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VAX2 Gene

protein-coding   GIFtS: 52
GCID: GC02P071127

Ventral Anterior Homeobox 2

  See VAX2-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Ventral Anterior Homeobox 21 2
DRES932

External Ids:    HGNC: 126611   Entrez Gene: 258062   Ensembl: ENSG000001160357   OMIM: 6042955   UniProtKB: Q9UIW03   

Export aliases for VAX2 gene to outside databases

Previous GC identifers: GC02P071137 GC02P071338 GC02P071085 GC02P071102 GC02P071039 GC02P070981 GC02P070864


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 corpus callosum agenesis. GO annotations related to this gene include chromatin DNA binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is NOTO.

UniProtKB/Swiss-Prot: VAX2_HUMAN, Q9UIW0
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




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NT_022184.16  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the VAX2 gene promoter:
         GATA-3   Sp1   RREB-1   HNF-4alpha2   POU6F1 (c2)   HNF-4alpha1   RORalpha1   PPAR-alpha   NF-Y   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidVAX2 promoter sequence
   Search Chromatin IP Primers for VAX2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VAX2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2p13   Ensembl cytogenetic band:  2p13.3   HGNC cytogenetic band: 2p13.3

VAX2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VAX2 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P071127:  view genomic region     (about GC identifiers)

Start:
71,127,720 bp from pter      End:
71,160,576 bp from pter
Size:
32,857 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: VAX2_HUMAN, Q9UIW0 (See protein sequence)
Recommended Name: Ventral anterior homeobox 2  
Size: 290 amino acids; 30874 Da
Developmental stage: Expressed in the ventral part of the optic vesicles at 7 week dpc
Secondary accessions: Q53Y33

Explore the universe of human proteins at neXtProt for VAX2: NX_Q9UIW0

Explore proteomics data for VAX2 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See VAX2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_036608.1  
    ENSEMBL proteins: 
     ENSP00000234392  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    NKL: Homeoboxes / ANTP class : NKL subclass

    5 InterPro protein domains:
     IPR020479 Homeobox_metazoa
     IPR000047 HTH_motif
     IPR017970 Homeobox_CS
     IPR001356 Homeobox_dom
     IPR009057 Homeodomain-like

    Graphical View of Domain Structure for InterPro Entry Q9UIW0

    ProtoNet protein and cluster: Q9UIW0

    1 Blocks protein domain: IPB000047 Lambda and other repressor helix-turn-helix signature

    UniProtKB/Swiss-Prot: VAX2_HUMAN, Q9UIW0
    Similarity: Belongs to the EMX homeobox family
    Similarity: Contains 1 homeobox DNA-binding domain


    Find genes that share domains with VAX2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: VAX2_HUMAN, Q9UIW0
    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

         Genatlas biochemistry entry for VAX2:
    ventral anterior homeobox 2,specifically expressed in the developing vertebral eye,controlling the patterning of
    the eye dorsoventral axis

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000976transcription regulatory region sequence-specific DNA binding IEA--
    GO:0003677DNA binding ----
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
    GO:0031490chromatin DNA binding IEA--
    GO:0043565sequence-specific DNA binding ----
         
    Find genes that share ontologies with VAX2           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for VAX2:
     Decreased homologous recombina 

         8 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Vax2):
     behavior/neurological  cellular  craniofacial  digestive/alimentary  growth/size/body 
     mortality/aging  nervous system  vision/eye 

    Find genes that share phenotypes with VAX2           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for VAX2: Vax2tm1Grl Vax2tm1Sba

       genOway: Develop your customized and physiologically relevant rodent model for VAX2

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    hsa-miR-623 hsa-miR-4303 hsa-miR-578 hsa-miR-597 hsa-miR-3921 hsa-miR-211 hsa-miR-1248 hsa-miR-146a*
    SwitchGear 3'UTR luciferase reporter plasmidVAX2 3' UTR sequence
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    VAX2_HUMAN, Q9UIW0: Nucleus (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus4

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IEA--

    Find genes that share ontologies with VAX2           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Pathway & Disease-focused RT2 Profiler PCR Array including VAX2: 
              Homeobox (HOX) Genes in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for VAX2

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    Selected Interacting proteins for VAX2 (Q9UIW03 ENSP000002343924) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RFXANKO145933, ENSP000003050714I2D: score=1 STRING: ENSP00000305071
    SIX6O954753, ENSP000003285964I2D: score=1 STRING: ENSP00000328596
    PAX6P263673, ENSP000003684014I2D: score=1 STRING: ENSP00000368401
    GMEB2Q9UKD13I2D: score=1 
    GTF2A1P526553I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 12):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IEA--
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated ----
    GO:0007398ectoderm development TAS10485894
    GO:0007409axonogenesis IEA--

    Find genes that share ontologies with VAX2           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for VAX2



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for VAX2 gene: 
    NM_012476.2  

    Unigene Cluster for VAX2:

    Ventral anterior homeobox 2
    Hs.249170  [show with all ESTs]
    Unigene Representative Sequence: Y17791
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000234392(uc002shh.3)
    miRNA
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    SwitchGear 3'UTR luciferase reporter plasmidVAX2 3' UTR sequence
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    Additional mRNA sequence: 

    AB593145.1 BC006336.2 BT007035.1 Y17791.1 

    1 DOTS entry:

    DT.75152909 

    13 AceView cDNA sequences:

    BC006336 NM_012476 BM710832 Y17791 BG601065 BQ637322 H92142 BF685044 
    BT007035 BF037978 BQ957193 BF684283 H92143 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for VAX2    About this scheme

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


    ECgene alternative splicing isoforms for VAX2

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    VAX2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGCGATGGGG
    VAX2 Expression
    About this image

    VAX2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    VAX2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.249170
        Pathway & Disease-focused RT2 Profiler PCR Array including VAX2: 
              Homeobox (HOX) Genes in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for VAX2 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vax21 , 5 ventral anterior homeobox containing gene 25
    ventral anterior homeobox 21
    86.04(n)1
    88.24(a)1
      6 (35.94 cM)5
    241131  NM_011912.31  NP_036042.11 
     837112645 
    chicken
    (Gallus gallus)
    Aves VAX16
    Gallus gallus ventral anterior homeobox 1 (VAX1), ...
    58(a)
    1 → many
    6(28618436-28621764)
    lizard
    (Anolis carolinensis)
    Reptilia VAX26
    ventral anterior homeobox 2
    64(a)
    1 ↔ 1
    AAWZ02036934(4216-19660)
    African clawed frog
    (Xenopus laevis)
    Amphibia AF113517.12   -- 74.81(n)    AF113517.1 
    zebrafish
    (Danio rerio)
    Actinopterygii vax22 ventral anterior homeobox 2 74.21(n)   373869  AY183363.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG185996
    --
    12(a)
    1 → many
    3R(14093510-14096895)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for VAX2 gene
    NOTO2  EN12  EMX22  VAX12  EMX12  EN22  
    2 SIMAP similar genes for VAX2 using alignment to 2 protein entries:     VAX2_HUMAN (see all proteins):
    VAX1    POU6F1

    Find genes that share paralogs with VAX2           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for VAX2 (see all 785)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs775391621,2
    C,F--70862236(+) GGGGAG/ACTTGG 1 -- us2k11Minor allele frequency- A:0.07NA 120
    rs1449703081,2
    C--70862569(+) CCCCC-/CGCCCA 1 -- us2k10--------
    rs38419071,2
    C--70884260(-) TGTGT-/GTGT  
            
    CTGTG
    1 -- int10--------
    rs621450691,2
    C--70884263(+) AGACAC/GACACA 1 -- int10--------
    rs1833835071,2
    --70991833(+) CCCTCC/TTACAT 1 -- us2k10--------
    rs1875510061,2
    --70991903(+) GTCCAC/TGCTGC 1 -- us2k10--------
    rs1443663911,2
    --70991935(+) AAGCCC/TTGGGC 1 -- us2k10--------
    rs1487967181,2
    --70992118(+) CCTCCC/TGACCT 1 -- us2k10--------
    rs1157790691,2
    F--70992198(+) ATAATT/CGGTGT 1 -- us2k11Minor allele frequency- C:0.01WA 118
    rs1910972961,2
    --70992402(+) TCCACG/TCCAGC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for VAX2 (71127720 - 71160576 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for VAX2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv519862CNV Gain19592680

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing VAX2
    DNA2.0 Custom Variant and Variant Library Synthesis for VAX2

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 604295    OMIM disorders: --

    1 disease for VAX2:    
    About MalaCards
    corpus callosum agenesis

    2 diseases from the University of Copenhagen DISEASES database for VAX2:
    Coloboma     Cleft lip

    Find genes that share disorders with VAX2           About GenesLikeMe

    Genetic Association Database (GAD): VAX2
    Human Genome Epidemiology (HuGE) Navigator: VAX2 (4 documents)

    Export disorders for VAX2 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for VAX2 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with VAX2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A homeobox gene, vax2, controls the patterning of the eye dorsoventral axis. (PubMed id 10485894)1, 2, 3, 9 Barbieri A.M.... Banfi S. (Proc. Natl. Acad. Sci. U.S.A. 1999)
    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. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    3. Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations. (PubMed id 16953426)1, 4 Beaty T.H....Scott A.F. (Hum. Genet. 2006)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    5. Identification of a candidate gene for astigmatism. (PubMed id 23322567)1 Lopes M.C....Hammond C.J. (amp 2013)
    6. VAX1 mutation associated with microphthalmia, corpus callosum agenesis, and orofacial clefting: The first description of a VAX1 phenotype in humans. (PubMed id 22095910)2 Slavotinek A.M.... Schorderet D.F. (Hum. Mutat. 2012)
    7. Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. (PubMed id 21697133)1 Oshikawa M.... Kato S. (Invest. Ophthalmol. Vis. Sci. 2011)
    8. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)1 Talmud P.J.... . (Am. J. Hum. Genet. 2009)
    9. Classification and nomenclature of all human homeobox genes. (PubMed id 17963489)1 Holland P.W.H.... Bruford E.A. (BMC Biol. 2007)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 25806 HGNC: 12661 AceView: VAX2 Ensembl:ENSG00000116035 euGenes: HUgn25806
    ECgene: VAX2 H-InvDB: VAX2

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for VAX2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for VAX2 gene:
    Search GeneIP for patents involving VAX2

    GeneCards and IP:
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