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

SDCBP2 Gene

protein-coding   GIFtS: 47
GCID: GC20M001238

syndecan binding protein (syntenin) 2

 Explore 3 diseases affiliated with
SDCBP2 via our new
 Human Malady Compendium 
Biological research products
for SDCBP2
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Syndecan Binding Protein (Syntenin) 21 2
SITAC181 2 3
ST-21 2
SITAC2
Syntenin-21
Syndecan-Binding Protein 23

External Ids:    HGNC: 157561   Entrez Gene: 271112   Ensembl: ENSG000001257757   UniProtKB: Q9H1903   

Export aliases for SDCBP2 gene to outside databases

Previous GC identifers: GC20M001278 GC20M001285


(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 SDCBP2:
The protein encoded by this gene contains two class II PDZ domains. PDZ domains facilitate protein-protein interactions
by binding to the cytoplasmic C-terminus of transmembrane proteins, and PDZ-containing proteins mediate cell signaling
and the organization of protein complexes. The encoded protein binds to phosphatidylinositol 4, 5-bisphosphate (PIP2)
and plays a role in nuclear PIP2 organization and cell division. Alternatively spliced transcript variants encoding
multiple isoforms have been observed for this gene. Read-through transcription also exists between this gene and the
upstream FKBP1A (FK506 binding protein 1A, 12kDa) gene, as represented in GeneID:100528031. (provided by RefSeq, Sep
2011)

Gene Wiki entry for SDCBP2


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000020.10  NC_018931.1  NT_011387.8  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SDCBP2 gene promoter:
         HEN1   RORalpha1   PPAR-gamma1   p300   ZIC2/Zic2   ZID   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSDCBP2 promoter sequence
   Search SABiosciences Chromatin IP Primers for SDCBP2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SDCBP2


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

Entrez Gene cytogenetic band: 20p13   Ensembl cytogenetic band:  20p13   HGNC cytogenetic band: 20p13

SDCBP2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SDCBP2 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20M001238:  view genomic region     (about GC identifiers)

Start:
1,290,619 bp from pter      End:
1,309,883 bp from pter
Size:
19,265 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: SDCB2_HUMAN, Q9H190 (See protein sequence)
Recommended Name: Syntenin-2  
Size: 292 amino acids; 31594 Da
Subunit: Monomer and homodimer. Interacts with SDCBP (By similarity)
Sequence caution: Sequence=AAH02727.2; Type=Erroneous initiation;
Secondary accessions: O95892 Q5W0X1 Q9BZ42 Q9H567 Q9NRY8
Alternative splicing: 2 isoforms:  Q9H190-1   Q9H190-3   

Explore the universe of human proteins at neXtProt for SDCBP2: NX_Q9H190

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9H190

  • SDCBP2 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (3 alternative transcripts): 
    NP_001186713.1  NP_056500.2  NP_536737.3  

    ENSEMBL proteins: 
     ENSP00000371229   ENSP00000371233   ENSP00000342935   ENSP00000354013  

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    Browse ProSpec Recombinant Proteins
    Browse Proteins at Uscn

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005737cytoplasm IDA11152476
    GO:0005886plasma membrane IC11152476


    SDCBP2 for ontologies           About GeneDecksing



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

    SDCBP2 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR001478 PDZ

    Graphical View of Domain Structure for InterPro Entry Q9H190

    ProtoNet protein and cluster: Q9H190

    1 Blocks protein family: IPB001478 PDZ/DHR/GLGF domain

    UniProtKB/Swiss-Prot: SDCB2_HUMAN, Q9H190
    Similarity: Contains 2 PDZ (DHR) domains


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

    miRNA
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    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008022protein C-terminus binding IPI11152476
    GO:0042803protein homodimerization activity IDA11152476
    GO:0046982protein heterodimerization activity IPI11152476


    SDCBP2 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for SDCBP2:
     Increased G1 DNA content 


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



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SDCBP2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 16)

    5/22 Interacting proteins for SDCBP2 (Q9H1902, 3 ENSP000003429354) via UniProtKB, MINT, STRING, and/or I2D (see all 22)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    C1orf35Q9BU762, 3, ENSP000002721394MINT-66267 I2D: score=5 STRING: ENSP00000272139
    PRR13Q9NZ812, 3, ENSP000004120644MINT-67666 I2D: score=4 STRING: ENSP00000412064
    DPPA2Q7Z7J52, 3MINT-67133 I2D: score=4 
    ZCCHC17Q9NP642, 3, ENSP000003435574MINT-66829 I2D: score=6 STRING: ENSP00000343557
    TIFAQ96CG32, 3, ENSP000003549114MINT-66594 I2D: score=5 STRING: ENSP00000354911
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007399nervous system development NAS11152476
    GO:0035556intracellular signal transduction NAS11152476
    GO:0046907intracellular transport NAS11152476


    SDCBP2 for ontologies           About GeneDecksing



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

    SDCBP2 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SDCBP2
    1 Novoseek chemical compound relationship for SDCBP2 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    pip2 81.8 10 16884951 (2), 15961997 (2), 17214441 (2)

    Search CenterWatch for drugs/clinical trials and news about SDCBP2 / SDCB2 

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

    REFSEQ mRNAs for SDCBP2 gene (3 alternative transcripts): 
    NM_001199784.1  NM_015685.5  NM_080489.4  

    Unigene Cluster for SDCBP2:

    Syndecan binding protein (syntenin) 2
    Hs.657015  [show with all ESTs]
    Unigene Representative Sequence: NR_037661
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000467129 ENST00000381808(uc002weu.4) ENST00000381812 ENST00000339987(uc021vzn.1 uc021vzo.1)
    ENST00000360779(uc002wev.4 uc010zpq.2)

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    hsa-miR-2117 hsa-miR-26b* hsa-miR-551b* hsa-miR-4273 hsa-miR-1205 hsa-miR-338-3p
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    Additional cDNA sequence: 

    AF131809.1 AF159228.1 AJ292244.1 AJ292245.1 AK296577.1 AK309026.1 BC002727.2 NR_037661.1 

    10 DOTS entries:

    DT.95074222  DT.120799427  DT.100792777  DT.100792776  DT.75109835  DT.443773  DT.95074209  DT.120799318 
    DT.91906301  DT.92422383 

    24/1172 AceView cDNA sequences (see all 1172):

    CR609321 AA907131 CR615284 CB131579 BM992587 CD366653 AA017692 BM127052 
    AA031472 F08881 BQ446756 BU684857 BM843185 AI092360 BM790715 BE910364 
    BM992499 CR593538 CA415722 BU184801 BM821877 X52220 H44875 CA420595 

    GeneLoc Exon Structure

    5/9 Alternative Splicing Database (ASD) splice patterns (SP) for SDCBP2 (see all 9)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b · 7c · 7d ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b
    SP1:                    -     -                 -     -                 -                 -                             -                     
    SP2:                          -                 -     -                 -                 -                             -                     
    SP3:                                                                                      -                             -                     
    SP4:                    -     -                 -     -                 -                                                                     
    SP5:                                            -     -                 -                                                                     


    ECgene alternative splicing isoforms for SDCBP2

    (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

    SDCBP2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GGATGGCTTA

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

    About this image
    See SDCBP2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SDCBP2

    SOURCE GeneReport for Unigene cluster: Hs.657015
        SABiosciences Custom PCR Arrays for SDCBP2
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    In Situ
    Assay Products:
     

     
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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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for SDCBP2 gene from 4/16 species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves LOC1008594391 syntenin-2-like 71.64(n)
    71.53(a)
      100859439  XM_003642488.1  XP_003642536.1 
    lizard
    (Anolis carolinensis)
    Reptilia SDCBP26
    --
    59(a)
    1 ↔ 1
    GL343346.1(835682-843264)
    zebrafish
    (Danio rerio)
    Actinopterygii sdcbp26
    syndecan binding protein (syntenin) 2
    57(a)
    1 ↔ 1
    23(16819339-16852904)
    honey bee
    (Apis mellifera)
    Insecta --
    --
    46(a)
    1 → many
    Group13.1(376222-377636)


    ENSEMBL Gene Tree for SDCBP2 (if available)
    TreeFam Gene Tree for SDCBP2 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SDCBP2 gene
    SDCBP2  
    1 SIMAP similar gene for SDCBP2 using alignment to 1 protein entry:     SDCB2_HUMAN:
    SDCBP

    SDCBP2 for paralogs           About GeneDecksing



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

    10/408 NCBI SNPs in SDCBP2 are shown (see all 408    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1151174041,2
    C,F,--1243263(+) GACACG/ACCCCC 3 -- ut311Minor allele frequency- A:0.05WA 118
    rs1133823041,2
    C,--1243269(+) CCCCCC/ATCATG 3 -- ut311Minor allele frequency- A:0.50NA 2
    rs1136316531,2
    --1243301(+) AGGCCA/GGCTGC 3 -- ut312Minor allele frequency- G:0.00CSA 2
    rs1117056101,2
    F--1243872(+) AAGGAC/TTGGGG 3 -- int12Minor allele frequency- T:0.50CSA 4
    rs454461951,2
    F,--1244078(+) TGAGCA/TTGCCT 3 -- int11Minor allele frequency- T:0.03NA 120
    rs61093901,2
    C,F,A,H,--1244127(+) GACGCG/ATAACA 3 -- int113Minor allele frequency- A:0.06NS EA NA WA 1214
    rs768112081,2
    F,--1244541(+) TGTTCG/AAAAAT 3 -- int11Minor allele frequency- A:0.14WA 118
    rs177180701,2
    C,F,--1244616(+) ACAAAC/TGATCT 3 -- int14Minor allele frequency- T:0.02NA 262
    rs743807831,2
    C,F,--1244996(+) CAGGTT/GTGCAC 3 -- int13Minor allele frequency- G:0.40WA CSA 5
    rs61345391,2
    H--1245223(+) AGCAAG/ACTGCC 3 -- int14Minor allele frequency- A:0.00NS EA 416

    HapMap Linkage Disequilibrium report for SDCBP2 (1290619 - 1309883 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for SDCBP2: --

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    SDCBP2 for disorders           About GeneDecksing

    3 diseases for SDCBP2:    About MalaCards
    intrahepatic cholangiocarcinoma    cholangiocarcinoma    melanoma


    Export disorders for SDCBP2 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 SDCBP2 gene, integrated from 9 sources (see all 20):
    (articles sorted by number of sources associating them with SDCBP2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The neural cell recognition molecule neurofascin interacts with syntenin-1 but not with syntenin-2, both of which reveal self- associating activity. (PubMed id 11152476)1, 2, 3, 9 Koroll M.... Volkmer H. (2001)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (2001)
    4. Nuclear speckles and nucleoli targeting by PIP2-PDZ domain interactions. (PubMed id 15961997)1, 9 Mortier E....Zimmermann P. (2005)
    5. The prevalence and significance of PDZ domain-phosphoinositide interactions. (PubMed id 16884951)1, 9 Zimmermann P. (2006)
    6. Human papillomavirus type 8 E6 oncoprotein inhibits tr anscription of the PDZ protein syntenin-2. (PubMed id 22623796)1 Lazic D....Akgul B. (2012)
    7. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (2006)
    8. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    9. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. (PubMed id 16712791)1 Wang A.G....Kim N.S. (2006)
    10. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (2005)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 27111 HGNC: 15756 AceView: FKBP1AandSDCBP2 Ensembl:ENSG00000125775 euGenes: HUgn27111
    ECgene: SDCBP2 H-InvDB: SDCBP2

    (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 SDCBP2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SDCBP2 gene:
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