FOXF1 Gene (Protein Coding)

Forkhead Box F1

GC16P086510
GIFtS:
43
This gene belongs to the forkhead family of transcription factors which is characterized by a distinct forkhead domain. The specific function of this gene has not yet been determined; however, it may play a role in the regulation of pulmonary genes as well as embryonic development. [provided by RefSeq, Jul 2008] See more...

Aliases for FOXF1 Gene

Aliases for FOXF1 Gene

  • Forkhead Box F1 2 3 5
  • FREAC1 2 3 4
  • Forkhead-Related Transcription Factor 1 3 4
  • Forkhead-Related Protein FKHL5 3 4
  • Forkhead-Related Activator 1 3 4
  • Forkhead Box Protein F1 3 4
  • FREAC-1 3 4
  • FKHL5 3 4
  • Forkhead, Drosophila, Homolog-Like 5 3
  • ACDMPV 3
  • FOXF1 5

External Ids for FOXF1 Gene

Previous HGNC Symbols for FOXF1 Gene

  • FKHL5

Previous GeneCards Identifiers for FOXF1 Gene

  • GC16P077898
  • GC16P087577
  • GC16P086284
  • GC16P086325
  • GC16P085101
  • GC16P086544
  • GC16P072284

Summaries for FOXF1 Gene

Entrez Gene Summary for FOXF1 Gene

  • This gene belongs to the forkhead family of transcription factors which is characterized by a distinct forkhead domain. The specific function of this gene has not yet been determined; however, it may play a role in the regulation of pulmonary genes as well as embryonic development. [provided by RefSeq, Jul 2008]

GeneCards Summary for FOXF1 Gene

FOXF1 (Forkhead Box F1) is a Protein Coding gene. Diseases associated with FOXF1 include Alveolar Capillary Dysplasia With Misalignment Of Pulmonary Veins and Persistent Fetal Circulation Syndrome. Among its related pathways are Embryonic and Induced Pluripotent Stem Cell Differentiation Pathways and Lineage-specific Markers and FOXA2 and FOXA3 transcription factor networks. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and transcription regulatory region DNA binding. An important paralog of this gene is FOXD2.

UniProtKB/Swiss-Prot Summary for FOXF1 Gene

  • Probable transcription activator for a number of lung-specific genes.

Gene Wiki entry for FOXF1 Gene

Additional gene information for FOXF1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for FOXF1 Gene

Genomics for FOXF1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for FOXF1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FOXF1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for FOXF1

Top Transcription factor binding sites by QIAGEN in the FOXF1 gene promoter:
  • E2F
  • FOXO1
  • FOXO1a
  • FOXO4
  • MyoD
  • p53
  • STAT3

Genomic Locations for FOXF1 Gene

Latest Assembly
chr16:86,510,527-86,515,422
(GRCh38/hg38)
Size:
4,896 bases
Orientation:
Plus strand

Previous Assembly
chr16:86,544,133-86,549,028
(GRCh37/hg19 by Entrez Gene)
Size:
4,896 bases
Orientation:
Plus strand

chr16:86,544,133-86,548,076
(GRCh37/hg19 by Ensembl)
Size:
3,944 bases
Orientation:
Plus strand

Genomic View for FOXF1 Gene

Genes around FOXF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FOXF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FOXF1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for FOXF1 Gene

Proteins for FOXF1 Gene

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  • Protein details for FOXF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q12946-FOXF1_HUMAN
    Recommended name:
    Forkhead box protein F1
    Protein Accession:
    Q12946
    Secondary Accessions:
    • B2RAF4
    • Q5FWE5

    Protein attributes for FOXF1 Gene

    Size:
    379 amino acids
    Molecular mass:
    40122 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAC50399.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAC61576.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAH89442.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAG36851.1; Type=Frameshift; Evidence={ECO:0000305};

neXtProt entry for FOXF1 Gene

Protein Expression for FOXF1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for FOXF1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for FOXF1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for FOXF1 Gene

Domains & Families for FOXF1 Gene

Gene Families for FOXF1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for FOXF1 Gene

InterPro:

Suggested Antigen Peptide Sequences for FOXF1 Gene

GenScript: Design optimal peptide antigens:
  • Forkhead-related transcription factor 1 (FOXF1_HUMAN)
  • Forkhead-related activator 1 (Q6JSE1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q12946

UniProtKB/Swiss-Prot:

FOXF1_HUMAN :
  • Activation domains C-terminal of (and distinct from) the forkhead domains are necessary for transcriptional activation.
Domain:
  • Activation domains C-terminal of (and distinct from) the forkhead domains are necessary for transcriptional activation.
genes like me logo Genes that share domains with FOXF1: view

Function for FOXF1 Gene

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  6. Cell Lines for research

Molecular function for FOXF1 Gene

UniProtKB/Swiss-Prot Function:
Probable transcription activator for a number of lung-specific genes.
GENATLAS Biochemistry:
transcription factor-like 5,with a Drosophila homeo fork head DNA binding domain homolog,containing a CGG repeat in 5'utr

Phenotypes From GWAS Catalog for FOXF1 Gene

Gene Ontology (GO) - Molecular Function for FOXF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding IEA --
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IMP 8626802
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA,IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IMP 8626802
genes like me logo Genes that share ontologies with FOXF1: view
genes like me logo Genes that share phenotypes with FOXF1: view

Human Phenotype Ontology for FOXF1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for FOXF1 Gene

MGI Knock Outs for FOXF1:

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FOXF1

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for FOXF1 Gene

Localization for FOXF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FOXF1 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for FOXF1 gene
Compartment Confidence
nucleus 5
extracellular 2
cytoskeleton 2
plasma membrane 1
mitochondrion 1
endoplasmic reticulum 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for FOXF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus TAS,IC 9769171
GO:0005667 transcription factor complex TAS 9722567
genes like me logo Genes that share ontologies with FOXF1: view

Pathways & Interactions for FOXF1 Gene

genes like me logo Genes that share pathways with FOXF1: view

Pathways by source for FOXF1 Gene

1 BioSystems pathway for FOXF1 Gene

SIGNOR curated interactions for FOXF1 Gene

Activates:
Is activated by:

Gene Ontology (GO) - Biological Process for FOXF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0001568 blood vessel development IMP 19500772
GO:0001570 vasculogenesis IEA --
GO:0001701 in utero embryonic development IMP 19500772
GO:0001756 somitogenesis IEA --
genes like me logo Genes that share ontologies with FOXF1: view

Drugs & Compounds for FOXF1 Gene

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No Compound Related Data Available

Transcripts for FOXF1 Gene

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mRNA/cDNA for FOXF1 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FOXF1

Alternative Splicing Database (ASD) splice patterns (SP) for FOXF1 Gene

No ASD Table

Relevant External Links for FOXF1 Gene

GeneLoc Exon Structure for
FOXF1

Expression for FOXF1 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for FOXF1 Gene

mRNA expression in normal human tissues for FOXF1 Gene
mRNA expression by BioGPS for FOXF1 GenemRNA expression by GTEx for FOXF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for FOXF1 Gene

This gene is overexpressed in Colon - Sigmoid (x7.1), Esophagus - Muscularis (x5.8), Esophagus - Gastroesophageal Junction (x5.7), and Bladder (x5.6).

Protein differential expression in normal tissues from HIPED for FOXF1 Gene

This gene is overexpressed in Bone (39.4), Fetal gut (16.1), and Pancreatic juice (13.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for FOXF1 Gene



Protein tissue co-expression partners for FOXF1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for FOXF1

SOURCE GeneReport for Unigene cluster for FOXF1 Gene:

Hs.155591

mRNA Expression by UniProt/SwissProt for FOXF1 Gene:

Q12946-FOXF1_HUMAN
Tissue specificity: Expressed in lung and placenta.

Evidence on tissue expression from TISSUES for FOXF1 Gene

  • Lung(4.5)
  • Intestine(4.5)
  • Gall bladder(2.4)
  • Stomach(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for FOXF1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • reproductive
  • respiratory
  • urinary
Regions:
Head and neck:
  • ear
Thorax:
  • esophagus
  • heart
  • heart valve
  • lung
Abdomen:
  • appendix
  • biliary tract
  • duodenum
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • stomach
Pelvis:
  • placenta
  • ureter
  • urinary bladder
  • uterus
General:
  • blood
  • blood vessel
genes like me logo Genes that share expression patterns with FOXF1: view

Primer products for research

Orthologs for FOXF1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for FOXF1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia FOXF1 29 30
  • 99.21 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia FOXF1 29 30
  • 94.28 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia FOXF1 29 30
  • 93.93 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia FOXF1 30
  • 92 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia FOXF1 30
  • 91 (a)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Foxf1 29 16 30
  • 88.92 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Foxf1 29
  • 88.74 (n)
Chicken
(Gallus gallus)
 Aves FOXF1 29 30
  • 84.91 (n)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia foxf1 29
  • 74.65 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.182 29
Zebrafish
(Danio rerio)
 Actinopterygii foxf1 29 30
  • 70.9 (n)
 OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.3557 29
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 30
  • 28 (a)
 OneToMany
Species where no ortholog for FOXF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for FOXF1 Gene

ENSEMBL:
Gene Tree for FOXF1 (if available)
TreeFam:
Gene Tree for FOXF1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for FOXF1: view image
Alliance of Genome Resources:
Additional Orthologs for FOXF1

Paralogs for FOXF1 Gene

Paralogs for FOXF1 Gene

(3) SIMAP similar genes for FOXF1 Gene using alignment to 2 proteins:

  • FOXF1_HUMAN
  • Q6JSE1_HUMAN
genes like me logo Genes that share paralogs with FOXF1: view

Variants for FOXF1 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for FOXF1 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
1030400 Pathogenic: Persistent fetal circulation syndrome 86,511,237(+) C/A
NM_001451.3(FOXF1):c.668C>A (p.Ser223Ter) 		NONSENSE
1033844 Uncertain Significance: Persistent fetal circulation syndrome 86,510,568(+) C/T
NM_001451.3(FOXF1):c.-2C>T 		FIVE_PRIME_UTR
869491 Likely Pathogenic: Persistent fetal circulation syndrome 86,510,735(+) C/G
NM_001451.3(FOXF1):c.166C>G (p.Leu56Val) 		MISSENSE
869492 Likely Pathogenic: Persistent fetal circulation syndrome 86,511,517(+) GA/G
NM_001451.3(FOXF1):c.950del (p.Asn317fs) 		FRAMESHIFT
916530 Pathogenic: Persistent fetal circulation syndrome 86,512,999(+) G/GCGTCCTCTTCCAT
NM_001451.3(FOXF1):c.1057_1078dup (p.Gly360fs) 		FRAMESHIFT

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for FOXF1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for FOXF1 Gene

Variant ID Type Subtype PubMed ID
dgv498n67 CNV gain 20364138
esv29890 CNV loss 19812545
esv4262 OTHER complex 18987735
nsv1065605 CNV gain 25217958
nsv1070364 CNV deletion 25765185
nsv483044 CNV gain 15286789
nsv525024 CNV loss 19592680
nsv527579 CNV loss 19592680
nsv9468 CNV gain 18304495

Variation tolerance for FOXF1 Gene

Residual Variation Intolerance Score: 38.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.00; 36.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FOXF1 Gene

Human Gene Mutation Database (HGMD)
FOXF1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
FOXF1
Leiden Open Variation Database (LOVD)
FOXF1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FOXF1 Gene

Disorders for FOXF1 Gene

MalaCards: The human disease database

(35) MalaCards diseases for FOXF1 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

Disorder Aliases PubMed IDs
alveolar capillary dysplasia with misalignment of pulmonary veins
  • acdmpv
persistent fetal circulation syndrome
  • congenital alveolar capillary dysplasia with misalignment of pulmonary veins
idiopathic/heritable pulmonary arterial hypertension
  • idiopathic and/or familial pulmonary arterial hypertension
vacterl association
  • vater syndrome
atresia of urethra
  • urethral atresia
- elite association - COSMIC cancer census association via MalaCards
Search FOXF1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

FOXF1_HUMAN
  • Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) [MIM:265380]: A rare developmental disorder characterized by abnormal development of the capillary vascular system in the lungs. Histological features include failure of formation and ingrowth of alveolar capillaries, medial muscular thickening of small pulmonary arterioles with muscularization of the intraacinar arterioles, thickened alveolar walls, and anomalously situated pulmonary veins running alongside pulmonary arterioles and sharing the same adventitial sheath. Less common features include a reduced number of alveoli and a patchy distribution of the histopathologic changes. Affected infants present with respiratory distress and the disease is fatal within the newborn period. Additional features include multiple congenital anomalies affecting the cardiovascular, gastrointestinal, genitourinary, and musculoskeletal systems, as well as disruption of the normal right-left asymmetry of intrathoracic or intraabdominal organs. ACDMPV is a rare cause of persistent pulmonary hypertension of the newborn, an abnormal physiologic state caused by failure of transition of the pulmonary circulation from the high pulmonary vascular resistance of the fetus to the low pulmonary vascular resistance of the newborn. {ECO:0000269 PubMed:19500772, ECO:0000269 PubMed:23505205, ECO:0000269 PubMed:27145217}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for FOXF1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with FOXF1: view

No data available for Genatlas for FOXF1 Gene

Publications for FOXF1 Gene

  1. Novel FOXF1 mutations in sporadic and familial cases of alveolar capillary dysplasia with misaligned pulmonary veins imply a role for its DNA binding domain. (PMID: 23505205) Sen P … Stankiewicz P (Human mutation 2013) 3 4 72
  2. Genomic and genic deletions of the FOX gene cluster on 16q24.1 and inactivating mutations of FOXF1 cause alveolar capillary dysplasia and other malformations. (PMID: 19500772) Stankiewicz P … Shaw-Smith C (American journal of human genetics 2009) 3 4 72
  3. Differential activation of lung-specific genes by two forkhead proteins, FREAC-1 and FREAC-2. (PMID: 8626802) Hellqvist M … Carlsson P (The Journal of biological chemistry 1996) 3 4 22
  4. Cloning and characterization of seven human forkhead proteins: binding site specificity and DNA bending. (PMID: 7957066) Pierrou S … Carlsson P (The EMBO journal 1994) 2 3 4
  5. Variable phenotypic presentation of a novel FOXF1 missense mutation in a single family. (PMID: 27145217) Reiter J … Kerem E (Pediatric pulmonology 2016) 3 4

ExternalLinks

View latest publications for FOXF1 gene in Mastermind

Products for FOXF1 Gene

  • Addgene plasmids for FOXF1

Sources for FOXF1 Gene