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    VCAN versican [ Homo sapiens (human) ]

    Gene ID: 1462, updated on 27-Nov-2024

    Summary

    Official Symbol
    VCANprovided by HGNC
    Official Full Name
    versicanprovided by HGNC
    Primary source
    HGNC:HGNC:2464
    See related
    Ensembl:ENSG00000038427 MIM:118661; AllianceGenome:HGNC:2464
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    WGN; ERVR; GHAP; PG-M; WGN1; CSPG2
    Summary
    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]
    Expression
    Broad expression in appendix (RPKM 45.0), placenta (RPKM 35.3) and 15 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See VCAN in Genome Data Viewer
    Location:
    5q14.2-q14.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (83471744..83582302)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (83960520..84071053)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (82767563..82878121)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379053 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16153 Neighboring gene ferritin heavy chain 1 pseudogene 9 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:82767992-82768864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16155 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:82771416-82771938 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:82771939-82772461 Neighboring gene VCAN antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:82849966-82851165 Neighboring gene uncharacterized LOC124901021 Neighboring gene hyaluronan and proteoglycan link protein 1 Neighboring gene RN7SK pseudogene 295 Neighboring gene RNA, U6 small nuclear 620, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Wagner syndrome
    MedGen: C1840452 OMIM: 143200 GeneReviews: Not available
    not available

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three susceptibility loci for laryngeal squamous cell carcinoma in the Chinese population.
    EBI GWAS Catalog
    Genome-wide association study of major recurrent depression in the U.K. population.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope transmembrane glycoprotein gp41 env A synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 upregulates the expression of versican (VCAN) in peptide-treated PBMCs PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • DKFZp686K06110

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables extracellular matrix structural constituent conferring compression resistance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables extracellular matrix structural constituent conferring compression resistance RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    enables glycosaminoglycan binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables hyaluronic acid binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein tyrosine phosphatase activator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell recognition TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in central nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in glial cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in osteoblast differentiation HDA PubMed 
    involved_in skeletal system development IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    versican core protein
    Names
    chondroitin sulfate proteoglycan core protein 2
    glial hyaluronate-binding protein
    large fibroblast proteoglycan
    versican proteoglycan

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_012682.1 RefSeqGene

      Range
      5034..115592
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001126336.3NP_001119808.1  versican core protein isoform 2 precursor

      See identical proteins and their annotated locations for NP_001119808.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), also known as PG-M(V3), omits two coding exons, compared to variant 1. This results in a shorter protein (isoform 2) with no chondroitin sulfate attachment domain.
      Source sequence(s)
      AC026696, BC050524, D32039, DA361670, DT217515
      Consensus CDS
      CCDS47242.1
      UniProtKB/Swiss-Prot
      P13611
      UniProtKB/TrEMBL
      Q86W61
      Related
      ENSP00000421362.2, ENST00000502527.2
      Conserved Domains (7) summary
      cd05901
      Location:36151
      Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican
      cd00033
      Location:555611
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00410
      Location:29147
      IG_like; Immunoglobulin like
      cd00054
      Location:386422
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd03517
      Location:150244
      Link_domain_CSPGs_modules_1_3; Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: ...
      cd03520
      Location:251346
      Link_domain_CSPGs_modules_2_4; Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The ...
      cl02432
      Location:428551
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
    2. NM_001164097.2NP_001157569.1  versican core protein isoform 3 precursor

      See identical proteins and their annotated locations for NP_001157569.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3), also known as PG-M(V1), lacks an exon in the coding region, compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.
      Source sequence(s)
      AA320958, AC026696, BX641036, DA361670, X15998
      Consensus CDS
      CCDS54876.1
      UniProtKB/TrEMBL
      Q6MZK8
      Related
      ENSP00000340062.5, ENST00000343200.9
      Conserved Domains (7) summary
      cd05901
      Location:36151
      Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican
      cd00033
      Location:23092365
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      cd03588
      Location:21822305
      CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins
      smart00410
      Location:29147
      IG_like; Immunoglobulin like
      cd00054
      Location:21402176
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd03517
      Location:150244
      Link_domain_CSPGs_modules_1_3; Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: ...
      cd03520
      Location:251346
      Link_domain_CSPGs_modules_2_4; Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The ...
    3. NM_001164098.2NP_001157570.1  versican core protein isoform 4 precursor

      See identical proteins and their annotated locations for NP_001157570.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4), also known as PG-M(V2), lacks an exon in the coding region, compared to variant 1. This results in a shorter protein (isoform 4), compared to isoform 1.
      Source sequence(s)
      AA320958, AC026696, DA361670, U26555
      Consensus CDS
      CCDS54875.1
      UniProtKB/TrEMBL
      E9PF17
      Related
      ENSP00000342768.4, ENST00000342785.8
      Conserved Domains (7) summary
      cd05901
      Location:36151
      Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican
      cd00033
      Location:15421598
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      cd03588
      Location:14151538
      CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins
      smart00410
      Location:29147
      IG_like; Immunoglobulin like
      cd00054
      Location:13731409
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd03517
      Location:150244
      Link_domain_CSPGs_modules_1_3; Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: ...
      cd03520
      Location:251346
      Link_domain_CSPGs_modules_2_4; Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The ...
    4. NM_004385.5NP_004376.2  versican core protein isoform 1 precursor

      See identical proteins and their annotated locations for NP_004376.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1), also known as PG-M(V0), encodes the longest isoform (1).
      Source sequence(s)
      AB209491, AC026696, DA361670, DT217515, U16306
      Consensus CDS
      CCDS4060.1
      UniProtKB/Swiss-Prot
      P13611, P20754, Q13010, Q13189, Q15123, Q9UCL9, Q9UNW5
      UniProtKB/TrEMBL
      Q59FG9
      Related
      ENSP00000265077.3, ENST00000265077.8
      Conserved Domains (7) summary
      cd05901
      Location:36151
      Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican
      cd00033
      Location:32963352
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      cd03588
      Location:31693292
      CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins
      smart00410
      Location:29147
      IG_like; Immunoglobulin like
      cd00054
      Location:31273163
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd03517
      Location:150244
      Link_domain_CSPGs_modules_1_3; Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: ...
      cd03520
      Location:251346
      Link_domain_CSPGs_modules_2_4; Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      83471744..83582302
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      83960520..84071053
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)