vax1 ventral anterior homeobox 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: vax1provided by ZNC
Official Full Name: ventral anterior homeobox 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-030904-9
See related: Ensembl:ENSDARG00000021916 AllianceGenome:ZFIN:ZDB-GENE-030904-9
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
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within several processes, including camera-type eye morphogenesis; negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator; and regulation of retinal ganglion cell axon guidance. Predicted to be active in nucleus. Is expressed in several structures, including anterior neural rod; eye; forebrain; forebrain neural keel; and optic vesicle. Human ortholog(s) of this gene implicated in syndromic microphthalmia 11. Orthologous to human VAX1 (ventral anterior homeobox 1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 17

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	17	NC_007128.7 (21432693..21441464, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	17	NC_007128.6 (21412857..21422148, complement)

Chromosome 17 - NC_007128.7 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?

vax1 and vax2 are expressed in overlapping domains encompassing the ventral retina, optic stalks and preoptic area; Hh signals act downstream of the Nodal pathway to promote Vax gene expression.
Title: Hedgehog signalling maintains the optic stalk-retinal interface through the regulation of Vax gene activity.

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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, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within closure of optic fissure	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator	IGI Inferred from Genetic Interaction more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within optic nerve development	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
acts_upstream_of_or_within regulation of retinal ganglion cell axon guidance	IMP Inferred from Mutant Phenotype 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 retina development in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retina morphogenesis in camera-type eye	IGI Inferred from Genetic Interaction more info	PubMed

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

General protein information

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Preferred Names: ventral anterior homeobox 1

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.