Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

SDCBP (syndecan binding protein (syntenin))

Written2012-10Rosaria Gangemi, Ulrich Pfeffer, Silvano Ferrini
Lab of Immunotherapy, Functional Genomics Istituto Nazionale per la Ricerca sul Cancro, 16132 Genova, Italy

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)SYCL
MDA-9
Other aliasST1
TACIP18
HGNC (Hugo) SDCBP
LocusID (NCBI) 6386
Atlas_Id 44377
Location 8q12.1  [Link to chromosome band 8q12]
Location_base_pair Starts at 59465728 and ends at 59495419 bp from pter ( according to hg19-Feb_2009)  [Mapping SDCBP.png]
Local_order The human SDCBP gene maps on 8q12 between the NSMAF (neutral sphingomyelinase activation associated factor) and the CYP7A1 (cytochrome P450, family 7, subfamily A, polypeptide 1) loci, which are both in the opposite orientation.
Fusion genes
(updated 2016)
CDK5 (7q36.1) / SDCBP (8q12.1)SDCBP (8q12.1) / RAB7A (3q21.3)SDCBP (8q12.1) / SDCBP (8q12.1)
Note No translocations reported.

DNA/RNA

 
  SDCBP gene organization, mRNA and encoded proteins. The SDCBP gene is comprised of 9 exons and results in 5 alternatively spliced transcript variants (TV), which encode for three different protein isoforms (additional transcripts variants were also reported). Coding exons are in blue and UTRs in yellow. Transcript variants 1 and 2 differ only in their 5' UTR regions and encode for the same full-length protein, named isoform 1. Transcript variant 3 derives from the usage of an alternative in frame splice-site in the 5' coding region (exon 1) and encodes for the protein isoform 2, lacking 6 residues. Transcript variant 4 uses an alternative splice site in exon 5 resulting in a protein isoform lacking one residue (isoform 3). Transcript variant 5 differs from variant 4 in the 5' UTR and encodes for the same protein isoform 3. Protein isoform 2 and 3 partial aa sequencies that differ from isoform 1 are in red characters.
Description The SDCBP gene is comprised of 9 exons, spanning 2,96 kb on chromosome 8q12.
The SDCBP promoter region has not been functionally explored, although two studies (Lin et al., 1998; Stier et al., 2000) describe SDCBP as an interferon-gamma and TNF-alpha inducible gene. Among predicted transcription factor binding sites upstream the transcription start site of SDCBP there are: Nf-KappaB, Nf-KappaB1 and p53.
Transcription Five alternatively spliced transcript variants of SDCBP, each comprising 9 exons, have been described.

Protein

Description SDCBP gene codes for a syntenin protein of 298 amino acid residues with a predicted molecular mass of 33 kDa (Lin et al., 1998; Grootjans et al., 1997). Three isoforms are produced by alternative splicing: isoform 1 (NP_001007068.1) which represents the full-length protein of 298 aa; isoform 2 (NP_001007069) of 292 aa missing residues 12-17; isoform 3 (NP_001007070) of 297 aa missing residue 81. Syntenin is a scaffolding protein, endowed with several biological activities and involved in cancer metastases development (reviewed in Das et al., 2012a). The molecule has four domains: an N-terminal domain (aa 1-113) with no homology to known structural motifs, two PDZ domains (PDZ-1 aa 114-193 and PDZ-2 aa 198-273) and a COOH-terminal domain. The crystal structure of the two PDZ domains showed independent interaction of each domain with protein targets (Cierpicki et al., 2005; Kang et al., 2004).
Postranslational modifications: syntenin can be phosphorylated on tyrosine (Sulka et al., 2009) and serine residues (Rajesh et al., 2011).
Expression SDCBP is expressed in fetal kidney, liver, lung and brain. In adult high expression is present in hearth and placenta (Lin et al., 1998; Zimmermann et al., 2001). It is also expressed in several human tumor cell lines. Several types of tumors express high levels of SDCBP such as gastric, colon and breast carcinomas (Koo et al., 2002), cutaneous (Helmke et al., 2004) and uveal melanoma (Gangemi et al., 2012).
Localisation SDCBP protein is localized to adherens junctions, focal adhesion plaques, inner side of the cell membrane, cytoplasm, endoplasmic reticulum, cytoskeleton (Zimmermann et al., 2001), nucleus (Gangemi et al., 2012) and melanosomes (Basrur et al., 2003). It is also present in cell-released exosomes (Baietti et al., 2012).
 
  Syntenin protein-protein interactions. Syntenin is an adaptor protein, which interacts with multiple proteins and has several intracellular functions.
Function SDCBP was identified as melanoma differentiation-associated gene (MDA)-9 (Lin et al., 1998). The same gene was independently cloned and named syntenin, by yeast two hybrid screening. Syntenin interacts through its PDZ domains with the heparan-sulfates syndecans, which are involved in molecular recognition, signaling, and cell trafficking (Grootjans et al., 1997). Through its binding with syndecans and PIP2, syntenin mediates syndecan recycling through endosomal compartments (Zimmermann et al., 2002). This process modulates the surface availability of growth factor receptors such as FGFR, which follows syndecan in the recycling pathway (Zimmermann et al., 2005). Syntenin binds the C-terminal domain of the pro-transforming growth factor α (proTGFα) (Fernández-Larrea et al., 1999) and to the Delta1 ligand of Notch (Estrach et al., 2007), tethering them to the cell surface. In addition, syntenin directly interacts with the C-terminal of Frizzled 7 and supports non-canonical Wnt signaling (Wawrzak et al., 2009).
Syntenin binds to the cytoplasmic tail of the tetraspanin CD63 at the plasma membrane and is therefore part of the tetraspanin-enriched microdomains (Latysheva et al., 2006). The over-expression of syntenin can limit internalization of CD63, suggesting a role for syntenin as a regulator of endocytosis.
Syntenin is involved in the establishment and maintenance of synaptic structures through its interaction with several adhesion molecules, such as neurofascin (Koroll et al., 2001). Presynaptic development also depends upon the interaction of the syntenin PDZ domains with ephrin-B1 and ephrin-B2 (McClelland et al., 2009). SDCBP participates in the formation and maturation of synapses and colocalizes with Glutamate receptors at growth cones (Hirbec et al., 2005). Outgrowth of developing axon is also regulated by syntenin, which provides a scaffold for the serine/threonine kinase Unc51.1 and for Rab5 GTPase (Tomoda et al., 2004).
Syntenin participates in B cell development and differentiation by interacting with interleukin-5 (IL-5) receptor α and the transcription factor Sox4 and mediates IL-5-induced Sox4 activation (Geijsen et al., 2001). Proteosomal degradation of Sox4 is prevented by the binding of its c terminal domain with SDCBP, which contributes to its localization into the nucleus (Beekman et al., 2012).
Syntenin mediates the generation of functional asymmetry in T cells during the cellular response to polarized extracellular cues, through the generation of polarized actin structures (Sala-Valdés et al., 2012).
Syntenin interacts with Ubiquitin through is C- and N-terminal regions and facilitates the recruitment of ubiquitinated proteins to its transmembrane partners. The process is facilitated by syntenin dimerization and is inhibited by phosphorylation of its serin in the N terminal domain mediated by Ulk1 (Rajesh et al., 2011).
Syntenin has a key role in exosome formation through the binding of syndecan 1, syndecan 2, syndecan 3, syndecan 4 with the PDZ domains and ALIX with the N-terminal domain (Baietti et al., 2012).
Homology The SDCBP gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and mosquito (NCBI).
Paralog: SDCBP2.
SDCBP is highly related to SDCBP2 at the amino acid level (70% over the PDZ domains) and in the domains organization (Koroll et al., 2001).

Mutations

Note Not yet described. Genetic polymorphisms of SDCBP (561 SNPs) have been reported (NCBI) but their relationship to disease is unknown.

Implicated in

Note
  
Entity Cutaneous melanoma
Note SDCBP gene was identified as an interferon-inducible gene in melanoma cells (Lin et al., 1998). A subtractory library approach of candidate metastasis genes identified the syntenin gene, which was overexpressed in cutaneous melanoma specimens relative to melanocytic nevi (Helmke et al., 2004). Altering syntenin expression by gene transduction modulates the metastatic ability of human melanoma cells (Boukerche et al., 2005). Syntenin over-expression increased phosphorylation of focal adhesion kinase, c-Jun-NH2-kinase, p38, and nuclear factor-kappaB (NF-kappaB) in human melanoma cells. As a consequence tumor cell growth and motility are enhanced. The induction of membrane-type matrix metalloproteinase (MMP)-1 and MMP-2 promotes extracellular matrix invasion (Boukerche et al., 2007). Syntenin binds c-Src and mediates the formation of an active FAK/c-Src complex, increasing melanoma cell invasive properties (Boukerche et al., 2008). In addition, src kinase activation is required for syntenin-mediated activation of NF-kappaB (Boukerche et al., 2010). Further studies indicated that syntenin acts as a molecular adaptor linking PKCalpha and FAK activation during human breast cancer and melanoma cell adhesion to fibronectin (Hwangbo et al., 2010).
The Raf kinase inhibitor RKIP, is downregulated in metastatic melanoma cells. The study of melanoma arrays and cell lines showed an inverse relationship between syntenin and RKIP expression during melanoma progression. Syntenin transcriptionally downregulated RKIP and also physically interacted with RKIP protein. Ectopic RKIP expression in melanoma cells inhibited syntenin signaling, cell invasion and growth and in vivo dissemination of melanoma cells. Therefore RKIP acts as an inhibitor of syntenin-dependent melanoma metastasis (Das et al., 2012b).
Disease Metastatic melanoma.
  
  
Entity Uveal melanoma
Note Uveal melanoma is a rare tumor of the eye, distinct from cutaneous melanoma on the basis of genetic alterations and clinical behavior. High expression of SDCBP gene correlated with metastatic progression in three gene expression profile datasets of primary uveal melanomas. High expression of syntenin protein in primary tumors was also related to metastatic recurrence. Syntenin was aslo highly expressed in liver metastases from patients and from xenografted mice. Silencing of syntenin inhibited uveal melanoma cell migration and hepatocyte growth factor (HGF)-triggered invasion, activation of FAK, AKT and Src. Conversely syntenin overexpression mediated opposite effects (Gangemi et al., 2012).
Disease Metastatic uveal melanoma.
  
  
Entity Gastric and breast cancers
Note The expression level of syntenin was related with invasive potential in human breast and gastric cancer cells in vitro. Syntenin gene was highly expressed in gastric cancer tissues. Syntenin overexpression in human gastric or breast cancer cells increased their migration in vitro and induced pseudopodia formation on collagen I. Mutation studies suggested that the PDZ2 domain of syntenin is involved in the stimulatory effect on cell migration (Koo et al., 2002).
  
  
Entity Colon cancer
Note The proteoglycan syndecan-2 is involved in tumorigenicity of colon cancer cells. Syndecan-2-induced migration requires the EFYA motif in its C-terminal region as its deletion inhibited cell migration and interaction with syntenin. In addition, overexpression of syntenin in colon cancer cells enhanced their migratory capacity, while syntenin silencing had opposite effects. Syntenin interaction with syndecan-2 mediates Rac activation, and colon cancer cell migration (Lee et al., 2011).
  
  
Entity HIV infection
Note Syntenin is recruited to the plasma membrane during HIV-1 attachment and associates with CD4. Syntenin overexpression inhibits HIV-1 production and HIV-mediated cell fusion, while syntenin depletion increases HIV-1 entry, suggesting a regulatory role of syntenin in HIV-1 entry (Gordón-Alonso et al., 2012).
Disease AIDS.
  

Bibliography

Syndecan-syntenin-ALIX regulates the biogenesis of exosomes.
Baietti MF, Zhang Z, Mortier E, Melchior A, Degeest G, Geeraerts A, Ivarsson Y, Depoortere F, Coomans C, Vermeiren E, Zimmermann P, David G.
Nat Cell Biol. 2012 Jun 3;14(7):677-85. doi: 10.1038/ncb2502.
PMID 22660413
 
Proteomic analysis of early melanosomes: identification of novel melanosomal proteins.
Basrur V, Yang F, Kushimoto T, Higashimoto Y, Yasumoto K, Valencia J, Muller J, Vieira WD, Watabe H, Shabanowitz J, Hearing VJ, Hunt DF, Appella E.
J Proteome Res. 2003 Jan-Feb;2(1):69-79.
PMID 12643545
 
Syntenin-mediated regulation of Sox4 proteasomal degradation modulates transcriptional output.
Beekman JM, Vervoort SJ, Dekkers F, van Vessem ME, Vendelbosch S, Brugulat-Panes A, van Loosdregt J, Braat AK, Coffer PJ.
Oncogene. 2012 May 24;31(21):2668-79. doi: 10.1038/onc.2011.445. Epub 2011 Oct 10.
PMID 21986941
 
Src kinase activation is mandatory for MDA-9/syntenin-mediated activation of nuclear factor-kappaB.
Boukerche H, Aissaoui H, Prevost C, Hirbec H, Das SK, Su ZZ, Sarkar D, Fisher PB.
Oncogene. 2010 May 27;29(21):3054-66. doi: 10.1038/onc.2010.65. Epub 2010 Mar 15.
PMID 20228839
 
Probing the supramodular architecture of a multidomain protein: the structure of syntenin in solution.
Cierpicki T, Bushweller JH, Derewenda ZS.
Structure. 2005 Feb;13(2):319-27.
PMID 15698575
 
Raf Kinase Inhibitor RKIP Inhibits MDA-9/Syntenin-Mediated Metastasis in Melanoma.
Das SK, Bhutia SK, Sokhi UK, Azab B, Su ZZ, Boukerche H, Anwar T, Moen EL, Chatterjee D, Pellecchia M, Sarkar D, Fisher PB.
Cancer Res. 2012b Dec 1;72(23):6217-26. doi: 10.1158/0008-5472.CAN-12-0402. Epub 2012 Oct 11.
PMID 23066033
 
Syntenin mediates Delta1-induced cohesiveness of epidermal stem cells in culture.
Estrach S, Legg J, Watt FM.
J Cell Sci. 2007 Aug 15;120(Pt 16):2944-52. Epub 2007 Jul 31.
PMID 17666427
 
A role for a PDZ protein in the early secretory pathway for the targeting of proTGF-alpha to the cell surface.
Fernandez-Larrea J, Merlos-Suarez A, Urena JM, Baselga J, Arribas J.
Mol Cell. 1999 Apr;3(4):423-33.
PMID 10230395
 
Mda-9/syntenin is expressed in uveal melanoma and correlates with metastatic progression.
Gangemi R, Mirisola V, Barisione G, Fabbi M, Brizzolara A, Lanza F, Mosci C, Salvi S, Gualco M, Truini M, Angelini G, Boccardo S, Cilli M, Airoldi I, Queirolo P, Jager MJ, Daga A, Pfeffer U, Ferrini S.
PLoS One. 2012;7(1):e29989. doi: 10.1371/journal.pone.0029989. Epub 2012 Jan 13.
PMID 22267972
 
Cytokine-specific transcriptional regulation through an IL-5Ralpha interacting protein.
Geijsen N, Uings IJ, Pals C, Armstrong J, McKinnon M, Raaijmakers JA, Lammers JW, Koenderman L, Coffer PJ.
Science. 2001 Aug 10;293(5532):1136-8.
PMID 11498591
 
The PDZ-adaptor protein syntenin-1 regulates HIV-1 entry.
Gordon-Alonso M, Rocha-Perugini V, Alvarez S, Moreno-Gonzalo O, Ursa A, Lopez-Martin S, Izquierdo-Useros N, Martinez-Picado J, Munoz-Fernandez MA, Yanez-Mo M, Sanchez-Madrid F.
Mol Biol Cell. 2012 Jun;23(12):2253-63. doi: 10.1091/mbc.E11-12-1003. Epub 2012 Apr 25.
PMID 22535526
 
Syntenin, a PDZ protein that binds syndecan cytoplasmic domains.
Grootjans JJ, Zimmermann P, Reekmans G, Smets A, Degeest G, Durr J, David G.
Proc Natl Acad Sci U S A. 1997 Dec 9;94(25):13683-8.
PMID 9391086
 
Melanoma metastasis is associated with enhanced expression of the syntenin gene.
Helmke BM, Polychronidis M, Benner A, Thome M, Arribas J, Deichmann M.
Oncol Rep. 2004 Aug;12(2):221-8.
PMID 15254681
 
Syntenin is involved in the developmental regulation of neuronal membrane architecture.
Hirbec H, Martin S, Henley JM.
Mol Cell Neurosci. 2005 Apr;28(4):737-46.
PMID 15797720
 
Activation of the integrin effector kinase focal adhesion kinase in cancer cells is regulated by crosstalk between protein kinase Calpha and the PDZ adapter protein mda-9/Syntenin.
Hwangbo C, Kim J, Lee JJ, Lee JH.
Cancer Res. 2010 Feb 15;70(4):1645-55. doi: 10.1158/0008-5472.CAN-09-2447. Epub 2010 Feb 9.
PMID 20145126
 
The PDZ2 domain of syntenin at ultra-high resolution: bridging the gap between macromolecular and small molecule crystallography.
Kang BS, Devedjiev Y, Derewenda U, Derewenda ZS.
J Mol Biol. 2004 Apr 30;338(3):483-93.
PMID 15081807
 
Syntenin is overexpressed and promotes cell migration in metastatic human breast and gastric cancer cell lines.
Koo TH, Lee JJ, Kim EM, Kim KW, Kim HD, Lee JH.
Oncogene. 2002 Jun 13;21(26):4080-8.
PMID 12037664
 
The neural cell recognition molecule neurofascin interacts with syntenin-1 but not with syntenin-2, both of which reveal self-associating activity.
Koroll M, Rathjen FG, Volkmer H.
J Biol Chem. 2001 Apr 6;276(14):10646-54. Epub 2001 Jan 4.
PMID 11152476
 
Syntenin-1 is a new component of tetraspanin-enriched microdomains: mechanisms and consequences of the interaction of syntenin-1 with CD63.
Latysheva N, Muratov G, Rajesh S, Padgett M, Hotchin NA, Overduin M, Berditchevski F.
Mol Cell Biol. 2006 Oct;26(20):7707-18. Epub 2006 Aug 14.
PMID 16908530
 
Syndecan-2 cytoplasmic domain regulates colon cancer cell migration via interaction with syntenin-1.
Lee H, Kim Y, Choi Y, Choi S, Hong E, Oh ES.
Biochem Biophys Res Commun. 2011 May 27;409(1):148-53. doi: 10.1016/j.bbrc.2011.04.135. Epub 2011 May 5.
PMID 21569759
 
Melanoma differentiation associated gene-9, mda-9, is a human gamma interferon responsive gene.
Lin JJ, Jiang H, Fisher PB.
Gene. 1998 Jan 30;207(2):105-10.
PMID 9511750
 
Ephrin-B1 and ephrin-B2 mediate EphB-dependent presynaptic development via syntenin-1.
McClelland AC, Sheffler-Collins SI, Kayser MS, Dalva MB.
Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20487-92. doi: 10.1073/pnas.0811862106. Epub 2009 Nov 13.
PMID 19915143
 
Binding to syntenin-1 protein defines a new mode of ubiquitin-based interactions regulated by phosphorylation.
Rajesh S, Bago R, Odintsova E, Muratov G, Baldwin G, Sridhar P, Rajesh S, Overduin M, Berditchevski F.
J Biol Chem. 2011 Nov 11;286(45):39606-14. doi: 10.1074/jbc.M111.262402. Epub 2011 Sep 26.
PMID 21949238
 
Association of syntenin-1 with M-RIP polarizes Rac-1 activation during chemotaxis and immune interactions.
Sala-Valdes M, Gordon-Alonso M, Tejera E, Ibanez A, Cabrero JR, Ursa A, Mittelbrunn M, Lozano F, Sanchez-Madrid F, Yanez-Mo M.
J Cell Sci. 2012 Mar 1;125(Pt 5):1235-46. doi: 10.1242/jcs.094912. Epub 2012 Feb 20.
PMID 22349701
 
Identification of syntenin and other TNF-inducible genes in human umbilical arterial endothelial cells by suppression subtractive hybridization.
Stier S, Totzke G, Grunewald E, Neuhaus T, Fronhoffs S, Sachinidis A, Vetter H, Schulze-Osthoff K, Ko Y.
FEBS Lett. 2000 Feb 11;467(2-3):299-304.
PMID 10675558
 
Tyrosine dephosphorylation of the syndecan-1 PDZ binding domain regulates syntenin-1 recruitment.
Sulka B, Lortat-Jacob H, Terreux R, Letourneur F, Rousselle P.
J Biol Chem. 2009 Apr 17;284(16):10659-71. doi: 10.1074/jbc.M807643200. Epub 2009 Feb 19.
PMID 19228696
 
Role of Unc51.1 and its binding partners in CNS axon outgrowth.
Tomoda T, Kim JH, Zhan C, Hatten ME.
Genes Dev. 2004 Mar 1;18(5):541-58. Epub 2004 Mar 10.
PMID 15014045
 
Frizzled-PDZ scaffold interactions in the control of Wnt signaling.
Wawrzak D, Luyten A, Lambaerts K, Zimmermann P.
Adv Enzyme Regul. 2009;49(1):98-106. doi: 10.1016/j.advenzreg.2009.01.002. (REVIEW)
PMID 19534027
 
Syndecan recycling [corrected] is controlled by syntenin-PIP2 interaction and Arf6.
Zimmermann P, Zhang Z, Degeest G, Mortier E, Leenaerts I, Coomans C, Schulz J, N'Kuli F, Courtoy PJ, David G.
Dev Cell. 2005 Sep;9(3):377-88.
PMID 16139226
 

Citation

This paper should be referenced as such :
Gangemi, R ; Pfeffer, U ; Ferrini, S
SDCBP (syndecan binding protein (syntenin))
Atlas Genet Cytogenet Oncol Haematol. 2013;17(4):240-244.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/SDCBPID44377ch8q12.html


External links

Nomenclature
HGNC (Hugo)SDCBP   10662
Cards
AtlasSDCBPID44377ch8q12
Entrez_Gene (NCBI)SDCBP  6386  syndecan binding protein
AliasesMDA-9; MDA9; ST1; SYCL; 
TACIP18
GeneCards (Weizmann)SDCBP
Ensembl hg19 (Hinxton)ENSG00000137575 [Gene_View]  chr8:59465728-59495419 [Contig_View]  SDCBP [Vega]
Ensembl hg38 (Hinxton)ENSG00000137575 [Gene_View]  chr8:59465728-59495419 [Contig_View]  SDCBP [Vega]
ICGC DataPortalENSG00000137575
TCGA cBioPortalSDCBP
AceView (NCBI)SDCBP
Genatlas (Paris)SDCBP
WikiGenes6386
SOURCE (Princeton)SDCBP
Genetics Home Reference (NIH)SDCBP
Genomic and cartography
GoldenPath hg19 (UCSC)SDCBP  -     chr8:59465728-59495419 +  8q12.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SDCBP  -     8q12.1   [Description]    (hg38-Dec_2013)
EnsemblSDCBP - 8q12.1 [CytoView hg19]  SDCBP - 8q12.1 [CytoView hg38]
Mapping of homologs : NCBISDCBP [Mapview hg19]  SDCBP [Mapview hg38]
OMIM602217   
Gene and transcription
Genbank (Entrez)AF000652 AF006636 AK128645 AK295198 AK298697
RefSeq transcript (Entrez)NM_001007067 NM_001007068 NM_001007069 NM_001007070 NM_005625
RefSeq genomic (Entrez)NC_000008 NC_018919 NT_008183 NW_004929339
Consensus coding sequences : CCDS (NCBI)SDCBP
Cluster EST : UnigeneHs.200804 [ NCBI ]
CGAP (NCI)Hs.200804
Alternative Splicing GalleryENSG00000137575
Gene ExpressionSDCBP [ NCBI-GEO ]   SDCBP [ EBI - ARRAY_EXPRESS ]   SDCBP [ SEEK ]   SDCBP [ MEM ]
Gene Expression Viewer (FireBrowse)SDCBP [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6386
GTEX Portal (Tissue expression)SDCBP
Protein : pattern, domain, 3D structure
UniProt/SwissProtO00560   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO00560  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO00560
Splice isoforms : SwissVarO00560
PhosPhoSitePlusO00560
Domaine pattern : Prosite (Expaxy)PDZ (PS50106)   
Domains : Interpro (EBI)PDZ    SDCBP   
Domain families : Pfam (Sanger)PDZ (PF00595)   
Domain families : Pfam (NCBI)pfam00595   
Domain families : Smart (EMBL)PDZ (SM00228)  
Conserved Domain (NCBI)SDCBP
DMDM Disease mutations6386
Blocks (Seattle)SDCBP
PDB (SRS)1N99    1NTE    1OBX    1OBY    1OBZ    1R6J    1V1T    1W9E    1W9O    1W9Q    1YBO   
PDB (PDBSum)1N99    1NTE    1OBX    1OBY    1OBZ    1R6J    1V1T    1W9E    1W9O    1W9Q    1YBO   
PDB (IMB)1N99    1NTE    1OBX    1OBY    1OBZ    1R6J    1V1T    1W9E    1W9O    1W9Q    1YBO   
PDB (RSDB)1N99    1NTE    1OBX    1OBY    1OBZ    1R6J    1V1T    1W9E    1W9O    1W9Q    1YBO   
Structural Biology KnowledgeBase1N99    1NTE    1OBX    1OBY    1OBZ    1R6J    1V1T    1W9E    1W9O    1W9Q    1YBO   
SCOP (Structural Classification of Proteins)1N99    1NTE    1OBX    1OBY    1OBZ    1R6J    1V1T    1W9E    1W9O    1W9Q    1YBO   
CATH (Classification of proteins structures)1N99    1NTE    1OBX    1OBY    1OBZ    1R6J    1V1T    1W9E    1W9O    1W9Q    1YBO   
SuperfamilyO00560
Human Protein AtlasENSG00000137575
Peptide AtlasO00560
HPRD03741
IPIIPI00299086   IPI00479018   IPI00478874   IPI00910606   IPI00980584   IPI01013352   IPI00794699   
Protein Interaction databases
DIP (DOE-UCLA)O00560
IntAct (EBI)O00560
FunCoupENSG00000137575
BioGRIDSDCBP
STRING (EMBL)SDCBP
ZODIACSDCBP
Ontologies - Pathways
QuickGOO00560
Ontology : AmiGOglycoprotein binding  negative regulation of receptor internalization  frizzled binding  interleukin-5 receptor binding  protein binding  extracellular space  nucleus  cytoplasm  endoplasmic reticulum membrane  cytosol  cytoskeleton  plasma membrane  interleukin-5 receptor complex  adherens junction  focal adhesion  protein targeting to membrane  substrate-dependent cell migration, cell extension  Ras protein signal transduction  synaptic transmission  regulation of mitotic cell cycle  protein C-terminus binding  cytoskeletal adaptor activity  positive regulation of cell proliferation  positive regulation of epithelial to mesenchymal transition  positive regulation of pathway-restricted SMAD protein phosphorylation  membrane  growth factor binding  actin cytoskeleton organization  positive regulation of cell growth  positive regulation of cell migration  positive regulation of transforming growth factor beta receptor signaling pathway  negative regulation of proteasomal ubiquitin-dependent protein catabolic process  intracellular signal transduction  neurexin family protein binding  positive regulation of phosphorylation  melanosome  identical protein binding  protein homodimerization activity  membrane raft  syndecan binding  syndecan binding  positive regulation of JNK cascade  ephrin receptor binding  protein heterodimerization activity  protein N-terminus binding  ephrin receptor signaling pathway  cell adhesion molecule binding  extracellular exosome  blood microparticle  positive regulation of exosomal secretion  positive regulation of extracellular exosome assembly  extracellular vesicle  
Ontology : EGO-EBIglycoprotein binding  negative regulation of receptor internalization  frizzled binding  interleukin-5 receptor binding  protein binding  extracellular space  nucleus  cytoplasm  endoplasmic reticulum membrane  cytosol  cytoskeleton  plasma membrane  interleukin-5 receptor complex  adherens junction  focal adhesion  protein targeting to membrane  substrate-dependent cell migration, cell extension  Ras protein signal transduction  synaptic transmission  regulation of mitotic cell cycle  protein C-terminus binding  cytoskeletal adaptor activity  positive regulation of cell proliferation  positive regulation of epithelial to mesenchymal transition  positive regulation of pathway-restricted SMAD protein phosphorylation  membrane  growth factor binding  actin cytoskeleton organization  positive regulation of cell growth  positive regulation of cell migration  positive regulation of transforming growth factor beta receptor signaling pathway  negative regulation of proteasomal ubiquitin-dependent protein catabolic process  intracellular signal transduction  neurexin family protein binding  positive regulation of phosphorylation  melanosome  identical protein binding  protein homodimerization activity  membrane raft  syndecan binding  syndecan binding  positive regulation of JNK cascade  ephrin receptor binding  protein heterodimerization activity  protein N-terminus binding  ephrin receptor signaling pathway  cell adhesion molecule binding  extracellular exosome  blood microparticle  positive regulation of exosomal secretion  positive regulation of extracellular exosome assembly  extracellular vesicle  
REACTOMEO00560 [protein]
REACTOME Pathways3928664 [pathway]   447043 [pathway]   6798695 [pathway]   
NDEx NetworkSDCBP
Atlas of Cancer Signalling NetworkSDCBP
Wikipedia pathwaysSDCBP
Orthology - Evolution
OrthoDB6386
GeneTree (enSembl)ENSG00000137575
Phylogenetic Trees/Animal Genes : TreeFamSDCBP
HOVERGENO00560
HOGENOMO00560
Homologs : HomoloGeneSDCBP
Homology/Alignments : Family Browser (UCSC)SDCBP
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSDCBP [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SDCBP
dbVarSDCBP
ClinVarSDCBP
1000_GenomesSDCBP 
Exome Variant ServerSDCBP
ExAC (Exome Aggregation Consortium)SDCBP (select the gene name)
Genetic variants : HAPMAP6386
Genomic Variants (DGV)SDCBP [DGVbeta]
DECIPHER (Syndromes)8:59465728-59495419  ENSG00000137575
CONAN: Copy Number AnalysisSDCBP 
Mutations
ICGC Data PortalSDCBP 
TCGA Data PortalSDCBP 
Broad Tumor PortalSDCBP
OASIS PortalSDCBP [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSDCBP  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSDCBP
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SDCBP
DgiDB (Drug Gene Interaction Database)SDCBP
DoCM (Curated mutations)SDCBP (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SDCBP (select a term)
intoGenSDCBP
NCG5 (London)SDCBP
Cancer3DSDCBP(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM602217   
Orphanet
MedgenSDCBP
Genetic Testing Registry SDCBP
NextProtO00560 [Medical]
TSGene6386
GENETestsSDCBP
Huge Navigator SDCBP [HugePedia]
snp3D : Map Gene to Disease6386
BioCentury BCIQSDCBP
ClinGenSDCBP
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6386
Chemical/Pharm GKB GenePA35592
Clinical trialSDCBP
Miscellaneous
canSAR (ICR)SDCBP (select the gene name)
Probes
Litterature
PubMed106 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSDCBP
EVEXSDCBP
GoPubMedSDCBP
iHOPSDCBP
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Wed Apr 12 11:39:17 CEST 2017

Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.