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Aliases for VSX2 Gene

Aliases for VSX2 Gene

  • Visual System Homeobox 2 2 3
  • CHX10 3 4 6
  • HOX10 3 4 6
  • Ceh-10 Homeodomain-Containing Homolog 3 4
  • Homeobox Protein CHX10 3 4
  • MCOPCB3 3 6
  • MCOP2 3 6
  • Ceh-10 Homeo Domain Containing Homolog (C. Elegans) 2
  • Ceh-10 Homeodomain Containing Homolog (C. Elegans) 2
  • C Elegans Ceh-10 Homeo Domain-Containing Homolog 2
  • Ceh-10 Homeo Domain Containing Homolog 3
  • RET1 3

External Ids for VSX2 Gene

Previous Symbols for VSX2 Gene

  • HOX10
  • CHX10

Summaries for VSX2 Gene

Entrez Gene Summary for VSX2 Gene

  • This gene encodes a homeobox protein originally described as a retina-specific transcription factor. Mutations in this gene are associated with microphthalmia, cataracts and iris abnormalities. [provided by RefSeq, Oct 2009]

GeneCards Summary for VSX2 Gene

VSX2 (Visual System Homeobox 2) is a Protein Coding gene. Diseases associated with VSX2 include microphthalmia, isolated 2 and microphthalmia with coloboma 3. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is PITX3.

UniProtKB/Swiss-Prot for VSX2 Gene

  • Plays a significant role in the specification and morphogenesis of the sensory retina. May also participate in the development of the cells of the inner nuclear layer, particularly bipolar cells (By similarity).

Gene Wiki entry for VSX2 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VSX2 Gene

Genomics for VSX2 Gene

Genomic Location for VSX2 Gene

Start:
74,239,472 bp from pter
End:
74,262,738 bp from pter
Size:
23,267 bases
Orientation:
Plus strand

Genomic View for VSX2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for VSX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VSX2 Gene

Regulatory Elements for VSX2 Gene

Proteins for VSX2 Gene

  • Protein details for VSX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P58304-VSX2_HUMAN
    Recommended name:
    Visual system homeobox 2
    Protein Accession:
    P58304
    Secondary Accessions:
    • A1A4X6

    Protein attributes for VSX2 Gene

    Size:
    361 amino acids
    Molecular mass:
    39411 Da
    Quaternary structure:
    No Data Available

neXtProt entry for VSX2 Gene

Proteomics data for VSX2 Gene at MOPED

Post-translational modifications for VSX2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VSX2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for VSX2 Gene

Domains for VSX2 Gene

Gene Families for VSX2 Gene

HGNC:
  • PRD :Homeoboxes / PRD class

Protein Domains for VSX2 Gene

Suggested Antigen Peptide Sequences for VSX2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P58304

UniProtKB/Swiss-Prot:

VSX2_HUMAN
Domain:
  • Contains 1 CVC domain.:
    • P58304
  • Contains 1 homeobox DNA-binding domain.:
    • P58304
Family:
  • Belongs to the paired homeobox family.:
    • P58304
genes like me logo Genes that share domains with VSX2: view

Function for VSX2 Gene

Molecular function for VSX2 Gene

UniProtKB/Swiss-Prot Function: Plays a significant role in the specification and morphogenesis of the sensory retina. May also participate in the development of the cells of the inner nuclear layer, particularly bipolar cells (By similarity).

Gene Ontology (GO) - Molecular Function for VSX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0005515 protein binding --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with VSX2: view
genes like me logo Genes that share phenotypes with VSX2: view

Transcription Factor Targeting for VSX2 Gene

Selected GeneGlobe predicted Target genes for VSX2

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA and HOMER Transcription for VSX2 Gene

Localization for VSX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VSX2 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VSX2 Gene COMPARTMENTS Subcellular localization image for VSX2 gene
Compartment Confidence
nucleus 5
cytoskeleton 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for VSX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular --
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with VSX2: view

Pathways for VSX2 Gene

SuperPathways for VSX2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for VSX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0007601 visual perception IEA --
GO:0008284 positive regulation of cell proliferation IEA --
GO:0008285 negative regulation of cell proliferation IEA --
GO:0043010 camera-type eye development --
genes like me logo Genes that share ontologies with VSX2: view

No data available for Pathways by source for VSX2 Gene

Transcripts for VSX2 Gene

mRNA/cDNA for VSX2 Gene

(2) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(17) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for VSX2 Gene

Visual system homeobox 2:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for VSX2 Gene

No ASD Table

Relevant External Links for VSX2 Gene

GeneLoc Exon Structure for
VSX2
ECgene alternative splicing isoforms for
VSX2

Expression for VSX2 Gene

mRNA expression in normal human tissues for VSX2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VSX2 Gene

This gene is overexpressed in Testis (8.0), Brain - Spinal cord (cervical c-1) (5.1), Brain - Substantia nigra (4.1), and Brain - Nucleus accumbens (basal ganglia) (4.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for VSX2 Gene

SOURCE GeneReport for Unigene cluster for VSX2 Gene Hs.449771

mRNA Expression by UniProt/SwissProt for VSX2 Gene

P58304-VSX2_HUMAN
Tissue specificity: Abundantly expressed in retinal neuroblasts during eye development and in the inner nuclear layer of the adult retina. Within this layer, expression is stronger in the outer margin where bipolar cells predominate
genes like me logo Genes that share expressions with VSX2: view

Orthologs for VSX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for VSX2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VSX2 35
  • 99.54 (n)
  • 99.72 (a)
VSX2 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VSX2 35
  • 91.14 (n)
  • 92.52 (a)
VSX2 36
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VSX2 35
  • 94.83 (n)
  • 96.12 (a)
VSX2 36
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vsx2 35
  • 91.41 (n)
  • 96.68 (a)
Vsx2 16
Vsx2 36
  • 97 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 86 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia Vsx2 35
  • 91.41 (n)
  • 96.95 (a)
chicken
(Gallus gallus)
Aves VSX2 35
  • 81.78 (n)
  • 83.29 (a)
VSX2 36
  • 78 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 71 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia vsx2 35
  • 67.2 (n)
  • 71.88 (a)
zebrafish
(Danio rerio)
Actinopterygii vsx2 35
vsx2 35
  • 69.77 (n)
  • 75.47 (a)
vsx2 36
  • 68 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta Vsx1 36
  • 15 (a)
ManyToMany
Vsx2 36
  • 21 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea ceh-10 36
  • 38 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2804 35
Species with no ortholog for VSX2:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VSX2 Gene

ENSEMBL:
Gene Tree for VSX2 (if available)
TreeFam:
Gene Tree for VSX2 (if available)

Paralogs for VSX2 Gene

Paralogs for VSX2 Gene

Selected SIMAP similar genes for VSX2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with VSX2: view

Variants for VSX2 Gene

Sequence variations from dbSNP and Humsavar for VSX2 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type MAF
rs917416 -- 74,258,170(-) GCAGC(A/G)CTCGC intron-variant
rs960198 -- 74,248,361(-) TTTTG(G/T)TTTTT intron-variant
rs1860713 -- 74,242,170(-) GCAGA(A/C)AGGCA intron-variant
rs1860714 -- 74,238,649(-) GTTCC(A/G)CAGTA upstream-variant-2KB
rs1860715 -- 74,238,544(-) GGAAG(C/G)GGGTG upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for VSX2 Gene

Variant ID Type Subtype PubMed ID
nsv902096 CNV Gain 21882294
nsv902097 CNV Gain 21882294
esv269970 CNV Insertion 20981092

Relevant External Links for VSX2 Gene

HapMap Linkage Disequilibrium report
VSX2
Human Gene Mutation Database (HGMD)
VSX2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VSX2 Gene

Disorders for VSX2 Gene

(2) OMIM Diseases for VSX2 Gene (142993)

UniProtKB/Swiss-Prot

VSX2_HUMAN
  • Microphthalmia, isolated, 2 (MCOP2) [MIM:610093]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. {ECO:0000269 PubMed:15257456, ECO:0000269 PubMed:21976963}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Microphthalmia with cataracts and iris abnormalities (MCOPCTI) [MIM:610092]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, cataract and other abnormalities like cataract may also be present. {ECO:0000269 PubMed:10932181}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Microphthalmia, isolated, with coloboma, 3 (MCOPCB3) [MIM:610092]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. Ocular colobomas are a set of malformations resulting from abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure (optic fissure). {ECO:0000269 PubMed:15257456}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for VSX2 Gene

(2) Novoseek inferred disease relationships for VSX2 Gene

Disease -log(P) Hits PubMed IDs
microphthalmia 87.2 11
anophthalmia 86 9

Relevant External Links for VSX2

GeneTests
VSX2
GeneReviews
VSX2
Genetic Association Database (GAD)
VSX2
Human Genome Epidemiology (HuGE) Navigator
VSX2
genes like me logo Genes that share disorders with VSX2: view

Publications for VSX2 Gene

  1. CHX10 mutations cause non-syndromic microphthalmia/ anophthalmia in Arab and Jewish kindreds. (PMID: 15257456) Bar-Yosef U. … Birk O.S. (Hum. Genet. 2004) 3 4 23
  2. Molecular analysis of CHX10 and MFRP in Chinese subjects with primary angle closure glaucoma and short axial length eyes. (PMID: 18648522) Aung T. … Vithana E.N. (Mol. Vis. 2008) 3 23 48
  3. Mutational screening of 10 genes in Chinese patients with microphthalmia and/or coloboma. (PMID: 20057906) Zhang X. … Zhang Q. (Mol. Vis. 2009) 3 23 48
  4. Nomenclature for human homeobox genes. (PMID: 1973146) McAlpine P.J. … Shows T.B. (Genomics 1990) 2 3
  5. Identification of novel mutations and sequence variants in the SOX2 and CHX10 genes in patients with anophthalmia/microphthalmia. (PMID: 18385794) Zhou J. … Young T.L. (Mol. Vis. 2008) 3 23

Products for VSX2 Gene

Sources for VSX2 Gene

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