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SDC1 Gene

protein-coding   GIFtS: 70
GCID: GC02M020400

Syndecan 1


(Previous symbol: SDC)
  See SDC1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Syndecan 11 2     CD1382
SDC1 2 3     Heparan Sulfate Proteoglycan Fibroblast Growth Factor Receptor2
Syndecan Proteoglycan 11 2     syndecan2
SYND12 3     syndecan-12
CD138 Antigen2 3     

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


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SDC1 Gene:
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)

GeneCards Summary for SDC1 Gene:
SDC1 (syndecan 1) is a protein-coding gene. Diseases associated with SDC1 include ameloblastic carcinoma, and monoclonal gammopathy of uncertain significance. GO annotations related to this gene include protein C-terminus binding and glycoprotein binding. An important paralog of this gene is SDC3.

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) 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NT_022184.16  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SDC1 gene promoter:
         STAT3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSDC1 promoter sequence
   Search Chromatin IP Primers for SDC1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SDC1_HUMAN, P18827 (See protein sequence)
Recommended Name: Syndecan-1 precursor  
Size: 310 amino acids; 32462 Da
Subunit: Interacts with CDCP1. Interacts (via C-terminus) with TIAM1 (via PDZ domain)
2 PDB 3D structures from and Proteopedia for SDC1:
4GVC (3D)        4GVD (3D)    
Secondary accessions: D6W523 Q53QV0 Q546D3 Q96HB7

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

Explore proteomics data for SDC1 at MOPED

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
  • Glycosylation2 at Ser37, Asn43, Ser45, Ser47, Thr61, Thr72, Thr76, Ser77, Thr81, Thr122,
                                 Thr164, Ser165, Thr166, Ser171, Thr177, Thr180, Ser186, Thr188, Ser206, Ser216 (see all 21)
  • Modification sites at PhosphoSitePlus

  • See SDC1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

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

    ENSEMBL proteins: 
     ENSP00000254351   ENSP00000384613   ENSP00000400773   ENSP00000390201   ENSP00000370542  
    Reactome Protein details: P18827

    SDC1 Human Recombinant Protein Products:

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    OriGene Protein Over-expression Lysate for SDC1
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    Novus Biologicals SDC1 Lysate
    Sino Biological Recombinant Protein for SDC1
    Sino Biological Cell Lysate for SDC1
    ProSpec Recombinant Protein for SDC1
    Cloud-Clone Corp. Proteins for SDC1

     
    Search eBioscience for Proteins for SDC1 

    SDC1 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of SDC1
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    SDC1 Assay Products:

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    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for SDC1
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    Search eBioscience for ELISAs for SDC1 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    CD: CD molecules
    SDC: Proteoglycans / Cell Surface : Syndecans

    3 InterPro protein domains:
     IPR001050 Syndecan
     IPR003585 Neurexin-like
     IPR027789 Syndecan/Neurexin_dom

    Graphical View of Domain Structure for InterPro Entry P18827

    ProtoNet protein and cluster: P18827

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


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


    Find genes that share domains with SDC1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: 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

         Gene Ontology (GO): 4 molecular function terms:    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--
         
    Find genes that share ontologies with SDC1           About GenesLikeMe


    Phenotypes:
         9 MGI mutant phenotypes (inferred from 1 allele(MGI details for Sdc1):
     cellular  endocrine/exocrine gland  hematopoietic system  homeostasis/metabolism  immune system 
     integument  mortality/aging  reproductive system  tumorigenesis 

    Find genes that share phenotypes with SDC1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Sdc1tm1Cma for SDC1

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SDC1
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       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SDC1

    miRNA
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    miRTarBase miRNAs that target SDC1:
    hsa-mir-9-5p (MIRT021459), hsa-mir-10b-5p (MIRT007072), hsa-mir-375 (MIRT019998), hsa-mir-149-5p (MIRT045538)

    Block miRNA regulation of human, mouse, rat SDC1 using miScript Target Protectors
    Selected qRT-PCR 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 plasmidSDC1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SDC1

    Gene Editing
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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
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SDC1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SDC1

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SDC1

    Flow Cytometry
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    eBioscience FlowRNA Probe Sets ( VA6-13168) for SDC1 


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SDC1_HUMAN, P18827: Membrane; Single-pass type I membrane protein. Secreted. Note=Shedding of the ectodomain
    produces a soluble form
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    golgi apparatus4
    lysosome4
    plasma membrane4
    vacuole4
    cytosol3
    cytoskeleton2
    endoplasmic reticulum1
    mitochondrion1
    nucleus1

    Gene Ontology (GO): Selected cellular component terms (see all 12):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region ----
    GO:0005737cytoplasm IDA--
    GO:0005796Golgi lumen TAS--
    GO:0005886plasma membrane TAS--
    GO:0005887integral component of plasma membrane TAS2324102

    Find genes that share ontologies with SDC1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for SDC1 About   (see all 24)  
    See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1Non-integrin membrane-ECM interactions
    Non-integrin membrane-ECM interactions0.35
    Proteogylcan syndecan-mediated signaling events0.00
    Syndecan interactions0.00
    2MPS VI - Maroteaux-Lamy syndrome
    MPS VI - Maroteaux-Lamy syndrome0.45
    MPS IIIB - Sanfilippo syndrome B0.45
    MPS IIIC - Sanfilippo syndrome C0.45
    MPS II - Hunter syndrome0.45
    MPS IV - Morquio syndrome A0.45
    Glycosaminoglycan metabolism0.45
    Mucopolysaccharidoses0.45
    MPS IV - Morquio syndrome B0.45
    3Lipoprotein metabolism
    Lipoprotein metabolism0.59
    Chylomicron-mediated lipid transport0.00
    Lipid digestion, mobilization, and transport0.59
    4Heparan sulfate/heparin (HS-GAG) metabolism
    Heparan sulfate/heparin (HS-GAG) metabolism0.57
    HS-GAG degradation0.39
    HS-GAG biosynthesis0.57
    5Diseases associated with visual transduction
    Visual phototransduction0.44
    Diseases associated with visual transduction0.43
    Retinoid metabolism and transport0.44


    Find genes that share SuperPaths with SDC1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    3 R&D Systems Pathways for SDC1
        Wnt Signaling Pathways
    Articular Cartilage Extracellular Matrix
    VEGF - VEGF R2 Signaling Pathways

    1 Downloadable PowerPoint Slide of GeneGlobe 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
        Arf6 trafficking events
    Integrins in angiogenesis
    Syndecan-1-mediated signaling events
    Proteogylcan syndecan-mediated signaling events

    2 Sino Biological Pathways for SDC1
        Canonical Wnt Pathway
    Non-Canonical Wnt Pathway

    Selected Reactome Pathways for SDC1 (see all 6)
        HS-GAG biosynthesis
    Retinoid metabolism and transport
    HS-GAG degradation
    Chylomicron-mediated lipid transport
    A tetrasaccharide linker sequence is required for GAG synthesis


    4 Kegg Pathways  (Kegg details for SDC1):
        ECM-receptor interaction
    Cell adhesion molecules (CAMs)
    Malaria
    Proteoglycans in cancer

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SDC1
    Interactions:

        GeneGlobe Interaction Network for SDC1

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

    Selected 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
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    Gene Ontology (GO): Selected biological process terms (see all 24):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001523retinoid metabolic process TAS--
    GO:0001657ureteric bud development IEA--
    GO:0005975carbohydrate metabolic process TAS--
    GO:0006024glycosaminoglycan biosynthetic process TAS--
    GO:0006027glycosaminoglycan catabolic process TAS--

    Find genes that share ontologies with SDC1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    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--



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    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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    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
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    GenScript: all cDNA clones in your preferred vector (see all 2): SDC1 (NM_002997)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SDC1
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    Additional mRNA 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 

    Selected AceView cDNA sequences (see all 627):

    AW516825 BQ016749 BM749794 BM560731 BM756752 BM758566 T97944 BM969244 
    BM758903 CB306068 AA586967 BM842749 BM757544 BQ644995 BM758625 BM772508 
    BM758468 BM742568 CR620183 BM757728 BM758946 AA588801 BE078507 AI660836 

    GeneLoc Exon Structure

    Selected 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

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    SDC1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTCATCTGCT
    SDC1 Expression
    About this image


    SDC1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 18) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 4 entries
             Mesenchymal Condensate Cells Zeugopod
             Bone Marrow
     
     Limb (Muscoskeletal System)    fully expand to see all 4 entries
             Mesenchymal Condensate Cells Zeugopod
             Limb Bud
     
     Cartilage (Muscoskeletal System)    fully expand to see all 3 entries
             Mesenchymal Condensate Cells Zeugopod
     
     Tooth (Integumentary System)    fully expand to see all 7 entries
             Early Ameloblasts Dental Enamel
     
     Epithelial Cells
             Early Ameloblasts Dental Enamel
    SDC1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SDC1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.224607
        Custom PCR Arrays for SDC1
    Primer
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    (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)
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    This gene was present in the common ancestor of animals.

    Orthologs for SDC1 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sdc11 , 5 syndecan 11, 5 80.15(n)1
    77.02(a)1
      12 (3.94 cM)5
    209691  NM_011519.21  NP_035649.11 
     87713235 
    chicken
    (Gallus gallus)
    Aves SDC11 syndecan 1 51.11(n)
    46.67(a)
      421960  XM_419972.3  XP_419972.2 
    lizard
    (Anolis carolinensis)
    Reptilia SDC16
    syndecan 1
    31(a)
    1 ↔ 1
    1(155040582-155080290)
    African clawed frog
    (Xenopus laevis)
    Amphibia U41628.12   -- 73.1(n)    U41628.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Sdc6
    Syndecan
    14(a)
    1 → many
    2R(17280111-17368680)
    worm
    (Caenorhabditis elegans)
    Secernentea sdn-16
    Protein SDN-1, isoform b (sdn-1) mRNA, complete cd...
    23(a)
    1 → many
    X(10589780-10593334) WBGene00004749


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

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

    Find genes that share paralogs with SDC1           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for SDC1
    PGOHUM00000250424


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SDC1 (see all 525)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    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--------
    rs1838653761,2
    --20400217(+) AATCAC/GAGTGA 2 -- ds50010--------
    rs113374841,2
    C--20400229(+) CAAAG-/AATAAA 2 -- ds50011Minor allele frequency- A:0.50NA 2
    rs43507031,2
    C,F,A,H--20400269(+) CATCAT/AGTCCT 2 -- ds500119Minor allele frequency- A:0.43NA NS EA WA 1152
    rs44324081,2
    C,F,A,H--20400300(+) TGGAGC/ACTTAA 2 -- ds500125Minor allele frequency- A:0.40NS EA NA WA CSA 2488
    rs1150194841,2
    F--20400343(+) GCCCCG/AGGAGG 2 -- ds50011Minor allele frequency- A:0.01WA 118
    rs1456353881,2
    --20400351(+) AGGAGG/TAAGGC 2 -- ds50010--------
    rs23484781,2
    C,F,A,H--20400430(+) GAGGGA/GCCAGC 2 -- ds500119Minor allele frequency- N:0.01NS EA NA WA CSA 1212

    HapMap Linkage Disequilibrium report for SDC1 (20400558 - 20425194 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for SDC1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv29269CNV Loss19812545
    esv29979CNV Loss17803354
    nsv819169CNV Gain19587683

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SDC1
    DNA2.0 Custom Variant and Variant Library Synthesis for SDC1

    (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.)
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    OMIM gene information: 186355    OMIM disorders: --

    5 diseases for SDC1:    
    About MalaCards
    ameloblastic carcinoma    monoclonal gammopathy of uncertain significance    breast carcinoma in situ    intestinal disease
    hiv-1

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

    Find genes that share disorders with SDC1           About GenesLikeMe

    3 Novoseek inferred 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)

    Genetic Association Database (GAD): SDC1
    Human Genome Epidemiology (HuGE) Navigator: SDC1 (2 documents)

    Export disorders for SDC1 gene to outside databases

    (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)
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    PubMed articles for SDC1 gene, integrated from 10 sources (see all 243):
    (articles sorted by number of sources associating them with SDC1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study. (PubMed id 19107206)1, 4 Dalmasso C....Theodorou I. (PLoS ONE 2008)
    2. Adhesion signaling by a novel mitotic substrate of src kinases. (PubMed id 16007225)1, 2 Bhatt A.S.... Moasser M.M. (Oncogene 2005)
    3. 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. (Genome Res. 2004)
    4. 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. (Hum. Genet. 1997)
    5. 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. (J. Biol. Chem. 1992)
    6. Sequence of human syndecan indicates a novel gene family of integral membrane proteoglycans. (PubMed id 2324102)1, 2 Mali M.... Jalkanen M. (J. Biol. Chem. 1990)
    7. Induction of syndecan-1 expression in stromal fibroblasts promotes proliferation of human breast cancer cells. (PubMed id 14744776)1, 9 Maeda T....Friedl A. (Cancer Res. 2004)
    8. 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. (J. Exp. Med. 2009)
    9. Membrane type 1 matrix metalloproteinase-mediated stromal syndecan-1 shedding stimulates breast carcinoma cell proliferation. (PubMed id 19010933)1, 9 Su G....Friedl A. (Cancer Res. 2008)
    10. 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. (amp 2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

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

    (According to HUGE)
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      --

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

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    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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