Format

Send to:

Choose Destination

VCAN versican [ Homo sapiens (human) ]

Gene ID: 1462, updated on 20-Dec-2019

Summary

Official Symbol
VCANprovided by HGNC
Official Full Name
versicanprovided by HGNC
Primary source
HGNC:HGNC:2464
See related
Ensembl:ENSG00000038427 MIM:118661
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

Genomic context

See VCAN in Genome Data Viewer
Location:
5q14.2-q14.3
Exon count:
15
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (83471674..83582303)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (82767493..82878122)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379053 Neighboring gene ferritin heavy chain 1 pseudogene 9 Neighboring gene uncharacterized LOC107986431 Neighboring gene VCAN antisense RNA 1 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: C0339540 OMIM: 143200 GeneReviews: VCAN-Related Vitreoretinopathy
Compare labs

NHGRI GWAS Catalog

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

Homology

Clone Names

  • DKFZp686K06110

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
carbohydrate binding IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix structural constituent conferring compression resistance ISS
Inferred from Sequence or Structural Similarity
more info
 
extracellular matrix structural constituent conferring compression resistance RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
glycosaminoglycan binding TAS
Traceable Author Statement
more info
PubMed 
hyaluronic acid binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
cell recognition TAS
Traceable Author Statement
more info
PubMed 
cellular protein metabolic process TAS
Traceable Author Statement
more info
 
central nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chondroitin sulfate biosynthetic process TAS
Traceable Author Statement
more info
 
chondroitin sulfate catabolic process TAS
Traceable Author Statement
more info
 
dermatan sulfate biosynthetic process TAS
Traceable Author Statement
more info
 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
multicellular organism development TAS
Traceable Author Statement
more info
PubMed 
osteoblast differentiation HDA PubMed 
post-translational protein modification TAS
Traceable Author Statement
more info
 
skeletal system development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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)

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_001164097.1NP_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/Swiss-Prot
    P13611
    UniProtKB/TrEMBL
    A0A024RAL1, 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_001164098.1NP_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/Swiss-Prot
    P13611
    UniProtKB/TrEMBL
    A0A024RAP3
    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
    UniProtKB/TrEMBL
    A0A024RAQ9, 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: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    83471674..83582303
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center