Tchem SDCBP Syntenin-1

Protein Summary

Description

Multifunctional adapter protein involved in diverse array of functions including trafficking of transmembrane proteins, neuro and immunomodulation, exosome biogenesis, and tumorigenesis (PubMed:26291527). Positively regulates TGFB1-mediated SMAD2/3 activation and TGFB1-induced epithelial-to-mesenchymal transition (EMT) and cell migration in various cell types. May increase TGFB1 signaling by enhancing cell-surface expression of TGFR1 by preventing the interaction between TGFR1 and CAV1 and subsequent CAV1-dependent internalization and degradation of TGFR1 (PubMed:25893292). In concert with SDC1/4 and PDCD6IP, regulates exosome biogenesis (PubMed:22660413). Regulates migration, growth, proliferation, and cell cycle progression in a variety of cancer types (PubMed:26539120). In adherens junctions may function to couple syndecans to cytoskeletal proteins or signaling components. Seems to couple transcription factor SOX4 to the IL-5 receptor (IL5RA) (PubMed:11498591). May also play a role in vesicular trafficking (PubMed:11179419). Seems to be required for the targeting of TGFA to the cell surface in the early secretory pathway (PubMed:10230395). 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]

Uniprot Accession IDs

• O00560
• B2R5Q7
• B4DUH3
• B7ZLN2
• O00173
• O43391
• Q14CP2

Gene Name

• SDCBP

Ensembl ID

• ENST00000260130
• ENSP00000260130
• ENSG00000137575
• ENST00000413219
• ENSP00000411771
• ENST00000424270
• ENSP00000395351
• ENST00000447182
• ENSP00000409288

Symbol

• MDA9
• SYCL
• ST1
• MDA9
• SYCL
• MDA-9
• TACIP18

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
disease perturbation	1
transcription factor perturbation	0.97
virus perturbation	0.94
cellular component	0.92
molecular function	0.86

Protein Classes

PANTHER Classes

Protein / Membrane Traffic Protein / Membrane Trafficking Regulatory Protein / Syntenin-1

DTO Classes

Protein / Transporter / Membrane Trafficking Regulatory Protein / Syntenin-1

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 647.64   (req: < 5)

Gene RIFs: 51   (req: <= 3)

Antibodies: 463   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 647.64   (req: >= 5)

Gene RIFs: 51   (req: > 3)

Antibodies: 463   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 28

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligands: 7

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Expression Data (0 Tissues)

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No expression data found

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Related Tools (4)

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Approved Drugs (0)

No approved drugs found

Active Ligands (7)

Explore Active Ligands

1 – 7 of 7

CHEMBL4750927

SDCBPTchem

pKi : 7.52

CHEMBL4781637

SDCBPTchem

pKi : 7.4

CHEMBL4799812

SDCBPTchem

pKi : 6.72

CHEMBL4749490

SDCBPTchem

pKi : 6.6

CHEMBL4758599

SDCBPTchem

pKi : 6.6

CHEMBL4792861

SDCBPTchem

pKi : 6.6

CHEMBL4747962

SDCBPTchem

pKi : 6.6

Protein-Protein Interactions (211)

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1 – 10 of 211

• See Interactions on String-DB

TARSL2

Tbio

Family:  Enzyme

Novelty:  0.02406282

p_int:  0.999942988

p_ni:  0.000057012

Score:  0.524

Data Source:  BioPlex,STRINGDB

AIMP1

Tbio

Family:  Enzyme

Novelty:  0.00743447

p_int:  0.999764334

p_ni:  0.000235666

Score:  0.828

Data Source:  BioPlex,STRINGDB

RARS

Tchem

Family:  Enzyme

Novelty:  0.00099479

p_int:  0.999487762

p_ni:  0.000512238

Score:  0.821

Data Source:  BioPlex,STRINGDB

AIMP2

Tchem

Family:  Enzyme

Novelty:  0.03283387

p_int:  0.997768809

p_ni:  0.002231191

Score:  0.815

Data Source:  BioPlex,STRINGDB

MANSC1

Tdark

Novelty:  0.91681036

p_int:  0.99687154

p_ni:  0.00312846

Data Source:  BioPlex

PCDHGA7

Tdark

Novelty:  1.67766171

p_int:  0.995036579

p_ni:  0.004955934

p_wrong:  0.000007487

Data Source:  BioPlex

WRAP73

Tbio

Novelty:  0.25394934

p_int:  0.993808405

p_ni:  0.006191595

Data Source:  BioPlex

LTBR

Tbio

Novelty:  0.003823

p_int:  0.991972423

p_ni:  0.008027577

Data Source:  BioPlex

DARS

Tbio

Family:  Enzyme

Novelty:  0.01101888

p_int:  0.983480748

p_ni:  0.016519252

Score:  0.817

Data Source:  BioPlex,STRINGDB

PSME2

Tbio

Novelty:  0.02624268

p_int:  0.978393776

p_ni:  0.02068423

p_wrong:  0.000921994

Score:  0.189

Data Source:  BioPlex,STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (17)

Reactome (9)

PathwayCommons (7)

WikiPathways (1)

Axon guidance (R-HSA-422475)

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5

1 – 5 of 9

Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Axon guidance	533 targets	R-HSA-422475
Reactome	Developmental Biology	1055 targets	R-HSA-1266738
Reactome	EPH-Ephrin signaling	92 targets	R-HSA-2682334
Reactome	Ephrin signaling	19 targets	R-HSA-3928664
Reactome	Immune System	2246 targets	R-HSA-168256

Name	Explore in Pharos	Explore in Source
Axon guidance	533 targets	R-HSA-422475
Developmental Biology	1055 targets	R-HSA-1266738
EPH-Ephrin signaling	92 targets	R-HSA-2682334
Ephrin signaling	19 targets	R-HSA-3928664
Immune System	2246 targets	R-HSA-168256

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (49)

Functions (8)

Components (21)

Processes (20)

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1 – 8 of 8

GO Term	Evidence	Assigned by
phosphatidylinositol-4,5-bisphosphate binding	Inferred from Direct Assay (IDA)	UniProtKB
frizzled binding	Inferred from Physical Interaction (IPI)	BHF-UCL
identical protein binding	Inferred from Physical Interaction (IPI)	IntAct
protein heterodimerization activity	Inferred from Physical Interaction (IPI)	UniProtKB
protein N-terminus binding	Inferred from Physical Interaction (IPI)	UniProtKB
syndecan binding	Inferred from Physical Interaction (IPI)	UniProtKB
interleukin-5 receptor binding	Inferred from Sequence or structural Similarity (ISS)	UniProtKB
cytoskeletal adaptor activity	Non-traceable Author Statement (NAS)	UniProtKB

Disease Associations (null)

No disease associations found

GWAS Traits (36)

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 36

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
low density lipoprotein cholesterol measurement	EFO_0004611	25	11	34		98.1
total cholesterol measurement	EFO_0004574	17	11	25		97.5
triglyceride measurement	EFO_0004530	18	8	19		95.6
apolipoprotein B measurement	EFO_0004615	3	4	4		93.1
serum gamma-glutamyl transferase measurement	EFO_0004532	2	3	3		87.9

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 36

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
low density lipoprotein cholesterol measurement	EFO_0004611	34		98.1
total cholesterol measurement	EFO_0004574	25		97.5
triglyceride measurement	EFO_0004530	19		95.6
apolipoprotein B measurement	EFO_0004615	4		93.1
serum gamma-glutamyl transferase measurement	EFO_0004532	3		87.9

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UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Acetylation
Alternative splicing
Cell junction
Cell membrane
Complete proteome
Cytoplasm
Cytoskeleton
Direct protein sequencing
Endoplasmic reticulum

GWAS Trait Find Similar Targets

No Header	No Header
apolipoprotein B measurement
aspartate aminotransferase measurement
basophil count
bile acid measurement
bilirubin measurement
Cholecystitis
cholelithiasis
cholesteryl ester measurement
chylomicron measurement
familial hyperlipidemia

IDG Resources

No IDG generated resources found

Orthologs (14)

1 – 5 of 14

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	syndecan binding protein	VGNC:800	464192
Macaque	syndecan binding protein		698381
Mouse	syndecan binding protein	MGI:1337026	53378
Rat	syndecan binding protein	RGD:621497	83841
Dog	syndecan binding protein		482977

Species	Name	OMA	EggNOG	Inparanoid
Chimp	syndecan binding protein
Macaque	syndecan binding protein
Mouse	syndecan binding protein
Rat	syndecan binding protein
Dog	syndecan binding protein

Publication Statistics

PubMed Score 647.64

PubMed score by year

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PubTator Score 275.44

PubTator score by year

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Related Publications

Text Mined References (97)

GeneRif Annotations (51)

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PMID	Year	Title