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Aliases for SDCBP Gene

Aliases for SDCBP Gene

  • Syndecan Binding Protein 2 3 5
  • Pro-TGF-Alpha Cytoplasmic Domain-Interacting Protein 18 3 4
  • Syndecan-Binding Protein 1 3 4
  • Scaffold Protein Pbp1 3 4
  • Syntenin-1 2 3
  • TACIP18 3 4
  • MDA-9 3 4
  • MDA9 3 4
  • SYCL 3 4
  • Melanoma Differentiation Associated Protein-9 3
  • Melanoma Differentiation-Associated Protein 9 4
  • Syndecan Binding Protein (Syntenin) 3
  • Syntenin 2
  • ST1 3

External Ids for SDCBP Gene

Previous GeneCards Identifiers for SDCBP Gene

  • GC08P059405
  • GC08P059188
  • GC08P059515
  • GC08P059628
  • GC08P054952

Summaries for SDCBP Gene

Entrez Gene Summary for SDCBP Gene

  • 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]

GeneCards Summary for SDCBP Gene

SDCBP (Syndecan Binding Protein) is a Protein Coding gene. Diseases associated with SDCBP include Pontiac Fever and Asthenopia. Among its related pathways are Innate Immune System and Syndecan-1-mediated signaling events. GO annotations related to this gene include protein homodimerization activity and protein heterodimerization activity. An important paralog of this gene is SDCBP2.

UniProtKB/Swiss-Prot for SDCBP Gene

  • 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).

Gene Wiki entry for SDCBP Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SDCBP Gene

Genomics for SDCBP Gene

Regulatory Elements for SDCBP Gene

Enhancers for SDCBP Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH08G058395 1.7 FANTOM5 Ensembl ENCODE dbSUPER 16.7 -156.1 -156102 3.2 SIX4 CTCF ATF1 MAX ZNF384 CEBPG ZNF48 RAD21 RFX5 ZNF316 SDCBP UBXN2B GC08P058299
GH08G058593 1.5 Ensembl ENCODE dbSUPER 10.9 +42.6 42622 4.0 PKNOX1 ATF1 ARNT SIN3A ZNF766 ELK1 GATA2 FOS JUNB NCOA1 SDCBP RPS26P7 GC08P058613
GH08G058616 1.2 FANTOM5 Ensembl dbSUPER 12.6 +63.8 63814 0.5 JUND ZNF589 ATF3 STAT3 CEBPB TRIM24 CEBPG EP300 SDCBP GC08P058613 GC08P058645
GH08G058552 1.3 ENCODE dbSUPER 9.5 +1.1 1090 3.2 HNRNPUL1 ARNT ARID4B SIN3A DMAP1 ZBTB7B YY1 ZNF143 ZNF207 FOS SDCBP RPS26P7
GH08G058557 1.1 Ensembl ENCODE dbSUPER 10.5 +5.4 5419 1.7 SREBF1 JUND ATF3 NR2C1 FOS HNF4A SDCBP RPS26P7
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SDCBP on UCSC Golden Path with GeneCards custom track

Promoters for SDCBP Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000224935 1176 3401 HNRNPUL1 ARNT ARID4B SIN3A DMAP1 ZBTB7B ZNF143 ZNF207 FOS SP3

Genomic Location for SDCBP Gene

Chromosome:
8
Start:
58,552,924 bp from pter
End:
58,582,860 bp from pter
Size:
29,937 bases
Orientation:
Plus strand

Genomic View for SDCBP Gene

Genes around SDCBP on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SDCBP Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SDCBP Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SDCBP Gene

Proteins for SDCBP Gene

  • Protein details for SDCBP Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O00560-SDCB1_HUMAN
    Recommended name:
    Syntenin-1
    Protein Accession:
    O00560
    Secondary Accessions:
    • B2R5Q7
    • B4DUH3
    • B7ZLN2
    • O00173
    • O43391
    • Q14CP2

    Protein attributes for SDCBP Gene

    Size:
    298 amino acids
    Molecular mass:
    32444 Da
    Quaternary structure:
    • Monomer and homodimer (By similarity). Interacts with SDC1, SDC2, SDC3, SDC4, NRXN2, EPHA7, EPHB1, NF2 isoform 1, TGFA and IL5RA. Interacts with neurofascin, SDCBP2 and PTPRJ (By similarity). Interacts with PDCD6IP (PubMed:22660413). Forms a complex with PDCD6IP and SDC2 (PubMed:22660413). Interacts (via C-terminus) with TGFBR1 (PubMed:25893292). Binds to FZD7; this interaction is increased by inositol trisphosphate (IP3) (PubMed:27386966).

    Three dimensional structures from OCA and Proteopedia for SDCBP Gene

    Alternative splice isoforms for SDCBP Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SDCBP Gene

Post-translational modifications for SDCBP Gene

No data available for DME Specific Peptides for SDCBP Gene

Domains & Families for SDCBP Gene

Gene Families for SDCBP Gene

Protein Domains for SDCBP Gene

InterPro:
Blocks:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SDCBP: view

No data available for UniProtKB/Swiss-Prot for SDCBP Gene

Function for SDCBP Gene

Molecular function for SDCBP Gene

UniProtKB/Swiss-Prot Function:
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).
UniProtKB/Swiss-Prot Induction:
By IFNG/IFN-gamma in melanoma cells.

Gene Ontology (GO) - Molecular Function for SDCBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005109 frizzled binding IPI 18256285
GO:0005137 interleukin-5 receptor binding IEA,ISS 11498591
GO:0005515 protein binding IPI 18256285
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding IDA 27386966
GO:0008022 protein C-terminus binding IEA --
genes like me logo Genes that share ontologies with SDCBP: view
genes like me logo Genes that share phenotypes with SDCBP: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SDCBP Gene

Localization for SDCBP Gene

Subcellular locations from UniProtKB/Swiss-Prot for SDCBP Gene

Cell junction, focal adhesion. Cell junction, adherens junction. Cell membrane; Peripheral membrane protein. Endoplasmic reticulum membrane; Peripheral membrane protein. Nucleus. Melanosome. Cytoplasm, cytosol. Cytoplasm, cytoskeleton. Secreted, exosome. Membrane raft. Note=Mainly membrane-associated. Localized to adherens junctions, focal adhesions and endoplasmic reticulum. Colocalized with actin stress fibers. Also found in the nucleus. Identified by mass spectrometry in melanosome fractions from stage I to stage IV. Associated to the plasma membrane in the presence of FZD7 and phosphatidylinositol 4,5-bisphosphate (PIP2) (PubMed:27386966). {ECO:0000269 PubMed:11179419, ECO:0000269 PubMed:12643545, ECO:0000269 PubMed:17081065, ECO:0000269 PubMed:27386966}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SDCBP gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytoskeleton 5
nucleus 5
cytosol 5
lysosome 4
endoplasmic reticulum 3
peroxisome 1

Gene Ontology (GO) - Cellular Components for SDCBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA,TAS --
GO:0005615 extracellular space IDA 16502470
GO:0005622 intracellular IEA --
GO:0005634 nucleus NAS 11179419
GO:0005654 nucleoplasm IDA --
genes like me logo Genes that share ontologies with SDCBP: view

Pathways & Interactions for SDCBP Gene

genes like me logo Genes that share pathways with SDCBP: view

Gene Ontology (GO) - Biological Process for SDCBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002091 negative regulation of receptor internalization IMP 25893292
GO:0006612 protein targeting to membrane NAS 10230395
GO:0006930 substrate-dependent cell migration, cell extension NAS 12037664
GO:0007265 Ras protein signal transduction IEA --
GO:0007268 chemical synaptic transmission NAS,IEA 9883737
genes like me logo Genes that share ontologies with SDCBP: view

No data available for SIGNOR curated interactions for SDCBP Gene

Drugs & Compounds for SDCBP Gene

(1) Drugs for SDCBP Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for SDCBP Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SDCBP: view

Transcripts for SDCBP Gene

Unigene Clusters for SDCBP Gene

Syndecan binding protein (syntenin):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SDCBP Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b · 8c · 8d · 8e · 8f ^ 9a · 9b · 9c ^ 10 ^ 11a ·
SP1: - - - - - - -
SP2: - - - - - - -
SP3: - - - - - - -
SP4: - - - - - -
SP5: - - - -
SP6: - - - - -
SP7: - - - - - - - -
SP8: - - - - - -
SP9: - - - - -
SP10: - - -
SP11: - -
SP12:
SP13: -
SP14:

ExUns: 11b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

Relevant External Links for SDCBP Gene

GeneLoc Exon Structure for
SDCBP
ECgene alternative splicing isoforms for
SDCBP

Expression for SDCBP Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SDCBP Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SDCBP Gene

This gene is overexpressed in Whole Blood (x9.5).

Protein differential expression in normal tissues from HIPED for SDCBP Gene

This gene is overexpressed in Urine (13.7), Amniocyte (9.4), and Milk (8.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SDCBP Gene



Protein tissue co-expression partners for SDCBP Gene

NURSA nuclear receptor signaling pathways regulating expression of SDCBP Gene:

SDCBP

SOURCE GeneReport for Unigene cluster for SDCBP Gene:

Hs.200804

mRNA Expression by UniProt/SwissProt for SDCBP Gene:

O00560-SDCB1_HUMAN
Tissue specificity: Expressed in lung cancers, including adenocarcinoma, squamous cell carcinoma and small-cell carcinoma (at protein level) (PubMed:25893292). Widely expressed. Expressed in fetal kidney, liver, lung and brain. In adult highest expression in heart and placenta.

Evidence on tissue expression from TISSUES for SDCBP Gene

  • Nervous system(5)
  • Blood(4.9)
  • Liver(4.7)
  • Intestine(4.5)
  • Skin(4.2)
  • Lung(3.9)
  • Kidney(3.7)
  • Pancreas(2.8)
  • Stomach(2.7)
  • Lymph node(2.5)
  • Spleen(2.3)
  • Gall bladder(2.1)
  • Bone marrow(2)
genes like me logo Genes that share expression patterns with SDCBP: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SDCBP Gene

Orthologs for SDCBP Gene

This gene was present in the common ancestor of animals.

Orthologs for SDCBP Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SDCBP 34 35
  • 99.89 (n)
dog
(Canis familiaris)
Mammalia -- 35
  • 95 (a)
OneToMany
SDCBP 34
  • 93.06 (n)
-- 35
  • 92 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Sdcbp 34 16 35
  • 87.25 (n)
rat
(Rattus norvegicus)
Mammalia Sdcbp 34
  • 86.35 (n)
cow
(Bos Taurus)
Mammalia SDCBP 34 35
  • 86.24 (n)
oppossum
(Monodelphis domestica)
Mammalia SDCBP 35
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SDCBP 35
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves SDCBP 34 35
  • 80.27 (n)
lizard
(Anolis carolinensis)
Reptilia SDCBP 35
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sdcbp 34
  • 74.58 (n)
Str.6014 34
African clawed frog
(Xenopus laevis)
Amphibia sdcbp-prov 34
zebrafish
(Danio rerio)
Actinopterygii sdcbp 34 35
  • 64.05 (n)
Dr.1778 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009569 34
  • 53.27 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6469 35
  • 56 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5544 34
Species where no ortholog for SDCBP was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SDCBP Gene

ENSEMBL:
Gene Tree for SDCBP (if available)
TreeFam:
Gene Tree for SDCBP (if available)

Paralogs for SDCBP Gene

Paralogs for SDCBP Gene

(1) SIMAP similar genes for SDCBP Gene using alignment to 4 proteins:

Pseudogenes.org Pseudogenes for SDCBP Gene

genes like me logo Genes that share paralogs with SDCBP: view

Variants for SDCBP Gene

Sequence variations from dbSNP and Humsavar for SDCBP Gene

SNP ID Clin Chr 08 pos Sequence Context AA Info Type
rs1000044173 -- 58,566,930(+) AAATC(C/G)TGACA intron-variant
rs1000135383 -- 58,553,819(+) GAAGT(A/G)TTTGT intron-variant
rs1000146784 -- 58,561,192(+) AAAAG(A/G)AAAAA intron-variant, utr-variant-5-prime
rs1000206805 -- 58,573,955(+) CAAAG(-/T)TCAAA intron-variant
rs1000213179 -- 58,565,317(+) TTACA(C/T)TTTTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SDCBP Gene

Variant ID Type Subtype PubMed ID
esv3307770 CNV mobile element insertion 20981092
esv3346499 CNV insertion 20981092
esv3617340 CNV gain 21293372
esv3891402 CNV gain 25118596
nsv1031537 CNV gain 25217958
nsv1075140 CNV deletion 25765185
nsv397168 CNV deletion 16902084
nsv831325 CNV gain 17160897
nsv981944 CNV duplication 23825009

Variation tolerance for SDCBP Gene

Residual Variation Intolerance Score: 38.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.43; 28.01% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SDCBP Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SDCBP

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SDCBP Gene

Disorders for SDCBP Gene

MalaCards: The human disease database

(3) MalaCards diseases for SDCBP Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
pontiac fever
asthenopia
  • accommodative strain
disuse amblyopia
  • deprivation amblyopia
- elite association - COSMIC cancer census association via MalaCards
Search SDCBP in MalaCards View complete list of genes associated with diseases

Relevant External Links for SDCBP

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SDCBP
genes like me logo Genes that share disorders with SDCBP: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SDCBP Gene

Publications for SDCBP Gene

  1. The PDZ2 domain of syntenin at ultra-high resolution: bridging the gap between macromolecular and small molecule crystallography. (PMID: 15081807) Kang B.S. … Derewenda Z.S. (J. Mol. Biol. 2004) 3 4 22 64
  2. PDZ tandem of human syntenin: crystal structure and functional properties. (PMID: 12679023) Kang B.S. … Derewenda Z.S. (Structure 2003) 3 4 22 64
  3. Characterization of syntenin, a syndecan-binding PDZ protein, as a component of cell adhesion sites and microfilaments. (PMID: 11179419) Zimmermann P. … David G. (Mol. Biol. Cell 2001) 3 4 22 64
  4. Schwannomin isoform-1 interacts with syntenin via PDZ domains. (PMID: 11432873) Jannatipour M. … Rouleau G.A. (J. Biol. Chem. 2001) 3 4 22 64
  5. Cytokine-specific transcriptional regulation through an IL-5Ralpha interacting protein. (PMID: 11498591) Geijsen N. … Coffer P.J. (Science 2001) 3 4 22 64

Products for SDCBP Gene

Sources for SDCBP Gene

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