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SDCBP syndecan binding protein [ Homo sapiens (human) ]

Gene ID: 6386, updated on 9-Dec-2018

Summary

Official Symbol
SDCBPprovided by HGNC
Official Full Name
syndecan binding proteinprovided by HGNC
Primary source
HGNC:HGNC:10662
See related
Ensembl:ENSG00000137575 MIM:602217
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]
Expression
Ubiquitous expression in placenta (RPKM 77.0), gall bladder (RPKM 73.7) and 25 other tissues See more
Orthologs

Genomic context

See SDCBP in Genome Data Viewer
Location:
8q12.1
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 8 NC_000008.11 (58552924..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 peptidylprolyl isomerase A pseudogene Neighboring gene uncharacterized LOC105375857 Neighboring gene ribosomal protein S26 pseudogene 7 Neighboring gene neutral sphingomyelinase activation associated factor Neighboring gene uncharacterized LOC105375858

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 FunctionsWhat's a GeneRIF?

HIV-1 interactions

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

Pathways from BioSystems

  • 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
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 HDA PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
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 HDA PubMed 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space HDA PubMed 
extracellular vesicle HDA 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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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

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_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, ENST00000413219.6
    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, ENST00000424270.6
    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, ENST00000447182.6
    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
    Related
    ENSP00000428184.1, ENST00000523483.5
    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
    Consensus CDS
    CCDS87610.1
    UniProtKB/TrEMBL
    B4DHN5
    Related
    ENSP00000430730.1, ENST00000520168.5
    Conserved Domains (2) summary
    cd00136
    Location:56132
    PDZ; PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. ...
    cd00992
    Location:137210
    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) ...
  7. NM_001348340.1NP_001335269.1  syntenin-1 isoform 6

    Status: REVIEWED

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

    Status: REVIEWED

    Source sequence(s)
    AC068522
    Conserved Domains (1) summary
    cd00992
    Location:133212
    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) ...
  9. NM_005625.4NP_005616.2  syntenin-1 isoform 1

    See identical proteins and their annotated locations for NP_005616.2

    Status: REVIEWED

    Source sequence(s)
    BC013254, BG772269, U83463
    Consensus CDS
    CCDS6172.1
    UniProtKB/Swiss-Prot
    O00560
    UniProtKB/TrEMBL
    A0A024R7Z5
    Related
    ENSP00000260130.4, ENST00000260130.8
    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 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p12 Primary Assembly

    Range
    58552924..58582860
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024447229.1XP_024302997.1  syntenin-1 isoform X1

    Conserved Domains (1) summary
    cd00992
    Location:133212
    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. XM_024447231.1XP_024302999.1  syntenin-1 isoform X3

    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_024447230.1XP_024302998.1  syntenin-1 isoform X2

    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) ...
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