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    SDCBP syndecan binding protein [ Homo sapiens (human) ]

    Gene ID: 6386, updated on 10-May-2017
    Official Symbol
    SDCBPprovided by HGNC
    Official Full Name
    syndecan binding proteinprovided by HGNC
    Primary source
    HGNC:HGNC:10662
    See related
    Ensembl:ENSG00000137575 MIM:602217; Vega:OTTHUMG00000164303
    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
    ST1; MDA9; SYCL; MDA-9; TACIP18
    Summary
    The protein encoded by this gene was initially identified as a molecule linking syndecan-mediated signaling to the cytoskeleton. The syntenin protein contains tandemly repeated PDZ domains that bind the cytoplasmic, C-terminal domains of a variety of transmembrane proteins. This protein may also affect cytoskeletal-membrane organization, cell adhesion, protein trafficking, and the activation of transcription factors. The protein is primarily localized to membrane-associated adherens junctions and focal adhesions but is also found at the endoplasmic reticulum and nucleus. Alternative splicing results in multiple transcript variants encoding different isoforms. Related pseudogenes have been identified on multiple chromosomes. [provided by RefSeq, Jan 2017]
    Orthologs
    Location:
    8q12.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 8 NC_000008.11 (58553169..58582860)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (59465566..59495419)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene cytochrome P450 family 7 subfamily A member 1 Neighboring gene uncharacterized LOC105375857 Neighboring gene ribosomal protein S26 pseudogene 7 Neighboring gene neutral sphingomyelinase activation associated factor Neighboring gene uncharacterized LOC105375858

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Syntenin-1 is recruited toward HIV-1 gp120/gp41-driven virus/cell and cell/cell contacts, associates with CD4, limits HIV-1-induced cell fusion and viral entry, and modulates gp120/gp41-triggered actin polymerization and PIP2 accumulation PubMed
    env Genes, including GABRP, ADF, HINT, PRSS2, SDCBP, PTK9, PPP2R5B, ITGA3, PRKCBP1, HMOX2, HAT1, PPP1cB, and ICAM-1, are upregulated after treatment of human astrocytes with HIV-1 gp120 PubMed
    Envelope transmembrane glycoprotein gp41 env Syntenin-1 is recruited toward HIV-1 gp120/gp41-driven virus/cell and cell/cell contacts, associates with CD4, limits HIV-1-induced cell fusion and viral entry, and modulates gp120/gp41-triggered actin polymerization and PIP2 accumulation PubMed
    Nef nef HIV-1 Nef inhibits the expression of syndecan binding protein (syntenin) in human podocyte PubMed
    matrix gag HIV-1 MA is identified to have a physical interaction with syndecan binding protein (SDCBP) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    • Axon guidance, organism-specific biosystem (from REACTOME)
      Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
    • Developmental Biology, organism-specific biosystem (from REACTOME)
      Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
    • EPH-Ephrin signaling, organism-specific biosystem (from REACTOME)
      EPH-Ephrin signaling, organism-specific biosystemDuring the development process cell migration and adhesion are the main forces involved in morphing the cells into critical anatomical structures. The ability of a cell to migrate to its correct dest...
    • Ectoderm Differentiation, organism-specific biosystem (from WikiPathways)
      Ectoderm Differentiation, organism-specific biosystemModel depicting ectoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
    • Ephrin signaling, organism-specific biosystem (from REACTOME)
      Ephrin signaling, organism-specific biosystemThe interaction between ephrin (EFN) ligands and EPH receptors results not only in forward signaling through the EPH receptor, but also in 'reverse' signaling through the EFN ligand itself. Reverse s...
    • Immune System, organism-specific biosystem (from REACTOME)
      Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
    • Innate Immune System, organism-specific biosystem (from REACTOME)
      Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
    • L1CAM interactions, organism-specific biosystem (from REACTOME)
      L1CAM interactions, organism-specific biosystemThe L1 family of cell adhesion molecules (L1CAMs) are a subfamily of the immunoglobulin superfamily of transmembrane receptors, comprised of four structurally related proteins: L1, Close Homolog of L...
    • Neurofascin interactions, organism-specific biosystem (from REACTOME)
      Neurofascin interactions, organism-specific biosystemNeurofascin is an L1 family immunoglobulin cell adhesion molecule involved in axon subcellular targeting and synapse formation during neural development. There are a range of different isoforms ident...
    • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
      Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...
    • 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
    • Syndecan-2-mediated signaling events, organism-specific biosystem (from Pathway Interaction Database)
      Syndecan-2-mediated signaling events, organism-specific biosystem
      Syndecan-2-mediated signaling events
    • Syndecan-4-mediated signaling events, organism-specific biosystem (from Pathway Interaction Database)
      Syndecan-4-mediated signaling events, organism-specific biosystem
      Syndecan-4-mediated signaling events
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    cadherin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoskeletal adaptor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    frizzled binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    interleukin-5 receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    phosphatidylinositol-4,5-bisphosphate binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein N-terminus binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    syndecan binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    syndecan binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    actin cytoskeleton organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    chemical synaptic transmission NAS
    Non-traceable Author Statement
    more info
    PubMed 
    ephrin receptor signaling pathway TAS
    Traceable Author Statement
    more info
     
    intracellular signal transduction NAS
    Non-traceable Author Statement
    more info
    PubMed 
    negative regulation of proteasomal ubiquitin-dependent protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of receptor internalization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    neutrophil degranulation TAS
    Traceable Author Statement
    more info
     
    positive regulation of JNK cascade IC
    Inferred by Curator
    more info
    PubMed 
    positive regulation of cell growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of epithelial to mesenchymal transition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of exosomal secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of extracellular exosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of pathway-restricted SMAD protein phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transforming growth factor beta receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein targeting to membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    regulation of mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    substrate-dependent cell migration, cell extension NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    adherens junction NAS
    Non-traceable Author Statement
    more info
    PubMed 
    azurophil granule lumen TAS
    Traceable Author Statement
    more info
     
    blood microparticle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoskeleton NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular region TAS
    Traceable Author Statement
    more info
     
    extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    focal adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    interleukin-5 receptor complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    melanosome IEA
    Inferred from Electronic Annotation
    more info
     
    membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear membrane IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    syntenin-1
    Names
    melanoma differentiation associated protein-9
    pro-TGF-alpha cytoplasmic domain-interacting protein 18
    scaffold protein Pbp1
    syndecan binding protein (syntenin)
    syndecan-binding protein 1

    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_001007067.1NP_001007068.1  syntenin-1 isoform 1

      See identical proteins and their annotated locations for NP_001007068.1

      Status: REVIEWED

      Source sequence(s)
      AF000652, BC013254, BG111210, BG772269, BU160865, U83463
      Consensus CDS
      CCDS6172.1
      UniProtKB/Swiss-Prot
      O00560
      UniProtKB/TrEMBL
      A0A024R7Z5
      Related
      ENSP00000411771.2, OTTHUMP00000226414, ENST00000413219.6, OTTHUMT00000378195
      Conserved Domains (1) summary
      cd00992
      Location:112191
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    2. NM_001007068.1NP_001007069.1  syntenin-1 isoform 2

      See identical proteins and their annotated locations for NP_001007069.1

      Status: REVIEWED

      Source sequence(s)
      AF000652, BC013254, BG111210, BG772269, BU160865, U83463
      Consensus CDS
      CCDS47863.1
      UniProtKB/Swiss-Prot
      O00560
      Related
      ENSP00000395351.2, OTTHUMP00000226415, ENST00000424270.6, OTTHUMT00000378196
      Conserved Domains (1) summary
      cd00992
      Location:106185
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    3. NM_001007069.1NP_001007070.1  syntenin-1 isoform 3

      See identical proteins and their annotated locations for NP_001007070.1

      Status: REVIEWED

      Source sequence(s)
      AF000652, BC013254, BG111210, BG772269, BU160865, U83463
      Consensus CDS
      CCDS47862.1
      UniProtKB/Swiss-Prot
      O00560
      Related
      ENSP00000409288.2, OTTHUMP00000226413, ENST00000447182.6, OTTHUMT00000378194
      Conserved Domains (1) summary
      cd00992
      Location:111190
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    4. NM_001007070.1NP_001007071.1  syntenin-1 isoform 3

      See identical proteins and their annotated locations for NP_001007071.1

      Status: REVIEWED

      Source sequence(s)
      AF000652, BC013254, BG111210, BG772269, BU160865, U83463
      Consensus CDS
      CCDS47862.1
      UniProtKB/Swiss-Prot
      O00560
      Conserved Domains (1) summary
      cd00992
      Location:111190
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    5. NM_001330537.1NP_001317466.1  syntenin-1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AA854128, AC068522, AK128645, DA466513
      Consensus CDS
      CCDS83298.1
      UniProtKB/TrEMBL
      G5EA09
      Conserved Domains (1) summary
      cd00992
      Location:132211
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    6. NM_001348339.1NP_001335268.1  syntenin-1 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC068522, AK295198, BC013254
      UniProtKB/TrEMBL
      B4DHN5
    7. NM_001348340.1NP_001335269.1  syntenin-1 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC068522
    8. NM_001348341.1NP_001335270.1  syntenin-1 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC068522
    9. NM_005625.3NP_005616.2  syntenin-1 isoform 1

      See identical proteins and their annotated locations for NP_005616.2

      Status: REVIEWED

      Source sequence(s)
      AF000652, BC013254, BG111210, BG772269, BU160865, U83463
      Consensus CDS
      CCDS6172.1
      UniProtKB/Swiss-Prot
      O00560
      UniProtKB/TrEMBL
      A0A024R7Z5
      Related
      ENSP00000260130.4, OTTHUMP00000226412, ENST00000260130.8, OTTHUMT00000378193
      Conserved Domains (1) summary
      cd00992
      Location:112191
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p7 Primary Assembly

      Range
      58553169..58582860
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017013727.1XP_016869216.1  syntenin-1 isoform X1

    2. XM_017013728.1XP_016869217.1  syntenin-1 isoform X2

      Related
      ENSP00000487245.1, ENST00000630925.1
      Conserved Domains (1) summary
      cd00992
      Location:132211
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    3. XM_011517571.2XP_011515873.2  syntenin-1 isoform X3

    Alternate CHM1_1.1

    Genomic

    1. NC_018919.2 Alternate CHM1_1.1

      Range
      59517611..59547302
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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