foxc1a forkhead box C1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: foxc1aprovided by ZNC
Official Full Name: forkhead box C1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-010302-1
See related: Ensembl:ENSDARG00000091481 AllianceGenome:ZFIN:ZDB-GENE-010302-1
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: foxc1.1
Summary: Enables chromatin binding activity. Acts upstream of or within with a positive effect on vascular associated smooth muscle cell differentiation. Acts upstream of or within several processes, including determination of left/right symmetry; glomerulus development; and regulation of signal transduction. Predicted to be located in nucleus. Is expressed in several structures, including cardiovascular system; head; mesenchyme; mesoderm; and trunk. Used to study Axenfeld-Rieger syndrome. Human ortholog(s) of this gene implicated in Axenfeld-Rieger syndrome; Axenfeld-Rieger syndrome type 3; anterior segment dysgenesis 3; and glaucoma. Orthologous to human FOXC1 (forkhead box C1). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 2

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	2	NC_007113.7 (686873..689052, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	2	NC_007113.6 (814507..816686, complement)

Chromosome 2 - NC_007113.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Foxc1 establishes enhancer accessibility for craniofacial cartilage differentiation.
Title: Foxc1 establishes enhancer accessibility for craniofacial cartilage differentiation.
Disruption of foxc1 genes in zebrafish results in dosage-dependent phenotypes overlapping Axenfeld-Rieger syndrome.
Title: Disruption of foxc1 genes in zebrafish results in dosage-dependent phenotypes overlapping Axenfeld-Rieger syndrome.
Our zebrafish model demonstrates that aberrant regulation of RGC number could act in concert with other known glaucoma risk factors to influence the development of congenital and early onset glaucoma due to FOXC1 mutation.
Title: Loss of foxc1 in zebrafish reduces optic nerve size and cell number in the retinal ganglion cell layer.
results indicate that during zebrafish cardiogenesis, Foxc1a is active directly upstream of nkx2.5.
Title: The transcription factor Foxc1a in zebrafish directly regulates expression of nkx2.5, encoding a transcriptional regulator of cardiac progenitor cells.
Zebrafish foxc1a plays a crucial role in early somitogenesis by restricting the expression of Raldh2 directly.
Title: Zebrafish foxc1a plays a crucial role in early somitogenesis by restricting the expression of aldh1a2 directly.
results reveal foxc1a as a key player in the development of connectivity between the spinal cord and paired appendages, which is crucial for appendage mobility.
Title: Zebrafish foxc1a drives appendage-specific neural circuit development.
Lmx1b and FoxC have roles in regulating podocin expression in podocytes
Title: Lmx1b and FoxC combinatorially regulate podocin expression in podocytes.
Identify mesodermal foxc1a/b as a direct upstream regulator of etsrp in angioblasts. This establishes a new molecular link in the process of mesoderm specification into angioblast.
Title: Etsrp/Etv2 is directly regulated by Foxc1a/b in the zebrafish angioblast.
embryos treated with morpholinos against wt1a, foxc1a, or the Notch transcriptional mediator rbpj develop fewer podocytes, as determined by wt1b, hey1 and nephrin expression, while embryos deficient in any two of these factors completely lack podocytes
Title: Wt1a, Foxc1a, and the Notch mediator Rbpj physically interact and regulate the formation of podocytes in zebrafish.
This study reveals an important role for FOXC1 in the direct regulation of the FGF19-FGFR4-MAPK pathway to promote both the development and maintenance of anterior segment structures within the eye.
Title: FGF19 is a target for FOXC1 regulation in ciliary body-derived cells.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation 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 chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within adrenal gland development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in anatomical structure morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within blood vessel development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within camera-type eye development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cerebellum vasculature development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within closure of optic fissure	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within determination of heart left/right asymmetry	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within determination of heart left/right asymmetry	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within determination of left/right symmetry	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within determination of left/right symmetry	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within determination of liver left/right asymmetry	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within determination of pancreatic left/right asymmetry	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic retina morphogenesis in camera-type eye	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within heart development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within motor neuron axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of retinoic acid receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural crest cell migration	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within pectoral fin development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within podocyte cell fate commitment	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within podocyte development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within podocyte development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pronephric glomerulus development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of Notch signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of bone mineralization	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of bone mineralization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of fibroblast growth factor receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of platelet-derived growth factor receptor-alpha signaling pathway	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 vascular permeability	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within somitogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within_positive_effect vascular associated smooth muscle cell differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within_positive_effect vascular associated smooth muscle cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within vasculature development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within vasculature development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: forkhead box C1-A

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.