foxn4 forkhead box N4 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: foxn4provided by ZNC
Official Full Name: forkhead box N4provided by ZNC
Primary source: ZFIN:ZDB-GENE-990415-277
See related: Ensembl:ENSDARG00000010591 AllianceGenome:ZFIN:ZDB-GENE-990415-277
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: whn; whna
Summary: Enables DNA-binding transcription factor activity and sequence-specific DNA binding activity. Involved in atrioventricular canal development; heart looping; and regulation of heart contraction. Acts upstream of or within heart valve development and positive regulation of DNA-templated transcription. Predicted to be active in nucleus. Is expressed in several structures, including forebrain neural keel; nervous system; optic vesicle; pericardial region; and presumptive neural retina. Orthologous to human FOXN4 (forkhead box N4). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 5

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	5	NC_007116.7 (19385503..19400164, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	5	NC_007116.6 (18881703..18896414, complement)

Chromosome 5 - NC_007116.7 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?

adult thymus is the only major site of foxn4 expression outside of the nervous system
Title: Expression of the winged helix/forkhead gene, foxn4, during zebrafish development.

Submit: New GeneRIF Correction

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	IBA Inferred from Biological aspect of Ancestor 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	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables cis-regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity 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 amacrine cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within atrioventricular canal development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in atrioventricular canal development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart looping	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart valve development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of heart contraction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of heart contraction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retina layer formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in ventral spinal cord interneuron fate commitment	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: forkhead box protein N4

Names: sli; slipjig; winged helix nude

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.

mRNA and Protein(s)

NM_131099.2 → NP_571174.1 forkhead box protein N4

See identical proteins and their annotated locations for NP_571174.1

Status: PROVISIONAL

Source sequence(s)

BC128811

UniProtKB/Swiss-Prot

A2BGM5, Q8UVH2, Q90X68, Q9DG30, Q9PT94

Related

ENSDARP00000020367.6, ENSDART00000008994.7

Conserved Domains (1) summary

pfam00250
Location:231 → 318

Forkhead; Forkhead domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

NC_007116.7 Reference GRCz11 Primary Assembly

Range

19385503..19400164 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005165100.5 → XP_005165157.2 forkhead box protein N4 isoform X1

UniProtKB/TrEMBL

A0A8M2BC99
XM_009301283.3 → XP_009299558.1 forkhead box protein N4 isoform X2

UniProtKB/Swiss-Prot

A2BGM5

Related

ENSDARP00000130721.2, ENSDART00000163771.2

Conserved Domains (1) summary

pfam00250
Location:92 → 179

Forkhead; Forkhead domain