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Aliases for VAX2 Gene

Aliases for VAX2 Gene

  • Ventral Anterior Homeobox 2 2 3 5
  • DRES93 3

External Ids for VAX2 Gene

Previous GeneCards Identifiers for VAX2 Gene

  • GC02P071137
  • GC02P071338
  • GC02P071085
  • GC02P071102
  • GC02P071039
  • GC02P070981
  • GC02P071127
  • GC02P070864

Summaries for VAX2 Gene

Entrez Gene Summary for VAX2 Gene

  • This gene encodes a homeobox protein and is almost exclusively expressed in the ventral portion of the retina during development. In mouse studies, this gene was found to be required for the correct formation of the optic fissure and other aspects of retinal development. [provided by RefSeq, Sep 2008]

GeneCards Summary for VAX2 Gene

VAX2 (Ventral Anterior Homeobox 2) is a Protein Coding gene. Diseases associated with VAX2 include Astigmatism and Coloboma Of Macula. Among its related pathways are Ectoderm Differentiation. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and chromatin DNA binding. An important paralog of this gene is VAX1.

UniProtKB/Swiss-Prot for VAX2 Gene

  • Transcription factor that may function in dorsoventral specification of the forebrain. Regulates the expression of Wnt signaling antagonists including the expression of a truncated TCF7L2 isoform that cannot bind CTNNB1 and acts therefore as a potent dominant-negative Wnt antagonist. Plays a crucial role in eye development and, in particular, in the specification of the ventral optic vesicle (By similarity). May be a regulator of axial polarization in the retina.

Additional gene information for VAX2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VAX2 Gene

Genomics for VAX2 Gene

GeneHancer (GH) Regulatory Elements for VAX2 Gene

Promoters and enhancers for VAX2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I070900 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 555.4 +0.6 608 2 HDGF MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B ZNF48 GLIS2 KLF7 VAX2 ENSG00000277764 CLEC4F ATP6V1B1
GH02I070898 Enhancer 0.5 ENCODE 550.8 -2.0 -1984 0.1 SP1 SUZ12 EZH2 ZBTB17 ENSG00000277764 VAX2 LINC01143
GH02I070551 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 9.7 -347.2 -347235 4.1 FOXA2 ARID4B SIN3A DMAP1 ZBTB7B ZNF48 YY1 GLIS2 ZNF143 SP3 TGFA CLEC4F TIA1 TEX261 PCBP1-AS1 CD207 VAX2 TGFA-IT1
GH02I070976 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 10 +77.3 77336 3.8 PKNOX1 ATF1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZNF48 FOS ATF7 ANKRD53 ZNF638 TEX261 ATP6V1B1-AS1 VAX2 NAGK OR7E62P CLEC4F LOC105374795 ENSG00000258881
GH02I070303 Enhancer 1 Ensembl ENCODE 10.1 -596.6 -596590 0.8 ARID4B RAD21 RFX5 ZNF335 EGR1 ZNF143 CREM MIXL1 EGR2 ZNF654 FAM136A ATP6V1B1-AS1 VAX2 BRD7P6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VAX2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VAX2 gene promoter:

Genomic Locations for VAX2 Gene

Genomic Locations for VAX2 Gene
chr2:70,900,590-70,933,446
(GRCh38/hg38)
Size:
32,857 bases
Orientation:
Plus strand
chr2:71,127,720-71,160,576
(GRCh37/hg19)

Genomic View for VAX2 Gene

Genes around VAX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VAX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VAX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VAX2 Gene

Proteins for VAX2 Gene

  • Protein details for VAX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UIW0-VAX2_HUMAN
    Recommended name:
    Ventral anterior homeobox 2
    Protein Accession:
    Q9UIW0
    Secondary Accessions:
    • Q53Y33

    Protein attributes for VAX2 Gene

    Size:
    290 amino acids
    Molecular mass:
    30874 Da
    Quaternary structure:
    No Data Available

neXtProt entry for VAX2 Gene

Post-translational modifications for VAX2 Gene

No Post-translational modifications

Other Protein References for VAX2 Gene

No data available for DME Specific Peptides for VAX2 Gene

Domains & Families for VAX2 Gene

Gene Families for VAX2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for VAX2 Gene

Graphical View of Domain Structure for InterPro Entry

Q9UIW0

UniProtKB/Swiss-Prot:

VAX2_HUMAN :
  • Belongs to the EMX homeobox family.
Family:
  • Belongs to the EMX homeobox family.
genes like me logo Genes that share domains with VAX2: view

Function for VAX2 Gene

Molecular function for VAX2 Gene

GENATLAS Biochemistry:
ventral anterior homeobox 2,specifically expressed in the developing vertebral eye,controlling the patterning of the eye dorsoventral axis
UniProtKB/Swiss-Prot Function:
Transcription factor that may function in dorsoventral specification of the forebrain. Regulates the expression of Wnt signaling antagonists including the expression of a truncated TCF7L2 isoform that cannot bind CTNNB1 and acts therefore as a potent dominant-negative Wnt antagonist. Plays a crucial role in eye development and, in particular, in the specification of the ventral optic vesicle (By similarity). May be a regulator of axial polarization in the retina.

Phenotypes From GWAS Catalog for VAX2 Gene

Gene Ontology (GO) - Molecular Function for VAX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001162 RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding IEA --
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity NAS 10485894
GO:0031490 chromatin DNA binding IEA --
genes like me logo Genes that share ontologies with VAX2: view
genes like me logo Genes that share phenotypes with VAX2: view

Animal Models for VAX2 Gene

MGI Knock Outs for VAX2:

miRNA for VAX2 Gene

miRTarBase miRNAs that target VAX2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VAX2 Gene

Localization for VAX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VAX2 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VAX2 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VAX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with VAX2: view

Pathways & Interactions for VAX2 Gene

SuperPathway Contained pathways
1 Ectoderm Differentiation
genes like me logo Genes that share pathways with VAX2: view

Pathways by source for VAX2 Gene

1 BioSystems pathway for VAX2 Gene

Gene Ontology (GO) - Biological Process for VAX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with VAX2: view

No data available for SIGNOR curated interactions for VAX2 Gene

Drugs & Compounds for VAX2 Gene

No Compound Related Data Available

Transcripts for VAX2 Gene

mRNA/cDNA for VAX2 Gene

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

Unigene Clusters for VAX2 Gene

Ventral anterior homeobox 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VAX2 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b
SP1:
SP2: -

Relevant External Links for VAX2 Gene

GeneLoc Exon Structure for
VAX2
ECgene alternative splicing isoforms for
VAX2

Expression for VAX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VAX2 Gene

mRNA differential expression in normal tissues according to GTEx for VAX2 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x9.0) and Brain - Cerebellum (x8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for VAX2 Gene



NURSA nuclear receptor signaling pathways regulating expression of VAX2 Gene:

VAX2

SOURCE GeneReport for Unigene cluster for VAX2 Gene:

Hs.249170

Evidence on tissue expression from TISSUES for VAX2 Gene

  • Eye(2.4)
genes like me logo Genes that share expression patterns with VAX2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VAX2 Gene

Orthologs for VAX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for VAX2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VAX2 33 34
  • 99.2 (n)
cow
(Bos Taurus)
Mammalia VAX2 33 34
  • 88.15 (n)
mouse
(Mus musculus)
Mammalia Vax2 33 16 34
  • 86.04 (n)
rat
(Rattus norvegicus)
Mammalia Vax2 33
  • 84.89 (n)
dog
(Canis familiaris)
Mammalia VAX2 34
  • 78 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VAX2 34
  • 65 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VAX2 34
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves VAX1 34
  • 58 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia VAX2 34
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100485836 33
  • 62.78 (n)
zebrafish
(Danio rerio)
Actinopterygii vax2 33 34
  • 64.87 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG18599 34
  • 12 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 35 (a)
OneToMany
Species where no ortholog for VAX2 was found in the sources mined by GeneCards:
  • 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)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for VAX2 Gene

ENSEMBL:
Gene Tree for VAX2 (if available)
TreeFam:
Gene Tree for VAX2 (if available)

Paralogs for VAX2 Gene

Paralogs for VAX2 Gene

(2) SIMAP similar genes for VAX2 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with VAX2: view

Variants for VAX2 Gene

Sequence variations from dbSNP and Humsavar for VAX2 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs869025255 likely-benign, Anophthalmia - microphthalmia 70,921,248(+) C/T coding_sequence_variant, missense_variant
rs1000261021 -- 70,910,318(+) G/T intron_variant
rs1000364536 -- 70,933,830(+) C/A downstream_transcript_variant
rs1000417775 -- 70,904,751(+) G/A intron_variant
rs1000470195 -- 70,904,933(+) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for VAX2 Gene

Variant ID Type Subtype PubMed ID
esv3591213 CNV loss 21293372
nsv1004459 CNV loss 25217958
nsv1013232 CNV gain 25217958
nsv953145 CNV deletion 24416366
nsv519862 CNV gain 19592680
nsv1146915 OTHER inversion 26484159
nsv1014516 CNV gain 25217958

Variation tolerance for VAX2 Gene

Residual Variation Intolerance Score: 90.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.84; 79.31% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VAX2 Gene

Human Gene Mutation Database (HGMD)
VAX2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VAX2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VAX2 Gene

Disorders for VAX2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for VAX2 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
astigmatism
coloboma of macula
  • agenesis of macula
- elite association - COSMIC cancer census association via MalaCards
Search VAX2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VAX2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VAX2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VAX2 Gene

Publications for VAX2 Gene

  1. A homeobox gene, vax2, controls the patterning of the eye dorsoventral axis. (PMID: 10485894) Barbieri AM … Banfi S (Proceedings of the National Academy of Sciences of the United States of America 1999) 2 3 4 22 58
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  3. Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations. (PMID: 16953426) Beaty TH … Scott AF (Human genetics 2006) 3 44 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for VAX2 Gene

Sources for VAX2 Gene

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