foxi1 forkhead box i1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: foxi1provided by ZNC
Official Full Name: forkhead box i1provided by ZNC
Primary source: ZFIN:ZDB-GENE-030505-1
See related: Ensembl:ENSDARG00000104566 AllianceGenome:ZFIN:ZDB-GENE-030505-1
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: foo; cb724
Summary: Enables DNA-binding transcription factor activity. Acts upstream of or within several processes, including animal organ development; epidermal cell fate specification; and neuron development. Predicted to be located in nucleus. Is expressed in several structures, including ectoderm; epibranchial ganglion; head; neural crest; and neurogenic field. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness 4. Orthologous to human FOXI1 (forkhead box I1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 12

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	12	NC_007123.7 (43662978..43664682, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	12	NC_007123.6 (43916243..43917947, complement)

Chromosome 12 - NC_007123.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Carbonic Anhydrase 2 Deletion Delays the Growth of Kidney Cysts Whereas Foxi1 Deletion Completely Abrogates Cystogenesis in TSC.
Title: Carbonic Anhydrase 2 Deletion Delays the Growth of Kidney Cysts Whereas Foxi1 Deletion Completely Abrogates Cystogenesis in TSC.
Fox1 activation of Wnt4a in the ectoderm signals the epithelial stabilization of pouch-forming cells during late-stage of pouch morphogenesis.
Title: Foxi1 promotes late-stage pharyngeal pouch morphogenesis through ectodermal Wnt4a activation.
Data indicate that foxi1 is expressed in branchial arch ectoderm and endoderm, and morpholino knock-down of foxi1 causes apoptosis of neural crest in the branchial arches, which is rescued by fgf3.
Title: Foxi transcription factors promote pharyngeal arch development by regulating formation of FGF signaling centers.
Foxi1 and Dlx3b/4b regulate the neuronal and sensory lineages of the inner ear.
Title: Zebrafish Foxi1 provides a neuronal ground state during inner ear induction preceding the Dlx3b/4b-regulated sensory lineage.
pax8 works with related genes pax2a/pax2b to downregulate otic expression of foxi1, a necessary step for further otic development
Title: Pax2/8 proteins coordinate sequential induction of otic and epibranchial placodes through differential regulation of foxi1, sox3 and fgf24.
Data show that the hearsay mutation disrupts foxi1, a forkhead domain-containing gene, expressed in otic precursor cells before placodes become visible, and which appears to be the earliest marker known for the otic anlage.[foxi1]
Title: Zebrafish foxi1 mediates otic placode formation and jaw development.
FoxI1 is capable of remodeling chromatin higher-order structure and can stably create site-specific changes in chromatin to either stably create or remove DNase I hypersensitive sites.
Title: The forkhead transcription factor FoxI1 remains bound to condensed mitotic chromosomes and stably remodels chromatin structure.
Foxi1 provide competence for cells to respond to Fgf and form an otic placode
Title: Fgf-dependent otic induction requires competence provided by Foxi1 and Dlx3b.
an extensive phylogenetic analysis of the FoxI class that includes these new sequences together with those previously reported
Title: Expression and phylogenetic analyses of three zebrafish FoxI class genes.

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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	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, 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 sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
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 cranial ganglion development	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within ectodermal placode development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within ectodermal placode formation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic viscerocranium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epidermal cell fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lateral line ganglion development	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within neural crest cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural crest cell migration	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within neuron development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otic placode formation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within otic placode formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otic vesicle development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otic vesicle formation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within otic vesicle formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otic vesicle morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

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 protein I1

Names: hearsay; hsy; no soul; nos; quadro; quo(l)

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.