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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

VCX3A Gene

protein-coding   GIFtS: 42
GCID: GC0XM006461

Variable Charge, X-Linked 3A

(Previous names: variable charge, X-linked 3)
(Previous symbol: VCX3)
  See related diseases
at  

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

Aliases
Variable Charge, X-Linked 3A1 2     VCX-8r2 3
VCX31 2 3     VCX-A2 3
VCX8R2 3 5     Variable Charge, X-Linked 31
VCXA2 3 5     Variable Charge X-Linked Protein 32
Variable Charge Protein On X With Eight Repeats2 3     Variably Charged X-A2
Variably Charged Protein X-A2 3     

External Ids:    HGNC: 181591   Entrez Gene: 514812   Ensembl: ENSG000001690597   OMIM: 3005335   UniProtKB: Q9NNX93   

Export aliases for VCX3A gene to outside databases

Previous GC identifers: GC0XP007622 GC0XP007623


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for VCX3A Gene:
This gene belongs to the VCX/Y gene family, which has multiple members on both X and Y chromosomes, and all are
expressed exclusively in male germ cells. The X-linked members are clustered on chromosome Xp22 and Y-linked
members are two identical copies of the gene within a palindromic region on Yq11. The family members share a high
degree of sequence identity, with the exception that a 30-bp unit is tandemly repeated in X-linked members but
occurs only once in Y-linked members. The VCX gene cluster is polymorphic in terms of copy number; different
individuals may have a different number of VCX genes. VCX/Y genes encode small and highly charged proteins of
unknown function. The presence of a putative bipartite nuclear localization signal suggests that VCX/Y members
are nuclear proteins. This gene contains 8 repeats of the 30-bp unit. (provided by RefSeq, Jul 2008)

GeneCards Summary for VCX3A Gene: 
VCX3A (variable charge, X-linked 3A) is a protein-coding gene. Diseases associated with VCX3A include x-linked ichthyosis, and ocular albinism. An important paralog of this gene is VCX3B.

UniProtKB/Swiss-Prot: VCX3_HUMAN, Q9NNX9
Function: May mediate a process in spermatogenesis or may play a role in sex ratio distortion




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.2  NT_167197.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the VCX3A gene promoter:
         POU2F2 (Oct-2.1)   POU2F2   POU2F2C   POU2F1   POU2F1a   FOXO1a   NF-Y   POU2F2B   CBF(2)   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidVCX3A promoter sequence
   Search SABiosciences Chromatin IP Primers for VCX3A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VCX3A


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

Entrez Gene cytogenetic band: Xp22   Ensembl cytogenetic band:  Xp22.31   HGNC cytogenetic band: Xp22.31

VCX3A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VCX3A gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM006461:  view genomic region     (about GC identifiers)

Start:
6,451,659 bp from pter      End:
6,453,159 bp from pter
Size:
1,501 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: VCX3_HUMAN, Q9NNX9 (See protein sequence)
Recommended Name: Variable charge X-linked protein 3  
Size: 186 amino acids; 20020 Da
Secondary accessions: Q9P0H4

Explore the universe of human proteins at neXtProt for VCX3A: NX_Q9NNX9

Explore proteomics data for VCX3A at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9NNX9

  • VCX3A Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    VCX3A Protein Expression
    REFSEQ proteins: NP_057463.2  
    ENSEMBL proteins: 
     ENSP00000370479   ENSP00000381713  

    Human Recombinant Protein Products for VCX3A: 
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    Cloud-Clone Corp. Proteins for VCX3A 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ISS--
    GO:0005730nucleolus ISS--

    VCX3A for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR026653 VCX/VCY1

    Graphical View of Domain Structure for InterPro Entry Q9NNX9

    ProtoNet protein and cluster: Q9NNX9

    UniProtKB/Swiss-Prot: VCX3_HUMAN, Q9NNX9
    Similarity: Belongs to the VCX/VCY family


    VCX3A for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: VCX3_HUMAN, Q9NNX9
    Function: May mediate a process in spermatogenesis or may play a role in sex ratio distortion

    Animal Models:

       inGenious Targeting Laboratory - Custom generated mouse model solutions for VCX3A 
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for VCX3A 
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    miRNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VCX3A


    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for VCX3A

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007420brain development IMP10903929

    VCX3A for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for VCX3A (VCX3)

    Search CenterWatch for drugs/clinical trials and news about VCX3A / VCX3

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for VCX3A gene: 
    NM_016379.3  

    Unigene Clusters for VCX3A:

    Variable charge, X-linked 3A
    Hs.170076  [show with all ESTs], Hs.278906  [show with all ESTs]
    Unigene Representative Sequences: BU595028, AF167078
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000381089(uc022bsg.1 uc004crs.3 uc010ndk.2) ENST00000398729

    miRNA
    Products:
         
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    Search QIAGEN for miScript miRNA Assays for microRNAs that regulate VCX3A
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for VCX3A
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat VCX3A
    Clone
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    OriGene clones in human, mouse for VCX3A (see all 5)
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    GenScript: all cDNA clones in your preferred vector: VCX3A (NM_016379)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for VCX3A
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VCX3A
    Sirion Biotech Customized lentivirus for stable overexpression of VCX3A 
                         Customized lentivirus expression plasmids for stable overexpression of VCX3A 
    Primer
    Products:
        
    OriGene qSTAR qPCR primer pairs in human, mouse for VCX3A
    SABiosciences RT2 qPCR Primer Assay in human, mouse / rat VCX3A
      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat VCX3A
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat VCX3A

    Additional mRNA sequence: 

    AF159128.1 AF167078.1 BC039722.1 BC098149.1 BC126902.1 

    5 DOTS entries:

    DT.120654203  DT.443460  DT.91679712  DT.121292751  DT.313846 

    10 AceView cDNA sequences:

    BQ212742 BV206645 AF167078 NM_016379 BC039722 CB160710 BV184444 AF159128 
    AA994122 AA897187 

    GeneLoc Exon Structure


    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    VCX3A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGGGATTTT
    VCX3A Expression
    About this image


    See VCX3A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for VCX3A

    SOURCE GeneReport for Unigene clusters: Hs.170076 Hs.278906

    UniProtKB/Swiss-Prot: VCX3_HUMAN, Q9NNX9
    Tissue specificity: Expressed exclusively in testis

        SABiosciences Custom PCR Arrays for VCX3A
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat VCX3A
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VCX3A

    (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)
    About This Section

    This gene was present in the common ancestor of human and chimp.

    Orthologs for VCX3A gene from 1 species (see representative species )    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chimpanzee
    (Pan troglodytes)
    Mammalia --
    LOC7404306
    (see all 6)
    --
    88(a)
    87(a)
    (see all 6)
    many ↔ many
    many ↔ many
    (see all 6)
    X(6358884-6359577)
    X(8312913-8313606)


    ENSEMBL Gene Tree for VCX3A (if available)
    TreeFam Gene Tree for VCX3A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for VCX3A gene
    VCX1 2  VCX3B1 2  VCY2  VCX22  VCY1B2  ENSG000002680802  
    5 SIMAP similar genes for VCX3A using alignment to 5 protein entries:     VCX3_HUMAN (see all proteins):
    VCX    VCX3B    VCY    VCX2    VCY1B

    VCX3A for paralogs           About GeneDecksing



    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/163 SNPs in VCX3A are shown (see all 163)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1871683021,2
    --6451368(+) CCTCCC/TCACAC 1 -- ds50010--------
    rs1912726031,2
    --6451610(+) CTTCCC/TCCCTC 1 -- ds50010--------
    rs2000710141,2
    C--6451752(+) TTAGTC/TGCTGC 1 -- ut310--------
    rs1836323281,2
    --6451762(+) CTCTCA/GGAGAT 1 -- ut310--------
    rs774135901,2
    C--6451777(+) GAGTAC/GCTGGC 1 -- ut311Minor allele frequency- G:0.00NA 2
    rs10582441,2
    C--6451778(-) GGCCAA/G/TCTACT 2 -- ut312MN NA 186
    rs1493650611,2
    C,F--6451784(+) TGGCCG/ATCTAC 1 -- ut311Minor allele frequency- A:0.01NA 4502
    rs743939381,2
    C--6451791(+) CTACAC/TACTCG 2 M V mis10--------
    rs59895111,2
    C,H--6451799(-) AGAACC/TACCGA 2 P L mis1 ese30--------
    rs1487486801,2
    F--6451804(+) AGTTCT/CTCCAT 2 /E syn11Minor allele frequency- C:0.00NA 4544

    HapMap Linkage Disequilibrium report for VCX3A (6451659 - 6453159 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for VCX3A:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2422345CNV Duplication17116639
    esv2422493CNV Duplication17116639
    nsv199CNV Insertion15895083
    nsv6783CNV Insertion18451855
    nsv508751CNV Insertion20534489
    dgv265e55CNV Gain17911159
    dgv2434e1CNV Complex17122850
    nsv511080CNV Complex20534489

    SABiosciences Cancer Mutation PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing VCX3A
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 300533    OMIM disorders: --

    8 diseases for VCX3A:    About MalaCards
    x-linked ichthyosis    ocular albinism    intellectual disability    ichthyosis
    kallmann syndrome    albinism    mental retardation, x-linked    mental retardation

    2 diseases from the University of Copenhagen DISEASES database for VCX3A:
    X-linked ichthyosis     Kallmann syndrome

    VCX3A for disorders           About GeneDecksing

    2 Novoseek inferred disease relationships for VCX3A gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    ichthyosis x-linked 91 4 15888481 (1), 18076704 (1)
    mental retardation 69.4 9 10903929 (2), 15888481 (2), 16470742 (1), 18076704 (1)


    Export disorders for VCX3A 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)
    About This Section

    PubMed articles for VCX3A gene, integrated from 9 sources (see all 15):
    (articles sorted by number of sources associating them with VCX3A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins. (PubMed id 10607842)1, 2, 3 Lahn B.T. and Page D.C. (2000)
    2. A member of a gene family on Xp22.3, VCX-A, is deleted in patients with X-linked nonspecific mental retardation. (PubMed id 10903929)1, 2, 9 Fukami M.... Rappold G.A. (2000)
    3. Analysis of the VCX3A, VCX2 and VCX3B genes shows that VCX3A gene deletion is not sufficient to result in mental retardation in X-linked ichthyosis. (PubMed id 18076704)1, 9 Cuevas-Covarrubias S.A. and Gonzalez-Huerta L.M. (2008)
    4. Modulation of neuritogenesis by a protein implicated in X-linked mental retardation. (PubMed id 19812318)1 Jiao X....Kiledjian M. (2009)
    5. The LIFEdb database in 2006. (PubMed id 16381901)1 Mehrle A....Wiemann S. (2006)
    6. Identification of an mRNA-decapping regulator implicated in X-linked mental retardation. (PubMed id 17157254)1 Jiao X....Kiledjian M. (2006)
    7. From ORFeome to biology: a functional genomics pipeline. (PubMed id 15489336)1 Wiemann S....Poustka A. (2004)
    8. 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. (2002)
    9. DNA cloning using in vitro site-specific recombination. (PubMed id 11076863)1 Hartley J.L....Brasch M.A. (2000)
    10. Characterization of a low copy repetitive element S232 involved in the generation of frequent deletions of the distal short arm of the human X chromosome. (PubMed id 1549475)1 Li X.M....Shapiro L.J. (1992)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 51481 HGNC: 18159 AceView: VCX3 Ensembl:ENSG00000169059 euGenes: HUgn51481
    ECgene: VCX3A H-InvDB: VCX3A

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for VCX3A Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for VCX3A gene:
    Search GeneIP for patents involving VCX3A

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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     inGenious Targeting Laboratory - Custom generated mouse model solutions for VCX3A
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    (GIFtS: 73)
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