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SDC2 Gene

protein-coding   GIFtS: 66
GCID: GC08P097575

Syndecan 2

(Previous names: heparan sulfate proteoglycan 1, cell surface-associated)
(Previous symbols: HSPG, HSPG1)
  See SDC2-related disease
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 21 2     CD3622
HSPG11 2 3 5     Cell Surface-Associated Heparan Sulfate Proteoglycan 12
HSPG1 2 3     fibroglycan2
Heparan Sulfate Proteoglycan 1, Cell Surface-Associated1 2     syndecan-22
Syndecan Proteoglycan 21 2     Fibroglycan3
Heparan Sulfate Proteoglycan Core Protein2 3     CD362 Antigen3
SYND22 3     

External Ids:    HGNC: 106591   Entrez Gene: 63832   Ensembl: ENSG000001694397   OMIM: 1424605   UniProtKB: P347413   

Export aliases for SDC2 gene to outside databases

Previous GC identifers: GC08P096514 GC08P097579 GC08P097174 GC08P097462 GC08P092711


(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 SDC2 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-2 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-2 expression has been detected
in several different tumor types. (provided by RefSeq, Jul 2008)

GeneCards Summary for SDC2 Gene:
SDC2 (syndecan 2) is a protein-coding gene. Diseases associated with SDC2 include hiv-1. GO annotations related to this gene include cytoskeletal protein binding and PDZ domain binding. An important paralog of this gene is SDC3.

UniProtKB/Swiss-Prot: SDC2_HUMAN, P34741
Function: Cell surface proteoglycan that bears heparan sulfate. Regulates dendritic arbor morphogenesis (By
similarity)

Gene Wiki entry for SDC2 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:
NC_000008.11  NT_008046.17  NC_018919.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SDC2 gene promoter:
         Bach1   AhR   NRSF form 1   Nkx2-5   E4BP4   LCR-F1   Evi-1   Arnt   MRF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSDC2 promoter sequence
   Search Chromatin IP Primers for SDC2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SDC2


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

Entrez Gene cytogenetic band: 8q22-q23   Ensembl cytogenetic band:  8q22.1   HGNC cytogenetic band: 8q22-q23

SDC2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SDC2 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08P097575:  view genomic region     (about GC identifiers)

Start:
97,505,579 bp from pter      End:
97,624,037 bp from pter
Size:
118,459 bases      Orientation:
plus 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: SDC2_HUMAN, P34741 (See protein sequence)
Recommended Name: Syndecan-2 precursor  
Size: 201 amino acids; 22160 Da
Subunit: Interacts (via cytoplasmic domain) with SARM1 (By similarity)
Sequence caution: Sequence=AAA52701.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: B3KQA3 Q6PIS6 Q9H6V1

Explore the universe of human proteins at neXtProt for SDC2: NX_P34741

Explore proteomics data for SDC2 at MOPED

Post-translational modifications: 

  • O-glycosylated with core 1 or possibly core 8 glycans. Contains heparan sulfate1
  • Glycosylation2 at Ser41, Ser55, Ser57, Thr80, Ser81, Thr88, Thr89, Thr90, Thr101, Thr107
  • Modification sites at PhosphoSitePlus

  • See SDC2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_002989.2  
    ENSEMBL proteins: 
     ENSP00000307046   ENSP00000429045   ENSP00000427784   ENSP00000428256   ENSP00000429121  
     ENSP00000429662  
    Reactome Protein details: P34741

    SDC2 Human Recombinant Protein Products:

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    OriGene Protein Over-expression Lysate for SDC2
    OriGene Custom MassSpec
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    Novus Biologicals SDC2 Proteins
    Novus Biologicals SDC2 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for SDC2 

    SDC2 Antibody Products:

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    LSBio Antibodies in human, mouse, rat for SDC2

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    Browse ELISAs at Cloud-Clone Corp.
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    Search eBioscience for ELISAs for SDC2 


    (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 P34741

    ProtoNet protein and cluster: P34741

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


    UniProtKB/Swiss-Prot: SDC2_HUMAN, P34741
    Similarity: Belongs to the syndecan proteoglycan family


    Find genes that share domains with SDC2           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: SDC2_HUMAN, P34741
    Function: Cell surface proteoglycan that bears heparan sulfate. Regulates dendritic arbor morphogenesis (By
    similarity)

         Genatlas biochemistry entry for SDC2:
    syndecan 2,heparan sulfate proteoglycan 1 (48kDa and 90kDa),cell surface-associated,lung,fibroblast,involved in a
    translocation t(X,8)(p22.13-q22.1) in a patient with autism and multiple exostoses

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI11356864
    GO:0008092cytoskeletal protein binding IEA--
    GO:0030165PDZ domain binding IPI18256285
         
    Find genes that share ontologies with SDC2           About GenesLikeMe


    Phenotypes:
         1 MGI phenotypic allele for Sdc2 (no phenotypes)

    Find genes that share phenotypes with SDC2           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SDC2
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    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SDC2 (see all 54):
    hsa-miR-21* hsa-miR-607 hsa-miR-429 hsa-miR-199a-3p hsa-miR-25 hsa-miR-200a hsa-miR-1245 hsa-miR-218
    SwitchGear 3'UTR luciferase reporter plasmidSDC2 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SDC2

    Gene Editing
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: SDC2 (NM_002998)
    Sino Biological Human cDNA Clone for SDC2
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SDC2

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    (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
    SDC2_HUMAN, P34741: Membrane; Single-pass type I membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    golgi apparatus4
    lysosome4
    vacuole4
    extracellular3
    cytoskeleton2
    nucleus1

    Gene Ontology (GO): Selected cellular component terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005796Golgi lumen TAS--
    GO:0005886plasma membrane TAS--
    GO:0005887integral component of plasma membrane ----
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with SDC2           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 SDC2 About   (see all 22)  
    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
    3Heparan sulfate/heparin (HS-GAG) metabolism
    Heparan sulfate/heparin (HS-GAG) metabolism0.57
    HS-GAG degradation0.39
    HS-GAG biosynthesis0.57
    4Diseases associated with visual transduction
    Visual phototransduction0.44
    Diseases associated with visual transduction0.43
    Retinoid metabolism and transport0.44
    5Non-Canonical Wnt Pathway
    Non-Canonical Wnt Pathway0.53
    Canonical Wnt Pathway0.53


    Find genes that share SuperPaths with SDC2           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 R&D Systems Pathways for SDC2
        Wnt Signaling Pathways
    VEGF - VEGF R2 Signaling Pathways

    3 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for SDC2
        Inhibition of Angiogenesis by TSP1
    Inhibition of Matrix Metalloproteinases
    Transendothelial Migration of Leukocytes

    2 GeneGo (Thomson Reuters) Pathways for SDC2
        Cell adhesion ECM remodeling
    Development FGFR signaling pathway

    4 BioSystems Pathways for SDC2
        TGF-beta Receptor Signaling Pathway
    FGF signaling pathway
    Syndecan-2-mediated signaling events
    Proteogylcan syndecan-mediated signaling events

    2 Sino Biological Pathways for SDC2
        Canonical Wnt Pathway
    Non-Canonical Wnt Pathway

    5 Reactome Pathways for SDC2
        HS-GAG biosynthesis
    Retinoid metabolism and transport
    HS-GAG degradation
    A tetrasaccharide linker sequence is required for GAG synthesis
    Syndecan interactions


    3 Kegg Pathways  (Kegg details for SDC2):
        Cell adhesion molecules (CAMs)
    Malaria
    Proteoglycans in cancer

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SDC2
    Interactions:

        GeneGlobe Interaction Network for SDC2

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

    Selected Interacting proteins for SDC2 (P347411, 2, 3 ENSP000003070464) via UniProtKB, MINT, STRING, and/or I2D (see all 135)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CASKO149361, 2, 3, ENSP000003674084EBI-1172957,EBI-1215506 MINT-14973 MINT-14974 MINT-58223 MINT-14972 I2D: score=5 STRING: ENSP00000367408
    NF1P213591, 3, ENSP000003510154EBI-1172957,EBI-1172917 I2D: score=3 STRING: ENSP00000351015
    SDCBPO005603, ENSP000002601304I2D: score=3 STRING: ENSP00000260130
    EPHB2P293233, ENSP000003637634I2D: score=2 STRING: ENSP00000363763
    EZRP153113, ENSP000003389344I2D: score=2 STRING: ENSP00000338934
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    Gene Ontology (GO): Selected biological process terms (see all 15):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001523retinoid metabolic process TAS--
    GO:0001666response to hypoxia IEA--
    GO:0005975carbohydrate metabolic process TAS--
    GO:0006024glycosaminoglycan biosynthetic process TAS--
    GO:0006027glycosaminoglycan catabolic process TAS--

    Find genes that share ontologies with SDC2           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 SDC2

    1 HMDB Compound for SDC2    About this table
    CompoundSynonyms CAS #PubMed Ids
    Heparan sulfateHHS 5 (see all 13)9050-30-0--

    1 DrugBank Compound for SDC2    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    SargramostimColony-stimulating factor (see all 5)83869-56-1targetagonist10734053 17139284 17016423

    1 Novoseek inferred chemical compound relationship for SDC2 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    heparan sulfate 74.8 4 15054905 (1), 12761845 (1), 15554942 (1), 8537400 (1)



    Find genes that share compounds with SDC2           About GenesLikeMe



    (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 SDC2 gene: 
    NM_002998.3  

    Unigene Cluster for SDC2:

    Syndecan 2
    Hs.1501  [show with all ESTs]
    Unigene Representative Sequence: BC030133
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000302190(uc003yhv.1 uc011lgu.1) ENST00000520233 ENST00000519587
    ENST00000518385 ENST00000522911 ENST00000519914 ENST00000521590 ENST00000523877

    miRNA
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    hsa-miR-21* hsa-miR-607 hsa-miR-429 hsa-miR-199a-3p hsa-miR-25 hsa-miR-200a hsa-miR-1245 hsa-miR-218
    SwitchGear 3'UTR luciferase reporter plasmidSDC2 3' UTR sequence
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    Primer
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    Additional mRNA sequence: 

    AK025488.1 AK074530.1 AK097839.1 AK130131.1 AK298643.1 AK298939.1 AK300067.1 BC030133.2 
    BC049836.1 J04621.1 

    17 DOTS entries:

    DT.318538  DT.100823371  DT.100823364  DT.95156202  DT.100823363  DT.100823369  DT.121482345  DT.91764066 
    DT.100644039  DT.100675643  DT.121482311  DT.121482328  DT.91764072  DT.91837226  DT.95156197  DT.91764069 
    DT.92014938 

    Selected AceView cDNA sequences (see all 382):

    AI337354 H64347 CB161866 BU154320 AW301666 AA122057 BQ716567 BU629078 
    BF061447 BQ575736 BM834669 AK130131 BQ721382 AK074530 AA043662 CA448604 
    CR596137 AA114891 BU625124 CA419078 T68006 BQ719666 CB162695 H81688 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for SDC2    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b
    SP1:                          -                                 
    SP2:                    -     -                                 
    SP3:                                                            


    ECgene alternative splicing isoforms for SDC2

    (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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    SDC2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGGCCTAATA
    SDC2 Expression
    About this image


    SDC2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 17) fully expand
     
     Kidney (Urinary System)    fully expand to see all 2 entries
             mK3
     
     Bone (Muscoskeletal System)    fully expand to see all 2 entries
             Endochondral Facial Bones
     
     Tooth (Integumentary System)    fully expand to see all 2 entries
             Odontoblasts Dentin
     
     Cartilage (Muscoskeletal System)
             Meckel's Cartilage
     
     Endothelium (Cardiovascular System)
             Extraembryonic Angioblasts Extraembryonic Capillary Plexus
    SDC2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SDC2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.1501
        Custom PCR Arrays for SDC2
    Primer
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    QuantiFast Probe-based Assays in human, mouse, rat SDC2
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SDC2

    (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 SDC2 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sdc21 , 5 syndecan 21, 5 84.41(n)1
    84.08(a)1
      15 (13.74 cM)5
    155291  NM_008304.21  NP_032330.11 
     329207235 
    chicken
    (Gallus gallus)
    Aves SDC21 syndecan 2 74.63(n)
    72.64(a)
      374102  NM_001001462.1  NP_001001462.1 
    lizard
    (Anolis carolinensis)
    Reptilia SDC26
    syndecan 2
    64(a)
    1 ↔ 1
    4(20103490-20112219)
    African clawed frog
    (Xenopus laevis)
    Amphibia sdc2-A-prov2 syndecan 2 81.16(n)    BC041490.1 
    zebrafish
    (Danio rerio)
    Actinopterygii sdc22 syndecan 2 78.47(n)   282667  AF262048.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Sdc6
    Syndecan
    13(a)
    1 → many
    2R(17280111-17368680)
    worm
    (Caenorhabditis elegans)
    Secernentea sdn-16
    Protein SDN-1, isoform b (sdn-1) mRNA, complete cd...
    21(a)
    1 → many
    X(10589780-10593334) WBGene00004749


    ENSEMBL Gene Tree for SDC2 (if available)
    TreeFam Gene Tree for SDC2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SDC2 gene
    SDC32  SDC42  SDC12  
    2 SIMAP similar genes for SDC2 using alignment to 5 protein entries:     SDC2_HUMAN (see all proteins):
    SDC4    SDC3

    Find genes that share paralogs with SDC2           About GenesLikeMe



    (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)
    About This Section

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    Selected SNPs for SDC2 (see all 2511)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs354835531,2
    C,F--97503892(+) CTGGCG/AAGTAG 1 -- us2k13Minor allele frequency- A:0.33NA 6
    rs39437311,2
    H--97504030(+) TCCATC/TTTAAA 1 -- us2k14Minor allele frequency- T:0.00NS EA 418
    rs1846796101,2
    --97504085(+) TTTGGA/GAGGCT 1 -- us2k10--------
    rs1401260001,2
    --97504119(+) CAAGAA/GTTTGA 1 -- us2k10--------
    rs1165495241,2
    F--97504256(+) GAGGTA/CGAGGC 1 -- us2k11Minor allele frequency- C:0.05WA 118
    rs114630101,2
    C--97504313(+) AAAAAA/-AAAAA 1 -- us2k1 trp31Minor allele frequency- -:0.00NA 2
    rs1438094451,2
    --97504339(+) AAAGGC/TTGTGG 1 -- us2k10--------
    rs1464403571,2
    --97504369(+) AGTGGA/GGCCCA 1 -- us2k10--------
    rs1158560181,2
    F--97504404(+) TGTCTG/ATGGAA 1 -- us2k11Minor allele frequency- A:0.01WA 118
    rs745918311,2
    F--97504606(+) TCTCCA/TGTTAA 1 -- us2k11Minor allele frequency- T:0.03EA 120

    HapMap Linkage Disequilibrium report for SDC2 (97505579 - 97624037 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SDC2 (see all 22):    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv821376CNV Deletion20802225
    esv2737335CNV Deletion23290073
    dgv1298e199CNV Deletion23128226
    esv1008392CNV Deletion20482838
    esv2737336CNV Deletion23290073
    esv2667295CNV Deletion23128226
    esv2661416CNV Deletion23128226
    esv2737334CNV Deletion23290073
    esv2537308CNV Insertion19546169
    nsv507475CNV Insertion20534489

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SDC2
    DNA2.0 Custom Variant and Variant Library Synthesis for SDC2

    (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: 142460    OMIM disorders: --

    1 disease for SDC2:    
    About MalaCards
    hiv-1


    Find genes that share disorders with SDC2           About GenesLikeMe

    1 Novoseek inferred disease relationship for SDC2 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    tumors 0 4 19288017 (1)

    Genetic Association Database (GAD): SDC2
    Human Genome Epidemiology (HuGE) Navigator: SDC2 (9 documents)

    Export disorders for SDC2 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

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    PubMed articles for SDC2 gene, integrated from 10 sources (see all 138):
    (articles sorted by number of sources associating them with SDC2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Common polymorphisms in ITGA2, PON1 and THBS2 are associated with coronary atherosclerosis in a candidate gene association study of the Chinese Han population. (PubMed id 20485444)1, 4 Wang Y....Huang W. (J. Hum. Genet. 2010)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    4. Genomic screening identifies novel linkages and provides further evidence for a role of MYH9 in nonsyndromic cleft lip and palate. (PubMed id 18716610)1, 4 Chiquet B.T....Hecht J.T. (Eur. J. Hum. Genet. 2009)
    5. Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment. (PubMed id 19086053)1, 4 GratacA^s M....Carracedo A. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2009)
    6. Signal sequence and keyword trap in silico for selection of full- length human cDNAs encoding secretion or membrane proteins from oligo- capped cDNA libraries. (PubMed id 16303743)1, 2 Otsuki T....Isogai T. (DNA Res. 2005)
    7. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    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. (Genome Res. 2004)
    9. Co-inheritance of specific genotypes of HSPG and ApoE gene increases risk of type 2 diabetic nephropathy. (PubMed id 14674716)1, 4 Liu L....Li J. (Mol. Cell. Biochem. 2003)
    10. The heparan sulfate proteoglycan gene polymorphism: association with type 2 diabetic nephropathy in Chinese. (PubMed id 12708751)1, 4 Liu L....Li J. (Mol. Cell. Biochem. 2003)

    (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: 6383 HGNC: 10659 AceView: SDC2 Ensembl:ENSG00000169439 euGenes: HUgn6383
    ECgene: SDC2 Kegg: 6383 H-InvDB: SDC2

    (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)
    About This Section

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    NameDescription
    PharmGKB entry for SDC2 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SDC2 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

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    Patent Information for SDC2 gene:
    Search GeneIP for patents involving SDC2

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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