not been fully characterized. [provided by RefSeq, Jul 2008]
Expression
Biased expression in small intestine (RPKM 14.5), duodenum (RPKM 13.0) and 4 other tissues See more
Orthologs
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Genomic context

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See NR1I2 in Genome Data Viewer
Location:
3q13.33
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (119782101..119818487)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (122501838..122538215)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (119500948..119537334)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20321 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20322 Neighboring gene uncharacterized LOC105374064 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:119419489-119420688 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:119421355-119422034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20325 Neighboring gene cytochrome c oxidase copper chaperone COX17 Neighboring gene cilia and flagella associated protein 91 Neighboring gene Sharpr-MPRA regulatory region 6912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:119528543-119529046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:119534511-119535011 Neighboring gene PHB1 pseudogene 8 Neighboring gene glycogen synthase kinase 3 beta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20328 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:119691277-119691494 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:119722393-119722919 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:119722920-119723445 Neighboring gene PARL pseudogene 1 Neighboring gene RFK pseudogene 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Investigation of associations between the pregnane-X receptor gene (NR1I2) and Crohn's disease in Canadian children using a gene-wide haplotype-based approach. Amre DK, et al. Inflamm Bowel Dis, 2008 Sep. PMID 18381611
  2. A pharmacogenetic study of pregnane X receptor (NR1I2) in Han Chinese. Wang XD, et al. Curr Drug Metab, 2007 Dec. PMID 18220558
  3. Regulation of hepatic energy metabolism by the nuclear receptor PXR. Hakkola J, et al. Biochim Biophys Acta, 2016 Sep. PMID 27041449
  4. Decreased Pregnane X Receptor Expression in Children with Active Crohn's Disease. Shakhnovich V, et al. Drug Metab Dispos, 2016 Jul. PMID 27013401, Free PMC Article
  5. Unique transcription start sites and distinct promoter regions differentiate the pregnane X receptor (PXR) isoforms PXR 1 and PXR 2. Tompkins LM, et al. Drug Metab Dispos, 2008 May. PMID 18276839

See all (394) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. DNA methylation determines the regulation of pregnane X receptor on CYP3A4 expression.
    Title: DNA methylation determines the regulation of pregnane X receptor on CYP3A4 expression.
  2. NEAT1_2 and DAZAP1, Paraspeckle Components, Interact with PXR to Negatively Regulate CYP3A4 Induction.
    Title: NEAT1_2 and DAZAP1, Paraspeckle Components, Interact with PXR to Negatively Regulate CYP3A4 Induction.
  3. Effect of pregnane X receptor and cytochrome P450 oxidoreductase gene polymorphisms on trough concentrations of rivaroxaban and edoxaban in patients with nonvalvular atrial fibrillation.
    Title: Effect of pregnane X receptor and cytochrome P450 oxidoreductase gene polymorphisms on trough concentrations of rivaroxaban and edoxaban in patients with nonvalvular atrial fibrillation.
  4. Pregnane X receptor gene variant rs7643645 and total mortality in subjects with nonalcoholic fatty liver disease.
    Title: Pregnane X receptor gene variant rs7643645 and total mortality in subjects with nonalcoholic fatty liver disease.
  5. Effects of NR1I2 and ABCB1 Genetic Polymorphisms on Everolimus Pharmacokinetics in Japanese Renal Transplant Patients.
    Title: Effects of NR1I2 and ABCB1 Genetic Polymorphisms on Everolimus Pharmacokinetics in Japanese Renal Transplant Patients.
  6. Relevance of gene polymorphisms of NAT2 and NR1I2 to anti-tuberculosis drug-induced hepatotoxicity.
    Title: Relevance of gene polymorphisms of NAT2 and NR1I2 to anti-tuberculosis drug-induced hepatotoxicity.
  7. Distinct Roles of the Sister Nuclear Receptors PXR and CAR in Liver Cancer Development.
    Title: Distinct Roles of the Sister Nuclear Receptors PXR and CAR in Liver Cancer Development.
  8. Protease-Activated Receptor 1 in Human Carotid Atheroma Is Significantly Related to Iron Metabolism, Plaque Vulnerability, and the Patient's Age.
    Title: Protease-Activated Receptor 1 in Human Carotid Atheroma Is Significantly Related to Iron Metabolism, Plaque Vulnerability, and the Patient's Age.
  9. No Effect of PXR (8055C>T) Polymorphism on the Pharmacokinetic Profiles of Piperaquine in Healthy Chinese Subjects.
    Title: No Effect of PXR (8055C>T) Polymorphism on the Pharmacokinetic Profiles of Piperaquine in Healthy Chinese Subjects.
  10. Molecular basis of crosstalk in nuclear receptors: heterodimerization between PXR and CAR and the implication in gene regulation.
    Title: Molecular basis of crosstalk in nuclear receptors: heterodimerization between PXR and CAR and the implication in gene regulation.
Submit: New GeneRIF Correction See all GeneRIFs (337)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables nuclear receptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables nuclear receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intracellular receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in signal transduction TAS
Traceable Author Statement
more info
 PubMed 
involved_in steroid metabolic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in xenobiotic catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in xenobiotic metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in xenobiotic transport IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in intermediate filament cytoskeleton IDA
Inferred from Direct Assay
more info
  
located_in nuclear body IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of transcription regulator complex IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
nuclear receptor subfamily 1 group I member 2
Names
orphan nuclear receptor PAR1
orphan nuclear receptor PXR
pregnane X receptor
steroid and xenobiotic receptor

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011856.2 RefSeqGene

    Range
    5002..41388
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_003889.4 → NP_003880.3  nuclear receptor subfamily 1 group I member 2 isoform 1

    See identical proteins and their annotated locations for NP_003880.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) contains an alternate 5' terminal exon compared to transcript variant 2, and initiates translation from an in-frame, downstream non-AUG (CUG) codon, resulting in a shorter isoform (1) with a different N-terminus compared to isoform 2.
    Source sequence(s)
    AC069444, KF457674
    Consensus CDS
    CCDS43136.1
    UniProtKB/Swiss-Prot
    O75469, Q006P5, Q008C8, Q96AC7, Q9UJ22, Q9UJ23, Q9UJ24, Q9UJ25, Q9UJ26, Q9UJ27, Q9UNW4
    UniProtKB/TrEMBL
    J3KPQ3
    Related
    ENSP00000377319.3, ENST00000393716.8
    Conserved Domains (2) summary
    cd06934
    Location:143 → 428
    NR_LBD_PXR_like; The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor
    cl02596
    Location:40 → 127
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers

  2. NM_022002.3 → NP_071285.1  nuclear receptor subfamily 1 group I member 2 isoform 2

    See identical proteins and their annotated locations for NP_071285.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) encodes the longest isoform (2) and initiates translation from the standard AUG codon present in its 5' terminal exon.
    Source sequence(s)
    AC069444, KF457674
    Consensus CDS
    CCDS2995.1
    UniProtKB/TrEMBL
    F1D8P9, F1DAL3
    Related
    ENSP00000336528.4, ENST00000337940.4
    Conserved Domains (2) summary
    cd06934
    Location:182 → 467
    NR_LBD_PXR_like; The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor
    cd07162
    Location:79 → 166
    NR_DBD_PXR; DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers

  3. NM_033013.3 → NP_148934.1  nuclear receptor subfamily 1 group I member 2 isoform 3

    See identical proteins and their annotated locations for NP_148934.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' terminal exon, and uses a different acceptor splice site at one of the internal coding exons, compared to transcript variant 2. It initiates translation from an in-frame, downstream non-AUG (CUG) codon, resulting in a shorter isoform (3) with a different N-terminus and missing an internal segment, compared to isoform 2.
    Source sequence(s)
    AC069444, KF457674
    Consensus CDS
    CCDS54627.1
    UniProtKB/TrEMBL
    H0Y8E2
    Related
    ENSP00000420297.2, ENST00000466380.6
    Conserved Domains (2) summary
    cd06934
    Location:143 → 391
    NR_LBD_PXR_like; The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor
    cl02596
    Location:40 → 127
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    119782101..119818487
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    122501838..122538215
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75469.1 GenPept UniProtKB/Swiss-Prot:O75469

Gene LinkOut

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