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    FOXA2 forkhead box A2 [ Homo sapiens (human) ]

    Gene ID: 3170, updated on 9-Dec-2024

    Summary

    Official Symbol
    FOXA2provided by HGNC
    Official Full Name
    forkhead box A2provided by HGNC
    Primary source
    HGNC:HGNC:5022
    See related
    Ensembl:ENSG00000125798 MIM:600288; AllianceGenome:HGNC:5022
    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
    HNF3B; TCF3B; HNF-3-beta
    Summary
    This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific genes such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. This gene has been linked to sporadic cases of maturity-onset diabetes of the young. Transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Oct 2008]
    Expression
    Biased expression in stomach (RPKM 15.2), lung (RPKM 9.0) and 8 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See FOXA2 in Genome Data Viewer
    Location:
    20p11.21
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (22580998..22585490, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (22640367..22644859, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (22561636..22566128, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:22493383-22493884 Neighboring gene Sharpr-MPRA regulatory region 10094 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:22543873-22544400 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:22544401-22544926 Neighboring gene long intergenic non-protein coding RNA 261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:22548490-22549308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:22549309-22550126 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:22552037-22552636 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:22558127-22559082 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:22559083-22560038 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:22560039-22560994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:22562671-22563242 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:22563243-22563815 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:22565240-22565995 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:22566751-22567506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:22567507-22568261 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr20:22571115-22571710 Neighboring gene lncRNA neighboring enhancer of FOXA2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:22592186-22592856 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:22643831-22644824 Neighboring gene long intergenic non-protein coding RNA 1747 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:22665133-22666332

    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 approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
    EBI GWAS Catalog
    A weighted false discovery rate control procedure reveals alleles at FOXA2 that influence fasting glucose levels.
    EBI GWAS Catalog
    Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
    EBI GWAS Catalog
    Six novel susceptibility Loci for early-onset androgenetic alopecia and their unexpected association with common diseases.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC19807

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in adult locomotory behavior ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in anatomical structure morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell fate specification ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in dopaminergic neuron differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in dopaminergic neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in dopaminergic neuron differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in endocrine pancreas development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of epithelial to mesenchymal transition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cell-cell adhesion mediated by cadherin IC
    Inferred by Curator
    more info
    PubMed 
    involved_in positive regulation of embryonic development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of gastrulation ISS
    Inferred from Sequence or Structural Similarity
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in primitive streak formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of blood coagulation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of insulin secretion involved in cellular response to glucose stimulus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to interleukin-6 TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cell junction IDA
    Inferred from Direct Assay
    more info
     
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    hepatocyte nuclear factor 3-beta
    Names
    forkhead box protein A2
    hepatic nuclear factor-3-beta
    transcription factor 3B

    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.

    mRNA and Protein(s)

    1. NM_021784.5NP_068556.2  hepatocyte nuclear factor 3-beta isoform 1

      See identical proteins and their annotated locations for NP_068556.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AL121722
      Consensus CDS
      CCDS46585.1
      UniProtKB/TrEMBL
      B0ZTD4
      Related
      ENSP00000400341.3, ENST00000419308.7
      Conserved Domains (3) summary
      pfam08430
      Location:23164
      Forkhead_N; Forkhead N-terminal region
      pfam09354
      Location:380452
      HNF_C; HNF3 C-terminal domain
      cd20039
      Location:163264
      FH_FOXA2; Forkhead (FH) domain found in Forkhead box protein A2 (FOXA2) and similar proteins
    2. NM_153675.3NP_710141.1  hepatocyte nuclear factor 3-beta isoform 2

      See identical proteins and their annotated locations for NP_710141.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has a different splice pattern at the 5' end compared to transcript variant 1, resulting in translation initiation from a downstream AUG, and a shorter isoform (2) missing 6 aa from the N-terminus compared to isoform 1.
      Source sequence(s)
      AA469087, AB028021, AI268650, AL121722
      Consensus CDS
      CCDS13147.1
      UniProtKB/Swiss-Prot
      Q8WUW4, Q96DF7, Q9Y261
      Related
      ENSP00000366319.4, ENST00000377115.4
      Conserved Domains (3) summary
      pfam08430
      Location:17158
      Forkhead_N; Forkhead N-terminal region
      pfam09354
      Location:374446
      HNF_C; HNF3 C-terminal domain
      cd20039
      Location:157258
      FH_FOXA2; Forkhead (FH) domain found in Forkhead box protein A2 (FOXA2) and similar proteins

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      22580998..22585490 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047440133.1XP_047296089.1  hepatocyte nuclear factor 3-beta isoform X1

      UniProtKB/Swiss-Prot
      Q8WUW4, Q96DF7, Q9Y261
    2. XM_047440134.1XP_047296090.1  hepatocyte nuclear factor 3-beta isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      22640367..22644859 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)