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SDCBP syndecan binding protein [ Homo sapiens (human) ]

Gene ID: 6386, updated on 6-Sep-2021

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
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Genomic context

See SDCBP in Genome Data Viewer
Location:
8q12.1
Exon count:
10
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (58553261..58582860)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (59465820..59495417)

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 Functions

What'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 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 cell adhesion molecule binding IEA
Inferred from Electronic Annotation
more info
 
enables cytoskeletal anchor activity NAS
Non-traceable Author Statement
more info
PubMed 
enables ephrin receptor binding IEA
Inferred from Electronic Annotation
more info
 
enables frizzled binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables growth factor binding IEA
Inferred from Electronic Annotation
more info
 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables interleukin-5 receptor binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
enables neurexin family protein binding IEA
Inferred from Electronic Annotation
more info
 
enables phosphatidylinositol-4,5-bisphosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein C-terminus binding IEA
Inferred from Electronic Annotation
more info
 
enables protein N-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
enables syndecan binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables syndecan binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables syndecan binding NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
involved_in Ras protein signal transduction IEA
Inferred from Electronic Annotation
more info
 
involved_in actin cytoskeleton organization NAS
Non-traceable Author Statement
more info
PubMed 
involved_in chemical synaptic transmission NAS
Non-traceable Author Statement
more info
PubMed 
involved_in intracellular signal transduction NAS
Non-traceable Author Statement
more info
PubMed 
involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of receptor internalization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of JNK cascade IC
Inferred by Curator
more info
PubMed 
involved_in positive regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of epithelial to mesenchymal transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 positive regulation of pathway-restricted SMAD protein phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of pathway-restricted SMAD protein phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transforming growth factor beta receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of transforming growth factor beta receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in presynapse assembly IEA
Inferred from Electronic Annotation
more info
 
involved_in protein targeting to membrane NAS
Non-traceable Author Statement
more info
PubMed 
involved_in regulation of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in substrate-dependent cell migration, cell extension NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
located_in adherens junction NAS
Non-traceable Author Statement
more info
PubMed 
located_in azurophil granule lumen TAS
Traceable Author Statement
more info
 
located_in blood microparticle HDA PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoskeleton NAS
Non-traceable Author Statement
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular exosome HDA PubMed 
located_in extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
 
located_in extracellular space HDA PubMed 
located_in extracellular vesicle HDA PubMed 
located_in focal adhesion IEA
Inferred from Electronic Annotation
more info
 
part_of interleukin-5 receptor complex ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
located_in melanosome IEA
Inferred from Electronic Annotation
more info
 
located_in membrane NAS
Non-traceable Author Statement
more info
PubMed 
located_in membrane raft IDA
Inferred from Direct Assay
more info
PubMed 
located_in nuclear membrane IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleus NAS
Non-traceable Author Statement
more info
PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in synapse IEA
Inferred from Electronic Annotation
more info
 

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)

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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_001007067.2NP_001007068.1  syntenin-1 isoform 1

    See identical proteins and their annotated locations for NP_001007068.1

    Status: REVIEWED

    Source sequence(s)
    BC013254, BG772269, 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_001007068.2NP_001007069.1  syntenin-1 isoform 2

    See identical proteins and their annotated locations for NP_001007069.1

    Status: REVIEWED

    Source sequence(s)
    BC013254, BG772269, 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_001007069.2NP_001007070.1  syntenin-1 isoform 3

    See identical proteins and their annotated locations for NP_001007070.1

    Status: REVIEWED

    Source sequence(s)
    BC013254, BG772269, 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_001007070.2NP_001007071.1  syntenin-1 isoform 3

    See identical proteins and their annotated locations for NP_001007071.1

    Status: REVIEWED

    Source sequence(s)
    BC013254, BG772269, 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_001330537.2NP_001317466.1  syntenin-1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC068522, AK128645
    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_001348339.2NP_001335268.1  syntenin-1 isoform 5

    Status: REVIEWED

    Source sequence(s)
    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_001348340.2NP_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_001348341.2NP_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, ENST00000260130.9
    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 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_000008.11 Reference GRCh38.p13 Primary Assembly

    Range
    58553261..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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