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Aliases for FOXC1 Gene

Aliases for FOXC1 Gene

  • Forkhead Box C1 2 3 5
  • Forkhead-Related Transcription Factor 3 3 4
  • Forkhead-Related Protein FKHL7 3 4
  • FREAC-3 3 4
  • FREAC3 3 4
  • FKHL7 3 4
  • Forkhead/Winged Helix-Like Transcription Factor 7 3
  • Forkhead, Drosophila, Homolog-Like 7 3
  • Forkhead-Related Activator 3 3
  • Forkhead Box C1 Protein 3
  • Forkhead Box Protein C1 3
  • Myeloid Factor-Delta 3
  • ASGD3 3
  • RIEG3 3
  • IRID1 3
  • IGDA 3
  • IHG1 3
  • ARA 3

External Ids for FOXC1 Gene

Previous HGNC Symbols for FOXC1 Gene

  • FKHL7
  • IRID1

Previous GeneCards Identifiers for FOXC1 Gene

  • GC06P001595
  • GC06P001555
  • GC06P001480

Summaries for FOXC1 Gene

Entrez Gene Summary for FOXC1 Gene

  • This gene belongs to the forkhead family of transcription factors which is characterized by a distinct DNA-binding forkhead domain. The specific function of this gene has not yet been determined; however, it has been shown to play a role in the regulation of embryonic and ocular development. Mutations in this gene cause various glaucoma phenotypes including primary congenital glaucoma, autosomal dominant iridogoniodysgenesis anomaly, and Axenfeld-Rieger anomaly. [provided by RefSeq, Jul 2008]

GeneCards Summary for FOXC1 Gene

FOXC1 (Forkhead Box C1) is a Protein Coding gene. Diseases associated with FOXC1 include Axenfeld-Rieger Syndrome, Type 3 and Iridogoniodysgenesis, Type 1. Among its related pathways are Mesodermal Commitment Pathway and Heart Development. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and transcription factor binding. An important paralog of this gene is FOXC2.

UniProtKB/Swiss-Prot for FOXC1 Gene

  • Binding of FREAC-3 and FREAC-4 to their cognate sites results in bending of the DNA at an angle of 80-90 degrees. Regulates FOXO1 through binding to a conserved element, 5-GTAAACAAA-3 in its promoter region, implicating FOXC1 as an important regulator of cell viability and resistance to oxidative stress in the eye.

Gene Wiki entry for FOXC1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FOXC1 Gene

Genomics for FOXC1 Gene

Regulatory Elements for FOXC1 Gene

Enhancers for FOXC1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G001608 1.6 FANTOM5 ENCODE dbSUPER 8.8 +1.8 1822 5.9 HDGF PKNOX1 ARNT SIN3A FEZF1 ZNF2 ZNF48 GLIS2 GATA2 FOS FOXC1 FOXQ1 GC06P001611 GC06P001612
GH06G001708 0.6 Ensembl ENCODE 14.3 +99.2 99230 0.8 SCRT2 FOXC1 GC06P001721 PIR36904
GH06G001723 0.9 Ensembl ENCODE 7.9 +114.8 114751 1.7 SOX13 KLF1 DPF2 FOXA1 PRDM6 CTBP1 SCRT2 KLF9 FOXP2 KLF7 FOXC1 GC06P001721 GC06M001726
GH06G001728 0.4 ENCODE 5.1 +119.5 119512 1.0 SCRT2 FOXC1 GC06M001726 GC06P001781
GH06G001607 1.2 ENCODE dbSUPER 0.7 -2.3 -2262 0.2 FOXA2 ARNT DMAP1 ZNF2 ZNF48 YY1 SLC30A9 ZNF263 ZNF202 SP5 FOXC1 FOXCUT
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around FOXC1 on UCSC Golden Path with GeneCards custom track

Promoters for FOXC1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000191970 1928 5001 HDGF PKNOX1 ARNT SIN3A FEZF1 ZNF2 ZNF48 GLIS2 GATA2 FOS

Genomic Location for FOXC1 Gene

Chromosome:
6
Start:
1,609,972 bp from pter
End:
1,613,897 bp from pter
Size:
3,926 bases
Orientation:
Plus strand

Genomic View for FOXC1 Gene

Genes around FOXC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FOXC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FOXC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FOXC1 Gene

Proteins for FOXC1 Gene

  • Protein details for FOXC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q12948-FOXC1_HUMAN
    Recommended name:
    Forkhead box protein C1
    Protein Accession:
    Q12948
    Secondary Accessions:
    • Q86UP7
    • Q9BYM1
    • Q9NUE5
    • Q9UDD0
    • Q9UP06

    Protein attributes for FOXC1 Gene

    Size:
    553 amino acids
    Molecular mass:
    56789 Da
    Quaternary structure:
    • Monomer. Interacts with C1QBP.

neXtProt entry for FOXC1 Gene

Post-translational modifications for FOXC1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for FOXC1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for FOXC1 Gene

Domains & Families for FOXC1 Gene

Gene Families for FOXC1 Gene

Protein Domains for FOXC1 Gene

Suggested Antigen Peptide Sequences for FOXC1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with FOXC1: view

No data available for UniProtKB/Swiss-Prot for FOXC1 Gene

Function for FOXC1 Gene

Molecular function for FOXC1 Gene

GENATLAS Biochemistry:
transcription factor-like 7,ubiquitously expressed,with a Drosophila homeo forkhead DNA binding domain homolog,homolog to the murine MF1,disrupted in congenital hydrocephalus
UniProtKB/Swiss-Prot Function:
Binding of FREAC-3 and FREAC-4 to their cognate sites results in bending of the DNA at an angle of 80-90 degrees. Regulates FOXO1 through binding to a conserved element, 5-GTAAACAAA-3 in its promoter region, implicating FOXC1 as an important regulator of cell viability and resistance to oxidative stress in the eye.

Gene Ontology (GO) - Molecular Function for FOXC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IDA 7957066
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding IBA --
GO:0001223 transcription coactivator binding ISS --
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding IC --
GO:0003677 DNA binding IDA 7957066
genes like me logo Genes that share ontologies with FOXC1: view
genes like me logo Genes that share phenotypes with FOXC1: view

Human Phenotype Ontology for FOXC1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for FOXC1 Gene

MGI Knock Outs for FOXC1:

Animal Model Products

CRISPR Products

miRNA for FOXC1 Gene

miRTarBase miRNAs that target FOXC1

Transcription Factor Targets for FOXC1 Gene

Selected GeneGlobe predicted Target genes for FOXC1

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) and HOMER Transcription for FOXC1 Gene

Localization for FOXC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FOXC1 Gene

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 FOXC1 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 1
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for FOXC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 11179011
GO:0005654 nucleoplasm IDA --
GO:0005720 nuclear heterochromatin IDA 15684392
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with FOXC1: view

Pathways & Interactions for FOXC1 Gene

genes like me logo Genes that share pathways with FOXC1: view

Pathways by source for FOXC1 Gene

2 BioSystems pathways for FOXC1 Gene

SIGNOR curated interactions for FOXC1 Gene

Activates:

Gene Ontology (GO) - Biological Process for FOXC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter ISS --
GO:0001501 skeletal system development IEA --
GO:0001503 ossification IEA --
GO:0001541 ovarian follicle development IEA --
GO:0001568 blood vessel development IEA --
genes like me logo Genes that share ontologies with FOXC1: view

Drugs & Compounds for FOXC1 Gene

(1) Drugs for FOXC1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with FOXC1: view

Transcripts for FOXC1 Gene

mRNA/cDNA for FOXC1 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(118) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for FOXC1 Gene

Forkhead box C1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for FOXC1 Gene

No ASD Table

Relevant External Links for FOXC1 Gene

GeneLoc Exon Structure for
FOXC1
ECgene alternative splicing isoforms for
FOXC1

Expression for FOXC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FOXC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for FOXC1 Gene

This gene is overexpressed in Artery - Tibial (x9.2), Artery - Aorta (x8.8), and Artery - Coronary (x5.1).

Protein differential expression in normal tissues from HIPED for FOXC1 Gene

This gene is overexpressed in Pancreas (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for FOXC1 Gene



Protein tissue co-expression partners for FOXC1 Gene

NURSA nuclear receptor signaling pathways regulating expression of FOXC1 Gene:

FOXC1

SOURCE GeneReport for Unigene cluster for FOXC1 Gene:

Hs.348883

mRNA Expression by UniProt/SwissProt for FOXC1 Gene:

Q12948-FOXC1_HUMAN
Tissue specificity: Expressed in all tissues and cell lines examined.

Evidence on tissue expression from TISSUES for FOXC1 Gene

  • Heart(3.9)
  • Stomach(3.7)
  • Nervous system(3.7)
  • Muscle(3.5)
  • Kidney(3.3)
  • Intestine(3)
  • Liver(2.9)
  • Eye(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for FOXC1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cheek
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • meninges
  • mouth
  • nose
  • pituitary gland
  • skull
  • tooth
Thorax:
  • heart
  • heart valve
Abdomen:
  • abdominal wall
  • intestine
  • large intestine
Pelvis:
  • anus
  • penis
  • rectum
  • testicle
  • urethra
General:
  • blood
  • blood vessel
  • hair
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with FOXC1: view

Primer Products

Orthologs for FOXC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for FOXC1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia FOXC1 34
  • 99.44 (n)
mouse
(Mus musculus)
Mammalia Foxc1 34 16 35
  • 90.03 (n)
rat
(Rattus norvegicus)
Mammalia Foxc1 34
  • 89.36 (n)
oppossum
(Monodelphis domestica)
Mammalia FOXC1 35
  • 85 (a)
OneToOne
dog
(Canis familiaris)
Mammalia FOXI3 35
  • 27 (a)
ManyToMany
cow
(Bos Taurus)
Mammalia -- 35
  • 26 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia foxc1 34
  • 73.02 (n)
African clawed frog
(Xenopus laevis)
Amphibia xfd-11 34
zebrafish
(Danio rerio)
Actinopterygii foxc1a 34 34 35
  • 72.06 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10228 34
fruit fly
(Drosophila melanogaster)
Insecta fd64A 36
  • 64 (a)
fd96Cb 36
  • 63 (a)
croc 35 36
  • 29 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 30 (a)
ManyToMany
Species where no ortholog for FOXC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • chicken (Gallus gallus)
  • 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)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 FOXC1 Gene

ENSEMBL:
Gene Tree for FOXC1 (if available)
TreeFam:
Gene Tree for FOXC1 (if available)

Paralogs for FOXC1 Gene

(20) SIMAP similar genes for FOXC1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with FOXC1: view

Variants for FOXC1 Gene

Sequence variations from dbSNP and Humsavar for FOXC1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs104893951 Pathogenic, Anterior segment dysgenesis 3 (ASGD3) [MIM:601631], Axenfeld-Rieger syndrome 3 (RIEG3) [MIM:602482] 1,610,780(+) CCGCT(A/C/T)CCCCT reference, missense
rs104893953 Pathogenic, Axenfeld-Rieger syndrome 3 (RIEG3) [MIM:602482] 1,610,690(+) CTATA(C/G)CTACA reference, missense
rs104893954 Pathogenic, Axenfeld-Rieger syndrome 3 (RIEG3) [MIM:602482] 1,610,706(+) CTCAT(C/G)ACCAT reference, missense
rs104893957 Pathogenic, Anterior segment dysgenesis 3 (ASGD3) [MIM:601631], Axenfeld-Rieger syndrome 3 (RIEG3) [MIM:602482] 1,610,837(+) CCTCT(C/T)GCTCA reference, missense
rs104893958 Pathogenic, Anterior segment dysgenesis 3 (ASGD3) [MIM:601631], Axenfeld-Rieger syndrome 3 (RIEG3) [MIM:602482] 1,610,823(+) AGCAT(A/C/G/T)CGCCA reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for FOXC1 Gene

Variant ID Type Subtype PubMed ID
dgv992n67 CNV gain 20364138
nsv1016859 CNV gain 25217958
nsv1073530 CNV deletion 25765185
nsv1073531 CNV deletion 25765185
nsv1119067 CNV deletion 24896259
nsv1119068 CNV deletion 24896259
nsv600807 CNV loss 21841781
nsv823397 CNV gain 20364138
nsv823399 CNV gain 20364138
nsv823400 CNV gain 20364138

Variation tolerance for FOXC1 Gene

Gene Damage Index Score: 7.63; 82.73% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for FOXC1 Gene

Human Gene Mutation Database (HGMD)
FOXC1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
FOXC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FOXC1 Gene

Disorders for FOXC1 Gene

MalaCards: The human disease database

(31) MalaCards diseases for FOXC1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
axenfeld-rieger syndrome, type 3
  • anterior segment mesenchymal dysgenesis
iridogoniodysgenesis, type 1
  • iris hypoplasia and glaucoma
isolated aniridia
peters anomaly
  • peters-plus syndrome
ring chromosome 6
  • chromosome 6 ring
- elite association - COSMIC cancer census association via MalaCards
Search FOXC1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

FOXC1_HUMAN
  • Anterior segment dysgenesis 3 (ASGD3) [MIM:601631]: A form of anterior segment dysgenesis, a group of defects affecting anterior structures of the eye including cornea, iris, lens, trabecular meshwork, and Schlemm canal. Anterior segment dysgeneses result from abnormal migration or differentiation of the neural crest derived mesenchymal cells that give rise to components of the anterior chamber during eye development. Different anterior segment anomalies may exist alone or in combination, including iris hypoplasia, enlarged or reduced corneal diameter, corneal vascularization and opacity, posterior embryotoxon, corectopia, polycoria, abnormal iridocorneal angle, ectopia lentis, and anterior synechiae between the iris and posterior corneal surface. Clinical conditions falling within the phenotypic spectrum of anterior segment dysgeneses include aniridia, Axenfeld anomaly, Reiger anomaly/syndrome, Peters anomaly, and iridogoniodysgenesis. ASGD3 inheritance is autosomal dominant. {ECO:0000269 PubMed:12614756, ECO:0000269 PubMed:9620769}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Axenfeld-Rieger syndrome 3 (RIEG3) [MIM:602482]: An autosomal dominant disorder of morphogenesis that results in abnormal development of the anterior segment of the eye, and results in blindness from glaucoma in approximately 50% of affected individuals. Features include posterior corneal embryotoxon, prominent Schwalbe line and iris adhesion to the Schwalbe line, hypertelorism, hypodontia, sensorineural deafness, redundant periumbilical skin, and cardiovascular defects such as patent ductus arteriosus and atrial septal defect. When associated with tooth anomalies, the disorder is known as Rieger syndrome. {ECO:0000269 PubMed:11170889, ECO:0000269 PubMed:11589884, ECO:0000269 PubMed:11740218, ECO:0000269 PubMed:12454026, ECO:0000269 PubMed:12592227, ECO:0000269 PubMed:14578375, ECO:0000269 PubMed:15277473, ECO:0000269 PubMed:15477465, ECO:0000269 PubMed:16936096, ECO:0000269 PubMed:17210863, ECO:0000269 PubMed:9620769, ECO:0000269 PubMed:9792859}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for FOXC1

Genetic Association Database (GAD)
FOXC1
Human Genome Epidemiology (HuGE) Navigator
FOXC1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
FOXC1
genes like me logo Genes that share disorders with FOXC1: view

No data available for Genatlas for FOXC1 Gene

Publications for FOXC1 Gene

  1. The transcription factor gene FOXC1 exhibits a limited role in primary congenital glaucoma. (PMID: 18708620) Chakrabarti S. … Thomas R. (Invest. Ophthalmol. Vis. Sci. 2009) 3 22 46 64
  2. Molecular analysis of FOXC1 in subjects presenting with severe developmental eye anomalies. (PMID: 19626132) Kaur K. … Ragoussis J. (Mol. Vis. 2009) 3 22 46 64
  3. FOXC1 is required for cell viability and resistance to oxidative stress in the eye through the transcriptional regulation of FOXO1A. (PMID: 17993506) Berry F.B. … Walter M.A. (Hum. Mol. Genet. 2008) 3 4 22 64
  4. Human p32 is a novel FOXC1-interacting protein that regulates FOXC1 transcriptional activity in ocular cells. (PMID: 18676636) Huang L. … Walter M.A. (Invest. Ophthalmol. Vis. Sci. 2008) 3 4 22 64
  5. Analyses of a novel L130F missense mutation in FOXC1. (PMID: 17210863) Ito Y.A. … Walter M.A. (Arch. Ophthalmol. 2007) 3 4 22 64

Products for FOXC1 Gene

Sources for FOXC1 Gene

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