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

Summary

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: mouse all
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Genomic context

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-T26531 (e-PCR)
- UniSTS:72997

NR1I3_2131 (e-PCR)
- UniSTS:280874

MARC_4339-4340:996679552:1 (e-PCR)
- UniSTS:269360

D3S3620 (e-PCR), detects polymorphism
- UniSTS:73032

G32262 (e-PCR)
- UniSTS:116861

A005P48 (e-PCR)
- UniSTS:42424

AFMA323WF9 (e-PCR)
- UniSTS:49099

SHGC-56597 (e-PCR)
- UniSTS:31448

SHGC-77233 (e-PCR)
- UniSTS:39416

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

NG_011856.2 RefSeqGene

Range

5002..41388

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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