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FOXA2 Gene(Protein Coding)

Forkhead Box A2

GCID:
GC20M022581
GIFtS:
53
Genes Participants
UDN Logo

Aliases for FOXA2 Gene

Aliases for FOXA2 Gene

  • Forkhead Box A2 2 3 5
  • Forkhead Box Protein A2 3 4
  • Transcription Factor 3B 3 4
  • HNF-3-Beta 3 4
  • HNF-3B 3 4
  • TCF-3B 3 4
  • HNF3B 3 4
  • TCF3B 3 4
  • Hepatocyte Nuclear Factor 3, Beta 2
  • Hepatocyte Nuclear Factor 3-Beta 3
  • Hepatic Nuclear Factor-3-Beta 3

External Ids for FOXA2 Gene

Previous HGNC Symbols for FOXA2 Gene

  • HNF3B

Previous GeneCards Identifiers for FOXA2 Gene

  • GC20M022550
  • GC20M022556
  • GC20M022509
  • GC20M022561
  • GC20M022523

Summaries for FOXA2 Gene

Entrez Gene Summary for FOXA2 Gene

  • This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific genes 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. This gene has been linked to sporadic cases of maturity-onset diabetes of the young. Transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Oct 2008]

GeneCards Summary for FOXA2 Gene

FOXA2 (Forkhead Box A2) is a Protein Coding gene. Diseases associated with FOXA2 include Meckel Diverticulum and Maturity-Onset Diabetes Of The Young. Among its related pathways are Ectoderm Differentiation and Mesodermal Commitment Pathway. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and transcription factor binding. An important paralog of this gene is FOXA1.

UniProtKB/Swiss-Prot for FOXA2 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). In embryonic development is required for notochord formation. Involved in the development of multiple endoderm-derived organ systems such as the liver, pancreas and lungs; FOXA1 and FOXA2 seem to have at least in part redundant roles. 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; regulates the expression of genes important for glucose sensing in pancreatic beta-cells and glucose homeostasis. Involved in regulation of fat metabolism. Binds to fibrinogen beta promoter and is involved in IL6-induced fibrinogen beta transcriptional activation.

Gene Wiki entry for FOXA2 Gene

Additional gene information for FOXA2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FOXA2 Gene

Genomics for FOXA2 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for FOXA2 Gene

Promoters and enhancers for FOXA2 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH20I022581 Promoter/Enhancer 1.7 EPDnew ENCODE dbSUPER 550.8 +1.8 1784 4.2 FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF48 YY1 GLIS2 PAF1 ENSG00000283932 FOXA2 LINC01384 LINC00261
GH20I022586 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 555.3 -1.5 -1476 0.3 ARID4B SIN3A DMAP1 ZNF48 SLC30A9 GLIS2 ARID2 ZNF143 RXRA NFYC FOXA2 LINC01384
GH20I022489 Enhancer 1.2 FANTOM5 ENCODE 16.7 +94.8 94849 2.2 PKNOX1 ATF1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF48 ETS1 YY1 FOXA2 LOC284788 GC20M022448
GH20I022652 Enhancer 0.6 ENCODE 26.5 -67.7 -67686 0.8 ZBTB8A E2F1 ZNF335 HIC1 PRDM6 GLIS2 GLIS1 ZNF341 PRDM10 FOS FOXA2 ENSG00000283072 LINC01384
GH20I022511 Enhancer 1.2 ENCODE dbSUPER 11.3 +72.8 72809 2.7 FOXA2 MLX ZFP64 ARID4B FEZF1 DMAP1 ZNF48 YY1 SLC30A9 TCF12 FOXA2 GC20M022448 LOC105372564 LOC284788
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around FOXA2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FOXA2 gene promoter:

Genomic Locations for FOXA2 Gene

Genomic Locations for FOXA2 Gene
chr20:22,581,004-22,585,463
(GRCh38/hg38)
Size:
4,460 bases
Orientation:
Minus strand
chr20:22,561,642-22,566,101
(GRCh37/hg19)

Genomic View for FOXA2 Gene

Genes around FOXA2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FOXA2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FOXA2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for FOXA2 Gene

Proteins for FOXA2 Gene

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  2. Protein
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  • Protein details for FOXA2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y261-FOXA2_HUMAN
    Recommended name:
    Hepatocyte nuclear factor 3-beta
    Protein Accession:
    Q9Y261
    Secondary Accessions:
    • Q8WUW4
    • Q96DF7

    Protein attributes for FOXA2 Gene

    Size:
    457 amino acids
    Molecular mass:
    48306 Da
    Quaternary structure:
    • Binds DNA as a monomer. Binds TLE1 (By similarity). Interacts with FOXA1 and FOXA3. Interacts with PRKDC.
    SequenceCaution:
    • Sequence=AAH11780.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for FOXA2 Gene

    Alternative splice isoforms for FOXA2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for FOXA2 Gene

Protein Expression for FOXA2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for FOXA2 Gene

  • Phosphorylation on Thr-156 abolishes binding to target promoters and subsequent transcription activation upon insulin stimulation.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for FOXA2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for FOXA2 Gene

Domains & Families for FOXA2 Gene

Gene Families for FOXA2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for FOXA2 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for FOXA2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with FOXA2: view

No data available for UniProtKB/Swiss-Prot for FOXA2 Gene

Function for FOXA2 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for FOXA2 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). In embryonic development is required for notochord formation. Involved in the development of multiple endoderm-derived organ systems such as the liver, pancreas and lungs; FOXA1 and FOXA2 seem to have at least in part redundant roles. 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; regulates the expression of genes important for glucose sensing in pancreatic beta-cells and glucose homeostasis. Involved in regulation of fat metabolism. Binds to fibrinogen beta promoter and is involved in IL6-induced fibrinogen beta transcriptional activation.

Phenotypes From GWAS Catalog for FOXA2 Gene

Gene Ontology (GO) - Molecular Function for FOXA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 12642491
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding IBA --
GO:0003677 DNA binding IEA,IDA 9931457
GO:0003700 DNA binding transcription factor activity IDA 9931457
GO:0008134 transcription factor binding IEA --
genes like me logo Genes that share ontologies with FOXA2: view
genes like me logo Genes that share phenotypes with FOXA2: view

Animal Models for FOXA2 Gene

MGI Knock Outs for FOXA2:

Animal Model Products

Targeted motifs for FOXA2 Gene
HOMER Transcription Factor Regulatory Elements motif FOXA2
  • Consensus sequence: CTTGTTTACATA Submotif: canonical Cell Type: Liver GEO ID: GSE25694

Clone Products

  • Addgene plasmids for FOXA2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Transcription Factor Targets for FOXA2 Gene

Localization for FOXA2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FOXA2 Gene

Nucleus. Cytoplasm. Note=Shuttles between the nucleus and cytoplasm in a CRM1-dependent manner; in response to insulin signaling via AKT1 is exported from the nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for FOXA2 gene
Compartment Confidence
nucleus 5
extracellular 2
cytosol 2
cytoskeleton 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Cell Junctions (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for FOXA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 9931457
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0030054 cell junction IDA --
genes like me logo Genes that share ontologies with FOXA2: view

Pathways & Interactions for FOXA2 Gene

genes like me logo Genes that share pathways with FOXA2: view

Interacting Proteins for FOXA2 Gene

Selected Interacting proteins: Q9Y261-FOXA2_HUMAN for FOXA2 Gene via IID MINT

SIGNOR curated interactions for FOXA2 Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for FOXA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000432 positive regulation of transcription from RNA polymerase II promoter by glucose ISS --
GO:0000433 negative regulation of transcription from RNA polymerase II promoter by glucose ISS --
GO:0001708 cell fate specification ISS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with FOXA2: view

Drugs & Compounds for FOXA2 Gene

Products:

  1. Drug

(1) Drugs for FOXA2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(4) Additional Compounds for FOXA2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with FOXA2: view

Transcripts for FOXA2 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for FOXA2 Gene

(2) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(78) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for FOXA2 Gene

Forkhead box A2:
Representative Sequences:

Clone Products

  • Addgene plasmids for FOXA2

Alternative Splicing Database (ASD) splice patterns (SP) for FOXA2 Gene

No ASD Table

Relevant External Links for FOXA2 Gene

GeneLoc Exon Structure for
FOXA2
ECgene alternative splicing isoforms for
FOXA2

Expression for FOXA2 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FOXA2 Gene

mRNA expression in normal human tissues for FOXA2 Gene
mRNA expression by BioGPS for FOXA2 GenemRNA expression by GTEx for FOXA2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for FOXA2 Gene

This gene is overexpressed in Liver (x15.7), Pancreas (x12.5), Stomach (x10.2), and Lung (x4.3).

Protein differential expression in normal tissues from HIPED for FOXA2 Gene

This gene is overexpressed in Islet of Langerhans (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for FOXA2 Gene



Protein tissue co-expression partners for FOXA2 Gene

NURSA nuclear receptor signaling pathways regulating expression of FOXA2 Gene:

FOXA2

SOURCE GeneReport for Unigene cluster for FOXA2 Gene:

Hs.155651

Evidence on tissue expression from TISSUES for FOXA2 Gene

  • Lung(4.7)
  • Liver(4.6)
  • Pancreas(2.7)
  • Intestine(2.2)
genes like me logo Genes that share expression patterns with FOXA2: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for FOXA2 Gene

Orthologs for FOXA2 Gene

This gene was present in the common ancestor of animals.

Orthologs for FOXA2 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
 Mammalia FOXA2 33 34
  • 94.38 (n)
cow
(Bos Taurus)
 Mammalia FOXA2 33 34
  • 94.1 (n)
mouse
(Mus musculus)
 Mammalia Foxa2 33 16 34
  • 90.23 (n)
rat
(Rattus norvegicus)
 Mammalia Foxa2 33
  • 89.18 (n)
oppossum
(Monodelphis domestica)
 Mammalia FOXA2 34
  • 88 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia FOXA2 34
  • 81 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves FOXA2 33
  • 78.78 (n)
tropical clawed frog
(Silurana tropicalis)
 Amphibia foxa2 33
  • 71.6 (n)
zebrafish
(Danio rerio)
 Actinopterygii foxa2 33 34
  • 68.63 (n)
-- 33
fruit fly
(Drosophila melanogaster)
 Insecta fkh 34
  • 35 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 53 (a)
 ManyToMany
CSA.7421 34
  • 29 (a)
 ManyToMany
Species where no ortholog for FOXA2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chimpanzee (Pan troglodytes)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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 FOXA2 Gene

ENSEMBL:
Gene Tree for FOXA2 (if available)
TreeFam:
Gene Tree for FOXA2 (if available)

Paralogs for FOXA2 Gene

Paralogs for FOXA2 Gene

(9) SIMAP similar genes for FOXA2 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with FOXA2: view

Variants for FOXA2 Gene

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Sequence variations from dbSNP and Humsavar for FOXA2 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1000160923 -- 22,584,371(-) C/A/G/T 5_prime_UTR_variant, intron_variant
rs1000296086 -- 22,584,531(-) G/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000920736 -- 22,582,825(-) C/T coding_sequence_variant, missense_variant
rs1001196477 -- 22,586,367(-) A/G upstream_transcript_variant
rs1002170329 -- 22,581,791(-) C/T 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for FOXA2 Gene

Variant ID Type Subtype PubMed ID
nsv1073050 CNV deletion 25765185
nsv1136325 CNV deletion 24896259
nsv953003 CNV deletion 24416366

Variation tolerance for FOXA2 Gene

Residual Variation Intolerance Score: 22.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.93; 49.04% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FOXA2 Gene

Human Gene Mutation Database (HGMD)
FOXA2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
FOXA2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FOXA2 Gene

Disorders for FOXA2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for FOXA2 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
meckel diverticulum
  • meckel's diverticulum
maturity-onset diabetes of the young
  • mody
non-functioning pancreatic endocrine tumor
  • non functioning pancreatic endocrine tumor
disuse amblyopia
  • deprivation amblyopia
- elite association - COSMIC cancer census association via MalaCards
Search FOXA2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for FOXA2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with FOXA2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for FOXA2 Gene

Publications for FOXA2 Gene

  1. Genetic predictors of interindividual variability in hepatic CYP3A4 expression. (PMID: 19934400) Lamba V … Schuetz EG (The Journal of pharmacology and experimental therapeutics 2010) 3 22 44 58
  2. Insulin regulates the activity of forkhead transcription factor Hnf-3beta/Foxa-2 by Akt-mediated phosphorylation and nuclear/cytosolic localization. (PMID: 14500912) Wolfrum C … Stoffel M (Proceedings of the National Academy of Sciences of the United States of America 2003) 3 4 22 58
  3. Foxa2 (HNF3beta ) controls multiple genes implicated in metabolism-secretion coupling of glucose-induced insulin release. (PMID: 11875061) Wang H … Wollheim CB (The Journal of biological chemistry 2002) 2 3 22 58
  4. Beta-cell transcription factors and diabetes: no evidence for diabetes-associated mutations in the hepatocyte nuclear factor-3beta gene (HNF3B) in Japanese patients with maturity-onset diabetes of the young. (PMID: 10868948) Hinokio Y … Bell GI (Diabetes 2000) 3 22 44 58
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58

Products for FOXA2 Gene

  • Addgene plasmids for FOXA2

Sources for FOXA2 Gene

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