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Aliases for FOXA1 Gene

Aliases for FOXA1 Gene

  • Forkhead Box A1 2 3
  • HNF3A 3 4 6
  • Forkhead Box Protein A1 3 4
  • Transcription Factor 3A 3 4
  • HNF-3-Alpha 3 4
  • HNF-3A 3 4
  • TCF-3A 3 4
  • TCF3A 3 4
  • Hepatocyte Nuclear Factor 3, Alpha 2
  • Hepatocyte Nuclear Factor 3-Alpha 3

External Ids for FOXA1 Gene

Previous HGNC Symbols for FOXA1 Gene

  • HNF3A

Previous GeneCards Identifiers for FOXA1 Gene

  • GC14M035439
  • GC14M031916
  • GC14M036049
  • GC14M037128
  • GC14M038059
  • GC14M018173

Summaries for FOXA1 Gene

Entrez Gene Summary for FOXA1 Gene

  • 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]

GeneCards Summary for FOXA1 Gene

FOXA1 (Forkhead Box A1) is a Protein Coding gene. Among its related pathways are Prostate Cancer and FOXA1 transcription factor network. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and transcription factor binding. An important paralog of this gene is FOXE3.

UniProtKB/Swiss-Prot for FOXA1 Gene

  • Transcription factor that is involved in embryonic development, establishment of tissue-specific gene expression and regulation of gene expression in differentiated tissues. Is thought to act as a pioneer factor opening the compacted chromatin for other proteins through interactions with nucleosomal core histones and thereby replacing linker histones at target enhancer and/or promoter sites. Binds DNA with the consensus sequence 5-[AC]A[AT]T[AG]TT[GT][AG][CT]T[CT]-3 (By similarity). Proposed to play a role in translating the epigenetic signatures into cell type-specific enhancer-driven transcriptional programs. Its differential recruitment to chromatin is dependent on distribution of histone H3 methylated at Lys-5 (H3K4me2) in estrogen-regulated genes. Involved in the development of multiple endoderm-derived organ systems such as liver, pancreas, lung and prostate; FOXA1 and FOXA2 seem to have at least in part redundant roles (By similarity). Modulates the transcriptional activity of nuclear hormone receptors. Is involved in ESR1-mediated transcription; required for ESR1 binding to the NKX2-1 promoter in breast cancer cells; binds to the RPRM promter and is required for the estrogen-induced repression of RPRM. Involved in regulation of apoptosis by inhibiting the expression of BCL2. Involved in cell cycle regulation by activating expression of CDKN1B, alone or in conjunction with BRCA1. Originally described as a transcription activator for a number of liver genes such as AFP, albumin, tyrosine aminotransferase, PEPCK, etc. Interacts with the cis-acting regulatory regions of these genes. Involved in glucose homeostasis.

Gene Wiki entry for FOXA1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FOXA1 Gene

Genomics for FOXA1 Gene

Regulatory Elements for FOXA1 Gene

Genomic Location for FOXA1 Gene

Start:
37,589,552 bp from pter
End:
37,596,059 bp from pter
Size:
6,508 bases
Orientation:
Minus strand

Genomic View for FOXA1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for FOXA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FOXA1 Gene

Proteins for FOXA1 Gene

  • Protein details for FOXA1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P55317-FOXA1_HUMAN
    Recommended name:
    Hepatocyte nuclear factor 3-alpha
    Protein Accession:
    P55317
    Secondary Accessions:
    • B2R9H6
    • B7ZAP5
    • Q9H2A0

    Protein attributes for FOXA1 Gene

    Size:
    472 amino acids
    Molecular mass:
    49148 Da
    Quaternary structure:
    • Binds DNA as a monomer (By similarity). Interacts with FOXA2. Interacts with NKX2-1. Interacts with HDAC7. Interacts with the histone H3-H4 heterodimer. Associates with nucleosomes containing histone H2A. Interacts with AR. Interacts with NR0B2 (By similarity).

    Alternative splice isoforms for FOXA1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for FOXA1 Gene

Proteomics data for FOXA1 Gene at MOPED

Post-translational modifications for FOXA1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for FOXA1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for FOXA1 Gene

Domains for FOXA1 Gene

Gene Families for FOXA1 Gene

HGNC:
  • FOX :Forkhead boxes

Protein Domains for FOXA1 Gene

Suggested Antigen Peptide Sequences for FOXA1 Gene

Graphical View of Domain Structure for InterPro Entry

P55317

UniProtKB/Swiss-Prot:

FOXA1_HUMAN :
  • P55317
Domain:
  • Contains 1 fork-head DNA-binding domain.
genes like me logo Genes that share domains with FOXA1: view

Function for FOXA1 Gene

Molecular function for FOXA1 Gene

UniProtKB/Swiss-Prot Function: Transcription factor that is involved in embryonic development, establishment of tissue-specific gene expression and regulation of gene expression in differentiated tissues. Is thought to act as a pioneer factor opening the compacted chromatin for other proteins through interactions with nucleosomal core histones and thereby replacing linker histones at target enhancer and/or promoter sites. Binds DNA with the consensus sequence 5-[AC]A[AT]T[AG]TT[GT][AG][CT]T[CT]-3 (By similarity). Proposed to play a role in translating the epigenetic signatures into cell type-specific enhancer-driven transcriptional programs. Its differential recruitment to chromatin is dependent on distribution of histone H3 methylated at Lys-5 (H3K4me2) in estrogen-regulated genes. Involved in the development of multiple endoderm-derived organ systems such as liver, pancreas, lung and prostate; FOXA1 and FOXA2 seem to have at least in part redundant roles (By similarity). Modulates the transcriptional activity of nuclear hormone receptors. Is involved in ESR1-mediated transcription; required for ESR1 binding to the NKX2-1 promoter in breast cancer cells; binds to the RPRM promter and is required for the estrogen-induced repression of RPRM. Involved in regulation of apoptosis by inhibiting the expression of BCL2. Involved in cell cycle regulation by activating expression of CDKN1B, alone or in conjunction with BRCA1. Originally described as a transcription activator for a number of liver genes such as AFP, albumin, tyrosine aminotransferase, PEPCK, etc. Interacts with the cis-acting regulatory regions of these genes. Involved in glucose homeostasis.

Gene Ontology (GO) - Molecular Function for FOXA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity IBA --
GO:0001077 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription ISS --
GO:0003677 DNA binding IDA 9931457
GO:0003700 sequence-specific DNA binding transcription factor activity TAS 8652662
GO:0008134 transcription factor binding IEA --
genes like me logo Genes that share ontologies with FOXA1: view
genes like me logo Genes that share phenotypes with FOXA1: view

miRNA for FOXA1 Gene

miRTarBase miRNAs that target FOXA1
Targeting motifs for FOXA1 Gene
HOMER Transcription Factor Regulatory Elements motif FOXA1
  • Consensus sequence: AAAGTAAACA Submotif: canonical Cell Type: MCF7 GeoId: GSE26831

No data available for Enzyme Numbers (IUBMB) , Animal Models and Transcription Factor Targeting for FOXA1 Gene

Localization for FOXA1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FOXA1 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for FOXA1 Gene COMPARTMENTS Subcellular localization image for FOXA1 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for FOXA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005730 nucleolus IDA --
GO:0005902 microvillus IEA --
genes like me logo Genes that share ontologies with FOXA1: view

Pathways for FOXA1 Gene

genes like me logo Genes that share pathways with FOXA1: view

Gene Ontology (GO) - Biological Process for FOXA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0006338 chromatin remodeling ISS --
GO:0006351 transcription, DNA-templated --
GO:0006355 regulation of transcription, DNA-templated --
GO:0006366 transcription from RNA polymerase II promoter IBA --
genes like me logo Genes that share ontologies with FOXA1: view

Transcripts for FOXA1 Gene

Unigene Clusters for FOXA1 Gene

Forkhead box A1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for FOXA1 Gene

No ASD Table

Relevant External Links for FOXA1 Gene

GeneLoc Exon Structure for
FOXA1
ECgene alternative splicing isoforms for
FOXA1

Expression for FOXA1 Gene

mRNA expression in normal human tissues for FOXA1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for FOXA1 Gene

This gene is overexpressed in Prostate (12.2), Liver (7.9), Stomach (6.3), Bladder (5.5), and Colon - Transverse (4.0).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for FOXA1 Gene

SOURCE GeneReport for Unigene cluster for FOXA1 Gene Hs.163484

mRNA Expression by UniProt/SwissProt for FOXA1 Gene

P55317-FOXA1_HUMAN
Tissue specificity: Highly expressed in prostate and ESR1-positive breast tumors. Overexpressed in esophageal and lung adenocarcinomas.
genes like me logo Genes that share expressions with FOXA1: view

Orthologs for FOXA1 Gene

This gene was present in the common ancestor of animals.

Orthologs for FOXA1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia FOXA1 35
  • 99.43 (n)
  • 99.15 (a)
FOXA1 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia FOXA1 35
  • 90.15 (n)
  • 94 (a)
FOXA1 36
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia FOXA1 35
  • 91.33 (n)
  • 94.39 (a)
FOXA1 36
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Foxa1 35
  • 91.52 (n)
  • 95.3 (a)
Foxa1 16
Foxa1 36
  • 96 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia FOXA1 36
  • 87 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Foxa1 35
  • 90.27 (n)
  • 92.49 (a)
lizard
(Anolis carolinensis)
Reptilia FOXA1 36
  • 65 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia foxa1-prov 35
tropical clawed frog
(Silurana tropicalis)
Amphibia foxa1 35
  • 70.81 (n)
  • 75.12 (a)
Hnf3a 35
zebrafish
(Danio rerio)
Actinopterygii foxa1 35
  • 67.23 (n)
  • 67.39 (a)
foxa1 36
  • 69 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta fkh 36
  • 35 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 53 (a)
ManyToMany
CSA.7421 36
  • 29 (a)
ManyToMany
Species with no ortholog for FOXA1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for FOXA1 Gene

ENSEMBL:
Gene Tree for FOXA1 (if available)
TreeFam:
Gene Tree for FOXA1 (if available)

Paralogs for FOXA1 Gene

Selected SIMAP similar genes for FOXA1 Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for FOXA1 Gene

genes like me logo Genes that share paralogs with FOXA1: view

Variants for FOXA1 Gene

Sequence variations from dbSNP and Humsavar for FOXA1 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type MAF
rs2698 -- 37,591,307(-) AAAAA(C/T)CAACA utr-variant-3-prime
rs2699 -- 37,591,293(-) AACAA(A/C)ACCAC utr-variant-3-prime
rs762083 -- 37,594,804(+) GGCCC(C/G)CCTGC intron-variant
rs911822 -- 37,591,222(+) AAGGT(A/T)GTGCA utr-variant-3-prime
rs1052935 -- 37,591,147(-) AAGAC(A/G)ACCCC utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for FOXA1 Gene

Variant ID Type Subtype PubMed ID
nsv826923 CNV Gain 20364138
nsv832772 CNV Loss 17160897
dgv1877n71 CNV Loss 21882294
dgv1878n71 CNV Loss 21882294

Relevant External Links for FOXA1 Gene

HapMap Linkage Disequilibrium report
FOXA1
Human Gene Mutation Database (HGMD)
FOXA1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FOXA1 Gene

Disorders for FOXA1 Gene

(2) University of Copenhagen DISEASES for FOXA1 Gene

Relevant External Links for FOXA1

Genetic Association Database (GAD)
FOXA1
Human Genome Epidemiology (HuGE) Navigator
FOXA1
genes like me logo Genes that share disorders with FOXA1: view

No data available for UniProtKB/Swiss-Prot for FOXA1 Gene

Publications for FOXA1 Gene

  1. Assignment of the human genes for hepatocyte nuclear factor 3-alpha, -beta, and -gamma (HNF3A, HNF3B, HNF3G) to 14q12-q13, 20p11, and 19q13.2-q13.4. (PMID: 9119385) Mincheva A. … Kaestner K.H. (Genomics 1997) 2 3 23
  2. The hepatocyte nuclear factor 3 alpha gene, HNF3alpha (FOXA1), on chromosome band 14q13 is amplified and overexpressed in esophageal and lung adenocarcinomas. (PMID: 12234996) Lin L. … Beer D.G. (Cancer Res. 2002) 3 4 23
  3. Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq. (PMID: 19919681) Motallebipour M. … Wadelius C. (Genome Biol. 2009) 3 4 23
  4. Molecular cloning of the forkhead transcription factor HNF-3 alpha from a human pulmonary adenocarcinoma cell line. (PMID: 8652662) Bingle C.D. … Gowan S. (Biochim. Biophys. Acta 1996) 2 3 4
  5. Hepatocyte nuclear factor-3alpha binding at P sequences of the human growth hormone locus is associated with pituitary repressor function. (PMID: 16239259) Norquay L.D. … Cattini P.A. (Mol. Endocrinol. 2006) 3 23

Products for FOXA1 Gene

Sources for FOXA1 Gene

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