Foxa1 forkhead box A1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Foxa1provided by MGI
Official Full Name: forkhead box A1provided by MGI
Primary source: MGI:MGI:1347472
See related: Ensembl:ENSMUSG00000035451 AllianceGenome:MGI:1347472
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Hnf3a; Tcf3a; Hnf-3a; Tcf-3a
Summary: Enables DNA-binding transcription factor activity; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in chromatin remodeling. Acts upstream of or within several processes, including lung development; prostate gland development; and regulation of transcription by RNA polymerase II. Located in microvillus and nucleus. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; respiratory system; and sensory organ. Human ortholog(s) of this gene implicated in breast cancer; gastrointestinal system cancer (multiple); and lung cancer (multiple). Orthologous to human FOXA1 (forkhead box A1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in stomach adult (RPKM 30.0), colon adult (RPKM 27.6) and 9 other tissues See more
Orthologs: human all
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Genomic context

Location:: 12 C1; 12 24.7 cM

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	12	NC_000078.7 (57585750..57594815, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	12	NC_000078.6 (57540628..57548029, complement)

Chromosome 12 - NC_000078.7 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: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The evolutionarily ancient FOXA transcription factors shape the murine gut microbiome via control of epithelial glycosylation.
Title: The evolutionarily ancient FOXA transcription factors shape the murine gut microbiome via control of epithelial glycosylation.
Impaired SUMOylation of FoxA1 promotes nonalcoholic fatty liver disease through down-regulation of Sirt6.
Title: Impaired SUMOylation of FoxA1 promotes nonalcoholic fatty liver disease through down-regulation of Sirt6.
Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4.
Title: Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4.
FOXA1 Suppresses Endoplasmic Reticulum Stress, Oxidative Stress, and Neuronal Apoptosis in Parkinson's Disease by Activating PON2 Transcription.
Title: FOXA1 Suppresses Endoplasmic Reticulum Stress, Oxidative Stress, and Neuronal Apoptosis in Parkinson's Disease by Activating PON2 Transcription.
Atypical inflammatory kinase IKBKE phosphorylates and inactivates FoxA1 to promote liver tumorigenesis.
Title: Atypical inflammatory kinase IKBKE phosphorylates and inactivates FoxA1 to promote liver tumorigenesis.
Neuroprotective role of FOXA1 in Parkinson's disease: Involvements of NF1 transcription activation and MAPK signaling pathway inhibition.
Title: Neuroprotective role of FOXA1 in Parkinson's disease: Involvements of NF1 transcription activation and MAPK signaling pathway inhibition.
Forkhead box A1 induces angiogenesis through activation of the S100A8/p38 MAPK axis in cutaneous wound healing.
Title: Forkhead box A1 induces angiogenesis through activation of the S100A8/p38 MAPK axis in cutaneous wound healing.
Lysosome-dependent FOXA1 ubiquitination contributes to luminal lineage of advanced prostate cancer.
Title: Lysosome-dependent FOXA1 ubiquitination contributes to luminal lineage of advanced prostate cancer.
Hepatocyte-specific HDAC3 ablation promotes hepatocellular carcinoma in females by suppressing Foxa1/2.
Title: Hepatocyte-specific HDAC3 ablation promotes hepatocellular carcinoma in females by suppressing Foxa1/2.
Knockdown of FOXA1 enhances the osteogenic differentiation of human bone marrow mesenchymal stem cells partly via activation of the ERK1/2 signalling pathway.
Title: Knockdown of FOXA1 enhances the osteogenic differentiation of human bone marrow mesenchymal stem cells partly via activation of the ERK1/2 signalling pathway.

Submit: New GeneRIF Correction See all GeneRIFs (72)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)
Targeted (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Foxa1 (e-PCR), detects polymorphism
- UniSTS:158731

Foxa1 (e-PCR), detects polymorphism
- UniSTS:506896

NoName (e-PCR)
- UniSTS:236853

PMC316377P6 (e-PCR)
- UniSTS:272973

Foxa1 (e-PCR), detects polymorphism
- UniSTS:532313

PMC316473P1 (e-PCR)
- UniSTS:272994

Foxa1 (e-PCR), detects polymorphism
- UniSTS:545935

Foxa1 (e-PCR), detects polymorphism
- UniSTS:499092

NoName (e-PCR)
- UniSTS:224681

Foxa1 (e-PCR), detects polymorphism
- UniSTS:547509

Foxa1 (e-PCR), detects polymorphism
- UniSTS:465386

Foxa2 (e-PCR), detects polymorphism
- UniSTS:465387

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor 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 RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables protein domain specific binding	IEA Inferred from Electronic Annotation more info
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription factor binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within Notch signaling pathway	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within alveolar secondary septum development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within anatomical structure formation involved in morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within connective tissue development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of dopaminergic neuron differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of dopaminergic neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within dorsal/ventral neural tube patterning	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within epithelial cell maturation involved in prostate gland development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epithelial tube branching involved in lung morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within glucose homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hormone metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lung development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within lung epithelial cell differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within lung morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mesenchymal-epithelial cell signaling involved in prostate gland development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of epithelial to mesenchymal transition	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of epithelial to mesenchymal transition	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of neuron differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron fate specification	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of dopaminergic neuron differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of dopaminergic neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of hydrogen peroxide-mediated programmed cell death	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of intracellular estrogen receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of intracellular estrogen receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of mitotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of smoothened signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within prostate gland epithelium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within prostate gland stromal morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of cell cycle	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within respiratory basal cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to estradiol	IEA Inferred from Electronic Annotation more info
involved_in response to estradiol	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of smoothened signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within tube morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in fibrillar center	IEA Inferred from Electronic Annotation more info
located_in fibrillar center	ISO Inferred from Sequence Orthology more info
located_in microvillus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: hepatocyte nuclear factor 3-alpha

Names: HNF-3-alpha; fork head domain; forkhead box protein A1; hepatocyte nuclear factor 3 alpha (winged helix transcription factor)

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.

mRNA and Protein(s)

NM_008259.4 → NP_032285.2 hepatocyte nuclear factor 3-alpha

See identical proteins and their annotated locations for NP_032285.2

Status: VALIDATED

Source sequence(s)

AC123067

Consensus CDS

CCDS25926.1

UniProtKB/Swiss-Prot

P35582, Q4VA63, Q61108

Related

ENSMUSP00000041118.7, ENSMUST00000044380.8

Conserved Domains (3) summary

smart00339
Location:170 → 258

FH; FORKHEAD

pfam08430
Location:17 → 169

Forkhead_N; Forkhead N-terminal region

pfam09354
Location:394 → 457

HNF_C; HNF3 C-terminal domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000078.7 Reference GRCm39 C57BL/6J

Range

57585750..57594815 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017314962.3 → XP_017170451.1 hepatocyte nuclear factor 3-alpha isoform X1

UniProtKB/Swiss-Prot

P35582, Q4VA63, Q61108

Conserved Domains (3) summary

smart00339
Location:170 → 258

FH; FORKHEAD

pfam08430
Location:17 → 169

Forkhead_N; Forkhead N-terminal region

pfam09354
Location:394 → 457

HNF_C; HNF3 C-terminal domain
XM_006515483.2 → XP_006515546.1 hepatocyte nuclear factor 3-alpha isoform X1

See identical proteins and their annotated locations for XP_006515546.1

UniProtKB/Swiss-Prot

P35582, Q4VA63, Q61108

Conserved Domains (3) summary

smart00339
Location:170 → 258

FH; FORKHEAD

pfam08430
Location:17 → 169

Forkhead_N; Forkhead N-terminal region

pfam09354
Location:394 → 457

HNF_C; HNF3 C-terminal domain
XM_006515479.5 → XP_006515542.1 hepatocyte nuclear factor 3-alpha isoform X1

See identical proteins and their annotated locations for XP_006515542.1

UniProtKB/Swiss-Prot

P35582, Q4VA63, Q61108

Conserved Domains (3) summary

smart00339
Location:170 → 258

FH; FORKHEAD

pfam08430
Location:17 → 169

Forkhead_N; Forkhead N-terminal region

pfam09354
Location:394 → 457

HNF_C; HNF3 C-terminal domain
XM_030246562.2 → XP_030102422.1 hepatocyte nuclear factor 3-alpha isoform X1

UniProtKB/Swiss-Prot

P35582, Q4VA63, Q61108

Conserved Domains (3) summary

smart00339
Location:170 → 258

FH; FORKHEAD

pfam08430
Location:17 → 169

Forkhead_N; Forkhead N-terminal region

pfam09354
Location:394 → 457

HNF_C; HNF3 C-terminal domain
XM_006515481.2 → XP_006515544.1 hepatocyte nuclear factor 3-alpha isoform X1

See identical proteins and their annotated locations for XP_006515544.1

UniProtKB/Swiss-Prot

P35582, Q4VA63, Q61108

Conserved Domains (3) summary

smart00339
Location:170 → 258

FH; FORKHEAD

pfam08430
Location:17 → 169

Forkhead_N; Forkhead N-terminal region

pfam09354
Location:394 → 457

HNF_C; HNF3 C-terminal domain