Foxa1 forkhead box A1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Foxa1provided by RGD
Official Full Name: forkhead box A1provided by RGD
Primary source: RGD:2807
See related: EnsemblRapid:ENSRNOG00000009284 AllianceGenome:RGD:2807
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Hnf3a
Summary: Enables several functions, including DNA binding activity; DNA-binding transcription activator activity, RNA polymerase II-specific; and RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in positive regulation of hydrogen peroxide-mediated programmed cell death and positive regulation of transcription by RNA polymerase II. Acts upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be located in fibrillar center; microvillus; and nucleoplasm. 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, Dec 2024]
Expression: Biased expression in Liver (RPKM 36.6), Lung (RPKM 18.7) and 1 other tissue See more
Orthologs: human mouse all
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Genomic context

Location:: 6q23

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (80838380..80871195, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (75099907..75136534, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (78516579..78549669, complement)

Chromosome 6 - NC_086024.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

LncRNA NKILA Exacerbates Alzheimer's Disease Progression by Regulating the FOXA1-Mediated Transcription of TNFAIP1.
Title: LncRNA NKILA Exacerbates Alzheimer's Disease Progression by Regulating the FOXA1-Mediated Transcription of TNFAIP1.
Foxa1 mediates eccrine sweat gland development through transcriptional regulation of Na-K-ATPase expression.
Title: Foxa1 mediates eccrine sweat gland development through transcriptional regulation of Na-K-ATPase expression.
Silencing of long noncoding RNA H19 alleviates pulmonary injury, inflammation, and fibrosis of acute respiratory distress syndrome through regulating the microRNA-423-5p/FOXA1 axis.
Title: Silencing of long noncoding RNA H19 alleviates pulmonary injury, inflammation, and fibrosis of acute respiratory distress syndrome through regulating the microRNA-423-5p/FOXA1 axis.
miR-194 relieve neuropathic pain and prevent neuroinflammation via targeting FOXA1.
Title: miR-194 relieve neuropathic pain and prevent neuroinflammation via targeting FOXA1.
In vitro, FOXA1 depletion by siRNA inhibited astrocyte proliferation and migration. Meanwhile, FOXA1 knockdown also reduce cell cycle related proteins.
Title: Spatiotemporal expression of FOXA1 correlates with reactive gliosis after spinal cord injury.
We conclude that Foxa1 can be used as a marker of eccrine sweat glands in skin and also as a marker of secretory coils, and Foxa1 is related to the development of secretory coils.
Title: Foxa1 gene and protein in developing rat eccrine sweat glands.
Foxa1 and Foxa2 control glucagon biosynthesis and secretion as well as alpha-cell differentiation with both common and unique target genes.
Title: Foxa1 and Foxa2 regulate α-cell differentiation, glucagon biosynthesis, and secretion.
Results suggest that Foxa1 may play an important role in acute lung injury by promoting apoptosis of pulmonary epithelial cells.
Title: A role for forkhead box A1 in acute lung injury.
GST-FOXA1 fusion protein interferes with the formation of NKX2.1 transcriptional complexes by potentially masking the latter's homeodomain DNA binding function
Title: Physical and functional interactions between homeodomain NKX2.1 and winged helix/forkhead FOXA1 in lung epithelial cells.

Submit: New GeneRIF Correction

General gene information

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Markers

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

AI105057 (e-PCR)
- UniSTS:250644

BM386117 (e-PCR)
- UniSTS:261147

RH94853 (e-PCR)
- UniSTS:120099

RH94854 (e-PCR)
- UniSTS:120100

PMC316473P1 (e-PCR)
- UniSTS:272994

BI301884 (e-PCR)
- UniSTS:247004

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation more info
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	IPI Inferred from Physical Interaction more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein domain specific binding	IDA Inferred from Direct Assay more info	PubMed
enables protein domain specific binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
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

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

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	IEA Inferred from Electronic Annotation more info
located_in microvillus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
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; HNF-3A; forkhead box protein A1

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_012742.2 → NP_036874.2 hepatocyte nuclear factor 3-alpha

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006

UniProtKB/Swiss-Prot

P23512

UniProtKB/TrEMBL

A0A8I6AF62, A6HBP6

Related

ENSRNOP00000090884.1, ENSRNOT00000119772.2

Conserved Domains (3) summary

pfam08430
Location:17 → 169

Forkhead_N; Forkhead N-terminal region

pfam09354
Location:394 → 457

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

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086024.1 Reference GRCr8

Range

80838380..80871195 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039111792.2 → XP_038967720.1 hepatocyte nuclear factor 3-alpha isoform X1

UniProtKB/Swiss-Prot

P23512

UniProtKB/TrEMBL

F1LR25

Related

ENSRNOP00000009940.7, ENSRNOT00000009940.8

Conserved Domains (3) summary

pfam08430
Location:17 → 169

Forkhead_N; Forkhead N-terminal region

pfam09354
Location:394 → 457

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
XM_039111793.2 → XP_038967721.1 hepatocyte nuclear factor 3-alpha isoform X2

UniProtKB/Swiss-Prot

P23512

Conserved Domains (3) summary

pfam08430
Location:17 → 169

Forkhead_N; Forkhead N-terminal region

pfam09354
Location:394 → 457

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