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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SDC1 Gene

protein-coding   GIFtS: 68
GCID: GC02M020400

syndecan 1


(Previous symbol: SDC)
 Explore 68 diseases affiliated with
SDC1 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for SDC1    

Aliases
for SDC1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Syndecan 11 2     CD138 Antigen2 3
SDC1 2 3     Heparan Sulfate Proteoglycan Fibroblast Growth Factor Receptor2
SYND11 2 3     Syndecan Proteoglycan 12
CD1381 2     Syndecan-11
Syndecan1     

External Ids:    HGNC: 106581   Entrez Gene: 63822   Ensembl: ENSG000001158847   OMIM: 1863555   UniProtKB: P188273   

Export aliases for SDC1 gene to outside databases

Previous GC identifers: GC02M020292 GC02M020469 GC02M020368 GC02M020385 GC02M020322 GC02M020264 GC02M020158


Summaries
for SDC1 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for SDC1:
The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan and is a member of the
syndecan proteoglycan family. The syndecans mediate cell binding, cell signaling, and cytoskeletal organization and
syndecan receptors are required for internalization of the HIV-1 tat protein. The syndecan-1 protein functions as an
integral membrane protein and participates in cell proliferation, cell migration and cell-matrix interactions via its
receptor for extracellular matrix proteins. Altered syndecan-1 expression has been detected in several different tumor
types. While several transcript variants may exist for this gene, the full-length natures of only two have been
described to date. These two represent the major variants of this gene and encode the same protein. (provided by
RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: SDC1_HUMAN, P18827
Function: Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the
cytoskeleton to the interstitial matrix

Gene Wiki entry for SDC1 (Syndecan 1)


Genomic Views
for SDC1 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NC_018913.1  NT_015926.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SDC1 gene promoter:
         STAT3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: SDC1 promoter sequence
   Search SABiosciences Chromatin IP Primers for SDC1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SDC1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2p24.1   Ensembl cytogenetic band:  2p24.1   HGNC cytogenetic band: 2p24.1

SDC1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SDC1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M020400:  view genomic region     (about GC identifiers)

Start:
 20,400,558 bp from pter      End:
 20,425,194 bp from pter
Size:
 24,637 bases      Orientation:
 minus strand

Proteins
for SDC1 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: SDC1_HUMAN, P18827 (See protein sequence)
Recommended Name: Syndecan-1 precursor  
Size: 310 amino acids; 32462 Da
Subunit: Interacts with CDCP1
Subcellular location: Membrane; Single-pass type I membrane protein. Secreted. Note=Shedding of the ectodomain produces
a soluble form
Secondary accessions: D6W523 Q53QV0 Q546D3 Q96HB7

Explore the universe of human proteins at neXtProt for SDC1: NX_P18827

Post-translational modifications:

  • Shedding is enhanced by a number of factors such as heparanase, thrombin or EGF. Also by stress and wound healing.
    • PMA-mediated shedding is inhibited by TIMP31
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P18827

    • SDC1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001006947.1  NP_002988.3  

    ENSEMBL proteins: 
     ENSP00000254351   ENSP00000384613   ENSP00000400773   ENSP00000390201   ENSP00000370542  
    Reactome Protein details: P18827
    Human Recombinant Protein Products: 
    Browse Purified and Recombinant Proteins at EMD Millipore
    R&D Systems Recombinant & Natural Proteins for SDC1 (Syndecan-1/CD138)
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    OriGene Protein Over-expression Lysate: SDC1
    OriGene Custom Protein Services for SDC1 
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    Novus Biologicals SDC1 Proteins
    Novus Biologicals SDC1 Lysate
    Browse Sino Biological Recombinant Proteins
    ProSpec Recombinant Protein for SDC1
    Uscn Proteins for SDC1

    Gene Ontology (GO): 5/12 cellular component terms (GO ID links to tree view) (see all 12):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001931uropod ----
    GO:0005576extracellular region IEA--
    GO:0005737cytoplasm IDA--
    GO:0005796Golgi lumen TAS--
    GO:0005886plasma membrane TAS--


    SDC1 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for SDC1

    Protein Domains /
    Families
    for SDC1 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    SDC1 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR003585 Neurexin-like
     IPR001050 Syndecan

    Graphical View of Domain Structure for InterPro Entry P18827

    ProtoNet protein and cluster: P18827

    2 Blocks protein families:
    IPB001050 Syndecan
    IPB003585 Neurexin/syndecan/glycophorin C


    UniProtKB/Swiss-Prot: SDC1_HUMAN, P18827
    Similarity: Belongs to the syndecan proteoglycan family


    Function
    for SDC1 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: SDC1_HUMAN, P18827
    Function: Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the
    cytoskeleton to the interstitial matrix

         Genatlas biochemistry entry for SDC1:
    syndecan,integral membrane heparan sulfate proteoglycan,matrix receptor,expressed in distinct stages of differentiation
    of normal lymphoid cells (pre-B) and in B chronic lymphoblastic leukemia (BCLL) in plamocytoid lymphomas and
    myelomas,underexpressed in squamous cell carcinoma of the head and neck

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SDC1
    8/60 QIAGEN miScript miRNA Assays for microRNAs that regulate SDC1 (see all 60):
    hsa-miR-3194-5p hsa-miR-302d hsa-miR-520e hsa-miR-19b-2* hsa-miR-218-1* hsa-let-7a-2* hsa-miR-342-3p hsa-miR-519a
    SwitchGear 3'UTR luciferase reporter plasmid: SDC1 3' UTR sequence
    Inhib. RNA
    Products:            		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for SDC1 (see all 7)
    OriGene shRNA RFP: SDC1
    OriGene siRNA: SDC1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SDC1

    Gene Editing
    Products:    		DNA2.0 Custom Protein Engineering Service for SDC1

    Clone
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    GenScript: all cDNA clones in your preferred vector (see all 2): SDC1 (NM_002997)
    Sino Biological Human cDNA Clone for SDC1
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SDC1 

    Cell Line
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    LifeMap BioReagents: cell line associated with SDC1: PureStem 4D20.8, NCr-fac Progenitor

    In Situ Assay
    Products:       
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SDC1

    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001948glycoprotein binding IEA--
    GO:0005515protein binding IPI15292202
    GO:0008022protein C-terminus binding IPI16982797
    GO:0008092cytoskeletal protein binding IEA--


    SDC1 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Sdc1tm1Cma for SDC1
         8 MGI mutant phenotypes (inferred from 1 allele) (MGI details for Sdc1):
     cellular  endocrine/exocrine gland  homeostasis/metabolism  immune system  integument 
     mortality/aging  reproductive system  tumorigenesis 

    SDC1 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for SDC1 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways - 5/19 super-pathways (see all 19) About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1MPS IIIC - Sanfilippo syndrome C
    8/16 pathways (see all 16)
    		MPS VI - Maroteaux-Lamy syndrome1.00
    		MPS IIIA - Sanfilippo syndrome A1.00
    		MPS IIIC - Sanfilippo syndrome C1.00
    		MPS IIID - Sanfilippo syndrome D1.00
    		MPS I - Hurler syndrome1.00
    		MPS IX - Natowicz syndrome1.00
    		Mucopolysaccharidoses1.00
    		MPS II - Hunter syndrome1.00
    2HS-GAGs translocate to the lysosome for degradation
    		HS-GAGs translocate to the lysosome for degradation1.00
    		HS-GAG degradation0.57
    		Some HSPGs are secreted to the plasma membrane1.00
    		Proteogylcan syndecan-mediated signaling events0.33
    3Lipoprotein metabolism
    		Lipoprotein metabolism1.00
    		Lipid digestion, mobilization, and transport0.56
    		Chylomicron-mediated lipid transport0.57
    4Retinoid metabolism and transport
    		Retinoid metabolism and transport1.00
    		Diseases associated with visual transduction0.73
    		Visual phototransduction0.74
    5Development HGF signaling pathway
    		Development HGF signaling pathway1.00
    		Development_HGF signaling pathway0.78

    Pathway sources
    See GeneCards unified pathways
    Show all pathways

    2 EMD Millipore Pathways for SDC1
        Development HGF signaling pathway
    Development FGFR signaling pathway

    2 R&D Systems Pathways for SDC1
        Wnt Signaling Pathway
    Articular Cartilage Extracellular Matrix

    1 Downloadable PowerPoint Slide of QIAGEN Pathway Central Maps for SDC1
        Transendothelial Migration of Leukocytes

    2 GeneGo (Thomson Reuters) Pathways for SDC1
        Development HGF signaling pathway
    Development FGFR signaling pathway

    4 BioSystems Pathways for SDC1 
        Integrins in angiogenesis
    Arf6 trafficking events
    Syndecan-1-mediated signaling events
    Proteogylcan syndecan-mediated signaling events

    5/31        Reactome Pathways for SDC1 (see all 31)
        Diseases associated with visual transduction
    Chondroitin sulfate/dermatan sulfate metabolism
    MPS VI - Maroteaux-Lamy syndrome
    Metabolism
    Chylomicron-mediated lipid transport


    3         Kegg Pathways  (Kegg details for SDC1):
        ECM-receptor interaction
    Cell adhesion molecules (CAMs)
    Malaria


    SDC1 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SDC1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/102 Interacting proteins for SDC1 (P188272, 3 ENSP000002543514) via UniProtKB, MINT, STRING, and/or I2D (see all 102)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CASKO149362, 3, ENSP000003674084MINT-58222 I2D: score=4 STRING: ENSP00000367408
    IL8P101453, ENSP000003065124I2D: score=4 STRING: ENSP00000306512
    SDCBPO005603, ENSP000002601304I2D: score=3 STRING: ENSP00000260130
    HGFP142103, ENSP000002223904I2D: score=2 STRING: ENSP00000222390
    IGFBP7Q162703, ENSP000002956664I2D: score=2 STRING: ENSP00000295666
    About this table

    Gene Ontology (GO): 5/21 biological process terms (GO ID links to tree view) (see all 21):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001657ureteric bud development IEA--
    GO:0005975carbohydrate metabolic process TAS--
    GO:0006024glycosaminoglycan biosynthetic process TAS--
    GO:0006027glycosaminoglycan catabolic process TAS--
    GO:0006629lipid metabolic process TAS--


    SDC1 for ontologies           About GeneDecksing



    Drugs & Compounds
    for SDC1 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SDC1

    1 HMDB Compound for SDC1    About this table
    CompoundSynonyms CAS #PubMed Ids
    Heparan sulfateHHS 5 (see all 13)9050-30-0--
    Search CenterWatch for drugs/clinical trials and news about SDC1 

    Transcripts
    for SDC1 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for SDC1 gene (2 alternative transcripts): 
    NM_001006946.1  NM_002997.4  

    Unigene Cluster for SDC1:

    Syndecan 1
    Hs.224607  [show with all ESTs]
    Unigene Representative Sequence: NM_001006946
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000254351(uc002rdo.1 uc010exv.3) ENST00000403076 ENST00000482879(uc010exw.1)
    ENST00000429035 ENST00000447124 ENST00000381150(uc002rdp.1)

    miRNA
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    8/60 QIAGEN miScript miRNA Assays for microRNAs that regulate SDC1 (see all 60):
    hsa-miR-3194-5p hsa-miR-302d hsa-miR-520e hsa-miR-19b-2* hsa-miR-218-1* hsa-let-7a-2* hsa-miR-342-3p hsa-miR-519a
    SwitchGear 3'UTR luciferase reporter plasmid: SDC1 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for SDC1 (see all 7)
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    Clone
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    Primer
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    Additional cDNA sequence: 

    AJ551176.1 AK222739.1 AK299385.1 AK307313.1 AK313974.1 BC008765.2 J05392.1 X60306.1 

    19 DOTS entries:

    DT.449752  DT.100727565  DT.100880464  DT.100880458  DT.100880469  DT.95269333  DT.100038526  DT.100880463 
    DT.95269365  DT.120996810  DT.85105565  DT.120996817  DT.120996820  DT.120996839  DT.91745597  DT.92455346 
    DT.95269334  DT.100774836  DT.120996874 

    24/627 AceView cDNA sequences (see all 627):

    BQ774844 BM742574 BM793548 BM766328 BM749304 CB852975 AA375599 AI922244 
    CB242749 BQ023676 AI695770 BM772526 BM766329 BM755910 BM750537 BG116748 
    BM791621 BM784366 CA411792 BM998847 BM785035 BM785432 CB243800 BM796313 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for SDC1 (see all 7)    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c · 6d · 6e · 6f · 6g ^ 7 ^ 8a · 8b
    SP1:                          -     -     -                                                                     
    SP2:        -     -           -     -     -                                                                     
    SP3:                          -     -     -                                         -     -     -     -         
    SP4:                          -     -                                                                           
    SP5:                          -     -     -           -                                                         


    ECgene alternative splicing isoforms for SDC1

    Expression
    for SDC1 gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SDC1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CTCATCTGCT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    SDC1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    4 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    LimbAutopodMesenchymal Condensate CellsBone, Cartilage
    LimbStylopodMesenchymal Condensate CellsBone, Cartilage
    LimbZeugopodMesenchymal Condensate CellsBone, Cartilage
    Lower Urinary TractUreterUreter CellsKidney
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 3 LifeMap Cells 
    NameCategory
    PureStem™ mesenchymal progenitor 4D20.8 (Embryonic Progenitor Cell)Lateral Plate Mesoderm, Neural Crest
    PureStem™ progenitor U31 (Embryonic Progenitor Cell)
    PureStem™ progenitor Z1 (Embryonic Progenitor Cell)

    See SDC1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SDC1

    SOURCE GeneReport for Unigene cluster: Hs.224607
        SABiosciences Custom PCR Arrays for SDC1
    Primer
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SDC1
    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SDC1

    Orthologs
    for SDC1 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for SDC1 gene from 5/15 species (see all 15)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves SDC11 syndecan 1 50.35(n)
    46.53(a)    		   421960  XM_419972.2  XP_419972.2 
    lizard
    (Anolis carolinensis)    		 Reptilia SDC16
    		 --
    		 39(a)
    		 1 ↔ 1
    		 1(155042696-155046166)
    African clawed frog
    (Xenopus laevis)    		 Amphibia U41628.12   -- 73.1(n)    U41628.1 
    fruit fly
    (Drosophila melanogaster)    		 Insecta Sdc6
    		 Syndecan
    		 11(a)
    		 1 → many
    		 2R(17280111-17368680)
    worm
    (Caenorhabditis elegans)    		 Secernentea sdn-16
    		 Probable syndecan
    		 17(a)
    		 1 → many
    		 X(10589718-10593274)


    ENSEMBL Gene Tree for SDC1 (if available)
    TreeFam Gene Tree for SDC1 (if available) 

    Paralogs
    for SDC1 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SDC1 gene
    SDC32  SDC42  SDC22  

    SDC1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for SDC1
    PGOHUM00000250424


    Genomic Variants
    for SDC1 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/477 NCBI SNPs in SDC1 are shown (see all 477)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 2 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs115448601,2
    		--20181952(-) CCTGCC/TGCTCT 1 -- us2k1 ese30--------
    rs37712261,2
    		C--20182287(-) TGGGGC/AGTTCC 1 -- us2k11Minor allele frequency- A:0.00NA 2
    rs102068121,2
    		C,F,--20182792(+) CACCCG/ACNNNN 1 -- us2k14Minor allele frequency- A:0.04NA WA 126
    rs101839061,2
    		C,F,--20182806(+) GGCTGC/TAAGAA 1 -- us2k14Minor allele frequency- T:0.04NA WA 126
    rs561756111,2
    		C,F,--20183109(+) AACGAC/TCTTCG 1 -- us2k13Minor allele frequency- T:0.16WA 122
    rs101990551,2
    		C,--20183387(+) AAAAGA/TTGATG 1 -- us2k13Minor allele frequency- T:0.11WA CSA 121
    rs786008721,2
    		F,--20183500(+) CATCAG/AGGTTC 1 -- us2k11Minor allele frequency- A:0.07WA 118
    rs23484771,2
    		C,F,A,H,--20400107(+) TGCAGT/CGTGCT 2 -- ds500110Minor allele frequency- C:0.44NA WA EA 374
    rs1864251271,2
    		--20400123(+) AACCTC/TCAGGT 2 -- ds50010--------
    rs1919540051,2
    		--20400191(+) AAGACC/TGTTGC 2 -- ds50010--------

    HapMap Linkage Disequilibrium report for SDC1 (20400558 - 20425194 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for SDC1
         1 CNV: 72933
         1 Indel: 58955

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SDC1
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    Disorders / Diseases
    for SDC1 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    SDC1 for disorders           About GeneDecksing

    OMIM gene information: 186355    OMIM disorders: --

    20/68 diseases for SDC1 (see all 68):    About MalaCards
    monoclonal gammopathy of uncertain significance    splenic marginal zone lymphoma    extrahepatic bile duct adenocarcinoma    diffuse large b-cell lymphoma
    central nervous system lymphoma    non-small cell lung carcinoma    lichen planus    b-cell lymphomas
    oral lichen planus    bile duct carcinoma    squamous cell carcinoma    type 2 diabetes mellitus
    primary effusion lymphoma    ameloblastic carcinoma    oral squamous cell carcinoma    squamous cell carcinoma of the head and neck
    esophageal squamous cell carcinoma    systemic lupus erythematosus    lupus erythematosus    diabetes mellitus

    2 diseases from the University of Copenhagen DISEASES database for SDC1:
    Multiple myeloma     Carcinoma

    3 Novoseek disease relationships for SDC1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    carcinoma 26.6 8 19010933 (3), 14744776 (1), 19253033 (1), 19255147 (1)
    tumors 2.02 3 14744776 (1), 14612567 (1)
    breast cancer 0 1 14744776 (1)

    Human Genome Epidemiology (HuGE) Navigator: SDC1 (2 documents)

    Export disorders for SDC1 gene to outside databases

    Publications
    for SDC1 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for SDC1 gene, integrated from 9 sources (see all 218):
    (articles sorted by number of sources associating them with SDC1)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Adhesion signaling by a novel mitotic substrate of src kinases. (PubMed id 16007225)1, 2 Bhatt A.S.... Moasser M.M. (2005)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. The mapping and visual ordering of the human syndecan-1 and N-myc genes near the telomeric region of chromosome 2p. (PubMed id 9050911)1, 2 Kaukonen J.... Palotie A. (1997)
    4. Differential expression of cell surface heparan sulfate proteoglycans in human mammary epithelial cells and lung fibroblasts. (PubMed id 1339431)1, 2 Lories V.... David G. (1992)
    5. Sequence of human syndecan indicates a novel gene family of integral membrane proteoglycans. (PubMed id 2324102)1, 2 Mali M.... Jalkanen M. (1990)
    6. Induction of syndecan-1 expression in stromal fibroblasts promotes proliferation of human breast cancer cells. (PubMed id 14744776)1, 9 Maeda T....Friedl A. (2004)
    7. Syndecan-1 regulates alphavbeta3 and alphavbeta5 integrin activation during angiogenesis and is blocked by synstatin, a novel peptide inhibitor. (PubMed id 19255147)1, 9 Beauvais D.M....Rapraeger A.C. (2009)
    8. Membrane type 1 matrix metalloproteinase-mediated stromal syndecan-1 shedding stimulates breast carcinoma cell proliferation. (PubMed id 19010933)1, 9 Su G....Friedl A. (2008)
    9. Evaluation of the association with cervical cancer of polymorphisms in syndecan-1, a heparan sulfate proteoglycan involved with viral cell entry. (PubMed id 18006945)1, 9 Yu K.J....Hildesheim A. (2007)
    10. Syndecan-1 expression is regulated in an isoform-specific manner by the farnesoid-X receptor. (PubMed id 12660231)1, 9 Anisfeld A.M....Edwards P.A. (2003)

    External Searches for SDC1 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing SDC1 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 6382 HGNC: 10658 AceView: SDC1 Ensembl:ENSG00000115884 euGenes: HUgn6382
    ECgene: SDC1 Kegg: 6382 H-InvDB: SDC1

    Other Databases showing SDC1 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing SDC1 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SDC1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SDC1 Genetics and Cytogenetics in Oncology and Haematology

    Intellectual Property
    for SDC1 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for SDC1 gene:
    Search GeneIP for patents involving SDC1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    About This Section

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     SDC1 Proteins, Antibodies, CLIAs, and ELISAs
     Cell Line associated with SDC1: PureStem 4D20.8, NCr-fac Progenitor
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