vsx2 visual system homeobox 2 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: vsx2provided by ZNC
Official Full Name: visual system homeobox 2provided by ZNC
Primary source: ZFIN:ZDB-GENE-001222-1
See related: Ensembl:ENSDARG00000005574 AllianceGenome:ZFIN:ZDB-GENE-001222-1
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: alx; Vsx-2; chx10
Summary: Enables sequence-specific DNA binding activity. Acts upstream of or within negative regulation of transcription by RNA polymerase II and regulation of neural retina development. Predicted to be active in nucleus. Is expressed in head; nervous system; neural tube; optic cup; and optic vesicle. Human ortholog(s) of this gene implicated in blindness and isolated microphthalmia 2. Orthologous to human VSX2 (visual system homeobox 2). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 17

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	17	NC_007128.7 (31650903..31659661, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	17	NC_007128.6 (31635676..31643308, 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?

These data support a model by which vsx2, operating through the effector gene opo, acts as a central transcriptional node that coordinates neural retina patterning and optic cup invagination in zebrafish.
Title: Analysis of opo cis-regulatory landscape uncovers Vsx2 requirement in early eye morphogenesis.
Mutual antagonism of the paired-type homeobox genes, vsx2 and dmbx1, regulates retinal progenitor cell cycle exit upstream of ccnd1 expression.
Title: Mutual antagonism of the paired-type homeobox genes, vsx2 and dmbx1, regulates retinal progenitor cell cycle exit upstream of ccnd1 expression.
Vsx2-positive RPCs are fully multipotent retinal progenitors and that when Vsx2 is downregulated, Vsx2-negative progenitors escape Vsx2 repression and so are able to express factors that restrict lineage potential.
Title: Vsx2 in the zebrafish retina: restricted lineages through derepression.

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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	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	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
acts_upstream_of_or_within regulation of neural retina development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of neural retina development	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 visual perception	IEA Inferred from Electronic Annotation 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

General protein information

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Preferred Names: visual system homeobox 2

Names: ceh-10 homeodomain containing homolog; homeobox protein ALX; homeobox protein CHX10; transcription factor VSX2

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_131462.2 → NP_571537.2 visual system homeobox 2

Status: VALIDATED

Source sequence(s)

CR628322

UniProtKB/Swiss-Prot

O42477, Q6NWA4, Q7SXI5

UniProtKB/TrEMBL

A0A8M1P5K9, F1QQE7

Related

ENSDARP00000038309.8, ENSDART00000030448.9

Conserved Domains (2) summary

pfam00046
Location:170 → 221

Homeobox; Homeobox domain

pfam03826
Location:317 → 334

OAR; OAR 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_007128.7 Reference GRCz11 Primary Assembly

Range

31650903..31659661 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005158805.5 → XP_005158862.1 visual system homeobox 2 isoform X1

UniProtKB/Swiss-Prot

O42477, Q6NWA4, Q7SXI5

UniProtKB/TrEMBL

A0A8M2B589

Conserved Domains (2) summary

pfam00046
Location:170 → 221

Homeobox; Homeobox domain

pfam03826
Location:338 → 355

OAR; OAR domain