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

VCX Gene

protein-coding   GIFtS: 45
GCID: GC0XP007770

Variable Charge, X-Linked

(Previous names: variable charge, X chromosome)
  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

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Variable Charge, X-Linked1 2     Variably Charged Protein X-B12 3
VCX10R2 3 5     VCX-10r2 3
VCXB12 3 5     VCX-B12 3
Variable Charge, X Chromosome1 2     VCX12 3
Variable Charge Protein On X With Ten Repeats2 3     Variable Charge X-Linked Protein 12

External Ids:    HGNC: 126671   Entrez Gene: 266092   Ensembl: ENSG000001825837   OMIM: 3002295   UniProtKB: Q9H3203   
ORGUL members:         
NONCODE14:n337625      

Export aliases for VCX gene to outside databases

Previous GC identifers: GC0XP006659 GC0XP007169 GC0XP007221 GC0XP007620 GC0XP005618


(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 VCX 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 10 repeats of the 30-bp unit. (provided by RefSeq, Jul 2008)

GeneCards Summary for VCX Gene: 
VCX (variable charge, X-linked) is a protein-coding gene, and is affiliated with the lncRNA class. Diseases associated with VCX include x-linked ichthyosis, and lung adenocarcinoma. GO annotations related to this gene include chromatin binding. An important paralog of this gene is VCX3B.

UniProtKB/Swiss-Prot: VCX1_HUMAN, Q9H320
Function: May mediate a process in spermatogenesis or may play a role in sex ratio distortion

Gene Wiki entry for VCX Gene


(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  NT_167197.1  NC_018934.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the VCX gene promoter:
         POU2F2 (Oct-2.1)   oct-B2   oct-B3   POU2F2   POU2F2C   POU2F1   POU2F1a   NF-Y   POU2F2B   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): VCX promoter sequence
   Search SABiosciences Chromatin IP Primers for VCX

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


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

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

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP007770:  view genomic region     (about GC identifiers)

Start:
7,810,303 bp from pter      End:
7,812,184 bp from pter
Size:
1,882 bases      Orientation:
plus 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: VCX1_HUMAN, Q9H320 (See protein sequence)
Recommended Name: Variable charge X-linked protein 1  
Size: 206 amino acids; 22289 Da
Secondary accessions: Q9P0H3

Explore the universe of human proteins at neXtProt for VCX: NX_Q9H320

Explore proteomics data for VCX at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9H320

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

    VCX Protein Expression
    REFSEQ proteins: NP_038480.2  
    ENSEMBL proteins: 
     ENSP00000370447   ENSP00000344144  

    Human Recombinant Protein Products for VCX: 
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    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA12862317
    GO:0005730nucleolus IDA12862317

    VCX 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 Q9H320

    ProtoNet protein and cluster: Q9H320

    UniProtKB/Swiss-Prot: VCX1_HUMAN, Q9H320
    Similarity: Belongs to the VCX/VCY family


    VCX 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: VCX1_HUMAN, Q9H320
    Function: May mediate a process in spermatogenesis or may play a role in sex ratio distortion

         Genatlas biochemistry entry for VCX:
    basic protein variable charge X/Y on chromosome X,testis specific,most likely present in germ cells,included in
    the CRI-S232 sequence flanking the STS gene

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003682chromatin binding TAS12862317
         
    VCX for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for VCX 
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    (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 VCX

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006325chromatin organization TAS12862317
    GO:0007283spermatogenesis TAS10607842
    GO:0042255ribosome assembly NAS12862317

    VCX 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 VCX (VCX1)

    Search CenterWatch for drugs/clinical trials and news about VCX / VCX1

    (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,
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    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 VCX gene: 
    NM_013452.2  

    Unigene Cluster for VCX:

    Variable charge, X-linked
    Hs.567503  [show with all ESTs]
    Unigene Representative Sequence: AF167081
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000381059(uc004crz.3) ENST00000341408
    miRNA
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    Additional mRNA sequence: 

    AF159129.1 AF167081.2 BC098123.1 BC126903.1 

    2 DOTS entries:

    DT.313846  DT.313845 

    11 AceView cDNA sequences:

    AF167081 AA565702 NM_013452 AF159129 AA206042 BE504628 BF885187 AU099954 
    BV184446 AI824821 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

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


    See VCX Protein Expression from SPIRE MOPED and PaxDB
    SOURCE GeneReport for Unigene cluster: Hs.567503

    UniProtKB/Swiss-Prot: VCX1_HUMAN, Q9H320
    Tissue specificity: Expressed exclusively in testis

        SABiosciences Custom PCR Arrays for VCX
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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VCX

    (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 VCX gene from 1 species (see representative species )    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chimpanzee
    (Pan troglodytes)
    Mammalia LOC7420756
    LOC7420756
    (see all 6)
    --
    89(a)
    89(a)
    (see all 6)
    many ↔ many
    many ↔ many
    (see all 6)
    Y(21572528-21573311)
    Y(21659699-21660482)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for VCX gene
    VCX3A1 2  VCX3B1 2  VCY2  VCX22  VCY1B2  ENSG000002680802  
    5 SIMAP similar genes for VCX using alignment to 4 protein entries:     VCX1_HUMAN (see all proteins):
    VCX3B    VCX3A    VCY    VCY1B    VCX2

    VCX 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

    10/165 SNPs in VCX are shown (see all 165)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs561429471,2
    C--7773188(+) TGGTG-/A/AA  
            
    AAAAA
    1 -- us2k11CSA 2
    rs1424546491,2
    C--7773188(+) TGGTG-/AAAAAAA 1 -- us2k10--------
    rs1854132591,2
    --7773299(+) GGGTGC/GTACAT 1 -- us2k10--------
    rs1446704171,2
    --7773454(+) TCCACA/GCCTTT 1 -- us2k10--------
    rs1909626341,2
    --7773611(+) TCTTTA/CGAGAA 1 -- us2k10--------
    rs348988621,2
    C--7773964(+) ATATT-/ACACACA 1 -- us2k10--------
    rs1835344591,2
    --7774066(+) CTGAGC/TGAGTG 1 -- us2k10--------
    rs1875138051,2
    --7774104(+) CAGTGC/TTTTAA 1 -- us2k10--------
    rs1916483471,2
    --7774310(+) CCAGGC/GTTGAG 1 -- us2k10--------
    rs1834854001,2
    --7774324(+) AATGGC/TGCTAT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for VCX (7810303 - 7812184 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for VCX:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2422194CNV Duplication17116639
    esv33658CNV Loss17666407
    dgv1n30CNV Gain18288195
    dgv499n21CNV Gain19592680

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 300229    OMIM disorders: --

    9 diseases for VCX:    About MalaCards
    x-linked ichthyosis    lung adenocarcinoma    intellectual disability    ocular albinism
    kallmann syndrome    albinism    ichthyosis    mental retardation
    adenocarcinoma

    3 diseases from the University of Copenhagen DISEASES database for VCX:
    X-linked ichthyosis     Kallmann syndrome     Ocular albinism

    VCX for disorders           About GeneDecksing

    Genetic Association Database (GAD): VCX

    Export disorders for VCX 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 VCX gene integrated from 9 sources:
    (articles sorted by number of sources associating them with VCX)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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, 3 Fukami M.... Rappold G.A. (2000)
    2. 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)
    3. A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT family. (PubMed id 17342728)1 Hansen M.A....Leffers H. (2008)
    4. Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness. (PubMed id 17903302)4 Levy D....Mitchell G.F. (2007)
    5. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (2007)
    6. Expression and localization of VCX/Y proteins and their possible involvement in regulation of ribosome assembly during spermatogenesis. (PubMed id 12862317)1 Zou S.W....Wang L.F. (2003)
    7. Genetic alterations of lung adenocarcinoma in relation to smoking and ethnicity. (PubMed id 12826317)1 Sy S.M....Yim A.P. (2003)
    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. Molecular cytogenetic analysis of a familial interstitial deletion Xp22.2-22.3 with a highly variable phenotype in female carriers. (PubMed id 16470742)9 Chocholska S....Kehrer-Sawatzki H. (2006)
    10. Deletion of VCX-A due to NAHR plays a major role in the occurrence of mental retardation in patients with X-linked ichthyosis. (PubMed id 15888481)9 Van Esch H....Froyen G. (2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    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: 26609 HGNC: 12667 AceView: VCX Ensembl:ENSG00000182583 euGenes: HUgn26609
    ECgene: VCX H-InvDB: VCX

    (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 VCX 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 VCX gene:
    Search GeneIP for patents involving VCX

    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)
    About This Section

     
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     Proteins for VCX
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

    View Random Gene

    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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