Human Gene FOXA1 (ENST00000250448.3) Description and Page Index
  Description: Homo sapiens forkhead box A1 (FOXA1), mRNA. (from RefSeq NM_004496)
RefSeq Summary (NM_004496): 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]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC033890.1, SRR7346977.1217667.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1966682, SAMEA1968189 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on manual assertion, conservation, expression, longest protein ##RefSeq-Attributes-END##
Gencode Transcript: ENST00000250448.3
Gencode Gene: ENSG00000129514.6
Transcript (Including UTRs)
   Position: hg38 chr14:37,589,552-37,595,113 Size: 5,562 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg38 chr14:37,591,365-37,594,972 Size: 3,608 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr14:37,589,552-37,595,113)mRNA (may differ from genome)Protein (472 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Hepatocyte nuclear factor 3-alpha; Short=HNF-3-alpha; Short=HNF-3A; AltName: Full=Forkhead box protein A1; AltName: Full=Transcription factor 3A; Short=TCF-3A;
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.
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).
TISSUE SPECIFICITY: Highly expressed in prostate and ESR1-positive breast tumors. Overexpressed in esophageal and lung adenocarcinomas.
SIMILARITY: Contains 1 fork-head DNA-binding domain.
WEB RESOURCE: Name=Wikipedia; Note=Hepatocyte nuclear factors entry; URL="";

-  MalaCards Disease Associations
  MalaCards Gene Search: FOXA1
Diseases sorted by gene-association score: estrogen-receptor positive breast cancer (9), luminal breast carcinoma (8), estrogen-receptor negative breast cancer (7), breast cancer (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 34.65 RPKM in Prostate
Total median expression: 108.44 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -66.20141-0.470 Picture PostScript Text
3' UTR -377.201813-0.208 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013638 - Fork-head_N
IPR018533 - Forkhead_box_C
IPR001766 - TF_fork_head
IPR018122 - TF_fork_head_CS
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00250 - Forkhead domain
PF08430 - Forkhead N-terminal region
PF09354 - HNF3 C-terminal domain

ModBase Predicted Comparative 3D Structure on P55317
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl WormBase 
Protein SequenceProtein Sequence  Protein Sequence 
AlignmentAlignment  Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0019904 protein domain specific binding
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0007219 Notch signaling pathway
GO:0007275 multicellular organism development
GO:0009653 anatomical structure morphogenesis
GO:0010468 regulation of gene expression
GO:0010719 negative regulation of epithelial to mesenchymal transition
GO:0021904 dorsal/ventral neural tube patterning
GO:0030324 lung development
GO:0032355 response to estradiol
GO:0033148 positive regulation of intracellular estrogen receptor signaling pathway
GO:0035239 tube morphogenesis
GO:0042445 hormone metabolic process
GO:0042593 glucose homeostasis
GO:0043065 positive regulation of apoptotic process
GO:0045666 positive regulation of neuron differentiation
GO:0045880 positive regulation of smoothened signaling pathway
GO:0045931 positive regulation of mitotic cell cycle
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048646 anatomical structure formation involved in morphogenesis
GO:0048665 neuron fate specification
GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity
GO:0051726 regulation of cell cycle
GO:0060425 lung morphogenesis
GO:0060441 epithelial tube branching involved in lung morphogenesis
GO:0060487 lung epithelial cell differentiation
GO:0060528 secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development
GO:0060738 epithelial-mesenchymal signaling involved in prostate gland development
GO:0060740 prostate gland epithelium morphogenesis
GO:0060741 prostate gland stromal morphogenesis
GO:0060743 epithelial cell maturation involved in prostate gland development
GO:0061144 alveolar secondary septum development
GO:0061448 connective tissue development
GO:0071542 dopaminergic neuron differentiation
GO:1902691 respiratory basal cell differentiation
GO:2000049 positive regulation of cell-cell adhesion mediated by cadherin

Cellular Component:
GO:0001650 fibrillar center
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005902 microvillus

-  Descriptions from all associated GenBank mRNAs
  BC033890 - Homo sapiens forkhead box A1, mRNA (cDNA clone MGC:33105 IMAGE:5269380), complete cds.
U39840 - Human hepatocyte nuclear factor-3 alpha (HNF-3 alpha) mRNA, complete cds.
JD496339 - Sequence 477363 from Patent EP1572962.
JD245236 - Sequence 226260 from Patent EP1572962.
JD119715 - Sequence 100739 from Patent EP1572962.
JD201222 - Sequence 182246 from Patent EP1572962.
JD192856 - Sequence 173880 from Patent EP1572962.
JD417521 - Sequence 398545 from Patent EP1572962.
JD109700 - Sequence 90724 from Patent EP1572962.
JD273526 - Sequence 254550 from Patent EP1572962.
JD299994 - Sequence 281018 from Patent EP1572962.
JD236233 - Sequence 217257 from Patent EP1572962.
AK316360 - Homo sapiens cDNA, FLJ79259 complete cds, highly similar to Hepatocyte nuclear factor 3-alpha.
AK304119 - Homo sapiens cDNA FLJ50362 complete cds, highly similar to Hepatocyte nuclear factor 3-alpha.
JD553463 - Sequence 534487 from Patent EP1572962.
JD094574 - Sequence 75598 from Patent EP1572962.
JD306680 - Sequence 287704 from Patent EP1572962.
JD303749 - Sequence 284773 from Patent EP1572962.
JD315937 - Sequence 296961 from Patent EP1572962.
JD301361 - Sequence 282385 from Patent EP1572962.
AK313785 - Homo sapiens cDNA, FLJ94394, Homo sapiens forkhead box A1 (FOXA1), mRNA.
KJ896991 - Synthetic construct Homo sapiens clone ccsbBroadEn_06385 FOXA1 gene, encodes complete protein.
AM392863 - Synthetic construct Homo sapiens clone IMAGE:100002618 for hypothetical protein (FOXA1 gene).
AM393239 - Synthetic construct Homo sapiens clone IMAGE:100002887 for hypothetical protein (FOXA1 gene).
AM393310 - Synthetic construct Homo sapiens clone IMAGE:100002629 for hypothetical protein (FOXA1 gene).
AM393369 - Synthetic construct Homo sapiens clone IMAGE:100002888 for hypothetical protein (FOXA1 gene).
AB463645 - Synthetic construct DNA, clone: pF1KB8365, Homo sapiens FOXA1 gene for forkhead box A1, without stop codon, in Flexi system.
CU689794 - Synthetic construct Homo sapiens gateway clone IMAGE:100019559 5' read FOXA1 mRNA.
LF212491 - JP 2014500723-A/19994: Polycomb-Associated Non-Coding RNAs.
MA448068 - JP 2018138019-A/19994: Polycomb-Associated Non-Coding RNAs.
JD543437 - Sequence 524461 from Patent EP1572962.
JD092749 - Sequence 73773 from Patent EP1572962.
JD281184 - Sequence 262208 from Patent EP1572962.
JD279722 - Sequence 260746 from Patent EP1572962.
JD220085 - Sequence 201109 from Patent EP1572962.
JD338350 - Sequence 319374 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P55317 (Reactome details) participates in the following event(s):

R-HSA-9009065 FOXA1 and GATA3 bind to CCND1 promoter
R-HSA-9018494 FOXA1 and GATA3 bind TFF genes
R-HSA-9009371 Binding of AP1 transcriptional activator complexes to CCND1 promoter
R-HSA-9018499 ESR1:ESTG and EP300 are recruited to TFF3 promoter
R-HSA-9009541 ESR1 binds to TFF1 gene promoter
R-HSA-9009536 DDX5 binds ESR1:estrogen:TFF1 gene promoter
R-HSA-9009533 TBP and TFIIA bind TATA box on ESR1:estrogen bound TFF1 gene promoter
R-HSA-9009526 CARM1 binds TBP:TFIIA:DDX5:ESR1:estrogen:TFF1 gene
R-HSA-9023861 PRMT1 binds TBP:TFIIA:DDX5:ESR1:estrogen:TFF1 gene
R-HSA-9023860 Histone acetyltransferases are recruited to the TFF1 gene
R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-8939211 ESR-mediated signaling
R-HSA-9006931 Signaling by Nuclear Receptors
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B2R9H6, FOXA1_HUMAN, HNF3A, NM_004496, P55317, Q9H2A0, TCF3A, uc001wuf.1, uc001wuf.2, uc001wuf.3, uc001wuf.4, uc001wuf.5, uc001wuf.6
UCSC ID: uc001wuf.6
RefSeq Accession: NM_004496
Protein: P55317 (aka FOXA1_HUMAN)
CCDS: CCDS9665.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.