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

SDC4 Gene

protein-coding   GIFtS: 69
GCID: GC20M043953

Syndecan 4

(Previous names: syndecan 4 (amphiglycan, ryudocan))
  See 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)
About This Section

Aliases
Syndecan 41 2     amphiglycan2
Syndecan 4 (Amphiglycan, Ryudocan)1 2     Ryudocan Amphiglycan2
Syndecan Proteoglycan 41 2     syndecan-42
Ryudocan Core Protein2 3     Amphiglycan3
SYND42 3     

External Ids:    HGNC: 106611   Entrez Gene: 63852   Ensembl: ENSG000001241457   OMIM: 6000175   UniProtKB: P314313   

Export aliases for SDC4 gene to outside databases

Previous GC identifers: GC20M043682 GC20M044592 GC20M044639 GC20M043387 GC20M040695


(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 SDC4 Gene:
The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan that functions as a
receptor in intracellular signaling. The encoded protein is found as a homodimer and is a member of the syndecan
proteoglycan family. This gene is found on chromosome 20, while a pseudogene has been found on chromosome 22.
(provided by RefSeq, Jul 2008)

GeneCards Summary for SDC4 Gene: 
SDC4 (syndecan 4) is a protein-coding gene. Diseases associated with SDC4 include morquio syndrome b, and bladder carcinoma, and among its related super-pathways are Non-integrin membrane-ECM interactions and Metabolism of carbohydrates. GO annotations related to this gene include cytoskeletal protein binding and fibronectin binding. An important paralog of this gene is SDC3.

UniProtKB/Swiss-Prot: SDC4_HUMAN, P31431
Function: Cell surface proteoglycan that bears heparan sulfate

Gene Wiki entry for SDC4 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000020.10  NT_011362.10  NC_018931.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SDC4 gene promoter:
         AP-1   ATF-2   MyoD   c-Jun   NF-kappaB   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSDC4 promoter sequence
   Search SABiosciences Chromatin IP Primers for SDC4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SDC4


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

Entrez Gene cytogenetic band: 20q12   Ensembl cytogenetic band:  20q13.12   HGNC cytogenetic band: 20q12

SDC4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SDC4 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20M043953:  view genomic region     (about GC identifiers)

Start:
43,953,928 bp from pter      End:
43,977,064 bp from pter
Size:
23,137 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SDC4_HUMAN, P31431 (See protein sequence)
Recommended Name: Syndecan-4 precursor  
Size: 198 amino acids; 21642 Da
Subunit: Homodimer. Interacts (via its cytoplasmic domain) with GIPC (via its PDZ domain). Interacts (via its
cytoplasmic domain) with NUDT16L1 (By similarity). Interacts with CDCP1 and SDCBP
Subcellular location: Isoform 1: Membrane; Single-pass type I membrane protein. Secreted. Note=Shedding of the
ectodomain produces a soluble form (By similarity)
Subcellular location: Isoform 2: Secreted
4 PDB 3D structures from and Proteopedia for SDC4:
1EJP (3D)        1EJQ (3D)        1OBY (3D)        1YBO (3D)    
Secondary accessions: O00773 Q16833 Q53FN9 Q6FGN3
Alternative splicing: 2 isoforms:  P31431-1   P31431-2   (Soluble form, lacks the transmembrane domain)

Explore the universe of human proteins at neXtProt for SDC4: NX_P31431

Explore proteomics data for SDC4 at MOPED 

Post-translational modifications:

  • UniProtKB: 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 TIMP3
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P31431

  • SDC4 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SDC4 Protein Expression
    REFSEQ proteins: NP_002990.2  
    ENSEMBL proteins: 
     ENSP00000361818   ENSP00000445353  
    Reactome Protein details: P31431
    Human Recombinant Protein Products for SDC4: 
    Browse Purified and Recombinant Proteins at EMD Millipore
    R&D Systems Recombinant & Natural Proteins for SDC4 (Syndecan-4)
    Enzo Life Sciences proteins for SDC4
    Browse OriGene full length recombinant human proteins expressed in human HEK293 cells
    OriGene Protein Over-expression Lysate for SDC4
    OriGene Custom MassSpec 
    OriGene Custom Protein Services for SDC4
    GenScript Custom Purified and Recombinant Proteins Services for SDC4
    Novus Biologicals SDC4 Proteins
    Novus Biologicals SDC4 Lysates
    Sino Biological Recombinant Protein for SDC4
    Sino Biological Cell Lysate for SDC4 
    ProSpec Recombinant Protein for SDC4
    Cloud-Clone Corp. Proteins for SDC4 

    Gene Ontology (GO): 5/11 cellular component terms (GO ID links to tree view) (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--
    GO:0005796Golgi lumen TAS--
    GO:0005886plasma membrane TAS--
    GO:0005887integral to plasma membrane NAS1500433
    GO:0005925focal adhesion IEA--

    SDC4 for ontologies           About GeneDecksing



    SDC4 Antibody Products: 
    EMD Millipore Mono- and Polyclonal Antibodies for the study of SDC4
    R&D Systems Antibodies for SDC4 (Syndecan-4)
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    Novus Biologicals SDC4 Antibodies
    Abcam antibodies for SDC4
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    ThermoFisher Antibodies for SDC4
    LSBio Antibodies in human, mouse, rat for SDC4 

    Assay Products for SDC4: 
    Browse Kits and Assays available from EMD Millipore
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    R&D Systems ELISAs for SDC4 (Syndecan-4)         (see all)
    GenScript Custom Assay Services for SDC4
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for SDC4 
    Cloud-Clone Corp. CLIAs for SDC4


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

    2 InterPro protein domains:
     IPR003585 Neurexin-like
     IPR001050 Syndecan

    Graphical View of Domain Structure for InterPro Entry P31431

    ProtoNet protein and cluster: P31431

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


    UniProtKB/Swiss-Prot: SDC4_HUMAN, P31431
    Similarity: Belongs to the syndecan proteoglycan family


    SDC4 for domains           About GeneDecksing


    (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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SDC4_HUMAN, P31431
    Function: Cell surface proteoglycan that bears heparan sulfate

         Genatlas biochemistry entry for SDC4:
    syndecan 4,heparan sulfate proteoglycan 3 (22kDa),endothelial cell surface associated,cooperating with integrins
    in a Rho dependent manner in the assembly of focal adhesion and actin stress fibers

         Gene Ontology (GO): 5 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001968fibronectin binding IEA--
    GO:0005080protein kinase C binding IEA--
    GO:0005515protein binding IPI12571249
    GO:0008092cytoskeletal protein binding IEA--
    GO:0070053thrombospondin receptor activity IMP17879962
         
    SDC4 for ontologies           About GeneDecksing


    Phenotypes:
         7 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Sdc4):
     cardiovascular system  cellular  embryogenesis  homeostasis/metabolism  mortality/aging 
     muscle  renal/urinary system 

    SDC4 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for SDC4: Sdc4tm1Goe Sdc4tm1Tmu

       inGenious Targeting Laboratory - Custom generated mouse model solutions for SDC4 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for SDC4

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SDC4 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SDC4 

    miRNA
    Products:
        
    miRTarBase miRNAs that target SDC4:
    hsa-mir-1 (MIRT002795)

    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SDC4
    8/22 QIAGEN miScript miRNA Assays for microRNAs that regulate SDC4 (see all 22):
    hsa-miR-142-3p hsa-miR-548k hsa-miR-16-1* hsa-miR-450b-3p hsa-miR-138-2* hsa-miR-764 hsa-miR-766 hsa-miR-3680
    SwitchGear 3'UTR luciferase reporter plasmidSDC4 3' UTR sequence
    Inhib. RNA
    Products:
        
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for SDC4
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SDC4

    Gene Editing
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    Clone
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: SDC4 (NM_002999)
    Sino Biological Human cDNA Clone for SDC4
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SDC4
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SDC4
    Sirion Biotech Customized lentivirus for stable overexpression of SDC4 
                         Customized lentivirus expression plasmids for stable overexpression of SDC4 

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for SDC4
    Search LifeMap BioReagents cell lines for SDC4
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SDC4


    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for SDC4 About   (see all 19)                                                                                              See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1Non-integrin membrane-ECM interactions
    Non-integrin membrane-ECM interactions0.44
    ECM-receptor interaction0.42
    Syndecan interactions0.44
    2MPS IIIC - Sanfilippo syndrome C
    MPS IIIC - Sanfilippo syndrome C0.48
    Mucopolysaccharidoses0.48
    MPS IV - Morquio syndrome A0.48
    MPS IIID - Sanfilippo syndrome D0.48
    MPS IV - Morquio syndrome B0.48
    MPS I - Hurler syndrome0.48
    MPS VI - Maroteaux-Lamy syndrome0.48
    MPS IX - Natowicz syndrome0.48
    3Heparan sulfate/heparin (HS-GAG) metabolism
    Heparan sulfate/heparin (HS-GAG) metabolism0.56
    HS-GAG degradation0.40
    HS-GAG biosynthesis0.56
    4Visual phototransduction
    Visual phototransduction0.48
    Diseases associated with visual transduction0.47
    Retinoid metabolism and transport0.48
    5A tetrasaccharide linker sequence is required for GAG synthesis
    Chondroitin sulfate/dermatan sulfate metabolism0.54
    A tetrasaccharide linker sequence is required for GAG synthesis0.54

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 EMD Millipore Pathway for SDC4
        Development FGFR signaling pathway

    2 R&D Systems Pathways for SDC4
        Wnt Signaling Pathway
    VEGF - VEGF R2 Signaling Pathways

    1 Downloadable PowerPoint Slide of QIAGEN Pathway Central Maps for SDC4
        Transendothelial Migration of Leukocytes

    1 Cell Signaling Technology (CST) Pathway for SDC4
        Adhesion

    1 GeneGo (Thomson Reuters) Pathway for SDC4
        Development FGFR signaling pathway

    2 BioSystems Pathways for SDC4
        Syndecan-4-mediated signaling events
    Proteogylcan syndecan-mediated signaling events

    2 Sino Biological Pathways for SDC4 
        Canonical Wnt Pathway
    Non-Canonical Wnt Pathway

    5/28        Reactome Pathways for SDC4 (see all 28)
        Diseases associated with visual transduction
    Chondroitin sulfate/dermatan sulfate metabolism
    MPS VI - Maroteaux-Lamy syndrome
    Metabolism
    Visual phototransduction


    3         Kegg Pathways  (Kegg details for SDC4):
        ECM-receptor interaction
    Cell adhesion molecules (CAMs)
    Proteoglycans in cancer


    SDC4 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SDC4

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

    5/101 Interacting proteins for SDC4 (P314311, 2, 3 ENSP000003618184) via UniProtKB, MINT, STRING, and/or I2D (see all 101)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PRKCAP172521, 3, ENSP000002843844EBI-3913237,EBI-1383528 I2D: score=2 STRING: ENSP00000284384
    GIPC1O149082, 3, ENSP000003406984MINT-72943 I2D: score=4 STRING: ENSP00000340698
    CASKO149363, ENSP000003674084I2D: score=2 STRING: ENSP00000367408
    CXCR4P610733, ENSP000003868844I2D: score=2 STRING: ENSP00000386884
    MDKP217413, ENSP000003528524I2D: score=2 STRING: ENSP00000352852
    About this table

    Gene Ontology (GO): 5/14 biological process terms (GO ID links to tree view) (see all 14):    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--

    SDC4 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 SDC4

    1 HMDB Compound for SDC4    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 SDC4

    (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,
    Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SDC4 gene: 
    NM_002999.3  

    Unigene Cluster for SDC4:

    Syndecan 4
    Hs.632267  [show with all ESTs]
    Unigene Representative Sequence: BC030805
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000372733(uc002xnu.3 uc010zws.2) ENST00000537976
    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SDC4
    8/22 QIAGEN miScript miRNA Assays for microRNAs that regulate SDC4 (see all 22):
    hsa-miR-142-3p hsa-miR-548k hsa-miR-16-1* hsa-miR-450b-3p hsa-miR-138-2* hsa-miR-764 hsa-miR-766 hsa-miR-3680
    SwitchGear 3'UTR luciferase reporter plasmidSDC4 3' UTR sequence
    Inhib. RNA
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    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SDC4
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SDC4
    Sirion Biotech Customized lentivirus for stable overexpression of SDC4 
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SDC4
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SDC4

    Additional mRNA sequence: 

    AK222695.1 AK223243.1 AK303964.1 AK312507.1 BC030805.1 CR542045.1 CR542074.1 D13292.1 
    X67016.1 

    12 DOTS entries:

    DT.452767  DT.95212585  DT.100797956  DT.120819104  DT.95212580  DT.417846  DT.95212589  DT.100777096 
    DT.91698455  DT.92442326  DT.97862180  DT.100033659 

    24/300 AceView cDNA sequences (see all 300):

    BM989767 BU624968 BU621133 BG149309 CA439231 AI027221 BI524082 X67016 
    AU118755 CR542045 BC030805 CD364886 BM050667 AW028728 BP353030 BX358362 
    AA313017 BQ689093 BM831837 NM_002999 AW514394 CR542074 BU727526 AA002237 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for SDC4    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b
    SP1:                                          
    SP2:              -                           


    ECgene alternative splicing isoforms for SDC4

    (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

    SDC4 expression in normal human tissues (normalized intensities)      SDC4 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TCCATCTGTT
    SDC4 Expression
    About this image


    SDC4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/12 selected tissues (see all 12) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 5 entries
             Endochondral Facial Bones
             skeleton/cranium/chondrocranium   
     
     Skeletal Muscle (Muscoskeletal System)    fully expand to see all 4 entries
             Muscle Satellite Cells Lumbar Muscle Satellite Pool
     
     Kidney (Urinary System)    fully expand to see all 3 entries
             Podocytes Podocyte Layer
             visceral organ/metanephros/calyx   
     
     Lower Urinary Tract (Urinary System)    fully expand to see all 3 entries
             visceral organ/urethra of male   
     
     Neural Crest (Gastrulation Derivatives)    fully expand to see all 2 entries
             skeleton/cranium/chondrocranium   

    See SDC4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SDC4

    SOURCE GeneReport for Unigene cluster: Hs.632267

    UniProtKB/Swiss-Prot: SDC4_HUMAN, P31431
    Tissue specificity: Expressed in epithelial and fibroblastic cells

        SABiosciences Custom PCR Arrays for SDC4
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SDC4
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SDC4

    (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 SDC4 gene from 5/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sdc41 , 5 syndecan 41, 5 81.52(n)1
    82.38(a)1
      2 (85.16 cM)5
    209711  NM_011521.21  NP_035651.11 
     1644242475 
    chicken
    (Gallus gallus)
    Aves SDC41 syndecan 4 63.26(n)
    60.22(a)
      419184  NM_001007869.1  NP_001007870.1 
    lizard
    (Anolis carolinensis)
    Reptilia SDC46
    Syndecan
    49(a)
    1 ↔ 1
    4(142913934-142920374)
    zebrafish
    (Danio rerio)
    Actinopterygii sdc41 syndecan 4 57.09(n)
    48.5(a)
      568593  NM_001048149.1  NP_001041614.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Sdc6
    Syndecan
    8(a)
    1 → many
    2R(17280111-17368680)


    ENSEMBL Gene Tree for SDC4 (if available)
    TreeFam Gene Tree for SDC4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SDC4 gene
    SDC32  SDC22  SDC12  
    5 SIMAP similar genes for SDC4 using alignment to 2 protein entries:     SDC4_HUMAN (see all proteins):
    R32    R34    SDC2    SDC4-ROS1_S2    SDC4-ROS1_S4

    SDC4 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for SDC4
    PGOHUM00000259702


    (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) 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

    10/651 SNPs in SDC4 are shown (see all 651)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0218514
    ----see VAR_0218512 F L mis40--------
    rs1852987661,2
    --43949510(+) ATGCTC/TCCCTA 1 -- us2k10--------
    rs1173010051,2
    C,F--43949558(+) TGCCAG/TAATAA 1 -- us2k11Minor allele frequency- T:0.03EA 120
    rs1177752311,2
    C,F--43953491(+) CCCACA/GTCTAG 1 -- ds50011Minor allele frequency- G:0.02EA 120
    rs670687371,2
    C,F--43953510(+) CTGCCG/ACTCAG 1 -- ds50017Minor allele frequency- A:0.20NA WA CSA EA 366
    rs1162925841,2
    --43953543(+) GCTGAC/TAGTTG 1 -- ds50010--------
    rs27433571,2
    H--43953603(+) ttatgA/Tgaaac 1 -- ds50014Minor allele frequency- T:0.00NS EA 418
    rs1445279591,2
    --43953637(+) CTGACA/GCAAAG 1 -- ds50010--------
    rs1838751531,2
    --43953651(+) TTTGTA/GTTTGC 1 -- ds50010--------
    rs1889451771,2
    --43953906(+) ATGAAC/TGAAAA 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for SDC4 (43953928 - 43977064 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SDC4: --
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing SDC4
    DNA2.0 Custom Variant and Variant Library Synthesis for SDC4

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 600017    OMIM disorders: --

    11 diseases for SDC4:    About MalaCards
    morquio syndrome b    bladder carcinoma    kaposi's sarcoma    osteoarthritis
    malaria    sarcoma    atherosclerosis    osteosarcoma
    endotheliitis    melanoma    hepatitis


    SDC4 for disorders           About GeneDecksing

    Genetic Association Database (GAD): SDC4
    Human Genome Epidemiology (HuGE) Navigator: SDC4 (6 documents)

    Export disorders for SDC4 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)
    About This Section

    PubMed articles for SDC4 gene, integrated from 9 sources (see all 109):
    (articles sorted by number of sources associating them with SDC4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Human ryudocan core protein: molecular cloning and characterization of the cDNA, and chromosomal localization of the gene. (PubMed id 7916598)1, 2, 3 Kojima T.... Saito H. (1993)
    2. Molecular cloning of amphiglycan, a novel integral membrane heparan sulfate proteoglycan expressed by epithelial and fibroblastic cells. (PubMed id 1500433)1, 2, 3 David G....van den Berghe H. (1992)
    3. The altered expression of syndecan 4 in the uninvolved skin of venous leg ulcer patients may predispose to venous leg ulcer. (PubMed id 18638267)1, 4, 9 Nagy N....Szell M. (2008)
    4. Common polymorphisms in ITGA2, PON1 and THBS2 are ass ociated with coronary atherosclerosis in a candidate gene association study of the Chinese Han population. (PubMed id 20485444)1, 4 Wang Y....Huang W. (2010)
    5. Genome-wide association analysis identifies three pso riasis susceptibility loci. (PubMed id 20953189)1, 4 Stuart P.E....Elder J.T. (2010)
    6. Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (2010)
    7. Adhesion signaling by a novel mitotic substrate of src kinases. (PubMed id 16007225)1, 2 Bhatt A.S.... Moasser M.M. (2005)
    8. 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)
    9. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (2001)
    10. Solution structure of the dimeric cytoplasmic domain of syndecan-4. (PubMed id 11456484)1, 2 Shin J.... Oh E.-S. (2001)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    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)
    About This Section
    Entrez Gene: 6385 HGNC: 10661 AceView: SDC4 Ensembl:ENSG00000124145 euGenes: HUgn6385
    ECgene: SDC4 Kegg: 6385 H-InvDB: SDC4

    (According to HUGE)
    About This Section
      --

    (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 SDC4 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SDC4 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SDC4 gene:
    Search GeneIP for patents involving SDC4

    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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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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