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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

FOXA1 Gene

protein-coding   GIFtS: 64
GCID: GC14M038059

Forkhead Box A1

(Previous names: hepatocyte nuclear factor 3, alpha)
(Previous symbol: HNF3A)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Forkhead Box A11 2     HNF-3A2 3
HNF3A1 2 3 5     TCF-3A2 3
Forkhead Box Protein A12 3     TCF3A2 3
Transcription Factor 3A2 3     Hepatocyte Nuclear Factor 3, Alpha1
HNF-3-alpha2 3     Hepatocyte Nuclear Factor 3-Alpha2

External Ids:    HGNC: 50211   Entrez Gene: 31692   Ensembl: ENSG000001295147   OMIM: 6022945   UniProtKB: P553173   

Export aliases for FOXA1 gene to outside databases

Previous GC identifers: GC14M035439 GC14M031916 GC14M036049 GC14M037128 GC14M018173


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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. Diseases associated with FOXA1 include mirror-image polydactyly, and lung adenocarcinoma, and among its related super-pathways are Integrated Cancer pathway. GO annotations related to this gene include transcription factor binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is FOXF1.

UniProtKB/Swiss-Prot: FOXA1_HUMAN, P55317
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 Wiki entry for FOXA1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000014.8  NT_026437.12  NC_018925.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the FOXA1 gene promoter:
         Sp1   NRSF form 1   HTF   FOXD3   NRSF form 2   GATA-1   PPAR-alpha   FOXO4   Sox9   ATF   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 3): FOXA1 promoter sequence
   Search SABiosciences Chromatin IP Primers for FOXA1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat FOXA1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 14q12-q13   Ensembl cytogenetic band:  14q21.1   HGNC cytogenetic band: 14q12-q13

FOXA1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FOXA1 gene location

GeneLoc information about chromosome 14         GeneLoc Exon Structure

GeneLoc location for GC14M038059:  view genomic region     (about GC identifiers)

Start:
38,059,189 bp from pter      End:
38,069,245 bp from pter
Size:
10,057 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: FOXA1_HUMAN, P55317 (See protein sequence)
Recommended Name: Hepatocyte nuclear factor 3-alpha  
Size: 472 amino acids; 49148 Da
Subunit: 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)
Subcellular location: Nucleus
Secondary accessions: B2R9H6 Q9H2A0

Explore the universe of human proteins at neXtProt for FOXA1: NX_P55317

Explore proteomics data for FOXA1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P55317

  • FOXA1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    FOXA1 Protein Expression
    REFSEQ proteins: NP_004487.2  
    ENSEMBL proteins: 
     ENSP00000250448   ENSP00000451704   ENSP00000440178  

    Human Recombinant Protein Products for FOXA1: 
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    OriGene MassSpec for FOXA1 
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    GenScript Custom Purified and Recombinant Proteins Services for FOXA1
    Novus Biologicals FOXA1 Proteins
    Novus Biologicals FOXA1 Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for FOXA1 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005667transcription factor complex IBA--

    FOXA1 for ontologies           About GeneDecksing



    FOXA1 Antibody Products: 
    EMD Millipore Mono- and Polyclonal Antibodies for the study of FOXA1
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    Novus Biologicals FOXA1 Antibodies
    Abcam antibodies for FOXA1
    Cloud-Clone Corp. Antibodies for FOXA1 
    ThermoFisher Antibody for FOXA1
    LSBio Antibodies in human, mouse, rat for FOXA1 

    Assay Products for FOXA1: 
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    GenScript Custom Assay Services for FOXA1
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for FOXA1 
    Cloud-Clone Corp. CLIAs for FOXA1


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    FOX: Forkhead boxes

    5 InterPro protein domains:
     IPR011991 WHTH_DNA-bd_dom
     IPR018533 Forkhead_box_C
     IPR018122 TF_fork_head_CS
     IPR013638 Fork-head_N
     IPR001766 TF_fork_head

    Graphical View of Domain Structure for InterPro Entry P55317

    ProtoNet protein and cluster: P55317

    1 Blocks protein domain: IPB013638 Fork-head N-terminal

    UniProtKB/Swiss-Prot: FOXA1_HUMAN, P55317
    Similarity: Contains 1 fork-head DNA-binding domain


    FOXA1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: FOXA1_HUMAN, P55317
    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): 5/10 molecular function terms (GO ID links to tree view) (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001077RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription ISS--
    GO:0003677DNA binding IDA9931457
    GO:0003690double-stranded DNA binding IBA--
    GO:0003700sequence-specific DNA binding transcription factor activity TAS8652662
    GO:0003705RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity IBA--
         
    FOXA1 for ontologies           About GeneDecksing


    Phenotypes:
         3 GenomeRNAi human phenotypes for FOXA1:
     Enable proliferation in B-Raf   G0/1 arrest  Increased G1 DNA content 

         9 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Foxa1):
     cellular  digestive/alimentary  endocrine/exocrine gland  growth/size  homeostasis/metabolism 
     immune system  integument  mortality/aging  tumorigenesis 

    FOXA1 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for FOXA1 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for FOXA1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for FOXA1 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for FOXA1 

    miRNA
    Products:
        
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat FOXA1
    8/61 QIAGEN miScript miRNA Assays for microRNAs that regulate FOXA1 (see all 61):
    hsa-miR-21* hsa-miR-548j hsa-miR-3607-3p hsa-miR-106a hsa-miR-200a hsa-miR-30d hsa-miR-519a hsa-miR-141
    SwitchGear 3'UTR luciferase reporter plasmidFOXA1 3' UTR sequence
    Inhib. RNA
    Products:
        
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for FOXA1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat FOXA1

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for FOXA1
    Sirion Biotech Customized adenovirus for overexpression of FOXA1

    Clone
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    Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: FOXA1 (NM_004496)
    Sino Biological Human cDNA Clone for FOXA1
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for FOXA1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat FOXA1
    Sirion Biotech Customized lentivirus for stable overexpression of FOXA1 
                         Customized lentivirus expression plasmids for stable overexpression of FOXA1 

    Cell Line
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    Search LifeMap BioReagents cell lines for FOXA1
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FOXA1


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for FOXA1 About   (see all 6)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Prostate Cancer
    Prostate Cancer0.32
    2Selected targets of ESR1
    Selected targets of ESR1
    3FOXA2 and FOXA3 transcription factor networks
    FOXA2 and FOXA3 transcription factor networks
    4FOXA1 transcription factor network
    FOXA1 transcription factor network
    5FOXA transcription factor networks
    FOXA transcription factor networks

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 EMD Millipore Pathway for FOXA1
        Selected targets of ESR1


    5 BioSystems Pathways for FOXA1
        Prostate Cancer
    FOXA2 and FOXA3 transcription factor networks
    Direct p53 effectors
    FOXA1 transcription factor network
    FOXA transcription factor networks




    FOXA1 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for FOXA1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/41 Interacting proteins for FOXA1 (P553172, 3 ENSP000002504484) via UniProtKB, MINT, STRING, and/or I2D (see all 41)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARP102753, ENSP000003638224I2D: score=2 STRING: ENSP00000363822
    HDAC7Q8WUI43, ENSP000000800594I2D: score=1 STRING: ENSP00000080059
    ONECUT1Q9UBC03, ENSP000003026304I2D: score=1 STRING: ENSP00000302630
    FOXA2Q9Y2612, ENSP000003159554MINT-7040448 STRING: ENSP00000315955
    HIST3H3Q166953, ENSP000003556574I2D: score=1 STRING: ENSP00000355657
    About this table

    Gene Ontology (GO): 5/27 biological process terms (GO ID links to tree view) (see all 27):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IBA--
    GO:0006338chromatin remodeling ISS--
    GO:0006355regulation of transcription, DNA-dependent ----
    GO:0007389pattern specification process IBA--
    GO:0009790embryo development IBA--

    FOXA1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for FOXA1

    Search CenterWatch for drugs/clinical trials and news about FOXA1

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for FOXA1 gene: 
    NM_004496.3  

    Unigene Cluster for FOXA1:

    Forkhead box A1
    Hs.163484  [show with all ESTs]
    Unigene Representative Sequence: NM_004496
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000250448(uc010tpz.2 uc001wuf.3) ENST00000545425 ENST00000553751
    ENST00000554607 ENST00000557418 ENST00000540786
    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat FOXA1
    8/61 QIAGEN miScript miRNA Assays for microRNAs that regulate FOXA1 (see all 61):
    hsa-miR-21* hsa-miR-548j hsa-miR-3607-3p hsa-miR-106a hsa-miR-200a hsa-miR-30d hsa-miR-519a hsa-miR-141
    SwitchGear 3'UTR luciferase reporter plasmidFOXA1 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for FOXA1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat FOXA1
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    OriGene ORF clones in mouse, rat for FOXA1
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    GenScript: all cDNA clones in your preferred vector: FOXA1 (NM_004496)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for FOXA1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat FOXA1
    Sirion Biotech Customized lentivirus for stable overexpression of FOXA1 
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    Primer
    Products:
        
    OriGene qPCR primer pairs and template standards for FOXA1
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat FOXA1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat FOXA1

    Additional mRNA sequence: 

    AK304119.1 AK313785.1 AK316360.1 BC033890.1 U39840.1 

    5 DOTS entries:

    DT.91827861  DT.120785835  DT.40232277  DT.446153  DT.202876 

    24/95 AceView cDNA sequences (see all 95):

    AI073898 BF195266 BU608051 BF449044 AI380832 BE222309 AA991871 AI299348 
    AA613671 AI347950 BX110546 NM_004496 AU119910 CF134672 BX089258 BF448367 
    BI819070 CB851712 AA693692 AI694151 AI318364 AI269801 CF138795 BX105480 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    FOXA1 expression in normal human tissues (normalized intensities)      FOXA1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTTTATTCTT
    FOXA1 Expression
    About this image


    FOXA1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/20 selected tissues (see all 20) fully expand
     
     Brain (Nervous System)    fully expand to see all 10 entries
             Thalamus
             GABA neuron-like cells ( Generation of motor and gamma-aminobutyric acid (GABA)...
             brain/midbrain   
     
     Gut Tube (Gastrointestinal Tract)    fully expand to see all 8 entries
             Hepatic Endoderm Cells Ventral Foregut Endoderm
             Foregut
             Primitive gut tube-like cells ( A scalable, suspension protocol for derivation of...
     
     Lung (Respiratory System)    fully expand to see all 5 entries
             Multipotent Lung Progenitor Cells Ventral Foregut Endoderm
             Stem Bronchi
             Human Tracheal Epithelial Cells (HTEpiC)   
     
     Pancreas (Endocrine System)    fully expand to see all 5 entries
             Alpha Progenitor Cells Dorsal Pancreatic Bud
             Posterior foregut-like cells ( A scalable, suspension protocol for derivation of...
     
     Liver (Hepatobiliary System)    fully expand to see all 4 entries
             Mature Hepatocytes Liver Lobule

    See FOXA1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for FOXA1

    SOURCE GeneReport for Unigene cluster: Hs.163484

    UniProtKB/Swiss-Prot: FOXA1_HUMAN, P55317
    Tissue specificity: Highly expressed in prostate and ESR1-positive breast tumors. Overexpressed in esophageal and
    lung adenocarcinomas

        SABiosciences Expression via Pathway-Focused PCR Arrays including FOXA1: 
              Estrogen Receptor Signaling in human mouse rat
              Cell Lineage Identification in human mouse rat
              Stem Cell Transcription Factors in human mouse rat
              Breast Cancer in human mouse rat

    Primer
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat FOXA1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FOXA1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for FOXA1 gene from 6/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Foxa11 , 5 forkhead box A11, 5 91.67(n)1
    95.73(a)1
      12 (24.70 cM)5
    153751  NM_008259.31  NP_032285.21 
     575406315 
    lizard
    (Anolis carolinensis)
    Reptilia FOXA36
    Uncharacterized protein
    46(a)
    possible ortholog
    GL344028.1(14068-49153)
    African clawed frog
    (Xenopus laevis)
    Amphibia foxa1-prov2 forkhead box A1 80.43(n)    BC047130.1 
    zebrafish
    (Danio rerio)
    Actinopterygii foxa12 forkhead box A1 80.57(n)   30541  BC056569.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta fkh6
    fork head
    27(a)
    1 → many
    3R(24406805-24410834)
    worm
    (Caenorhabditis elegans)
    Secernentea pha-46
    Defective pharyngeal development protein 4
    23(a)
    1 → many
    V(20752936-20760303)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for FOXA1 gene
    FOXF12  FOXA22  FOXF22  FOXD4L12  FOXC22  FOXI22  FOXB12  FOXE32  
    FOXC12  FOXD4L22  FOXD4L32  FOXA32  FOXD4L52  FOXD12  FOXD32  FOXD4L42  
    FOXL12  FOXE12  FOXB22  FOXI12  FOXD4L62  FOXS12  FOXD22  FOXL22  
    FOXD42  
    6 SIMAP similar genes for FOXA1 using alignment to 3 protein entries:     FOXA1_HUMAN (see all proteins):
    FOXA2    FOXC1    FOXL2    FOXE3    FOXI2    FOXL1

    FOXA1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for FOXA1
    PGOHUM00000233095


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/181 SNPs in FOXA1 are shown (see all 181)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 14 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0151854
    ----see VAR_0151852 Q R mis40--------
    VAR_0151834
    ----see VAR_0151832 G A mis40--------
    rs37425961,2
    C--18172634(+) CGGCTA/CCCTAA 1 -- ds50010--------
    rs602351851,2
    C--18180194(+) TTTTT-/T/TT  
            
    TTTTT
    1 -- us2k11NA 2
    rs1813348641,2
    --19055587(+) AGGATA/GGAGTT 1 -- ds50010--------
    rs1996878911,2
    C--19055867(+) CGGCT-/ACCCTA 1 -- ds50012Minor allele frequency- A:0.25NA 4
    rs1157148531,2
    C,F--19056024(+) CTATCA/CGCCAC 1 -- ut311Minor allele frequency- C:0.03WA 118
    rs342916301,2
    C--19056185(+) AAAAA-/A/AA  
            
    TGAAG
    2 -- ut311NA 2
    rs1406116001,2
    --19056232(+) CAACTC/TTTGGA 1 -- ut310--------
    rs101302051,2
    C,F,H--19056375(+) AATATC/TGTATT 1 -- ut318Minor allele frequency- T:0.03NS NA 1066

    HapMap Linkage Disequilibrium report for FOXA1 (38059189 - 38069245 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for FOXA1:    About this table     
    Variant IDTypeSubtypePubMed ID
    dgv1877n71CNV Loss21882294
    dgv1878n71CNV Loss21882294
    nsv832772CNV Loss17160897
    nsv826923CNV Gain20364138


    Human Gene Mutation Database (HGMD): FOXA1
    SABiosciences Cancer Mutation PCR Assays
    1 SABiosciences qBiomarker Copy Number PCR Array containing FOXA1:
    Oncogenes & Tumor Suppressor Genes 384HC
    SeqTarget long-range PCR primers for resequencing FOXA1
    DNA2.0 Custom Variant and Variant Library Synthesis for FOXA1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 602294    OMIM disorders: --

    20 diseases for FOXA1:    About MalaCards
    mirror-image polydactyly    lung adenocarcinoma    polydactyly    pharyngitis
    maturity-onset diabetes of the young    estrogen-receptor negative breast cancer    conjunctivitis    esophageal squamous cell carcinoma
    esophagitis    neuroblastoma    squamous cell carcinoma    pancreatic cancer
    adenocarcinoma    pancreatitis    prostate cancer    thyroiditis
    prostatitis    breast cancer    neuronitis    lung cancer

    2 diseases from the University of Copenhagen DISEASES database for FOXA1:
    Breast cancer     Prostate cancer

    FOXA1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): FOXA1
    Human Genome Epidemiology (HuGE) Navigator: FOXA1 (4 documents)

    Export disorders for FOXA1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for FOXA1 gene, integrated from 9 sources (see all 118):
    (articles sorted by number of sources associating them with FOXA1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning of the forkhead transcription factor HNF-3 alpha from a human pulmonary adenocarcinoma cell line. (PubMed id 8652662)1, 2, 3 Bingle C.D. and Gowan S. (1996)
    2. Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq. (PubMed id 19919681)1, 2, 9 Motallebipour M.... Wadelius C. (2009)
    3. The hepatocyte nuclear factor 3 alpha gene, HNF3alpha (FOXA1), on chromosome band 14q13 is amplified and overexpressed in esophageal and lung adenocarcinomas. (PubMed id 12234996)1, 2, 9 Lin L....Beer D.G. (2002)
    4. 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. (PubMed id 9119385)1, 3, 9 Mincheva A....Kaestner K.H. (1997)
    5. Histone deacetylase 7 and FoxA1 in estrogen-mediated repression of RPRM. (PubMed id 19917725)1, 2 Malik S.... Oesterreich S. (2010)
    6. Screening and association testing of common coding variation in steroid hormone receptor co-activator and co-repressor genes in relation to breast cancer risk: the Multiethnic Cohort. (PubMed id 19183483)1, 4 Haiman C.A....Press M.F. (2009)
    7. Role of Foxa1 in regulation of bcl2 expression during oxidative- stress-induced apoptosis in A549 type II pneumocytes. (PubMed id 19127412)1, 2 Song L.... Xiao X. (2009)
    8. FoxA1 translates epigenetic signatures into enhancer-driven lineage- specific transcription. (PubMed id 18358809)1, 2 Lupien M.... Brown M. (2008)
    9. BRCA1 and FOXA1 proteins coregulate the expression of the cell cycle- dependent kinase inhibitor p27(Kip1). (PubMed id 16331276)1, 2 Williamson E.A....Koeffler H.P. (2006)
    10. Location analysis of estrogen receptor alpha target promoters reveals that FOXA1 defines a domain of the estrogen response. (PubMed id 16087863)1, 2 Laganiere J....Giguere V. (2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 3169 HGNC: 5021 AceView: FOXA1 Ensembl:ENSG00000129514 euGenes: HUgn3169
    ECgene: FOXA1 H-InvDB: FOXA1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for FOXA1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for FOXA1 Genetics and Cytogenetics in Oncology and Haematology
    Wikipedia http://en.wikipedia.org/wiki/Hepatocyte_nuclear_factors

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for FOXA1 gene:
    Search GeneIP for patents involving FOXA1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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