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FOXA1 Gene

protein-coding   GIFtS: 65
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)
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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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 estrogen-receptor negative breast cancer, and mirror-image polydactyly. 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 FOXA2.

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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000014.9  NC_018925.2  NT_026437.13  
Regulatory elements:
   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 Chromatin IP Primers for FOXA1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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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)
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: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See FOXA1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_004487.2  
    ENSEMBL proteins: 
     ENSP00000250448   ENSP00000451704   ENSP00000440178  

    FOXA1 Human Recombinant Protein Products:

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    Browse Sino Biological Cell Lysates
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    Cloud-Clone Corp. Proteins for FOXA1

    FOXA1 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of FOXA1
    R&D Systems Antibodies for FOXA1 (HNF-3 alpha/FoxA1)
    OriGene Antibodies for FOXA1
    OriGene Custom Antibody Services for FOXA1
    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

    FOXA1 Assay Products:

    EMD Millipore Kits and Assays for the Analysis of FOXA1
    OriGene Custom Assay Services for FOXA1
    Browse R&D Systems for biochemical assays
    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)
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    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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    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): Selected molecular function terms (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/body  homeostasis/metabolism 
     immune system  integument  mortality/aging  tumorigenesis 

    FOXA1 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for FOXA1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models 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

    Transcription Factor Targeting: 
    Targeting motifs: HOMER Transcription Factor Regulatory Elements motif viewer 
                                          Consensus sequence:  AAAGTAAACA 

    miRNA
    Products:
        
    miRTarBase miRNAs that target FOXA1:
    hsa-mir-192-5p (MIRT026509), hsa-let-7a-5p (MIRT002078), hsa-mir-215-5p (MIRT024644)

    Block miRNA regulation of human, mouse, rat FOXA1 using miScript Target Protectors
    Selected qRT-PCR 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:
        
    OriGene RNAi products in human, mouse, rat for FOXA1
    Predesigned siRNA for gene silencing in human, mouse, rat FOXA1

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for FOXA1

    Clone
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    OriGene clones in human, mouse for FOXA1 (see all 7)
    OriGene ORF clones in mouse, rat for FOXA1
    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

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for FOXA1
    Browse ESI BIO Cell Lines and PureStem Progenitors for FOXA1 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FOXA1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    FOXA1_HUMAN, P55317: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2

    Gene Ontology (GO): 2 cellular component terms:    About this table

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

    FOXA1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for FOXA1 About    
    See pathways by source

    SuperPathContained pathways About
    1FOXA1 transcription factor network
    FOXA1 transcription factor network
    FOXA transcription factor networks0.00
    2Prostate Cancer
    Prostate Cancer0.32
    3Selected targets of ESR1
    Selected targets of ESR1
    4FOXA2 and FOXA3 transcription factor networks
    FOXA2 and FOXA3 transcription factor networks
    5Direct p53 effectors
    Direct p53 effectors


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



        Pathway & Disease-focused RT2 Profiler 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

    Interactions:

        GeneGlobe Interaction Network for FOXA1

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

    Selected Interacting proteins for FOXA1 (P553172, 3 ENSP000002504484) via UniProtKB, MINT, STRING, and/or I2D (see all 57)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARP102753, ENSP000003638224I2D: score=2 STRING: ENSP00000363822
    HDAC7Q8WUI43, ENSP000000800594I2D: score=1 STRING: ENSP00000080059
    ONECUT1Q9UBC03, ENSP000003026304I2D: score=1 STRING: ENSP00000302630
    HIST3H3Q166953, ENSP000003556574I2D: score=1 STRING: ENSP00000355657
    TLE1Q047243, ENSP000003656824I2D: score=1 STRING: ENSP00000365682
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 32):    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-templated ----
    GO:0006366transcription from RNA polymerase II promoter IBA--
    GO:0007389pattern specification process IBA--

    FOXA1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for 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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    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
    Products:
         
    Block miRNA regulation of human, mouse, rat FOXA1 using miScript Target Protectors
    Selected qRT-PCR 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
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    Predesigned siRNA for gene silencing in human, mouse, rat FOXA1
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    GenScript: all cDNA clones in your preferred vector: FOXA1 (NM_004496)
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    Primer
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    OriGene qPCR primer pairs and template standards for FOXA1
    OriGene qSTAR qPCR primer pairs in human, mouse for FOXA1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat FOXA1
      QuantiTect SYBR Green Assays in human, mouse, rat FOXA1
      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 

    Selected AceView cDNA sequences (see all 95):

    AU119910 AI347950 BX089258 BF449044 BF195266 CF138795 BE222309 BE348594 
    AI694151 BI819070 AI269801 AI299348 NM_004496 AI073898 BX105480 AI380832 
    AA613671 AA991871 BM854964 BX110546 BF000514 CF134672 AA693692 BU608051 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    FOXA1 expression in normal human tissues (normalized intensities)
    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
     selected tissues (see all 17) fully expand
     
     Brain (Nervous System)    fully expand to see all 7 entries
             Thalamus
             GABA neuron-like cells
     
     Gut Tube (Gastrointestinal Tract)    fully expand to see all 5 entries
             Hepatic Endoderm Cells Ventral Foregut Endoderm
     
     Liver (Hepatobiliary System)    fully expand to see all 4 entries
             Mature Hepatocytes Liver Lobule
     
     Lung (Respiratory System)    fully expand to see all 3 entries
             Multipotent Lung Progenitor Cells Ventral Foregut Endoderm
             Stem Bronchi
     
     NULL (Uncategorized)    fully expand to see all 3 entries
             Posterior foregut-like cells
    FOXA1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    FOXA1 Protein Expression

    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

        Pathway & Disease-focused RT2 Profiler 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
    Products:
    OriGene qPCR primer pairs and template standards for FOXA1
    OriGene qSTAR qPCR primer pairs in human, mouse for FOXA1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat FOXA1
    QuantiTect SYBR Green Assays in human, mouse, rat FOXA1
    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)
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    This gene was present in the common ancestor of animals.

    Orthologs for FOXA1 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Foxa11 , 5 forkhead box A11, 5 91.52(n)1
    95.3(a)1
      12 (24.70 cM)5
    153751  NM_008259.31  NP_032285.21 
     575406315 
    lizard
    (Anolis carolinensis)
    Reptilia FOXA16
    forkhead box A1
    65(a)
    1 ↔ 1
    1(25570112-25581834)
    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
    35(a)
    1 → many
    3R(24406805-24410834)


    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

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    Paralogs for FOXA1 gene
    FOXA22  FOXD4L12  FOXC22  FOXI22  FOXB12  FOXE32  FOXC12  FOXD4L22  
    FOXD4L32  FOXA32  FOXD4L52  FOXD12  FOXD32  FOXD4L42  FOXE12  FOXL12  
    FOXB22  FOXI12  FOXD4L62  FOXS12  FOXD22  FOXL22  FOXD42  
    7 SIMAP similar genes for FOXA1 using alignment to 3 protein entries:     FOXA1_HUMAN (see all proteins):
    FOXN4    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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for FOXA1 (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
    ----------
    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
    rs1510468501,2
    --19056618(+) TGTAAA/GGAAAA 1 -- ut310--------
    rs2009072051,2
    --19056864(+) TACTG-/AAAAAA 1 -- ut310--------

    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
    Site Specific Mutation Identification with PCR Assays
    1 Copy Number PCR Panel 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, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 602294    OMIM disorders: --

    Selected diseases for FOXA1 (see all 23):    
    About MalaCards
    estrogen-receptor negative breast cancer    mirror-image polydactyly    polydactyly    pharyngitis
    lung adenocarcinoma    maturity-onset diabetes of the young    conjunctivitis    esophageal squamous cell carcinoma
    osteoporosis    esophagitis    neuroblastoma    breast cancer
    squamous cell carcinoma    peritonitis    pancreatic cancer    pancreatitis
    adenocarcinoma    prostate cancer    thyroiditis    prostatitis

    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)
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    PubMed articles for FOXA1 gene, integrated from 10 sources (see all 121):
    (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. (Biochim. Biophys. Acta 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. (Genome Biol. 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. (Cancer Res. 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. (Genomics 1997)
    5. Histone deacetylase 7 and FoxA1 in estrogen-mediated repression of RPRM. (PubMed id 19917725)1, 2 Malik S.... Oesterreich S. (Mol. Cell. Biol. 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. (BMC Cancer 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. (Cell Stress Chaperones 2009)
    8. FoxA1 translates epigenetic signatures into enhancer-driven lineage- specific transcription. (PubMed id 18358809)1, 2 Lupien M.... Brown M. (Cell 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. (Oncogene 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. (Proc. Natl. Acad. Sci. U.S.A. 2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 3169 HGNC: 5021 AceView: FOXA1 Ensembl:ENSG00000129514 euGenes: HUgn3169
    ECgene: FOXA1 H-InvDB: FOXA1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    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.)
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    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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