FOXA1 forkhead box A1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: FOXA1provided by HGNC
Official Full Name: forkhead box A1provided by HGNC
Primary source: HGNC:HGNC:5021
See related: Ensembl:ENSG00000129514 MIM:602294; AllianceGenome:HGNC:5021
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HNF3A; TCF3A
Summary: 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]
Expression: Biased expression in prostate (RPKM 46.5), urinary bladder (RPKM 12.0) and 6 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q21.1

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (37589552..37595249, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (31778686..31784378, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (38058757..38064454, complement)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

LINC01133 contributes to the malignant phenotypes of non-small cell lung cancer by targeting miR-30b-5p/FOXA1 pathway.
Title: LINC01133 contributes to the malignant phenotypes of non-small cell lung cancer by targeting miR-30b-5p/FOXA1 pathway.
Dynamic phosphorylation of FOXA1 by Aurora B guides post-mitotic gene reactivation.
Title: Dynamic phosphorylation of FOXA1 by Aurora B guides post-mitotic gene reactivation.
The Role of FOXA1 in Human Normal Development and Its Functions in Sex Hormone-Related Cancers.
Title: The Role of FOXA1 in Human Normal Development and Its Functions in Sex Hormone-Related Cancers.
FOXA1 regulates ribosomal RNA transcription in prostate cancer.
Title: FOXA1 regulates ribosomal RNA transcription in prostate cancer.
FOXA1 co-activates circODC1 and ODC1 in HPV-positive cervical cancer cell growth.
Title: FOXA1 co-activates circODC1 and ODC1 in HPV-positive cervical cancer cell growth.
FOXA1/UBE2T Inhibits CD8[+]T Cell Activity by Inducing Mediates Glycolysis in Lung Adenocarcinoma.
Title: FOXA1/UBE2T Inhibits CD8(+)T Cell Activity by Inducing Mediates Glycolysis in Lung Adenocarcinoma.
Expression of BCL2, TP53, FOXA1, and GATA3 in pTa bladder cancer recurrence.
Title: Expression of BCL2, TP53, FOXA1, and GATA3 in pTa bladder cancer recurrence.
The role of transcription factor FOXA1/C2/M1/O3/P1/Q1 in breast cancer.
Title: The role of transcription factor FOXA1/C2/M1/O3/P1/Q1 in breast cancer.
Clinically-observed FOXA1 mutations upregulate SEMA3C through transcriptional derepression in prostate cancer.
Title: Clinically-observed FOXA1 mutations upregulate SEMA3C through transcriptional derepression in prostate cancer.
Staufen1 Represses the FOXA1-Regulated Transcriptome by Destabilizing FOXA1 mRNA in Colorectal Cancer Cells.
Title: Staufen1 Represses the FOXA1-Regulated Transcriptome by Destabilizing FOXA1 mRNA in Colorectal Cancer Cells.

Submit: New GeneRIF Correction See all GeneRIFs (300)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of chronic periodontitis in a general German population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-35681 (e-PCR)
- UniSTS:55858

RH70624 (e-PCR)
- UniSTS:5742

RH79152 (e-PCR)
- UniSTS:26290

HNF3A (e-PCR)
- UniSTS:479974

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IC Inferred by Curator more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription factor activity	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in Notch signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in alveolar secondary septum development	IEA Inferred from Electronic Annotation more info
involved_in anatomical structure formation involved in morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in anatomical structure morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	ISS Inferred from Sequence or Structural Similarity more info
involved_in dopaminergic neuron differentiation	TAS Traceable Author Statement more info	PubMed
involved_in dorsal/ventral neural tube patterning	IEA Inferred from Electronic Annotation more info
involved_in epithelial cell maturation involved in prostate gland development	IEA Inferred from Electronic Annotation more info
involved_in epithelial tube branching involved in lung morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in glucose homeostasis	IEA Inferred from Electronic Annotation more info
involved_in hormone metabolic process	IEA Inferred from Electronic Annotation more info
involved_in lung epithelial cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in mesenchymal-epithelial cell signaling involved in prostate gland development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of epithelial to mesenchymal transition	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in neuron fate specification	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell-cell adhesion mediated by cadherin	IC Inferred by Curator more info	PubMed
involved_in positive regulation of dopaminergic neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of intracellular estrogen receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of miRNA transcription	IC Inferred by Curator more info	PubMed
involved_in positive regulation of mitotic cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in prostate gland epithelium morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in prostate gland stromal morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in respiratory basal cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in response to estradiol	IDA Inferred from Direct Assay more info	PubMed
involved_in secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development	IEA Inferred from Electronic Annotation more info
involved_in smoothened signaling pathway	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in fibrillar center	IDA Inferred from Direct Assay more info
located_in microvillus	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: hepatocyte nuclear factor 3-alpha

Names: HNF-3-alpha; HNF-3A; TCF-3A; forkhead box protein A1; transcription factor 3A

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_033028.1 RefSeqGene

Range

4872..10569

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1415

mRNA and Protein(s)

NM_004496.5 → NP_004487.2 hepatocyte nuclear factor 3-alpha

See identical proteins and their annotated locations for NP_004487.2

Status: REVIEWED

Source sequence(s)

AL121790

Consensus CDS

CCDS9665.1

UniProtKB/Swiss-Prot

B2R9H6, B7ZAP5, P55317, Q9H2A0

UniProtKB/TrEMBL

B4E257

Related

ENSP00000250448.3, ENST00000250448.5

Conserved Domains (3) summary

pfam08430
Location:17 → 169

Forkhead_N; Forkhead N-terminal region

pfam09354
Location:398 → 461

HNF_C; HNF3 C-terminal domain

cd20038
Location:157 → 268

FH_FOXA1; Forkhead (FH) domain found in Forkhead box protein A1 (FOXA1) and similar proteins