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    Vcan versican [ Rattus norvegicus (Norway rat) ]

    Gene ID: 114122, updated on 18-Apr-2019

    Summary

    Official Symbol
    Vcanprovided by RGD
    Official Full Name
    versicanprovided by RGD
    Primary source
    RGD:619940
    See related
    Ensembl:ENSRNOG00000029212
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Cspg2
    Summary
    extracellular matrix protein secreted by many cell types; part of the large chondroitin sulfate proteoglycan (CSPG) family [RGD, Feb 2006]
    Annotation information
    Annotation category: partial on reference assembly
    Expression
    Biased expression in Heart (RPKM 115.3), Uterus (RPKM 98.0) and 8 other tissues See more
    Orthologs

    Genomic context

    See Vcan in Genome Data Viewer
    Location:
    2q12
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (18490102..18587340, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 2 NC_005101.3 (18363890..18463115, complement)

    Chromosome 2 - NC_005101.4Genomic Context describing neighboring genes Neighboring gene similar to eukaryotic translation elongation factor 1 alpha 2 Neighboring gene hyaluronan and proteoglycan link protein 1 Neighboring gene X-ray repair cross complementing 4 Neighboring gene 40S ribosomal protein S6 pseudogene Neighboring gene transmembrane protein 167A

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
     
    hyaluronic acid binding IEA
    Inferred from Electronic Annotation
    more info
     
    low-density lipoprotein particle binding TAS
    Traceable Author Statement
    more info
    PubMed 
    protein phosphatase binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    Process Evidence Code Pubs
    axon regeneration IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    central nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    glial cell migration ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    heart development ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    response to wounding IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    skeletal system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    ureteric bud development ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    Component Evidence Code Pubs
    cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    collagen-containing extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular matrix ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    perineuronal net IDA
    Inferred from Direct Assay
    more info
    PubMed 
    synapse EXP
    Inferred from Experiment
    more info
    PubMed 
    synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    versican core protein
    Names
    GHAP
    PG-M
    chondroitin sulfate proteoglycan 2 (versican)
    chondroitin sulfate proteoglycan core protein 2
    glial hyaluronate-binding protein
    large fibroblast 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.

    mRNA and Protein(s)

    1. NM_001170558.1NP_001164029.1  versican core protein isoform 1 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1, also referred to as V0).
      Source sequence(s)
      AABR07007554, AF062402, AF072892, AY007691
      UniProtKB/Swiss-Prot
      Q9ERB4
      Related
      ENSRNOP00000045935.4, ENSRNOT00000045532.6
      Conserved Domains (7) summary
      cd05901
      Location:36151
      Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican
      cd00033
      Location:32573313
      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:31303253
      CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins
      smart00410
      Location:30147
      IG_like; Immunoglobulin like
      cd00054
      Location:30883124
      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 ...
    2. NM_001170559.1NP_001164030.1  versican core protein isoform 4 precursor

      See identical proteins and their annotated locations for NP_001164030.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks two alternate in-frame exons, compared to variant 1, resulting in a shorter protein (isoform 4, also referred to as V3), compared to isoform 1.
      Source sequence(s)
      AF072892, AY007691
      UniProtKB/Swiss-Prot
      Q9ERB4
      Related
      ENSRNOP00000062961.2, ENSRNOT00000063821.3
      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:30147
      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
    3. NM_001170560.1NP_001164031.1  versican core protein isoform 3 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 3, also referred to as V2), compared to isoform 1.
      Source sequence(s)
      AABR07007554, AF062402, AF072892, AY007691
      UniProtKB/Swiss-Prot
      Q9ERB4
      Related
      ENSRNOP00000058873.2, ENSRNOT00000067456.4
      Conserved Domains (8) summary
      cd05901
      Location:36151
      Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican
      cd00033
      Location:15211577
      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:13941517
      CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins
      smart00410
      Location:30147
      IG_like; Immunoglobulin like
      cd00054
      Location:13521388
      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 ...
      pfam05109
      Location:7661193
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    4. NM_053663.1NP_446115.1  versican core protein isoform 2 precursor

      See identical proteins and their annotated locations for NP_446115.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2, also referred to as V1), compared to isoform 1.
      Source sequence(s)
      CH473955
      Related
      ENSRNOP00000074854.1, ENSRNOT00000088313.1
      Conserved Domains (7) summary
      cd05901
      Location:36151
      Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican
      cd00033
      Location:22912347
      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:21642287
      CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins
      smart00410
      Location:30147
      IG_like; Immunoglobulin like
      cd00054
      Location:21222158
      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: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005101.4 Reference Rnor_6.0 Primary Assembly

      Range
      18490102..18587340 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate Rn_Celera

    Genomic

    1. AC_000070.1 Alternate Rn_Celera

      Range
      16903548..17002158 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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