Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   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

SDC3 (syndecan 3)

Identity

Alias_namessyndecan 3 (N-syndecan)
Alias_symbol (synonym)N-syndecan
SYND3
Other aliasSDCN
HGNC (Hugo) SDC3
LocusID (NCBI) 9672
Atlas_Id 42225
Location 1p35.2  [Link to chromosome band 1p35]
Location_base_pair Starts at 30869466 and ends at 30908633 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
ADGRE5 (19p13.12) / SDC3 (1p35.2)LAS1L (Xq12) / SDC3 (1p35.2)LOC100507412 (-) / SDC3 (1p35.2)
MAP7D2 (Xp22.12) / SDC3 (1p35.2)MYH11 (16p13.11) / SDC3 (1p35.2)SDC3 (1p35.2) / SDC3 (1p35.2)
SDC3 (1p35.2) / SLC1A3 (5p13.2)SDC3 (1p35.2) / TAF12 (1p35.3)SDC3 (1p35.2) / ZNF827 (4q31.21)
SIRT6 (19p13.3) / SDC3 (1p35.2)YWHAH (22q12.3) / SDC3 (1p35.2)SDC3 1p35.2 / SLC1A3 5p13.2
SDC3 1p35.2 / ZNF827 4q31.21

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)SDC3   10660
Cards
Entrez_Gene (NCBI)SDC3  9672  syndecan 3
AliasesSDCN; SYND3
GeneCards (Weizmann)SDC3
Ensembl hg19 (Hinxton)ENSG00000162512 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000162512 [Gene_View]  chr1:30869466-30908633 [Contig_View]  SDC3 [Vega]
ICGC DataPortalENSG00000162512
TCGA cBioPortalSDC3
AceView (NCBI)SDC3
Genatlas (Paris)SDC3
WikiGenes9672
SOURCE (Princeton)SDC3
Genetics Home Reference (NIH)SDC3
Genomic and cartography
GoldenPath hg38 (UCSC)SDC3  -     chr1:30869466-30908633 -  1p35.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SDC3  -     1p35.2   [Description]    (hg19-Feb_2009)
EnsemblSDC3 - 1p35.2 [CytoView hg19]  SDC3 - 1p35.2 [CytoView hg38]
Mapping of homologs : NCBISDC3 [Mapview hg19]  SDC3 [Mapview hg38]
OMIM186357   601665   
Gene and transcription
Genbank (Entrez)AB007937 AF248634 AK295698 AL049426 BC013974
RefSeq transcript (Entrez)NM_014654
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SDC3
Cluster EST : UnigeneHs.158287 [ NCBI ]
CGAP (NCI)Hs.158287
Alternative Splicing GalleryENSG00000162512
Gene ExpressionSDC3 [ NCBI-GEO ]   SDC3 [ EBI - ARRAY_EXPRESS ]   SDC3 [ SEEK ]   SDC3 [ MEM ]
Gene Expression Viewer (FireBrowse)SDC3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)9672
GTEX Portal (Tissue expression)SDC3
Protein : pattern, domain, 3D structure
UniProt/SwissProtO75056   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO75056  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO75056
Splice isoforms : SwissVarO75056
PhosPhoSitePlusO75056
Domaine pattern : Prosite (Expaxy)SYNDECAN (PS00964)   
Domains : Interpro (EBI)Neurexin-like    Syndecan    Syndecan-3    Syndecan/Neurexin_dom    Syndecan_CS   
Domain families : Pfam (Sanger)Syndecan (PF01034)   
Domain families : Pfam (NCBI)pfam01034   
Domain families : Smart (EMBL)4.1m (SM00294)  
Conserved Domain (NCBI)SDC3
DMDM Disease mutations9672
Blocks (Seattle)SDC3
SuperfamilyO75056
Human Protein AtlasENSG00000162512
Peptide AtlasO75056
HPRD01719
IPIIPI00395366   IPI00749234   IPI00023942   
Protein Interaction databases
DIP (DOE-UCLA)O75056
IntAct (EBI)O75056
FunCoupENSG00000162512
BioGRIDSDC3
STRING (EMBL)SDC3
ZODIACSDC3
Ontologies - Pathways
QuickGOO75056
Ontology : AmiGOretinoid metabolic process  Golgi lumen  plasma membrane  glycosaminoglycan biosynthetic process  glycosaminoglycan catabolic process  membrane  integral component of membrane  glycosaminoglycan metabolic process  lysosomal lumen  leukocyte migration  
Ontology : EGO-EBIretinoid metabolic process  Golgi lumen  plasma membrane  glycosaminoglycan biosynthetic process  glycosaminoglycan catabolic process  membrane  integral component of membrane  glycosaminoglycan metabolic process  lysosomal lumen  leukocyte migration  
Pathways : KEGGCell adhesion molecules (CAMs)   
NDEx NetworkSDC3
Atlas of Cancer Signalling NetworkSDC3
Wikipedia pathwaysSDC3
Orthology - Evolution
OrthoDB9672
GeneTree (enSembl)ENSG00000162512
Phylogenetic Trees/Animal Genes : TreeFamSDC3
HOVERGENO75056
HOGENOMO75056
Homologs : HomoloGeneSDC3
Homology/Alignments : Family Browser (UCSC)SDC3
Gene fusions - Rearrangements
Fusion : MitelmanSDC3/SLC1A3 [1p35.2/5p13.2]  
Fusion : MitelmanSDC3/ZNF827 [1p35.2/4q31.21]  [t(1;4)(p35;q31)]  
Fusion: TCGASDC3 1p35.2 SLC1A3 5p13.2 LGG
Fusion: TCGASDC3 1p35.2 ZNF827 4q31.21 LGG
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSDC3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SDC3
dbVarSDC3
ClinVarSDC3
1000_GenomesSDC3 
Exome Variant ServerSDC3
ExAC (Exome Aggregation Consortium)SDC3 (select the gene name)
Genetic variants : HAPMAP9672
Genomic Variants (DGV)SDC3 [DGVbeta]
DECIPHERSDC3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSDC3 
Mutations
ICGC Data PortalSDC3 
TCGA Data PortalSDC3 
Broad Tumor PortalSDC3
OASIS PortalSDC3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSDC3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSDC3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SDC3
DgiDB (Drug Gene Interaction Database)SDC3
DoCM (Curated mutations)SDC3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SDC3 (select a term)
intoGenSDC3
Cancer3DSDC3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM186357    601665   
Orphanet
MedgenSDC3
Genetic Testing Registry SDC3
NextProtO75056 [Medical]
TSGene9672
GENETestsSDC3
Target ValidationSDC3
Huge Navigator SDC3 [HugePedia]
snp3D : Map Gene to Disease9672
BioCentury BCIQSDC3
ClinGenSDC3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD9672
Chemical/Pharm GKB GenePA35590
Clinical trialSDC3
Miscellaneous
canSAR (ICR)SDC3 (select the gene name)
Probes
Litterature
PubMed50 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSDC3
EVEXSDC3
GoPubMedSDC3
iHOPSDC3
Genes in titleautomatic search in PubMed
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 : Tue Aug 1 17:13:54 CEST 2017

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

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.