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

Gene ID: 15375, updated on 19-Feb-2024

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. Orthologous to human FOXA1 (forkhead box A1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in stomach adult (RPKM 30.0), colon adult (RPKM 27.6) and 9 other tissues See more
Orthologs
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Genomic context

See Foxa1 in Genome Data Viewer
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_000078.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_32225 Neighboring gene predicted gene, 20016 Neighboring gene TAR DNA-binding protein 43 pseudogene Neighboring gene tetratricopeptide repeat domain 6 Neighboring gene RIKEN cDNA 4921518K17 gene Neighboring gene predicted gene, 30518

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (4)  1 citation
  • Endonuclease-mediated (2) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 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
 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
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 
acts_upstream_of_or_within multicellular organism development 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 ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
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 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
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 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 ISO
Inferred from Sequence Orthology
more info
 
located_in microvillus IDA
Inferred from Direct Assay
more info
PubMed 
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

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)

  1. NM_008259.4NP_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:170258
    FH; FORKHEAD
    pfam08430
    Location:17169
    Forkhead_N; Forkhead N-terminal region
    pfam09354
    Location:394457
    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

  1. NC_000078.7 Reference GRCm39 C57BL/6J

    Range
    57585750..57594815 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/Swiss-Prot
    P35582, Q4VA63, Q61108
    Conserved Domains (3) summary
    smart00339
    Location:170258
    FH; FORKHEAD
    pfam08430
    Location:17169
    Forkhead_N; Forkhead N-terminal region
    pfam09354
    Location:394457
    HNF_C; HNF3 C-terminal domain
  2. XM_006515483.2XP_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:170258
    FH; FORKHEAD
    pfam08430
    Location:17169
    Forkhead_N; Forkhead N-terminal region
    pfam09354
    Location:394457
    HNF_C; HNF3 C-terminal domain
  3. XM_006515479.5XP_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:170258
    FH; FORKHEAD
    pfam08430
    Location:17169
    Forkhead_N; Forkhead N-terminal region
    pfam09354
    Location:394457
    HNF_C; HNF3 C-terminal domain
  4. XM_030246562.2XP_030102422.1  hepatocyte nuclear factor 3-alpha isoform X1

    UniProtKB/Swiss-Prot
    P35582, Q4VA63, Q61108
    Conserved Domains (3) summary
    smart00339
    Location:170258
    FH; FORKHEAD
    pfam08430
    Location:17169
    Forkhead_N; Forkhead N-terminal region
    pfam09354
    Location:394457
    HNF_C; HNF3 C-terminal domain
  5. XM_006515481.2XP_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:170258
    FH; FORKHEAD
    pfam08430
    Location:17169
    Forkhead_N; Forkhead N-terminal region
    pfam09354
    Location:394457
    HNF_C; HNF3 C-terminal domain