foxd3 forkhead box D3 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: foxd3provided by ZNC
Official Full Name: forkhead box D3provided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-143
See related: Ensembl:ENSDARG00000021032 AllianceGenome:ZFIN:ZDB-GENE-980526-143
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: fkd6; fkh6; fkd-6; forkhead-6; zgc:111934
Summary: Enables DNA-binding transcription factor activity and sequence-specific DNA binding activity. Acts upstream of or within several processes, including iridophore differentiation; negative regulation of macromolecule biosynthetic process; and nervous system development. Predicted to be located in nucleus. Is expressed in several structures, including mesoderm; nervous system; neural crest; neural keel; and neural plate. Human ortholog(s) of this gene implicated in vitiligo. Orthologous to human FOXD3 (forkhead box D3). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 6

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	6	NC_007117.7 (32092032..32093830, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	6	NC_007117.6 (32105118..32106916, complement)

Chromosome 6 - NC_007117.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Embryonic stem cell factor FOXD3 (Genesis) defects in gastrointestinal stromal tumors.
Title: Embryonic stem cell factor FOXD3 (Genesis) defects in gastrointestinal stromal tumors.
Mitochondrial dysfunction interferes with neural crest specification through the FoxD3 transcription factor.
Title: Mitochondrial dysfunction interferes with neural crest specification through the FoxD3 transcription factor.
foxd3 acts bimodally in the neural crest as a switch from "permissive" to "repressive" nucleosome and chromatin organization to maintain multipotency and define cell fates.
Title: From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo.
Foxd3 rescues the prdm1a loss-of-function neural crest phenotype.
Title: Prdm1a directly activates foxd3 and tfap2a during zebrafish neural crest specification.
These results reveal dynamic and differential regulation of FoxD3 in distinct neural crest subpopulations, suggesting that heterogeneity is encrypted at the regulatory level
Title: Dynamic and differential regulation of stem cell factor FoxD3 in the neural crest is Encrypted in the genome.
analysis of how a FoxD3 gene trap line reveals neural crest precursor movement and a role for FoxD3 in their specification
Title: A novel FoxD3 gene trap line reveals neural crest precursor movement and a role for FoxD3 in their specification.
tfap2a and foxd3 are expressed during gastrulation prior to neural crest induction in distinct, complementary, domains; tfap2a is expressed in the ventral non-neural ectoderm and foxd3 in the dorsal mesendoderm and ectoderm
Title: Tfap2a and Foxd3 regulate early steps in the development of the neural crest progenitor population.
analysis of a Foxd3/mitfa transcriptional switch that governs whether a bi-potent pigment precursor will attain either an iridophore or a melanophore fate
Title: Interplay between Foxd3 and Mitf regulates cell fate plasticity in the zebrafish neural crest.
foxd3 is an essential Nodal-dependent regulator of zebrafish mesoderm development.
Title: Foxd3 is an essential Nodal-dependent regulator of zebrafish dorsal mesoderm development.
Disc1 functions in the transcriptional repression of foxd3 and sox10, thus mediating cranial neural crest cell migration and differentiation.
Title: Disc1 regulates foxd3 and sox10 expression, affecting neural crest migration and differentiation.

Submit: New GeneRIF Correction See all GeneRIFs (18)

General gene information

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Markers

fkd6 (e-PCR)
- UniSTS:205631

Z13538 (e-PCR)
- UniSTS:204698

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	IDA Inferred from Direct Assay more info	PubMed
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
acts_upstream_of_or_within cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cartilage development involved in endochondral bone morphogenesis	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 enteric nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within iridophore differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lateral line nerve glial cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within melanocyte differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural crest cell development	IGI Inferred from Genetic Interaction more info	PubMed
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	PubMed
acts_upstream_of_or_within peripheral nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pigment cell differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within pigment cell differentiation	IMP Inferred from Mutant Phenotype 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
acts_upstream_of_or_within response to thyroid hormone	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within sympathetic nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within transcription by RNA polymerase II	IDA Inferred from Direct Assay 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 protein D3

Names: fork head domain protein 6; mother superior

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.