SDCBP syndecan binding protein [Homo sapiens (human)] - Gene

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; AllianceGenome:HGNC:10662
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; SDCBP1; 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: mouse all
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Genomic context

Location:: 8q12.1

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (58553261..58582858)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (58974408..59004011)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (59465820..59495417)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Syntenin-1-mediated arthritogenicity is advanced by reprogramming RA metabolic macrophages and Th1 cells.
Title: Syntenin-1-mediated arthritogenicity is advanced by reprogramming RA metabolic macrophages and Th1 cells.
Anaplasma phagocytophilum Ats-1 enhances exosome secretion through Syntenin-1.
Title: Anaplasma phagocytophilum Ats-1 enhances exosome secretion through Syntenin-1.
SDCBP promotes pancreatic cancer progression by preventing YAP1 from beta-TrCP-mediated proteasomal degradation.
Title: SDCBP promotes pancreatic cancer progression by preventing YAP1 from β-TrCP-mediated proteasomal degradation.
The Multifunctional Protein Syntenin-1: Regulator of Exosome Biogenesis, Cellular Function, and Tumor Progression.
Title: The Multifunctional Protein Syntenin-1: Regulator of Exosome Biogenesis, Cellular Function, and Tumor Progression.
Syntenin-1-mediated small extracellular vesicles promotes cell growth, migration, and angiogenesis by increasing onco-miRNAs secretion in lung cancer cells.
Title: Syntenin-1-mediated small extracellular vesicles promotes cell growth, migration, and angiogenesis by increasing onco-miRNAs secretion in lung cancer cells.
Downregulation of SDCBP inhibits cell proliferation and induces apoptosis by regulating PI3K/AKT/mTOR pathway in gastric carcinoma.
Title: Downregulation of SDCBP inhibits cell proliferation and induces apoptosis by regulating PI3K/AKT/mTOR pathway in gastric carcinoma.
Pharmacological inhibition of MDA-9/Syntenin blocks breast cancer metastasis through suppression of IL-1beta.
Title: Pharmacological inhibition of MDA-9/Syntenin blocks breast cancer metastasis through suppression of IL-1β.
Quantitative proteomics identifies the core proteome of exosomes with syntenin-1 as the highest abundant protein and a putative universal biomarker.
Title: Quantitative proteomics identifies the core proteome of exosomes with syntenin-1 as the highest abundant protein and a putative universal biomarker.
Downregulation of exosomal miR1273a increases cisplatin resistance of nonsmall cell lung cancer by upregulating the expression of syndecan binding protein.
Title: Downregulation of exosomal miR‑1273a increases cisplatin resistance of non‑small cell lung cancer by upregulating the expression of syndecan binding protein.
Single-cell RNA sequencing identify SDCBP in ACE2-positive bronchial epithelial cells negatively correlates with COVID-19 severity.
Title: Single-cell RNA sequencing identify SDCBP in ACE2-positive bronchial epithelial cells negatively correlates with COVID-19 severity.

Submit: New GeneRIF Correction See all GeneRIFs (72)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-83 (e-PCR)
- UniSTS:88120

SGC32650 (e-PCR)
- UniSTS:44357

RH47142 (e-PCR)
- UniSTS:44358

STS-G07282 (e-PCR)
- UniSTS:29044

RH91764 (e-PCR)
- UniSTS:90255

D8S1955 (e-PCR)
- UniSTS:8592

NoName (e-PCR)
- UniSTS:486293

SHGC-35930 (e-PCR)
- UniSTS:19658

RH64949 (e-PCR)
- UniSTS:19659

RH16388 (e-PCR)
- UniSTS:72444

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 ionotropic glutamate receptor binding	IEA Inferred from Electronic Annotation more info
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 binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables protein sequestering activity	IDA Inferred from Direct Assay 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
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 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 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
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 more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
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 more info	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 more info	PubMed
located_in extracellular vesicle	HDA more info	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
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in presynapse	IEA Inferred from Electronic Annotation more info

General protein information

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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)

NM_001007067.2 → NP_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

B2R5Q7, B4DUH3, B7ZLN2, O00173, O00560, O43391, Q14CP2

UniProtKB/TrEMBL

B4DQ93

Related

ENSP00000411771.2, ENST00000413219.6

Conserved Domains (1) summary

cd00992
Location:112 → 191

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) ...
NM_001007068.2 → NP_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/TrEMBL

B4DQ93

Related

ENSP00000395351.2, ENST00000424270.6

Conserved Domains (1) summary

cd00992
Location:106 → 185

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) ...
NM_001007069.2 → NP_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/TrEMBL

B4DQ93

Related

ENSP00000409288.2, ENST00000447182.6

Conserved Domains (1) summary

cd00992
Location:111 → 190

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) ...
NM_001007070.2 → NP_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/TrEMBL

B4DQ93

Conserved Domains (1) summary

cd00992
Location:111 → 190

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) ...
NM_001330537.2 → NP_001317466.1 syntenin-1 isoform 4

Status: REVIEWED

Source sequence(s)

AC068522, AK128645

Consensus CDS

CCDS83298.1

UniProtKB/TrEMBL

B4DQ93, G5EA09

Related

ENSP00000428184.1, ENST00000523483.5

Conserved Domains (1) summary

cd00992
Location:132 → 211

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) ...
NM_001348339.2 → NP_001335268.1 syntenin-1 isoform 5

Status: REVIEWED

Source sequence(s)

AK295198, BC013254

Consensus CDS

CCDS87610.1

UniProtKB/TrEMBL

B4DHN5, E9PBU7

Related

ENSP00000430730.1, ENST00000520168.5

Conserved Domains (2) summary

cd00136
Location:56 → 132

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:137 → 210

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) ...
NM_001348340.2 → NP_001335269.1 syntenin-1 isoform 6

Status: REVIEWED

Source sequence(s)

AC068522

UniProtKB/TrEMBL

B4DQ93

Conserved Domains (1) summary

cd00992
Location:132 → 211

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) ...
NM_001348341.2 → NP_001335270.1 syntenin-1 isoform 7

Status: REVIEWED

Source sequence(s)

AC068522

UniProtKB/TrEMBL

B4DQ93

Conserved Domains (1) summary

cd00992
Location:133 → 212

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) ...
NM_005625.4 → NP_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

B2R5Q7, B4DUH3, B7ZLN2, O00173, O00560, O43391, Q14CP2

UniProtKB/TrEMBL

B4DQ93

Related

ENSP00000260130.4, ENST00000260130.9

Conserved Domains (1) summary

cd00992
Location:112 → 191

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) ...