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

TBC1D9 Gene

protein-coding   GIFtS: 49
GCID: GC04M141541

TBC1 domain family, member 9 (with GRAM domain)

(Previous names: TBC1 domain family, member 9 )
 Explore 2 diseases affiliated with
TBC1D9 via our new
 Human Malady Compendium 
Biological research products
for TBC1D9
    

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

Aliases
TBC1 Domain Family, Member 9 (With GRAM Domain)1 2     TBC1 Domain Family, Member 91
MDR11 2     TBC1 Domain Family Member 92
KIAA08821 3     TBC1D9A3
TBC1 Domain Family Member 9A2 3     

External Ids:    HGNC: 217101   Entrez Gene: 231582   Ensembl: ENSG000001094367   UniProtKB: Q6ZT073   

Export aliases for TBC1D9 gene to outside databases

Previous GC identifers: GC04M141900 GC04M141761 GC04M137272


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

UniProtKB/Swiss-Prot: TBCD9_HUMAN, Q6ZT07
Function: May act as a GTPase-activating protein for Rab family protein(s)

Gene Wiki entry for TBC1D9


(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_000004.11  NC_018915.1  NT_016354.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the TBC1D9 gene promoter:
         NF-1   NF-1/L   AML1a   ATF-2   Nkx2-5   AP-2gamma   Pax-3   HSF2   ATF   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTBC1D9 promoter sequence
   Search SABiosciences Chromatin IP Primers for TBC1D9

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TBC1D9


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

Entrez Gene cytogenetic band: 4q31.21   Ensembl cytogenetic band:  4q31.21   HGNC cytogenetic band: 4q31.1

TBC1D9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TBC1D9 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M141541:  view genomic region     (about GC identifiers)

Start:
141,541,919 bp from pter      End:
141,677,471 bp from pter
Size:
135,553 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: TBCD9_HUMAN, Q6ZT07 (See protein sequence)
Recommended Name: TBC1 domain family member 9  
Size: 1266 amino acids; 143229 Da
Sequence caution: Sequence=BAA74905.2; Type=Erroneous initiation; Sequence=BAC86789.1; Type=Erroneous initiation;
Note=Translation N-terminally extended; Sequence=BAC86789.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing;
Secondary accessions: A6H8U8 D3DNZ1 O94958

Explore the universe of human proteins at neXtProt for TBC1D9: NX_Q6ZT07

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q6ZT07

  • TBC1D9 Protein expression data from MOPED and PaxDb:    About this image 
    TBC1D9 Protein Expression
    REFSEQ proteins: NP_055945.2  
    ENSEMBL proteins: 
     ENSP00000411197  

    Human Recombinant Protein Products for TBC1D9: 
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    Uscn Proteins for TBC1D9

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular IEA--

    TBC1D9 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

    TBC1D9 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR011992 EF-hand-like_dom
     IPR002048 EF_hand_Ca-bd
     IPR000195 Rab-GTPase-TBC_dom
     IPR004182 GRAM

    Graphical View of Domain Structure for InterPro Entry Q6ZT07

    ProtoNet protein and cluster: Q6ZT07

    2 Blocks protein families:
    IPB000195 RabGAP/TBC domain
    IPB004182 GRAM domain


    UniProtKB/Swiss-Prot: TBCD9_HUMAN, Q6ZT07
    Similarity: Contains 1 EF-hand domain
    Similarity: Contains 2 GRAM domains
    Similarity: Contains 1 Rab-GAP TBC domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, 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, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TBCD9_HUMAN, Q6ZT07
    Function: May act as a GTPase-activating protein for Rab family protein(s)

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005097Rab GTPase activator activity IEA--
    GO:0005509calcium ion binding IEA--
         
    TBC1D9 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for TBC1D9:
     Decreased circadian period len 

    Animal Models:
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for TBC1D9 

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    hsa-miR-579 hsa-miR-142-5p hsa-miR-3678-3p hsa-miR-15a hsa-miR-106a hsa-miR-519a hsa-miR-764 hsa-miR-570
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TBC1D9


    (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 TBC1D9

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    4 Interacting proteins for TBC1D9 (ENSP000004111974) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GABARAPL1ENSP000002664584STRING: ENSP00000266458
    MAP1LC3AENSP000003639704STRING: ENSP00000363970
    GABARAPL2ENSP000000372434STRING: ENSP00000037243
    MAP1LC3BENSP000002686074STRING: ENSP00000268607
    About this table

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

    Browse Tocris compounds for TBC1D9
    Search CenterWatch for drugs/clinical trials and news about TBC1D9 / TBCD9 

    (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, Sirion Biotech, 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 TBC1D9 gene: 
    NM_015130.2  

    Unigene Cluster for TBC1D9:

    TBC1 domain family, member 9 (with GRAM domain)
    Hs.480819  [show with all ESTs]
    Unigene Representative Sequence: NM_015130
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000442267(uc010ioj.3) ENST00000502786 ENST00000514787

    miRNA
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    hsa-miR-579 hsa-miR-142-5p hsa-miR-3678-3p hsa-miR-15a hsa-miR-106a hsa-miR-519a hsa-miR-764 hsa-miR-570
    SwitchGear 3'UTR luciferase reporter plasmidTBC1D9 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AB020689.2 AB449892.1 AF131785.1 AK127020.1 BC038804.1 BC114935.1 BC128046.1 BC146758.1 

    3 DOTS entries:

    DT.448316  DT.97801758  DT.100749422 

    24/119 AceView cDNA sequences (see all 119):

    BF195944 CA407301 BU607767 AA328052 AW029567 AW500368 BC038804 AA243858 
    T35177 BQ631274 AL138320 AI969557 BM129070 BF594750 AI203736 AB020689 
    AW070660 CA426926 CA772060 BM711973 BM666137 BE010649 BM128646 BF436600 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for TBC1D9    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21a · 21b
    SP1:                                            -                                                                                             
    SP2:                                                                                                                                          
    SP3:                                                                                                                                          


    ECgene alternative splicing isoforms for TBC1D9

    (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

    TBC1D9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GTCTCATTTC
    TBC1D9 Expression
    About this image

    TBC1D9 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table

    Stem Cell Differentiation: 3 LifeMap Cells 
    NameCategory
    Definitive endoderm-like cells (Generation and expan...)
    Definitive endoderm-like cells (Generation of mesend...)
    Mesendoderm-like cells (Generation of mesend...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See TBC1D9 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TBC1D9

    SOURCE GeneReport for Unigene cluster: Hs.480819
        SABiosciences Custom PCR Arrays for TBC1D9
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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 TBC1D9 gene from 5/24 species (see all 24)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves TBC1D91 TBC1 domain family, member 9 (with GRAM domain) 81.05(n)
    91.28(a)
      422452  XM_001232385.1  XP_001232386.1 
    lizard
    (Anolis carolinensis)
    Reptilia TBC1D96
    --
    91(a)
    1 ↔ 1
    5(119609555-119680711)
    zebrafish
    (Danio rerio)
    Actinopterygii tbc1d91 TBC1 domain family, member 9 (with GRAM domain) 73.74(n)
    80.95(a)
      563578  XM_686942.5  XP_692034.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG73241 CG7324 49.12(n)
    39.79(a)
      40361  NM_141048.1  NP_649305.1 
    worm
    (Caenorhabditis elegans)
    Secernentea tbc-91 Protein TBC-9 50(n)
    44.5(a)
      178316  NM_001129340.1  NP_001122812.1 


    ENSEMBL Gene Tree for TBC1D9 (if available)
    TreeFam Gene Tree for TBC1D9 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for TBC1D9 gene
    TBC1D8B2  TBC1D302  TBC1D9B2  TBC1D82  
    7 SIMAP similar genes for TBC1D9 using alignment to 1 protein entry:     TBCD9_HUMAN:
    TBC1D9B    TBC1D8B    SGSM3    TBC1D8    FLJ00006    GRTP1
    FLJ00288

    TBC1D9 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

    10/2126 NCBI SNPs in TBC1D9 are shown (see all 2126    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1382144171,2
    --141541457(+) TATATG/TCCCAG 1 -- ds50010--------
    rs1919931991,2
    --141541770(+) TAAATA/GTAGTC 1 -- ds50010--------
    rs1387913901,2
    C--141541799(+) GTATT-/TCTC  
            
    TCTCT
    1 -- ds50010--------
    rs1839412621,2
    --141541850(+) GTTGCC/TTGATA 1 -- ds50010--------
    rs1412758801,2
    --141542270(+) AAATAC/GAGCAT 1 -- ut310--------
    rs115450271,2
    C--141542333(+) TTATCT/CTGCAG 1 -- ut312Minor allele frequency- C:0.00NA 4
    rs1860681191,2
    --141542372(+) ATTGAG/TTTGAT 1 -- ut310--------
    rs1909724161,2
    --141542437(+) ACGGAA/GATGGT 1 -- ut310--------
    rs68544571,2
    C,F,A,H--141542490(+) ACATCC/GAGTAT 1 -- ut3113Minor allele frequency- G:0.13NS EA NA WA 922
    rs1450750691,2
    --141542596(+) CTCTGA/TGACAA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for TBC1D9 (141541919 - 141677471 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for TBC1D9: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing TBC1D9
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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

    TBC1D9 for disorders           About GeneDecksing

    2 diseases for TBC1D9:    About MalaCards
    mantle cell lymphoma    osteochondrosis

    1 disease from the University of Copenhagen DISEASES database for TBC1D9:
    Osteochondrosis
    Human Genome Epidemiology (HuGE) Navigator: TBC1D9 (1 document)

    Export disorders for TBC1D9 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 TBC1D9 gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with TBC1D9)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of a novel Tre-2/Bub2/Cdc16 (TBC) protein that possesses Rab3A-GAP activity. (PubMed id 19077034)1, 2 Ishibashi K.... Fukuda M. (2009)
    2. High level of cannabinoid receptor 1, absence of regulator of G protein signalling 13 and differential expression of Cyclin D1 in mantle cell lymphoma. (PubMed id 12970790)1, 3 Islam T.C....Sander B. (2003)
    3. Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10048485)1, 2 Nagase T....Ohara O. (1998)
    4. Rab GTPase-activating proteins in autophagy: regulatio n of endocytic and autophagy pathways by direct binding to human ATG8 modifiers. (PubMed id 22354992)1 Popovic D....Dikic I. (2012)
    5. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    6. MDR1 gene C3435T polymorphism is associated with clini cal outcomes in gastric cancer patients treated with postoperative adjuvant chem otherapy. (PubMed id 22296392)1 Li Y....Li C.G. (2011)
    7. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    8. CD34+ leukemic subpopulation predominantly displays lower spontaneous apoptosis and has higher expression levels of Bcl-2 and MDR1 genes than CD34- cells in childhood AML. (PubMed id 18228020)1 Shman T.V....Aleinikova O.V. (2008)
    9. Plasma levels of atazanavir and the risk of hyperbilirubinemia are predicted by the 3435C-->T polymorphism at the multidrug resistance gene 1. (PubMed id 16355344)1 Rodriguez Novoa S....Soriano V. (2006)
    10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 23158 HGNC: 21710 AceView: KIAA0882 Ensembl:ENSG00000109436 euGenes: HUgn23158
    ECgene: TBC1D9 H-InvDB: TBC1D9

    (According to HUGE)
    About This Section
    HUGE: KIAA0882

    (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 TBC1D9 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for TBC1D9 gene:
    Search GeneIP for patents involving TBC1D9

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



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