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

Gene ID: 30598, updated on 2-Nov-2024

Summary

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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
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Genomic context

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See vsx1 in Genome Data Viewer
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_007128.7Genomic Context describing neighboring genes Neighboring gene BicC family RNA binding protein 1a Neighboring gene ubiquitin-conjugating enzyme E2D 1a Neighboring gene ectonucleoside triphosphate diphosphohydrolase 6 Neighboring gene phosphorylase, glycogen; brain

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Ubiquitination and degradation of the zebrafish paired-like homeobox protein VSX-1. Kurtzman AL, et al. J Neurochem, 2000 Jul. PMID 10854246
  2. Sequence divergence in the 3'-untranslated region has an effect on the subfunctionalization of duplicate genes. Tong Y, et al. J Exp Zool B Mol Dev Evol, 2012 Nov. PMID 22674856
  3. Mismatch of Synaptic Patterns between Neurons Produced in Regeneration and during Development of the Vertebrate Retina. D'Orazi FD, et al. Curr Biol, 2016 Sep 12. PMID 27524481, Free PMC Article
  4. MicroRNA-20a is essential for normal embryogenesis by targeting vsx1 mRNA in fish. Sun L, et al. RNA Biol, 2015. PMID 25833418, Free PMC Article
  5. Ubc9 interacts with a nuclear localization signal and mediates nuclear localization of the paired-like homeobox protein Vsx-1 independent of SUMO-1 modification. Kurtzman AL, et al. Proc Natl Acad Sci U S A, 2001 May 8. PMID 11331779, Free PMC Article

See all (52) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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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Markers

Homology

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)

  1. 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

  1. NC_007128.7 Reference GRCz11 Primary Assembly

    Range
    21063403..21066091 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018394984.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    123985..126655 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O42250.2 GenPept UniProtKB/Swiss-Prot:O42250

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