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IBSP Gene

protein-coding   GIFtS: 57

GC04P088939
integrin-binding sialoprotein
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
BNSP 2, 3
BSP 1, 2
BSP-II 1, 2
SP-II 1, 2
Descriptions
BSP II 3
Bone sialoprotein II 2, 3
Cell-binding sialoprotein 3
integrin-binding sialoprotein 2, 3
External Ids
HGNC: 53411
Entrez Gene: 33812
UniProtKB: P218153
Ensembl: ENSG000000295597
Search outside databases for aliases for IBSP gene

Previous GC identifers: GC04P088878 GC04P089022 GC04P089179 GC04P089077

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

EntrezGene summary for IBSP:
The protein encoded by this gene is a major structural protein of the bone matrix. It constitutes
approximately 12% of the noncollagenous proteins in human bone and is synthesized by
skeletal-associated cell types, including hypertrophic chondrocytes, osteoblasts, osteocytes, and
osteoclasts. The only extraskeletal site of its synthesis is the trophoblast. This protein binds
to calcium and hydroxyapatite via its acidic amino acid clusters, and mediates cell attachment
through an RGD sequence that recognizes the vitronectin receptor. [provided by RefSeq]

UniProtKB/Swiss-Prot: SIAL_HUMAN, P21815
Function: Binds tightly to hydroxyapatite. Appears to form an integral part of the mineralized
matrix. Probably important to cell-matrix interaction. Promotes Arg-Gly-Asp-dependent cell
attachment

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the IBSP gene  

Entrez Gene cytogenetic band: 4q21-q25   Ensembl cytogenetic band:  4q22.1   HGNC cytogenetic band: 4q21.1

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

GeneLoc gene densities for chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P088939:     (about GC identifiers)

Start:
88,939,726 bp from pter
End:
88,952,098 bp from pter
Size:
12,373 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000004.10  NT_016354.18  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: SIAL_HUMAN, P21815 (See protein sequence)
Recommended Name: Bone sialoprotein 2 precursor  
Size: 317 amino acids; 35018 Da
Subcellular location: Secreted
Miscellaneous: It is possible that the segments of clustered carboxyl groups mediate the strong
binding to hydroxyapatite

Post-translational modifications:

  • N-glycosylated; glycans consist of sialated and core-fucosylated bi-, tri- and tetraantennary
    chains1
  • O-glycosylated at eight sites; mucin-type glycans contain Gal, GlcNAc, GalNAc and terminal NeuAc1
  • Sulfated on either Tyr-313 or Tyr-3141
  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_004958.2  

    ENSEMBL proteins: 
    ENSP00000226284 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    R&D Systems Recombinant & Natural Proteins for IBSP (IBSP/Sialoprotein II)
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (Bone Sialoprotein)
    Browse Abnova for Human Recombinant Proteins
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    1 Gene Ontology (GO) cellular component term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576 extracellular region IEA--
    About this table

    Antibodies for IBSP: 
    Browse Antibodies Central at Invitrogen
    Millipore Mono- and Polyclonal Antibodies for the study of IBSP
    Sigma-Aldrich Antibodies for IBSP
    R&D Systems Antibodies for IBSP (IBSP/Sialoprotein II)
    Antibodies from Abcam (Bone Sialoprotein), each with their AbpromiseSM
    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Search Novus for antibodies for IBSP

    Assays for IBSP: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

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

    1 InterPro domain/family:
     IPR008412 BSP_II


       GeneDecks  IBSP for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry P21815

    ProtoNet protein and cluster: P21815

    1 Blocks protein family: IPB008412 Bone sialoprotein II

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (IBSP)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_004967

                  Applied Biosystems Silencer® siRNAs for IBSP

                  Sigma-Aldrich siRNA for IBSP  
                         Sigma-Aldrich shRNA for IBSP  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Browse Clone Ranger at Invitrogen for clones
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_004967
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_004967
                                     untagged cDNA clone in CMV expression vector: NM_004967 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_004967

    UniProtKB/Swiss-Prot: SIAL_HUMAN, P21815
    Function: Binds tightly to hydroxyapatite. Appears to form an integral part of the mineralized
    matrix. Probably important to cell-matrix interaction. Promotes Arg-Gly-Asp-dependent cell
    attachment

    Genatlas biochemistry entry for IBSP:
    sialoprotein,bone (cell adhesion molecule,RGD containing)

    3 MGI mutant phenotypes (inferred from 1 allele(MGI details for Ibsp):

    growth/sizelimbs/digits/tailskeleton

    1 Gene Ontology (GO) molecular function term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515 protein binding IEA--
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    2 Invitrogen iPath™ Online BioAtlas - Pathways for IBSP (Maps provided by GeneGo):
     Hedgehog and PTH signaling pathways participation in bone and cartilage development
     Interactions of Integrins with extracellular matrix

       GeneDecks  IBSP for the pathways selected above  
    About GeneDecksing

    1 Millipore Pathway for IBSP
     Development Hedgehog and PTH signaling pathways in bone and cartilage development

       GeneDecks  IBSP for the pathways selected above  
    About GeneDecksing

    2 Kegg Pathways  (Kegg details for IBSP):
     hsa04510 Focal adhesion
     hsa04512 ECM-receptor interaction

       GeneDecks  IBSP for the pathways selected above  
    About GeneDecksing
     Gene Network CentralTM Interacting Genes and Proteins Network for  IBSP 


    5/69 Interacting proteins for IBSP (ENSP000002262843) via UniProtKB, MINT, and/or STRING (see all 69 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SPP1ENSP000002376233STRING (score=.979)
    RUNX2ENSP000003525143STRING (score=.948)
    VWFENSP000002614053STRING (score=.942)
    FN1ENSP000003235343STRING (score=.935)
    COL1A1ENSP000002259643STRING (score=.915)
    About this table

    2 Gene Ontology (GO) biological process terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001503 ossification IEA--
    GO:0007155 cell adhesion IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for IBSP
    10/47 Novoseek chemical compound relationships for IBSP gene (see all 47 )
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    alizarin 79.61 10 16530029 (1), 15003788 (1), 17651131 (1), 15853967 (1) (see all 7)
    hydroxyapatite 76.88 81 8397409 (4), 9181551 (3), 7915111 (3), 15004030 (3) (see all 36)
    grgdsp 66.42 6 9639398 (3), 9699501 (1)
    deoxypyridinoline 54.15 24 10794751 (4), 11148806 (2), 8784085 (2), 11763409 (2) (see all 9)
    pyridinoline 53.58 21 10794751 (3), 11763409 (2), 8784085 (2), 11148806 (1) (see all 8)
    titanium 51.85 9 12472226 (1), 12419636 (1), 12798071 (1), 17437306 (1) (see all 5)
    strontium ranelate 48.27 5 17300752 (2), 17579299 (1), 17945546 (1)
    fibroin 44.04 1 15478212 (1)
    calcium 40.63 21 1447223 (3), 16327496 (1), 16637042 (1), 9893065 (1) (see all 16)
    toluidine 35.98 1 15642592 (1)
    About this table


    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (IBSP)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_004967

                  Sigma-Aldrich siRNA for IBSP  
                         Sigma-Aldrich shRNA for IBSP  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_004967  

    REFSEQ mRNAs for IBSP gene: 

    NM_004967.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_004967  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_004967
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_004967
                                     untagged cDNA clone in CMV expression vector: NM_004967 

    Additional cDNA sequence: J05213.1 

    1 DOTS entry:

    DT.308799 

    24/33 AceView cDNA sequences (see all 33 ):

    BQ573754 BQ028857 CA412935 C01831 CA413768 CA412904 BQ183053 CA436814 
    AW196683 BF478125 BU615775 CA415063 BI493249 CA427677 AI963900 CA427673 
    AA452255 CA436452 BQ182386 CA426254 CA427111 BQ181439 N66529 J05213 

    highest scoring ESTs for IBSP:

    J05213 AA452431 AI421654 BE466675 BQ028857 BQ182386 CA412904 CA412935 CA413768 CA415063 

    Unigene Cluster for IBSP:

    Integrin-binding sialoprotein
    Hs.518726  [show with all ESTs]
    Unigene Representative Sequence: NM_004967


    GeneLoc Exon Structure

    1 Ensembl transcript including schematic representation:
    ENST00000226284  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    IBSP expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for IBSP

    1 / 2 / 3

    6 probe-sets matching IBSP gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    35131_at2, 3 U95-A 1 1.00 1.00 0.78 1.18 J05213 1.00 1.00 1.00 1

    53238_at2, 3 U95-C 1 0.94 1.00 0.92 1.15 AI421654 0.80 1.00 0.91 1

    236028_at2, 3 U133-B 1 1.00 1.00 -- -- BE466675 0.80 1.00 0.91 1

    207370_at2, 3 U133-A 1 1.00 1.00 -- -- NM_004967 0.60 1.00 0.82 1

    236028_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    207370_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: --

    SOURCE GeneReport for Unigene cluster: Hs.518726

    Expression variation in blood from EXPOLDB for IBSP

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for IBSP gene from 5/6 species (see all 6 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    IBSP1   -- integrin-binding sialoprotein 85.96(n)
    82.32(a)
    609146  XM_846356.1  XP_851449.1 
    chimpanzee
    (Pan troglodytes)
    IBSP1   -- integrin-binding sialoprotein 98.74(n)
    98.11(a)
    471249  XM_526631.2  XP_526631.1 
    cow
    (Bos taurus)
    IBSP1   -- integrin-binding sialoprotein 84(n)
    81.79(a)
    281233  NM_174084.2  NP_776509.1 
    rat
    (Rattus norvegicus)
    Ibsp1   -- integrin binding sialoprotein 74.5(n)
    71.43(a)
    24477  NM_012587.1  NP_036719.1 
    mouse
    (Mus musculus)
    Ibsp1, 5 5 (56.00 cM)5
    integrin binding sialoprotein1, 5 76.54(n)1
    73.89(a)1
    158911  NM_008318.11  NP_032344.11 
     AK1323715  AK1626405  (see all 10)
    About this table        Species with no ortholog for IBSP

    ENSEMBL Gene Tree for IBSP
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

      --
    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/77 NCBI SNPs in IBSP are shown (see all 77 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 50)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 4 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs10546291,2
    C,F,H,O88951942(+) AATGAA/TTACGA 1 E/D mis1 ese313Minor allele frequency- T:0.16MN NA EU EA WA 1232
    rs170131871,2
    C,F,H88952555(+) GTGACC/TTGTAT 1 -- ut317Minor allele frequency- T:0.09NA EU EA WA 560
    rs131443711,2
    C,F,H88951770(+) AGAAGG/ACACCA 1 G/D mis1 ese312Minor allele frequency- A:0.24NA EU EA WA 1034
    rs170131821,2
    C,F,H88951898(+) CCACCA/GCCGTT 1 T/A mis1 ese312Minor allele frequency- G:0.09NA EU EA WA 1052
    rs170131811,2
    C,F,H88951787(+) CCGGAA/GGGCAG 1 R/G mis1 ese313Minor allele frequency- N:0.00NA EA EU WA 1100
    rs10546281,2
    C,F,H88951935(+) GGGCGC/TCAATG 1 A/V mis1 ese314Minor allele frequency- T:0.24MN EA NA EU WA 1302
    rs10546271,2
    C,F,H88951716(+) CGGAGG/AAGACA 1 E/G mis1 ese313Minor allele frequency- A:0.18MN EA NA EU WA 1238
    rs19037981,2
    A,H88939042(-) TTTTTC/TCTTGG 1 -- ng51 trp33Minor allele frequency- T:0.00EU EA 298
    --
    rs74359741,2
    C88937933(+) cagacA/Ccttct 1 -- ng510--------
    rs38053781,2
    C88939418(-) AATTAC/TACAAG 1 -- ng510--------
    About this table

    HapMap Linkage Disequilibrium images for IBSP (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 147563

    10/52 Novoseek disease relationships for IBSP gene (see all 52 )

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    bone metastases 64.80 33 10804012 (4), 17213971 (3), 9157781 (3), 10632320 (3) (see all 16)
    calcification 64.74 35 8769669 (1), 9539200 (1), 16637042 (1), 9099263 (1) (see all 24)
    osteosarcoma 57.33 17 12569382 (2), 15203941 (2), 9069166 (1), 10716620 (1) (see all 9)
    bone diseases 50.81 7 11125546 (1), 8990227 (1), 10632320 (1)
    collagen fibril 48.12 11 1451011 (4), 15846504 (2), 10441531 (1), 9458064 (1)
    osteolytic 43.00 4 15688393 (2), 14647232 (1)
    osteogenesis imperfecta 39.79 1 2068957 (1)
    osteoporosis 32.35 3 11125546 (2)
    bone lesion 32.13 1 14524533 (1)
    lytic lesion 31.99 1 15688393 (1)
    About this table

    Human Genome Epidemiology Navigator: IBSP (1 document)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

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

    10/517 PubMed articles for IBSP gene (see all 517 ):
    (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, and/or H-InvDB)
    About This Section

    Entrez Gene: 3381 HGNC: 5341 AceView: IBSP Ensembl:ENSG00000029559 euGenes: HUgn3381
    ECgene: IBSP H-InvDB: IBSP
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    ATLAS Chromosomes in Cancer entry for IBSP Genetics and Cytogenetics in Oncology and Haematology
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for IBSP:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



      Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
      Invitrogen Antibodies  Invitrogen Assays
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      Invitrogen Human Recombinant Kinases  Invitrogen Custom Antibody and Peptide Service
      Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for IBSP-related products

     Millipore Custom Antibody & Bulk Services
     Millipore Preclinical / Clinical Development Services
     Millipore Immunoassay Services
     Millipore Target Screening & Profiling Services


     Predesigned and custom siRNAs for IBSP Antibodies for IBSP
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for IBSP Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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