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Vsx2 visual system homeobox 2 [ Mus musculus (house mouse) ]

Gene ID: 12677, updated on 21-Mar-2023

Summary

Official Symbol
Vsx2provided by MGI
Official Full Name
visual system homeobox 2provided by MGI
Primary source
MGI:MGI:88401
See related
Ensembl:ENSMUSG00000021239 AllianceGenome:MGI:88401
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
or; Chx10; Hox10; Hox-10
Summary
This gene encodes a member of the Vsx (visual system homeobox) family which belongs to the larger PRD homeobox class. The encoded protein is required for eye organogenesis and controls retinal development. Disruption of this gene is associated with ocular retardation J (orJ), a mouse disease which causes microphthalmia, retinal degeneration and optic nerve aplasia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014]
Expression
Biased expression in whole brain E14.5 (RPKM 1.2), CNS E14 (RPKM 0.9) and 8 other tissues See more
Orthologs
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Genomic context

See Vsx2 in Genome Data Viewer
Location:
12 D1; 12 39.28 cM
Exon count:
5
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (84616602..84642231)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (84569828..84595457)

Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene basal body orientation factor 1 Neighboring gene aldehyde dehydrogenase family 6, subfamily A1 Neighboring gene lin-52 DREAM MuvB core complex component Neighboring gene ATP-binding cassette, sub-family D (ALD), member 4 Neighboring gene vertebrae development associated

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Gene Ontology Provided by MGI

Process Evidence Code Pubs
acts_upstream_of_or_within camera-type eye development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within cell fate commitment IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of neuroblast proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of neuroblast proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within response to stimulus IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within retina morphogenesis in camera-type eye IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within retinal bipolar neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within visual perception IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in intracellular anatomical structure IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
visual system homeobox 2
Names
C. elegans ceh-10 homeo domain containing homolog
ceh-10 homeodomain-containing homolog
homeobox protein CHX10
ocular retardation

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_001301427.1NP_001288356.1  visual system homeobox 2 isoform 1

    See identical proteins and their annotated locations for NP_001288356.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK143461, BC058806
    Consensus CDS
    CCDS79136.1
    UniProtKB/TrEMBL
    Q6PDC1, Q80WF9
    Related
    ENSMUSP00000131009.3, ENSMUST00000169934.4
    Conserved Domains (2) summary
    pfam00046
    Location:153204
    Homeobox; Homeobox domain
    pfam03826
    Location:319336
    OAR; OAR domain
  2. NM_007701.3NP_031727.1  visual system homeobox 2 isoform 2

    See identical proteins and their annotated locations for NP_031727.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1
    Source sequence(s)
    AK143461, BC031869, BC051245
    Consensus CDS
    CCDS36493.1
    UniProtKB/Swiss-Prot
    Q61412
    UniProtKB/TrEMBL
    Q80WF9
    Related
    ENSMUSP00000021665.6, ENSMUST00000021665.12
    Conserved Domains (2) summary
    pfam00046
    Location:153204
    Homeobox; Homeobox domain
    pfam03826
    Location:300317
    OAR; OAR domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000078.7 Reference GRCm39 C57BL/6J

    Range
    84616602..84642231
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)