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

Gene ID: 2494, updated on 22-Aug-2020

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
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

Genomic context

See NR5A2 in Genome Data Viewer
Location:
1q32.1
Exon count:
13
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (200027710..200177415)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (199996730..200146552)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 716, pseudogene Neighboring gene RNA, U6 small nuclear 609, pseudogene Neighboring gene RNA, U6 small nuclear 570, pseudogene Neighboring gene heart enhancer 1 Neighboring gene uncharacterized LOC107985244 Neighboring gene collagen type XXII alpha 1 chain pseudogene Neighboring gene CCNQ pseudogene 1 Neighboring gene long intergenic non-protein coding RNA 862

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33.
GeneReviews: Not available
A genome-wide association study of serum uric acid in African Americans.
GeneReviews: Not available
Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.
GeneReviews: Not available
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
GeneReviews: Not available
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear receptor activity TAS
Traceable Author Statement
more info
PubMed 
phospholipid binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
bile acid metabolic process IEA
Inferred from Electronic Annotation
more info
 
calcineurin-mediated signaling IEA
Inferred from Electronic Annotation
more info
 
cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
 
cholesterol homeostasis IEA
Inferred from Electronic Annotation
more info
 
embryo development ending in birth or egg hatching TAS
Traceable Author Statement
more info
PubMed 
epithelial cell differentiation IEA
Inferred from Electronic Annotation
more info
 
homeostatic process NAS
Non-traceable Author Statement
more info
PubMed 
hormone-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
pancreas morphogenesis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated TAS
Traceable Author Statement
more info
PubMed 
positive regulation of viral genome replication IDA
Inferred from Direct Assay
more info
PubMed 
regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated TAS
Traceable Author Statement
more info
PubMed 
tissue development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
RNA polymerase II transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II transcription factor complex ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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
liver nuclear receptor homolog-1 variant 2

NCBI Reference Sequences (RefSeq)

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_050913.1 RefSeqGene

    Range
    5109..154814
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001276464.2NP_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/Swiss-Prot
    O00482
    Related
    ENSP00000439116.1, ENST00000544748.5
    Conserved Domains (2) summary
    cd07069
    Location:229469
    NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,
    cd07167
    Location:14106
    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
  2. NM_003822.5NP_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/Swiss-Prot
    O00482
    UniProtKB/TrEMBL
    F1D8R9
    Related
    ENSP00000236914.3, ENST00000236914.7
    Conserved Domains (2) summary
    cd07069
    Location:255495
    NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,
    cd07167
    Location:40132
    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
  3. NM_205860.3NP_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
    O00482
    Related
    ENSP00000356331.3, ENST00000367362.8
    Conserved Domains (2) summary
    cd07069
    Location:301541
    NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,
    cd07167
    Location:86178
    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: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    200027710..200177415
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509380.1XP_011507682.1  nuclear receptor subfamily 5 group A member 2 isoform X1

    See identical proteins and their annotated locations for XP_011507682.1

    Conserved Domains (2) summary
    cd07069
    Location:261501
    NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,
    cd07167
    Location:46138
    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
  2. XM_011509382.1XP_011507684.1  nuclear receptor subfamily 5 group A member 2 isoform X2

    See identical proteins and their annotated locations for XP_011507684.1

    UniProtKB/Swiss-Prot
    O00482
    Conserved Domains (2) summary
    cd07069
    Location:229469
    NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,
    cd07167
    Location:14106
    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
  3. XM_011509381.3XP_011507683.1  nuclear receptor subfamily 5 group A member 2 isoform X1

    See identical proteins and their annotated locations for XP_011507683.1

    Conserved Domains (2) summary
    cd07069
    Location:261501
    NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,
    cd07167
    Location:46138
    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
  4. XM_011509384.2XP_011507686.1  nuclear receptor subfamily 5 group A member 2 isoform X1

    See identical proteins and their annotated locations for XP_011507686.1

    Conserved Domains (2) summary
    cd07069
    Location:261501
    NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,
    cd07167
    Location:46138
    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
  5. XM_017000904.1XP_016856393.1  nuclear receptor subfamily 5 group A member 2 isoform X1

    Conserved Domains (2) summary
    cd07069
    Location:261501
    NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,
    cd07167
    Location:46138
    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
  6. XM_005245062.3XP_005245119.1  nuclear receptor subfamily 5 group A member 2 isoform X2

    See identical proteins and their annotated locations for XP_005245119.1

    UniProtKB/Swiss-Prot
    O00482
    Conserved Domains (2) summary
    cd07069
    Location:229469
    NR_LBD_Lrh-1; The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,
    cd07167
    Location:14106
    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
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