Format

Send to:

Choose Destination
    • Showing Current items.

    SDC1 syndecan 1 [ Homo sapiens (human) ]

    Gene ID: 6382, updated on 19-Sep-2021

    Summary

    Official Symbol
    SDC1provided by HGNC
    Official Full Name
    syndecan 1provided by HGNC
    Primary source
    HGNC:HGNC:10658
    See related
    Ensembl:ENSG00000115884 MIM:186355
    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]
    Expression
    Broad expression in esophagus (RPKM 110.6), skin (RPKM 101.9) and 14 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SDC1 in Genome Data Viewer
    Location:
    2p24.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (20200797..20225475, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (20400558..20425236, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 140, pseudogene Neighboring gene RNA, U6 small nuclear 961, pseudogene Neighboring gene DRG1 pseudogene 1 Neighboring gene RNA, U7 small nuclear 113 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
    Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
    GeneReviews: Not available

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of syndecan 1 (SDC1) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    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 HIV-1 Tat tethered to the surface of syndecan-1 expression B-lymphoid cells or of peripheral blood monocytes promotes their transendothelial migration in vitro in response to CXCL12 or CCL5, respectively PubMed
    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 Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein C-terminus binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in Sertoli cell development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in canonical Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in myoblast development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in odontogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of exosomal secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of extracellular exosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to cAMP IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to calcium ion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to glucocorticoid IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to hydrogen peroxide IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to toxic substance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in striated muscle cell development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in ureteric bud development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in wound healing IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in Golgi lumen TAS
    Traceable Author Statement
    more info
     
    is_active_in cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in external side of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in integral component of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in lysosomal lumen TAS
    Traceable Author Statement
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    part_of protein-containing complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

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

    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_050639.1 RefSeqGene

      Range
      5001..29637
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001006946.2NP_001006947.2  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)
      AC104792
      Consensus CDS
      CCDS1697.1
      Related
      ENSP00000370542.1, ENST00000381150.5
      Conserved Domains (1) summary
      pfam01034
      Location:245308
      Syndecan; Syndecan domain
    2. NM_002997.5NP_002988.4  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)
      AC104792
      Consensus CDS
      CCDS1697.1
      Related
      ENSP00000254351.4, ENST00000254351.9
      Conserved Domains (1) summary
      pfam01034
      Location:245308
      Syndecan; Syndecan domain

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

      Range
      20200797..20225475 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005262622.2XP_005262679.1  syndecan-1 isoform X3

      Conserved Domains (1) summary
      pfam01034
      Location:227290
      Syndecan; Syndecan domain
    2. XM_005262620.4XP_005262677.1  syndecan-1 isoform X1

      Conserved Domains (1) summary
      pfam01034
      Location:269332
      Syndecan; Syndecan domain
    3. XM_005262621.3XP_005262678.3  syndecan-1 isoform X2

    Support Center