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

    Gene ID: 2494, updated on 3-Dec-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NR5A2 in Genome Data Viewer
    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_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 716, pseudogene Neighboring gene RNA, U6 small nuclear 609, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:199998502-199999002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:199999003-199999503 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:200005053-200005953 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:200009541-200010343 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:200017388-200018327 Neighboring gene RNA, U6 small nuclear 570, pseudogene Neighboring gene heart enhancer 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:200049926-200050612 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:200050613-200051298 Neighboring gene uncharacterized LOC107985244 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1668 Neighboring gene collagen type XXII alpha 1 chain pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2295 Neighboring gene NANOG hESC enhancer GRCh37_chr1:200193434-200193952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:200195876-200196563 Neighboring gene CCNQ pseudogene 1 Neighboring gene uncharacterized LOC124904479

    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

    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
    A genome-wide association study of serum uric acid in African Americans.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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/TrEMBL
      B4E2M6, B6ZGU9
      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/TrEMBL
      B4E2M6, B6ZGU9, 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
      B4E2P3, O00482, O95642, Q147U3
      UniProtKB/TrEMBL
      Q9UEC0
      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: 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_000001.11 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_047416753.1XP_047272709.1  nuclear receptor subfamily 5 group A member 2 isoform X1

      UniProtKB/TrEMBL
      B4E2M6, B6ZGU9
    2. XM_011509381.4XP_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: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
    3. XM_017000904.2XP_016856393.1  nuclear receptor subfamily 5 group A member 2 isoform X3

      UniProtKB/TrEMBL
      B4E2M6, B6ZGU9
      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_011509384.3XP_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: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_047416762.1XP_047272718.1  nuclear receptor subfamily 5 group A member 2 isoform X2

      UniProtKB/TrEMBL
      B4E2M6, B6ZGU9
    6. XM_005245062.4XP_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: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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      199284725..199434351
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335750.1XP_054191725.1  nuclear receptor subfamily 5 group A member 2 isoform X3

      UniProtKB/TrEMBL
      B4E2M6, B6ZGU9
    2. XM_054335749.1XP_054191724.1  nuclear receptor subfamily 5 group A member 2 isoform X3

      UniProtKB/TrEMBL
      B4E2M6, B6ZGU9
    3. XM_054335752.1XP_054191727.1  nuclear receptor subfamily 5 group A member 2 isoform X3

      UniProtKB/TrEMBL
      B4E2M6, B6ZGU9
    4. XM_054335751.1XP_054191726.1  nuclear receptor subfamily 5 group A member 2 isoform X4

      UniProtKB/TrEMBL
      B4E2M6, B6ZGU9