NR5A2 nuclear receptor subfamily 5 group A member 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NR5A2provided by HGNC
Official Full Name: nuclear receptor subfamily 5 group A member 2provided by HGNC
Primary source: HGNC:HGNC:7984
See related: Ensembl:ENSG00000116833 MIM:604453; AllianceGenome:HGNC:7984
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: B1F; CPF; FTF; B1F2; LRH1; LRH-1; FTZ-F1; hB1F-2; FTZ-F1beta
Summary: The protein encoded by this gene is a DNA-binding zinc finger transcription factor and is a member of the fushi tarazu factor-1 subfamily of orphan nuclear receptors. The encoded protein is involved in the expression of genes for hepatitis B virus and cholesterol biosynthesis, and may be an important regulator of embryonic development. [provided by RefSeq, Jun 2016]
Expression: Biased expression in liver (RPKM 6.4), small intestine (RPKM 5.8) and 13 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q32.1

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (200027710..200177415)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (199284725..199434351)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (199996838..200146543)

Chromosome 1 - NC_000001.11 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

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Lineage regulators TFAP2C and NR5A2 function as bipotency activators in totipotent embryos.
Title: Lineage regulators TFAP2C and NR5A2 function as bipotency activators in totipotent embryos.
Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition.
Title: Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition.
Aberrant phosphorylation of human LRH1 at serine 510 is predictable of hepatocellular carcinoma recurrence.
Title: Aberrant phosphorylation of human LRH1 at serine 510 is predictable of hepatocellular carcinoma recurrence.
Nuclear receptor 5A2 regulation of Agrp underlies olanzapine-induced hyperphagia.
Title: Nuclear receptor 5A2 regulation of Agrp underlies olanzapine-induced hyperphagia.
MicroRNA-433-3p enhances chemosensitivity of glioma to cisplatin by downregulating NR5A2.
Title: MicroRNA-433-3p enhances chemosensitivity of glioma to cisplatin by downregulating NR5A2.
LRH-1/NR5A2 interacts with the glucocorticoid receptor to regulate glucocorticoid resistance.
Title: LRH-1/NR5A2 interacts with the glucocorticoid receptor to regulate glucocorticoid resistance.
Nuclear receptor subfamily 5 group A member 2 (NR5A2): role in health and diseases.
Title: Nuclear receptor subfamily 5 group A member 2 (NR5A2): role in health and diseases.
Nuclear-mitochondrial crosstalk: On the role of the nuclear receptor liver receptor homolog-1 (NR5A2) in the regulation of mitochondrial metabolism, cell survival, and cancer.
Title: Nuclear-mitochondrial crosstalk: On the role of the nuclear receptor liver receptor homolog-1 (NR5A2) in the regulation of mitochondrial metabolism, cell survival, and cancer.
NF-kappaB Regulation of LRH-1 and ABCG5/8 Potentiates Phytosterol Role in the Pathogenesis of Parenteral Nutrition-Associated Cholestasis.
Title: NF-κB Regulation of LRH-1 and ABCG5/8 Potentiates Phytosterol Role in the Pathogenesis of Parenteral Nutrition-Associated Cholestasis.
Nuclear receptor NR5A2 negatively regulates cell proliferation and tumor growth in nervous system malignancies.
Title: Nuclear receptor NR5A2 negatively regulates cell proliferation and tumor growth in nervous system malignancies.

Submit: New GeneRIF Correction See all GeneRIFs (133)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study of serum uric acid in African Americans. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer. EBI GWAS Catalog EBI GWAS CatalogPubMed
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

AFM292vd5 (e-PCR)
- UniSTS:34605

D1S2622 (e-PCR), detects polymorphism
- UniSTS:38232

RH122291 (e-PCR)
- UniSTS:137818

SHGC-76109 (e-PCR)
- UniSTS:51306

SHGC-76105 (e-PCR)
- UniSTS:29807

RH94232 (e-PCR)
- UniSTS:92305

PMC193920P3 (e-PCR)
- UniSTS:271762

A009V39 (e-PCR)
- UniSTS:1180

D1S2817 (e-PCR)
- UniSTS:72608

G30215 (e-PCR)
- UniSTS:16803

G32891 (e-PCR)
- UniSTS:117470

SHGC-76125 (e-PCR)
- UniSTS:65262

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	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 cis-regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables nuclear receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables nuclear receptor activity	TAS Traceable Author Statement more info	PubMed
enables phospholipid binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription coregulator binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in acinar cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in bile acid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in calcineurin-mediated signaling	IEA Inferred from Electronic Annotation more info
involved_in cellular response to leukemia inhibitory factor	IEA Inferred from Electronic Annotation more info
involved_in cholesterol homeostasis	IEA Inferred from Electronic Annotation more info
involved_in embryo development ending in birth or egg hatching	TAS Traceable Author Statement more info	PubMed
involved_in homeostatic process	NAS Non-traceable Author Statement more info	PubMed
involved_in hormone-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in pancreas morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
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	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of viral genome replication	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	TAS Traceable Author Statement more info	PubMed
involved_in regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in tissue development	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	IBA Inferred from Biological aspect of Ancestor more info
part_of RNA polymerase II transcription regulator complex	ISS Inferred from Sequence or Structural Similarity more info
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: nuclear receptor subfamily 5 group A member 2

Names: CYP7A promoter-binding factor; b1-binding factor, hepatocyte transcription factor which activates enhancer II of hepatitis B virus; fetoprotein-alpha 1 (AFP) transcription factor; hepatocytic transcription factor hB1F-3

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_050913.1 RefSeqGene

Range

5109..154814

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001276464.2 → NP_001263393.1 nuclear receptor subfamily 5 group A member 2 isoform 3

See identical proteins and their annotated locations for NP_001263393.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) has an alternate exon in place of the first two exons compared to variant 1. The resulting isoform (3) uses a downstream translation start site and has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AC096633, AF146343, AK304365, CA776772

Consensus CDS

CCDS60383.1

UniProtKB/TrEMBL

B4E2M6, B6ZGU9

Related

ENSP00000439116.1, ENST00000544748.5

Conserved Domains (2) summary

cd07069
Location:229 → 469

NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,

cd07167
Location:14 → 106

NR_DBD_Lrh-1_like; The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers
NM_003822.5 → NP_003813.1 nuclear receptor subfamily 5 group A member 2 isoform 2

See identical proteins and their annotated locations for NP_003813.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AC096633, AF146343, CA776772

Consensus CDS

CCDS1400.1

UniProtKB/TrEMBL

B4E2M6, B6ZGU9, F1D8R9

Related

ENSP00000236914.3, ENST00000236914.7

Conserved Domains (2) summary

cd07069
Location:255 → 495

NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,

cd07167
Location:40 → 132

NR_DBD_Lrh-1_like; The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers
NM_205860.3 → NP_995582.1 nuclear receptor subfamily 5 group A member 2 isoform 1

See identical proteins and their annotated locations for NP_995582.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC096633, AF124247, AF146343, CA776772

Consensus CDS

CCDS1401.1

UniProtKB/Swiss-Prot

B4E2P3, O00482, O95642, Q147U3

UniProtKB/TrEMBL

Q9UEC0

Related

ENSP00000356331.3, ENST00000367362.8

Conserved Domains (2) summary

cd07069
Location:301 → 541

NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,

cd07167
Location:86 → 178

NR_DBD_Lrh-1_like; The DNA-binding domain of Lrh-1 like nuclear receptor family like 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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

200027710..200177415

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047416753.1 → XP_047272709.1 nuclear receptor subfamily 5 group A member 2 isoform X1
XM_011509381.4 → XP_011507683.1 nuclear receptor subfamily 5 group A member 2 isoform X3

See identical proteins and their annotated locations for XP_011507683.1

UniProtKB/TrEMBL

B4E2M6, B6ZGU9

Conserved Domains (2) summary

cd07069
Location:261 → 501

NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,

cd07167
Location:46 → 138

NR_DBD_Lrh-1_like; The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers
XM_017000904.2 → XP_016856393.1 nuclear receptor subfamily 5 group A member 2 isoform X3

UniProtKB/TrEMBL

B4E2M6, B6ZGU9

Conserved Domains (2) summary

cd07069
Location:261 → 501

NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,

cd07167
Location:46 → 138

NR_DBD_Lrh-1_like; The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers
XM_011509384.3 → XP_011507686.1 nuclear receptor subfamily 5 group A member 2 isoform X3

See identical proteins and their annotated locations for XP_011507686.1

UniProtKB/TrEMBL

B4E2M6, B6ZGU9

Conserved Domains (2) summary

cd07069
Location:261 → 501

NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,

cd07167
Location:46 → 138

NR_DBD_Lrh-1_like; The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers
XM_047416762.1 → XP_047272718.1 nuclear receptor subfamily 5 group A member 2 isoform X2
XM_005245062.4 → XP_005245119.1 nuclear receptor subfamily 5 group A member 2 isoform X4

See identical proteins and their annotated locations for XP_005245119.1

UniProtKB/TrEMBL

B4E2M6, B6ZGU9

Conserved Domains (2) summary

cd07069
Location:229 → 469

NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,

cd07167
Location:14 → 106

NR_DBD_Lrh-1_like; The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

199284725..199434351

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054335750.1 → XP_054191725.1 nuclear receptor subfamily 5 group A member 2 isoform X3
XM_054335749.1 → XP_054191724.1 nuclear receptor subfamily 5 group A member 2 isoform X3
XM_054335752.1 → XP_054191727.1 nuclear receptor subfamily 5 group A member 2 isoform X3
XM_054335751.1 → XP_054191726.1 nuclear receptor subfamily 5 group A member 2 isoform X4