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VCAN Gene

protein-coding   GIFtS: 66
GCID: GC05P082804

Versican

(Previous name: chondroitin sulfate proteoglycan 2)
(Previous symbol: CSPG2)
  See VCAN-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)
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Aliases
versican1 2     GHAP2 3
CSPG21 2 3 5     PG-M2 3
Chondroitin Sulfate Proteoglycan 21 2 3     ERVR2 5
Versican Proteoglycan1 2     WGN2 5
Chondroitin Sulfate Proteoglycan Core Protein 22 3     WGN12 5
Glial Hyaluronate-Binding Protein2 3     Versican Core Protein2
Large Fibroblast Proteoglycan2 3     

External Ids:    HGNC: 24641   Entrez Gene: 14622   Ensembl: ENSG000000384277   OMIM: 1186615   UniProtKB: P136113   

Export aliases for VCAN gene to outside databases

Previous GC identifer: GC05P077975


(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 VCAN Gene:
This gene is a member of the aggrecan/versican proteoglycan family. The protein encoded is a large chondroitin
sulfate proteoglycan and is a major component of the extracellular matrix. This protein is involved in cell
adhesion, proliferation, proliferation, migration and angiogenesis and plays a central role in tissue
morphogenesis and maintenance. Mutations in this gene are the cause of Wagner syndrome type 1. Multiple
transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Aug 2009)

GeneCards Summary for VCAN Gene:
VCAN (versican) is a protein-coding gene. Diseases associated with VCAN include wagner syndrome, and vcan-related vitreoretinopathy. GO annotations related to this gene include hyaluronic acid binding and calcium ion binding. An important paralog of this gene is HAPLN3.

UniProtKB/Swiss-Prot: CSPG2_HUMAN, P13611
Function: May play a role in intercellular signaling and in connecting cells with the extracellular matrix. May
take part in the regulation of cell motility, growth and differentiation. Binds hyaluronic acid

Gene Wiki entry for VCAN (Versican) 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000005.9  NC_018916.2  NT_034772.7  
Regulatory elements:
   Regulatory transcription factor binding sites in the VCAN gene promoter:
         Egr-3   AML1a   GCNF   MyoD   HNF-3beta   GATA-1   E47   GCNF-1   IRF-7A   GCNF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidVCAN promoter sequence
   Search Chromatin IP Primers for VCAN

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


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

Entrez Gene cytogenetic band: 5q14.3   Ensembl cytogenetic band:  5q14.2   HGNC cytogenetic band: 5q14.2-q14.3

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

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P082804:  view genomic region     (about GC identifiers)

Start:
82,767,284 bp from pter      End:
82,878,122 bp from pter
Size:
110,839 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: CSPG2_HUMAN, P13611 (See protein sequence)
Recommended Name: Versican core protein precursor  
Size: 3396 amino acids; 372820 Da
Subunit: Interacts with FBLN1 (By similarity)
Developmental stage: Disappears after the cartilage development
Secondary accessions: P20754 Q13010 Q13189 Q15123 Q9UCL9 Q9UNW5
Alternative splicing: 5 isoforms:  P13611-1   P13611-2   P13611-3   P13611-4   P13611-5   

Explore the universe of human proteins at neXtProt for VCAN: NX_P13611

Explore proteomics data for VCAN at MOPED

Post-translational modifications: 

  • Phosphorylation sites are present in the extracellular medium1
  • Glycosylation2 at Asn57, Asn330, Ser510, Thr516, Thr518, Thr522, Asn615, Thr627, Thr632, Ser641,
                                 Thr642, Thr643, Thr687, Thr689, Thr716, Thr751, Thr754, Asn782, Thr792, Thr799 (see all 133)
  • Modification sites at PhosphoSitePlus

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

    REFSEQ proteins (4 alternative transcripts): 
    NP_001119808.1  NP_001157569.1  NP_001157570.1  NP_004376.2  

    ENSEMBL proteins: 
     ENSP00000265077   ENSP00000425959   ENSP00000426251   ENSP00000426715   ENSP00000421362  
     ENSP00000340062   ENSP00000342768  
    Reactome Protein details: P13611

    VCAN Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Browse OriGene full length recombinant human proteins expressed in human HEK293 cells
    Browse OriGene Protein Over-expression Lysates
    OriGene Custom MassSpec
    OriGene Custom Protein Services for VCAN
    GenScript Custom Purified and Recombinant Proteins Services for VCAN
    Novus Biologicals VCAN Proteins
    Novus Biologicals VCAN Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for VCAN 

     
    antibodies-online proteins for VCAN (4 products) 

     
    Search antibodies-online for peptides for VCAN

    VCAN Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of VCAN
    R&D Systems Antibodies for VCAN (Versican)
    OriGene Antibodies for VCAN
    OriGene Custom Antibody Services for VCAN
    Novus Biologicals VCAN Antibodies
    Abcam antibodies for VCAN
    Browse Antibodies at Cloud-Clone Corp.
    ThermoFisher Antibody for VCAN
    antibodies-online antibodies for VCAN (74 products) 

    VCAN Assay Products:

    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for VCAN
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for VCAN
    Browse Enzo Life Sciences for kits & assays
    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.
    Search eBioscience for ELISAs for VCAN 
    antibodies-online kits for VCAN (28 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    VSET: Immunoglobulin superfamily / V-set domain containing
    HYALECTAN: Proteoglycans / Extracellular Matrix : Hyalectans

    Selected InterPro protein domains (see all 15):
     IPR000742 EG-like_dom
     IPR000436 Sushi_SCR_CCP
     IPR000152 EGF-type_Asp/Asn_hydroxyl_site
     IPR018097 EGF_Ca-bd_CS
     IPR013783 Ig-like_fold

    Graphical View of Domain Structure for InterPro Entry P13611

    ProtoNet protein and cluster: P13611

    Selected Blocks protein domains (see all 8):
    IPB000152 Aspartic acid and asparagine hydroxylation site
    IPB000436 Sushi domain/SCR domain/CCP module
    IPB000538 Link domain
    IPB001438 Type II EGF-like signature
    IPB001881 EGF-like calcium-binding


    UniProtKB/Swiss-Prot: CSPG2_HUMAN, P13611
    Similarity: Belongs to the aggrecan/versican proteoglycan family
    Similarity: Contains 1 C-type lectin domain
    Similarity: Contains 2 EGF-like domains
    Similarity: Contains 1 Ig-like V-type (immunoglobulin-like) domain
    Similarity: Contains 2 Link domains
    Similarity: Contains 1 Sushi (CCP/SCR) domain


    Find genes that share domains with VCAN           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: CSPG2_HUMAN, P13611
    Function: May play a role in intercellular signaling and in connecting cells with the extracellular matrix. May
    take part in the regulation of cell motility, growth and differentiation. Binds hyaluronic acid

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
    GO:0005515protein binding IPI--
    GO:0005539glycosaminoglycan binding TAS7528742
    GO:0005540hyaluronic acid binding IEA--
    GO:0030246carbohydrate binding IEA--
         
    Find genes that share ontologies with VCAN           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for VCAN:
     Decreased number of cells in m 

         4 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Vcan):
     limbs/digits/tail  nervous system  normal  skeleton 

    Find genes that share phenotypes with VCAN           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Vcantm1.1Dzim for VCAN

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

    miRNA
    Products:
        
    Block miRNA regulation of human, mouse, rat VCAN using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate VCAN (see all 40):
    hsa-miR-579 hsa-miR-3164 hsa-miR-200a hsa-miR-485-3p hsa-miR-141 hsa-miR-9 hsa-miR-1184 hsa-miR-124
    SwitchGear 3'UTR luciferase reporter plasmidVCAN 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for VCAN
    Predesigned siRNA for gene silencing in human, mouse, rat VCAN

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for VCAN

    Clone
    Products:
         
    OriGene clones in human, mouse for VCAN (see all 23)
    OriGene ORF clones in mouse, rat for VCAN
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 4): VCAN (NM_004385)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for VCAN
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VCAN

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for VCAN
    ESI BIO PureStem Progenitors for VCAN: 
    PureStem 4D20.8, NCr-fac Progenitor, PureStem E15, Meso-prx/latp Progenitor,
    PureStem SK11, NCr-fac & Meso-prx Progenitor
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VCAN


    (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
    CSPG2_HUMAN, P13611: Secreted, extracellular space, extracellular matrix
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    golgi apparatus4
    lysosome4
    vacuole4
    cytoskeleton2
    cytosol1
    mitochondrion1
    nucleus1
    plasma membrane1

    Gene Ontology (GO): Selected cellular component terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005578proteinaceous extracellular matrix IEA--
    GO:0005615extracellular space IDA--
    GO:0005796Golgi lumen TAS--
    GO:0031012colocalizes with extracellular matrix ISS--

    Find genes that share ontologies with VCAN           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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    SuperPaths for VCAN About   (see all 13)  
    See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1MPS VI - Maroteaux-Lamy syndrome
    MPS VI - Maroteaux-Lamy syndrome0.45
    MPS IIIB - Sanfilippo syndrome B0.45
    MPS IIIC - Sanfilippo syndrome C0.45
    MPS II - Hunter syndrome0.45
    MPS IV - Morquio syndrome A0.45
    Glycosaminoglycan metabolism0.45
    Mucopolysaccharidoses0.45
    MPS IV - Morquio syndrome B0.45
    2Chondroitin sulfate/dermatan sulfate metabolism
    Chondroitin sulfate/dermatan sulfate metabolism0.51
    CS/DS degradation0.00
    A tetrasaccharide linker sequence is required for GAG synthesis0.51
    Dermatan sulfate biosynthesis0.00
    Chondroitin sulfate biosynthesis0.41
    3Heparan sulfate/heparin (HS-GAG) metabolism
    Heparan sulfate/heparin (HS-GAG) metabolism0.57
    4Metabolism
    Metabolism0.38
    5Degradation of the extracellular matrix
    Extracellular matrix organization0.34


    Find genes that share SuperPaths with VCAN           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for VCAN (see all 13)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway

    2 GeneGo (Thomson Reuters) Pathways for VCAN
        Cell adhesion Cell-matrix glycoconjugates
    Cell adhesion ECM remodeling

    3 BioSystems Pathways for VCAN
        Spinal Cord Injury
    Direct p53 effectors
    Regulation of Wnt-mediated beta catenin signaling and target gene transcription

    5 Reactome Pathways for VCAN
        Dermatan sulfate biosynthesis
    ECM proteoglycans
    CS/DS degradation
    A tetrasaccharide linker sequence is required for GAG synthesis
    Chondroitin sulfate biosynthesis


    1 Kegg Pathway  (Kegg details for VCAN):
        Cell adhesion molecules (CAMs)

        Pathway & Disease-focused RT2 Profiler PCR Arrays including VCAN: 
              Extracellular Matrix & Adhesion Molecules in human mouse rat
              Epithelial to Mesenchymal Transition (EMT) in human mouse rat
              Cardiotoxicity in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for VCAN

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for VCAN (P136111, 2, 3 ENSP000002650774) via UniProtKB, MINT, STRING, and/or I2D (see all 74)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MMP9P147801, 2EBI-8515977,EBI-1382326 MINT-8427495 MINT-8427508 MINT-8427443
    CCL2P135003, ENSP000002258314I2D: score=4 STRING: ENSP00000225831
    CXCL12P480613, ENSP000003635484I2D: score=2 STRING: ENSP00000363548
    HAPLN1P109153, ENSP000002743414I2D: score=2 STRING: ENSP00000274341
    PF4P027763, ENSP000002960294I2D: score=2 STRING: ENSP00000296029
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005975carbohydrate metabolic process TAS--
    GO:0007155cell adhesion IEA--
    GO:0007275multicellular organismal development TAS2583089
    GO:0007507heart development IEA--
    GO:0008037cell recognition TAS2583089

    Find genes that share ontologies with VCAN           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 VCAN (CSPG2)

    1 HMDB Compound for VCAN    About this table
    CompoundSynonyms CAS #PubMed Ids
    Hyaluronic acidhyaluronic acid 9004-61-9--

    Selected Novoseek inferred chemical compound relationships for VCAN gene (see all 22)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    neurocan 80 10 11038354 (2), 20420122 (2), 10400671 (2), 15590670 (1) (see all 7)
    dermatan sulfate 74.6 14 12530013 (1), 12844226 (1), 18442658 (1), 19479939 (1) (see all 12)
    glycosaminoglycan 74.4 13 8970376 (1), 7921538 (1), 16636652 (1), 11918305 (1) (see all 9)
    chondroitin sulfate 73.2 36 10950950 (5), 12530013 (2), 7822336 (2), 16730906 (2) (see all 15)
    keratan sulfate 67 6 10399179 (2), 11918305 (1), 16151708 (1), 11980843 (1)
    chondroitin 65.7 6 10950950 (1), 19479939 (1), 9474087 (1), 11474365 (1) (see all 6)
    dermatan 64 1 11474365 (1)
    hyaluronic acid 55.4 19 1720020 (4), 10399179 (3), 7921538 (1), 12844226 (1) (see all 8)
    iduronic acid 54 2 12530013 (1), 16118286 (1)
    tgf beta1 36.1 6 15599946 (3), 15302416 (2), 15336555 (1)



    Find genes that share compounds with VCAN           About GenesLikeMe



    (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 VCAN gene (4 alternative transcripts): 
    NM_001126336.2  NM_001164097.1  NM_001164098.1  NM_004385.4  

    Unigene Cluster for VCAN:

    Versican
    Hs.643801  [show with all ESTs]
    Unigene Representative Sequence: NM_004385
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000265077(uc003kii.3) ENST00000503923 ENST00000512590 ENST00000513960
    ENST00000513984(uc003kih.4) ENST00000502527 ENST00000515397 ENST00000513016(uc003kil.3)
    ENST00000507162 ENST00000505615 ENST00000343200(uc003kij.3) ENST00000342785(uc010jau.2 uc003kik.3)

    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat VCAN using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate VCAN (see all 40):
    hsa-miR-579 hsa-miR-3164 hsa-miR-200a hsa-miR-485-3p hsa-miR-141 hsa-miR-9 hsa-miR-1184 hsa-miR-124
    SwitchGear 3'UTR luciferase reporter plasmidVCAN 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for VCAN
    Predesigned siRNA for gene silencing in human, mouse, rat VCAN
    Clone
    Products:
         
    OriGene clones in human, mouse for VCAN (see all 23)
    OriGene ORF clones in mouse, rat for VCAN
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 4): VCAN (NM_004385)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for VCAN
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VCAN
    Primer
    Products:
        
    OriGene qSTAR qPCR primer pairs in human, mouse for VCAN
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat VCAN
      QuantiTect SYBR Green Assays in human, mouse, rat VCAN
      QuantiFast Probe-based Assays in human, mouse, rat VCAN

    Additional mRNA sequence: 

    AB209491.1 AF084545.1 AK296285.1 AK299770.1 AK307642.1 BC050524.1 BX641036.1 D32039.1 
    J02814.1 U16306.1 U26555.1 X15998.1 

    17 DOTS entries:

    DT.92004195  DT.97816723  DT.102833978  DT.449140  DT.92450898  DT.97772672  DT.100827290  DT.100827289 
    DT.120890777  DT.95080321  DT.95309059  DT.100827284  DT.100827292  DT.100827297  DT.120890730  DT.120890748 
    DT.100728649 

    Selected AceView cDNA sequences (see all 485):

    AA554374 AU137695 AI367672 AI701083 AU117861 AA665903 AW474973 AA669728 
    AW074103 CA414846 AW612845 AU120576 AI920899 AI174666 AI677801 W42959 
    CA447917 BU753353 AI193987 AI659750 AW128957 BX493025 W79765 W76054 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for VCAN (see all 9)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^
    SP1:                                                  -                 -     -     -     -     -     -                                                         
    SP2:                                                  -     -     -     -     -     -     -     -     -                                                         
    SP3:                                                                                            -     -                                                         
    SP4:                                                                                            -     -                       -                                 
    SP5:                                                                                                                                                            

    ExUns: 18a · 18b ^ 19a · 19b · 19c · 19d
    SP1:  -                                 
    SP2:  -                                 
    SP3:  -                                 
    SP4:                                    
    SP5:                                    


    ECgene alternative splicing isoforms for VCAN

    (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)
    About This Section

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


    VCAN expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 27) fully expand
     
     Heart (Cardiovascular System)    fully expand to see all 4 entries
             Atrioventricular Valve Cells Atrioventricular Valves
     
     Cartilage (Muscoskeletal System)    fully expand to see all 4 entries
             Intervertebral Disc Annulus Fibrosus Cells Annulus Fibrosus
             Chondrocytes (Carticel®)
             Chondrocytes
     
     Paraxial Mesoderm (Gastrulation Derivatives)    fully expand to see all 2 entries
             PureStem SK11, NCr-fac & Meso-prx Progenitor
     
     Bone (Muscoskeletal System)    fully expand to see all 4 entries
             Mesenchymal Condensate Cells Zeugopod
             Zeugopod Epiphyseal End
             HyStem+BMP4-induced MEL2 cells
     
     Dermis (Integumentary System)    fully expand to see all 6 entries
             Zigzag Dermal Papilla Cells Dermal Papilla
    VCAN Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    VCAN Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.643801

    UniProtKB/Swiss-Prot: CSPG2_HUMAN, P13611
    Tissue specificity: Cerebral white matter and plasma. Isoform V0 and isoform V1 are expressed in normal brain,
    gliomas, medulloblastomas, schwannomas, neurofibromas, and meningiomas. Isoform V2 is restricted to normal brain
    and gliomas. Isoform V3 is found in all these tissues except medulloblastomas

        Pathway & Disease-focused RT2 Profiler PCR Arrays including VCAN: 
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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 VCAN gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vcan1 , 5 versican1, 5 76.67(n)1
    64.38(a)1
      13 (45.50 cM)5
    130031  NM_001081249.11  NP_001074718.11 
     896553125 
    chicken
    (Gallus gallus)
    Aves VCAN6
    Gallus gallus versican (VCAN), mRNA.
    28(a)
    1 ↔ 1
    Z(62474981-62580840)
    lizard
    (Anolis carolinensis)
    Reptilia VCAN6
    versican
    33(a)
    1 ↔ 1
    2(18585597-18724394)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.247762 Xenopus laevis transcribed sequence with moderate similarity more 79.6(n)    CA988094.1 
    zebrafish
    (Danio rerio)
    Actinopterygii 570519802   -- 72.32(n)   322700  57051980 
    worm
    (Caenorhabditis elegans)
    Secernentea clec-1496
    Protein CLEC-149 (clec-149) mRNA, complete cds
    25(a)
    1 → many
    III(823222-826412) WBGene00019328


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for VCAN gene
    HAPLN32  BCAN2  CLEC19A2  NCAN2  HAPLN12  HAPLN42  ACAN2  HAPLN22  
    18 SIMAP similar genes for VCAN using alignment to 4 protein entries:     CSPG2_HUMAN (see all proteins):
    DKFZp686K06110    DKFZp761L191    BCAN    ACAN    NOTCH3    PROS1
    CLEC4E    F9    HAPLN1    HAPLN3    CSPG3 variant protein    HAPLN2
    CLEC1B    REG1A    CLEC4C    CLEC4D    SNED1    HAPLN4

    Find genes that share paralogs with VCAN           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)
    About This Section

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    Selected SNPs for VCAN (see all 2562)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs803565561,2
    Cpathogenic183125230(+) TTTTTA/C/TTCAGG 4 -- int10--------
    rs599489951,2
    Cuntested183129287(+) TAGACA/GTTTTA 6 I V mis1 int10--------
    rs1441775641,2
    C--78010633(+) ATATC-/AT    
       T
    /TAT
    ATCAG
    8 -- cds10--------
    rs1414391711,2
    C--78028647(+) CTGCG-/TACCTAC
    CTACCTACC
    TACCT
    4 -- int10--------
    rs716058571,2
    C--78033085(+) AAGAT-/AC/ACA
    CACACACAC
    ACACA
    8 -- int1 cds11NA 2
    rs721004041,2
    C--78033086(+) AAGAT-/ACAC  
      ACACAC
    ACACA
    4 -- int10--------
    rs23082291,2
    C,F--78038284(-) ATCTT-/CTTATTGA 8 -- int1 cds14Minor allele frequency- CTT:0.34EU NA EA 342
    rs1384692731,2
    C--78038284(+) TCAAT-/AAGAAGAT 4 -- int10--------
    rs2017395431,2
    C--78038286(+) AATAAG/TAAGAT 4 -- int10--------
    rs2011697641,2
    C--78038288(+) TAAGAA/TGATCA 4 -- int10--------

    HapMap Linkage Disequilibrium report for VCAN (82767284 - 82878122 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for VCAN:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv4903CNV Insertion18451855
    nsv462227CNV Loss19166990
    esv7817CNV Gain19470904
    nsv830366CNV Gain17160897
    nsv830367CNV Gain+Loss17160897

    Human Gene Mutation Database (HGMD): VCAN
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing VCAN
    DNA2.0 Custom Variant and Variant Library Synthesis for VCAN

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

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    OMIM gene information: 118661   
    OMIM disorders: 143200  
    UniProtKB/Swiss-Prot: CSPG2_HUMAN, P13611
  • Wagner vitreoretinopathy (WGVRP) [MIM:143200]: A rare vitreoretinopathy characterized by an optically
    empty vitreous cavity with fibrillary condensations and a preretinal avascular membrane. Other optical features
    include progressive chorioretinal atrophy, perivascular sheating, subcapsular cataract and myopia. Note=The
    disease is caused by mutations affecting the gene represented in this entry. The pathological mechanism involves
    a quantitave imbalance of the normally occurring splice variants (PubMed:22739342)

  • 3 diseases for VCAN:    
    About MalaCards
    wagner syndrome    vcan-related vitreoretinopathy    odontogenic myxoma


    Find genes that share disorders with VCAN           About GenesLikeMe

    Selected Novoseek inferred disease relationships for VCAN gene (see all 22)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    solar elastosis 55.3 2 7783424 (1), 10504457 (1)
    vascular stenosis 46.8 1 16493581 (1)
    aggressiveness 24.5 4 18383852 (1), 12534600 (1), 19269971 (1), 16730906 (1)
    atherosclerosis 19.5 3 16845893 (1), 10397680 (1), 15539621 (1)
    tumors 17.2 30 19160015 (3), 19608024 (3), 20420122 (2), 15073129 (2) (see all 19)
    metastasis 14.2 18 19608024 (4), 17065588 (2), 17446061 (2), 17163843 (1) (see all 9)
    medulloblastoma 12.1 1 8627343 (1)
    melanoma 9.94 18 19269971 (6), 15645431 (3), 12972299 (2), 16847433 (2) (see all 6)
    cancer 8.55 23 19160015 (5), 19608024 (3), 16730906 (2), 12530013 (1) (see all 12)
    inflammation 3.51 5 19608024 (2), 15694131 (1), 2222452 (1), 9493652 (1)

    GeneTests: VCAN
    GeneReviews: VCAN
    Genetic Association Database (GAD): VCAN
    Human Genome Epidemiology (HuGE) Navigator: VCAN (11 documents)

    Export disorders for VCAN 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 VCAN gene, integrated from 10 sources (see all 276):
    (articles sorted by number of sources associating them with VCAN)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mapping of the versican proteoglycan gene (CSPG2) to the long arm of human chromosome 5 (5q12-5q14). (PubMed id 1478664)1, 2, 3, 9 Iozzo R.V.... McPherson J.D. (Genomics 1992)
    2. Isolation of a large aggregating proteoglycan from human brain. (PubMed id 1429726)1, 2, 9 Perides G.... Bignami A. (J. Biol. Chem. 1992)
    3. Versican/PG-M isoforms in vascular smooth muscle cells. (PubMed id 10397680)1, 2, 9 Lemire J.M....Wight T.N. (Arterioscler. Thromb. Vasc. Biol. 1999)
    4. Identification of the proteoglycan versican in aorta and smooth muscle cells by DNA sequence analysis, in situ hybridization and immunohistochemistry. (PubMed id 7921538)1, 2, 9 Yao L.Y.... Sandell L.J. (Matrix Biol. 1994)
    5. Identification of a novel splice site mutation of the CSPG2 gene in a Japanese family with Wagner syndrome. (PubMed id 16043844)1, 2, 9 Miyamoto T.... Itakura M. (Invest. Ophthalmol. Vis. Sci. 2005)
    6. Differential expression of versican isoforms in brain tumors. (PubMed id 8627343)1, 2, 9 Paulus W.... Zimmermann D.R. (J. Neuropathol. Exp. Neurol. 1996)
    7. Characterization of the complete genomic structure of the human versican gene and functional analysis of its promoter. (PubMed id 7528742)1, 2, 9 Naso M.F.... Iozzo R.V. (J. Biol. Chem. 1994)
    8. Chondroitin sulfate proteoglycan 2 (CSPG2) gene polymorphisms rs173686 and rs251124 are not associated with intracranial aneurysms in Chinese Han nationality. (PubMed id 18484070)1, 4, 9 Sun H....Zhao J. (Ups. J. Med. Sci. 2007)
    9. Novel VCAN mutations and evidence for unbalanced alternative splicing in the pathogenesis of Wagner syndrome. (PubMed id 22739342)1, 2 Kloeckener-Gruissem B.... Berger W. (Eur. J. Hum. Genet. 2013)
    10. Molecular evidence for differences in endometrium in severe versus mild endometriosis. (PubMed id 21063030)1, 3 Aghajanova L. and Giudice L.C. (Reprod Sci 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 1462 HGNC: 2464 AceView: CSPG2 Ensembl:ENSG00000038427 euGenes: HUgn1462
    ECgene: VCAN Kegg: 1462 H-InvDB: VCAN

    (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)
    About This Section

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    NameDescription
    PharmGKB entry for VCAN Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for VCAN Genetics and Cytogenetics in Oncology and Haematology
    Functional Glycomics Gateway - Glycan Bindinghttp://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Ctlect_214

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

    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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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