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Aliases for SDCBP Gene

Aliases for SDCBP Gene

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

External Ids for SDCBP Gene

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. [provided by RefSeq, Jul 2008]

GeneCards Summary for SDCBP Gene

SDCBP (Syndecan Binding Protein (Syntenin)) is a Protein Coding gene. Diseases associated with SDCBP include melanoma and asthenopia. Among its related pathways are L1CAM interactions and Syndecan-4-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

  • Seems to function as an adapter protein. 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). May also play a role in vesicular trafficking. Seems to be required for the targeting of TGFA to the cell surface in the early secretory pathway.

Gene Wiki entry for SDCBP Gene

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

Genomics for SDCBP Gene

Genomic Location for SDCBP Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SDCBP Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SDCBP Gene

Regulatory Elements 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).

    Three dimensional structures from OCA and Proteopedia for SDCBP Gene

    Alternative splice isoforms for SDCBP Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SDCBP Gene

Proteomics data for SDCBP Gene at MOPED

Post-translational modifications for SDCBP Gene

No data available for DME Specific Peptides for SDCBP Gene

Domains for SDCBP Gene

Protein Domains for SDCBP Gene

InterPro:
Blocks:
ProtoNet:

UniProtKB/Swiss-Prot:

SDCB1_HUMAN
Domain:
  • Contains 2 PDZ (DHR) domains.:
    • O00560
genes like me logo Genes that share domains with SDCBP: view

No data available for Gene Families for SDCBP Gene

Function for SDCBP Gene

Molecular function for SDCBP Gene

UniProtKB/Swiss-Prot Function: Seems to function as an adapter protein. 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). May also play a role in vesicular trafficking. Seems to be required for the targeting of TGFA to the cell surface in the early secretory pathway.
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:0001948 glycoprotein binding IEA --
GO:0005109 frizzled binding IPI 18256285
GO:0005137 interleukin-5 receptor binding ISS 11498591
GO:0005515 protein binding IPI 18256285
GO:0008022 protein C-terminus binding IEA --
genes like me logo Genes that share ontologies with SDCBP: view

Phenotypes for SDCBP Gene

GenomeRNAi human phenotypes for SDCBP:
genes like me logo Genes that share phenotypes with SDCBP: view

miRNA for SDCBP Gene

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting 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. 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.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SDCBP Gene COMPARTMENTS Subcellular localization image for SDCBP gene
Compartment Confidence
cytoskeleton 5
cytosol 5
endoplasmic reticulum 5
extracellular 5
nucleus 5
plasma membrane 5
chloroplast 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for SDCBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA 16502470
GO:0005634 nucleus NAS 11179419
GO:0005737 cytoplasm IDA 18256285
GO:0005783 endoplasmic reticulum --
GO:0005789 endoplasmic reticulum membrane IEA --
genes like me logo Genes that share ontologies with SDCBP: view

Pathways 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: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 synaptic transmission NAS 9883737
GO:0007411 axon guidance TAS --
genes like me logo Genes that share ontologies with SDCBP: view

Compounds for SDCBP Gene

(4) Novoseek inferred chemical compound relationships for SDCBP Gene

Compound -log(P) Hits PubMed IDs
pip2 65.7 4
heparan sulfate 28.4 1
kainate 20.6 4
glutamate 1.07 1
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:

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 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 (9.5).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for SDCBP Gene

SOURCE GeneReport for Unigene cluster for SDCBP Gene Hs.200804

mRNA Expression by UniProt/SwissProt for SDCBP Gene

O00560-SDCB1_HUMAN
Tissue specificity: Widely expressed. Expressed in fetal kidney, liver, lung and brain. In adult highest expression in heart and placenta
genes like me logo Genes that share expressions with SDCBP: view

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 36
  • 99.89 (n)
  • 100 (a)
SDCBP 37
  • 93 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SDCBP 36
  • 86.24 (n)
  • 92.95 (a)
SDCBP 37
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 37
  • 92 (a)
OneToMany
-- 37
  • 95 (a)
OneToMany
SDCBP 36
  • 93.06 (n)
  • 94.63 (a)
mouse
(Mus musculus)
Mammalia Sdcbp 36
  • 87.25 (n)
  • 90.6 (a)
Sdcbp 16
Sdcbp 37
  • 90 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SDCBP 37
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SDCBP 37
  • 77 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sdcbp 36
  • 86.35 (n)
  • 89.93 (a)
chicken
(Gallus gallus)
Aves SDCBP 36
  • 80.27 (n)
  • 88.78 (a)
SDCBP 37
  • 88 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SDCBP 37
  • 87 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia sdcbp-prov 36
tropical clawed frog
(Silurana tropicalis)
Amphibia sdcbp 36
  • 74.58 (n)
  • 78.98 (a)
Str.6014 36
zebrafish
(Danio rerio)
Actinopterygii Dr.1778 36
sdcbp 36
  • 64.05 (n)
  • 70.65 (a)
sdcbp 37
  • 59 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009569 36
  • 53.27 (n)
  • 51.01 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5544 36
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6469 37
  • 56 (a)
OneToMany
Species with no ortholog for SDCBP:
  • 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

Selected 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 MAF
rs2997 -- 58,581,917(+) ATTTC(A/C)AAATA utr-variant-3-prime
rs1044304 -- 58,582,798(+) TTCTT(C/T)TTTTT utr-variant-3-prime
rs1803071 -- 58,581,856(+) GGACC(C/T)TTCTA utr-variant-3-prime
rs1803072 -- 58,581,798(+) CAACT(C/T)CTGTA utr-variant-3-prime
rs1976162 -- 58,580,347(+) AAGCA(A/G)TTTGG intron-variant

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

Variant ID Type Subtype PubMed ID
nsv890938 CNV Gain 21882294
nsv890939 CNV Gain 21882294
esv272044 CNV Insertion 20981092
nsv397168 CNV Loss 16902084
nsv831325 CNV Gain 17160897

Relevant External Links for SDCBP Gene

HapMap Linkage Disequilibrium report
SDCBP

Disorders for SDCBP Gene

(2) MalaCards Diseases for SDCBP Gene

Search for SDCBP Gene in MalaCards »

(1) University of Copenhagen DISEASES for SDCBP Gene

(5) Novoseek inferred disease relationships for SDCBP Gene

Disease -log(P) Hits PubMed IDs
neurofibromatosis type 2 58.3 1
melanoma 40.4 26
metastasis 28.9 18
cancer 14.9 13
tumors 6.64 10
genes like me logo Genes that share disorders with SDCBP: view

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

Publications for SDCBP Gene

  1. 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 23
  2. Schwannomin isoform-1 interacts with syntenin via PDZ domains. (PMID: 11432873) Jannatipour M. … Rouleau G.A. (J. Biol. Chem. 2001) 3 4 23
  3. Cytokine-specific transcriptional regulation through an IL-5Ralpha interacting protein. (PMID: 11498591) Geijsen N. … Coffer P.J. (Science 2001) 3 4 23
  4. A role for a PDZ protein in the early secretory pathway for the targeting of proTGF-alpha to the cell surface. (PMID: 10230395) Fernandez-Larrea J. … Arribas J. (Mol. Cell 1999) 3 4 23
  5. 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 23

Products for SDCBP Gene

Sources for SDCBP Gene

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