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FOXA1 forkhead box A1 [ Homo sapiens (human) ]

Gene ID: 3169, updated on 10-Dec-2024

Summary

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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
mouse all
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. Time-varying effects of FOXA1 on breast cancer prognosis. Chen QX, et al. Breast Cancer Res Treat, 2021 Jun. PMID 33604715
  2. Switch in FOXA1 status associates with endometrial cancer progression. Tangen IL, et al. PLoS One, 2014. PMID 24849812, Free PMC Article
  3. NFI transcription factors interact with FOXA1 to regulate prostate-specific gene expression. Grabowska MM, et al. Mol Endocrinol, 2014 Jun. PMID 24801505, Free PMC Article
  4. FOXA1 Mutations Reveal Distinct Chromatin Profiles and Influence Therapeutic Response in Breast Cancer. Arruabarrena-Aristorena A, et al. Cancer Cell, 2020 Oct 12. PMID 32888433, Free PMC Article
  5. Down-regulated FOXA1 in early-onset pre-eclampsia induces apoptosis, and inhibits migration and invasion of trophoblast cells. Zhu J, et al. J Gene Med, 2020 Dec. PMID 32894789

See all (356) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LINC01133 contributes to the malignant phenotypes of non-small cell lung cancer by targeting miR-30b-5p/FOXA1 pathway.
    Title: LINC01133 contributes to the malignant phenotypes of non-small cell lung cancer by targeting miR-30b-5p/FOXA1 pathway.
  2. Dynamic phosphorylation of FOXA1 by Aurora B guides post-mitotic gene reactivation.
    Title: Dynamic phosphorylation of FOXA1 by Aurora B guides post-mitotic gene reactivation.
  3. The Role of FOXA1 in Human Normal Development and Its Functions in Sex Hormone-Related Cancers.
    Title: The Role of FOXA1 in Human Normal Development and Its Functions in Sex Hormone-Related Cancers.
  4. FOXA1 regulates ribosomal RNA transcription in prostate cancer.
    Title: FOXA1 regulates ribosomal RNA transcription in prostate cancer.
  5. FOXA1 co-activates circODC1 and ODC1 in HPV-positive cervical cancer cell growth.
    Title: FOXA1 co-activates circODC1 and ODC1 in HPV-positive cervical cancer cell growth.
  6. FOXA1/UBE2T Inhibits CD8[+]T Cell Activity by Inducing Mediates Glycolysis in Lung Adenocarcinoma.
    Title: FOXA1/UBE2T Inhibits CD8(+)T Cell Activity by Inducing Mediates Glycolysis in Lung Adenocarcinoma.
  7. Expression of BCL2, TP53, FOXA1, and GATA3 in pTa bladder cancer recurrence.
    Title: Expression of BCL2, TP53, FOXA1, and GATA3 in pTa bladder cancer recurrence.
  8. The role of transcription factor FOXA1/C2/M1/O3/P1/Q1 in breast cancer.
    Title: The role of transcription factor FOXA1/C2/M1/O3/P1/Q1 in breast cancer.
  9. Clinically-observed FOXA1 mutations upregulate SEMA3C through transcriptional derepression in prostate cancer.
    Title: Clinically-observed FOXA1 mutations upregulate SEMA3C through transcriptional derepression in prostate cancer.
  10. Staufen1 Represses the FOXA1-Regulated Transcriptome by Destabilizing FOXA1 mRNA in Colorectal Cancer Cells.
    Title: Staufen1 Represses the FOXA1-Regulated Transcriptome by Destabilizing FOXA1 mRNA in Colorectal Cancer Cells.
Submit: New GeneRIF Correction See all GeneRIFs (300)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC33105

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 IC
Inferred by Curator
more info
 PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISS
Inferred from Sequence or Structural Similarity
more info
  
enables DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
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 IDA
Inferred from Direct Assay
more info
 PubMed 
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein domain specific binding IEA
Inferred from Electronic Annotation
more info
  
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 
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

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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)

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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_004496.5 → NP_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:17 → 169
    Forkhead_N; Forkhead N-terminal region
    pfam09354
    Location:398 → 461
    HNF_C; HNF3 C-terminal domain
    cd20038
    Location:157 → 268
    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)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P55317.2 GenPept UniProtKB/Swiss-Prot:P55317

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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