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    FOXA1 forkhead box A1 [ Homo sapiens (human) ]

    Gene ID: 3169, updated on 9-Oct-2024

    Summary

    Official Symbol
    FOXA1provided by HGNC
    Official Full Name
    forkhead box A1provided by HGNC
    Primary source
    HGNC:HGNC:5021
    See related
    Ensembl:ENSG00000129514 MIM:602294; AllianceGenome:HGNC:5021
    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
    HNF3A; TCF3A
    Summary
    This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts 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. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in prostate (RPKM 46.5), urinary bladder (RPKM 12.0) and 6 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See FOXA1 in Genome Data Viewer
    Location:
    14q21.1
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (37589552..37595249, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (31778686..31784378, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (38058757..38064454, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene mirror-image polydactyly 1 Neighboring gene uncharacterized LOC107984702 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:37866371-37867570 Neighboring gene RNA, U6 small nuclear 886, pseudogene Neighboring gene FOXA motif-containing MPRA enhancer 271 Neighboring gene Sharpr-MPRA regulatory region 2445 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:38057104-38057944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:38060408-38060957 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:38064763-38065962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:38068389-38069060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:38069061-38069730 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:38124049-38125248 Neighboring gene tetratricopeptide repeat domain 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:38255187-38255688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:38255689-38256188 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:38304329-38304828 Neighboring gene RNA, U6 small nuclear 1277, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5683 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:38363413-38364243 Neighboring gene long intergenic non-protein coding RNA 517

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci.
    EBI GWAS Catalog
    Genome-wide association study of chronic periodontitis in a general German population.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC33105

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in Notch signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in alveolar secondary septum development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in anatomical structure formation involved in morphogenesis IEA
    Inferred from Electronic Annotation
    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 chromatin remodeling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in dopaminergic neuron differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in dorsal/ventral neural tube patterning IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in epithelial cell maturation involved in prostate gland development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in epithelial tube branching involved in lung morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in glucose homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in hormone metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lung epithelial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mesenchymal-epithelial cell signaling involved in prostate gland development IEA
    Inferred from Electronic Annotation
    more info
     
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron fate specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell-cell adhesion mediated by cadherin IC
    Inferred by Curator
    more info
    PubMed 
    involved_in positive regulation of dopaminergic neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of intracellular estrogen receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of miRNA transcription IC
    Inferred by Curator
    more info
    PubMed 
    involved_in positive regulation of mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in prostate gland epithelium morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in prostate gland stromal morphogenesis 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 respiratory basal cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to estradiol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
     
    located_in microvillus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    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
    hepatocyte nuclear factor 3-alpha
    Names
    HNF-3-alpha
    HNF-3A
    TCF-3A
    forkhead box protein A1
    transcription factor 3A

    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_033028.1 RefSeqGene

      Range
      4872..10569
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1415

    mRNA and Protein(s)

    1. NM_004496.5NP_004487.2  hepatocyte nuclear factor 3-alpha

      See identical proteins and their annotated locations for NP_004487.2

      Status: REVIEWED

      Source sequence(s)
      AL121790
      Consensus CDS
      CCDS9665.1
      UniProtKB/Swiss-Prot
      B2R9H6, B7ZAP5, P55317, Q9H2A0
      UniProtKB/TrEMBL
      B4E257
      Related
      ENSP00000250448.3, ENST00000250448.5
      Conserved Domains (3) summary
      pfam08430
      Location:17169
      Forkhead_N; Forkhead N-terminal region
      pfam09354
      Location:398461
      HNF_C; HNF3 C-terminal domain
      cd20038
      Location:157268
      FH_FOXA1; Forkhead (FH) domain found in Forkhead box protein A1 (FOXA1) 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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      37589552..37595249 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      31778686..31784378 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)