vsx1 visual system homeobox 1 homolog, chx10-like [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: vsx1provided by ZNC
Official Full Name: visual system homeobox 1 homolog, chx10-likeprovided by ZNC
Primary source: ZFIN:ZDB-GENE-990415-205
See related: Ensembl:ENSDARG00000056292 AllianceGenome:ZFIN:ZDB-GENE-990415-205
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: Enables chromatin binding activity and transcription cis-regulatory region binding activity. Acts upstream of or within several processes, including negative regulation of axial mesodermal cell fate specification; nervous system development; and paraxial mesodermal cell fate specification. Predicted to be active in nucleus. Is expressed in blastomere; immature eye; nervous system; and neural tube. Human ortholog(s) of this gene implicated in corneal dystrophy; keratoconus; and posterior polymorphous corneal dystrophy 1. Orthologous to human VSX1 (visual system homeobox 1). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: 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 (21063403..21066091, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	17	NC_007128.6 (21043567..21046274, 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 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?

Zygotic Vsx1 Plays a Key Role in Defining V2a Interneuron Sub-Lineage by Directly Repressing tal1 Transcription in Zebrafish.
Title: Zygotic Vsx1 Plays a Key Role in Defining V2a Interneuron Sub-Lineage by Directly Repressing tal1 Transcription in Zebrafish.
miR-20a is essential for normal embryogenesis by restricting Vsx1 expression in goldfish and zebrafish, and that post-transcriptional regulation is an essential mechanism for Vsx1 playing different roles in diverse developmental processes.
Title: MicroRNA-20a is essential for normal embryogenesis by targeting vsx1 mRNA in fish.
Maternal Vsx1 plays an essential role in regulating prechordal mesendoderm and forebrain formation in zebrafish.
Title: Maternal Vsx1 plays an essential role in regulating prechordal mesendoderm and forebrain formation in zebrafish.

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, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IBA Inferred from Biological aspect of Ancestor more info
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within axial mesoderm development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within forebrain development	IMP Inferred from Mutant Phenotype 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 axial mesodermal cell fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within paraxial mesoderm development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within paraxial mesodermal cell fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within prechordal plate formation	IMP Inferred from Mutant Phenotype more info	PubMed
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
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 1

Names: etID309864.17; paired-like homeobox protein; transcription factor VSX1; visual system homeobox 1 protein

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_131333.1 → NP_571408.1 visual system homeobox 1

See identical proteins and their annotated locations for NP_571408.1

Status: PROVISIONAL

Source sequence(s)

AF025348

UniProtKB/Swiss-Prot

O42250

Related

ENSDARP00000073224.2, ENSDART00000078763.3

Conserved Domains (2) summary

COG5576
Location:101 → 221

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:154 → 207

Homeobox; Homeobox 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

21063403..21066091 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005158663.5 → XP_005158720.1 visual system homeobox 1 isoform X1

UniProtKB/TrEMBL

A0A8M2B5L9, F1QBH3

Related

ENSDARP00000095102.4, ENSDART00000104327.7

Conserved Domains (2) summary

COG5576
Location:101 → 221

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:154 → 207

Homeobox; Homeobox domain