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    SDC1 syndecan 1 [ Homo sapiens ]

    Gene ID: 6382, updated on 20-May-2012

    Summary

    Official Symbol
    SDC1provided by HGNC
    Official Full Name
    syndecan 1provided by HGNC
    Primary source
    HGNC:10658
    See related
    Ensembl:ENSG00000115884; HPRD:01718; MIM:186355; Vega:OTTHUMG00000090751
    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
    SDC; CD138; SYND1; syndecan
    Summary
    The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan and is a member of the syndecan proteoglycan family. The syndecans mediate cell binding, cell signaling, and cytoskeletal organization and syndecan receptors are required for internalization of the HIV-1 tat protein. The syndecan-1 protein functions as an integral membrane protein and participates in cell proliferation, cell migration and cell-matrix interactions via its receptor for extracellular matrix proteins. Altered syndecan-1 expression has been detected in several different tumor types. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode the same protein. [provided by RefSeq, Jul 2008]

    Genomic context

    Location :
    2p24.1
    Sequence :
    Chromosome: 2; NC_000002.11 (20400558..20425194, complement)
    See SDC1 in Epigenomics, MapViewer

    Chromosome 2 - NC_000002.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100506455 Neighboring gene lysosomal protein transmembrane 4 alpha Neighboring gene ribosomal protein S16 pseudogene 2 Neighboring gene uncharacterized LOC100131373 Neighboring gene developmentally regulated GTP binding protein 1 pseudogene Neighboring gene pumilio homolog 2 (Drosophila) Neighboring gene retinitis pigmentosa 9 (autosomal dominant) pseudogene

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    HIV-1 protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env The V3 region (amino acids 298-329) of HIV-1 gp120 contains the syndecan-binding site for HIV-1 via 6-O sulfated motifs; a single conserved arginine (Arg-298) in the V3 region of gp120 governs HIV-1 binding to syndecans PubMed
    Tat tat Binding of HIV-1 Tat to heparan sulfate proteoglycans is competed out by the heparin-binding factor bFGF PubMed
    tat Cell membrane heparin sulfate proteoglycans bind to the basic region of HIV-1 Tat (amino acids 49-57) and act as receptors for extracellular Tat uptake, an effect that may contribute to the angiogenic properties of Tat in promoting Kaposi's sarcoma PubMed

    Go to the HIV-1, Human Protein Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    P18827 O14936 CASK    HPRD  PubMed  
    P18827 P13501 CCL5    HPRD  PubMed  
    P18827 P08311 CTSG    HPRD  PubMed  
    P18827 P08246 ELANE    HPRD  PubMed  
    P18827 P09038 FGF2    HPRD  PubMed  
    P18827 P14210 HGF    HPRD  PubMed  
    P18827 Q16270 IGFBP7    HPRD  PubMed  
    P18827 P10145 IL8    HPRD  PubMed  
    P18827 Q9GZZ8 LACRT    HPRD  PubMed  
    P18827 P21741 MDK    HPRD  PubMed  
    P18827 P50281 MMP14    HPRD  PubMed  
    P18827 P21246 PTN    HPRD  PubMed  
    P18827 O00560 SDCBP    HPRD  PubMed  
    BioGRID:112284 BioGRID:114141 CASK    BioGRID  PubMed Reconstituted Complex 
    BioGRID:112284 BioGRID:112255 CCL5    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:112284 BioGRID:107891 CTSG    BioGRID  PubMed Reconstituted Complex 
    BioGRID:112284 BioGRID:108538 FGF2    BioGRID  PubMed Co-purification 
    BioGRID:112284 BioGRID:109330 HGF    BioGRID  PubMed Reconstituted Complex 
    BioGRID:112284 BioGRID:109790 IL8    BioGRID  PubMed Reconstituted Complex 
    BioGRID:112284 BioGRID:124659 LACRT    BioGRID  PubMed Co-purification 
    BioGRID:112284 BioGRID:111731 PTN    BioGRID  PubMed Reconstituted Complex 
    BioGRID:112284 BioGRID:112287 SDCBP    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:112284 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-MS 

    General gene information

    Markers

    Homology

    Pathways from BioSystems

    • Arf6 trafficking events, organism-specific biosystem (from Pathway Interaction Database)
      Arf6 trafficking events, organism-specific biosystem
      Arf6 trafficking events
    • Cell adhesion molecules (CAMs), organism-specific biosystem (from KEGG)
      Cell adhesion molecules (CAMs), organism-specific biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
    • Cell adhesion molecules (CAMs), conserved biosystem (from KEGG)
      Cell adhesion molecules (CAMs), conserved biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
    • Chylomicron-mediated lipid transport, organism-specific biosystem (from REACTOME)
      Chylomicron-mediated lipid transport, organism-specific biosystemChylomicrons transport triacylglycerol, phospholipid, and cholesterol derived from dietary lipid from the small intestine to other tissues of the body. Each chylomicron assembles around a single mole...
    • ECM-receptor interaction, organism-specific biosystem (from KEGG)
      ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
    • ECM-receptor interaction, conserved biosystem (from KEGG)
      ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
    • Integrins in angiogenesis, organism-specific biosystem (from Pathway Interaction Database)
      Integrins in angiogenesis, organism-specific biosystem
      Integrins in angiogenesis
    • Lipid digestion, mobilization, and transport, organism-specific biosystem (from REACTOME)
      Lipid digestion, mobilization, and transport, organism-specific biosystemProcesses annotated here include the digestion of dietary lipids, sterol uptake, the formation and turnover of lipoproteins (chylomicrons, VLDL, LDL, and HDL), and the mobilization of fatty acids thr...
    • Lipoprotein metabolism, organism-specific biosystem (from REACTOME)
      Lipoprotein metabolism, organism-specific biosystemBecause of their hydrophobicity, lipids are found in the extracellular spaces of the human body primarily in the form of lipoprotein complexes. Chylomicrons form in the small intestine and transport ...
    • Malaria, organism-specific biosystem (from KEGG)
      Malaria, organism-specific biosystemPlasmodium protozoa are parasites that account for malaria infection. Sporozoite forms of the parasite are injected by mosquito bites under the skin and are carried to the liver where they develop in...
    • Malaria, conserved biosystem (from KEGG)
      Malaria, conserved biosystemPlasmodium protozoa are parasites that account for malaria infection. Sporozoite forms of the parasite are injected by mosquito bites under the skin and are carried to the liver where they develop in...
    • Metabolism, organism-specific biosystem (from REACTOME)
      Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
    • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
      Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
    • Proteogylcan syndecan-mediated signaling events, organism-specific biosystem (from Pathway Interaction Database)
      Proteogylcan syndecan-mediated signaling events, organism-specific biosystem
      Proteogylcan syndecan-mediated signaling events
    • Syndecan-1-mediated signaling events, organism-specific biosystem (from Pathway Interaction Database)
      Syndecan-1-mediated signaling events, organism-specific biosystem
      Syndecan-1-mediated signaling events

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    cytoskeletal protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    glycoprotein binding IEA
    Inferred from Electronic Annotation
    more info
     
    lipoprotein lipase activity TAS
    Traceable Author Statement
    more info
     
    protein C-terminus binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    Sertoli cell development IEA
    Inferred from Electronic Annotation
    more info
     
    canonical Wnt receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    lipid metabolic process TAS
    Traceable Author Statement
    more info
     
    lipoprotein metabolic process TAS
    Traceable Author Statement
    more info
     
    myoblast development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    odontogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    response to cAMP IEA
    Inferred from Electronic Annotation
    more info
     
    response to calcium ion IEA
    Inferred from Electronic Annotation
    more info
     
    response to glucocorticoid stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    response to hydrogen peroxide IEA
    Inferred from Electronic Annotation
    more info
     
    response to toxin IEA
    Inferred from Electronic Annotation
    more info
     
    small molecule metabolic process TAS
    Traceable Author Statement
    more info
     
    striated muscle cell development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    ureteric bud development IEA
    Inferred from Electronic Annotation
    more info
     
    wound healing IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cell surface IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    focal adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral to plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    protein complex IEA
    Inferred from Electronic Annotation
    more info
     
    uropod IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    syndecan-1
    Names
    syndecan-1
    CD138 antigen
    syndecan proteoglycan 1
    heparan sulfate proteoglycan fibroblast growth factor receptor

    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_001006946.1NP_001006947.1  syndecan-1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AJ551176, BC008765, BM785035, CB321970, X60306
      Consensus CDS
      CCDS1697.1
      UniProtKB/Swiss-Prot
      P18827
      Related
      ENSP00000370542, ENST00000381150
      Conserved Domains (2) summary
      smart00294
      Location:275293
      Blast Score: 93
      4.1m; putative band 4.1 homologues' binding motif
      pfam01034
      Location:220308
      Blast Score: 252
      Syndecan; Syndecan domain
    2. NM_002997.4NP_002988.3  syndecan-1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AJ551176, BC008765, BM910157, CB321970, X60306
      Consensus CDS
      CCDS1697.1
      UniProtKB/Swiss-Prot
      P18827
      Related
      ENSP00000254351, OTTHUMP00000115942, ENST00000254351, OTTHUMT00000207495
      Conserved Domains (2) summary
      smart00294
      Location:275293
      Blast Score: 93
      4.1m; putative band 4.1 homologues' binding motif
      pfam01034
      Location:220308
      Blast Score: 252
      Syndecan; Syndecan domain

    RefSeqs of Annotated Genomes: Build 37.3

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

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000002.11 Reference GRCh37.p5 Primary Assembly

      Range
      20400558..20425194, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000134.1 Alternate HuRef

      Range
      20158155..20182491, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Related Sequences

    Nucleotide Protein
    Heading Accession and Version
    genomic AC104792.5 AAX93151.1
    genomic CH471053.2 EAX00828.1
      EAX00829.1
      EAX00830.1
      EAX00831.1
    genomic Z48199.1 CAA88235.1
    mRNA AJ551176.1 CAD80245.1
    mRNA AK222739.1 BAD96459.1
    mRNA AK299385.1 BAG61371.1
    mRNA AK313974.1 None
    mRNA BC008765.2 AAH08765.1
    mRNA BM785035.1 None
    mRNA BM910157.1 None
    mRNA CB321970.1 None
    mRNA J05392.1 AAA60605.1
    mRNA X60306.1 CAA42851.1
    other-genetic DQ893265.2 ABM84191.1
    other-genetic DQ896595.2 ABM87594.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    AAB21434.1 GenPept
    AAB23935.1 GenPept
    P18827.3 GenPept UniProtKB/Swiss-Prot:P18827
    Q53H42 GenPept UniProtKB/TrEMBL:Q53H42

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