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

RIMS3 Gene

protein-coding   GIFtS: 52
GCID: GC01M041086

regulating synaptic membrane exocytosis 3

 Explore 2 diseases affiliated with
RIMS3 via our new
 Human Malady Compendium 
Biological research products
for RIMS3
    

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

Aliases
Regulating Synaptic Membrane Exocytosis 31 2     Rab-3 Interacting Molecule 32
NIM31 2 5     Regulating Synaptic Membrane Exocytosis Protein 32
RIM31 2     KIAA02373
Rab-3-Interacting Molecule 32 3     Nim33
RIM 32 3     KIAA01375
RIM3 Gamma2 3     

External Ids:    HGNC: 212921   Entrez Gene: 97832   Ensembl: ENSG000001170167   OMIM: 6116005   UniProtKB: Q9UJD03   

Export aliases for RIMS3 gene to outside databases

Previous GC identifers: GC01M040549 GC01M040499 GC01M040505 GC01M040755 GC01M040858 GC01M039204


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

UniProtKB/Swiss-Prot: RIMS3_HUMAN, Q9UJD0
Function: Regulates synaptic membrane exocytosis (By similarity)




(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_000001.10  NC_018912.1  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RIMS3 gene promoter:
         E2F-4   E2F-3a   E2F-5   NRSF form 1   E2F-2   NRSF form 2   GATA-1   YY1   E2F-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRIMS3 promoter sequence
   Search SABiosciences Chromatin IP Primers for RIMS3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RIMS3


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

Entrez Gene cytogenetic band: 1pter-p22.2   Ensembl cytogenetic band:  1p34.2   HGNC cytogenetic band: 1pter-p22.2

RIMS3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RIMS3 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M041086:  view genomic region     (about GC identifiers)

Start:
41,086,351 bp from pter      End:
41,131,329 bp from pter
Size:
44,979 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: RIMS3_HUMAN, Q9UJD0 (See protein sequence)
Recommended Name: Regulating synaptic membrane exocytosis protein 3  
Size: 308 amino acids; 32796 Da
Subunit: Binds PPFIA3 (By similarity). Does not bind RAB3
Subcellular location: Cell junction, synapse (By similarity)
Sequence caution: Sequence=BAA13243.2; Type=Erroneous initiation;
Secondary accessions: D3DPV8 Q92511

Explore the universe of human proteins at neXtProt for RIMS3: NX_Q9UJD0

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9UJD0

  • RIMS3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_055562.2  
    ENSEMBL proteins: 
     ENSP00000361769   ENSP00000361768  

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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for RIMS3

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030054cell junction IEA--
    GO:0045202synapse IEA--


    RIMS3 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for RIMS3


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

    RIMS3 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR008973 C2_Ca/lipid-bd_dom_CaLB
     IPR018029 C2_membr_targeting
     IPR000008 C2_Ca-dep

    Graphical View of Domain Structure for InterPro Entry Q9UJD0

    ProtoNet protein and cluster: Q9UJD0

    1 Blocks protein family: IPB000008 C2 domain

    UniProtKB/Swiss-Prot: RIMS3_HUMAN, Q9UJD0
    Similarity: Contains 1 C2 domain


    (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

    Function Summary:

         UniProtKB/Swiss-Prot: RIMS3_HUMAN, Q9UJD0
    Function: Regulates synaptic membrane exocytosis (By similarity)

    miRNA
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0044325ion channel binding IEA--


    RIMS3 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for RIMS3:
     Decreased TP53 protein express 


    (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 RIMS3

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    3 Interacting proteins for RIMS3 (Q9UJD03 ENSP000003617684) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CREB3O438893I2D: score=1 
    YWHAEP622583I2D: score=1 
    GJA5ENSP000002713484STRING: ENSP00000271348
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006836neurotransmitter transport IEA--
    GO:0006887exocytosis IEA--
    GO:0017156calcium ion-dependent exocytosis ----
    GO:0042391regulation of membrane potential IEA--


    RIMS3 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
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RIMS3
    Search CenterWatch for drugs/clinical trials and news about RIMS3 

    (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 RIMS3 gene: 
    NM_014747.2  

    Unigene Cluster for RIMS3:

    Regulating synaptic membrane exocytosis 3
    Hs.654808  [show with all ESTs]
    Unigene Representative Sequence: D87074
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000372684(uc001cfu.1 uc001cfv.1) ENST00000372683

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    hsa-miR-579 hsa-miR-607 hsa-miR-642a hsa-miR-3194-5p hsa-miR-15a hsa-miR-1258 hsa-miR-128 hsa-miR-3921
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RIMS3
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    Additional cDNA sequence: 

    AY326956.1 BC003103.1 D87074.1 

    2 DOTS entries:

    DT.413753  DT.91748411 

    24/102 AceView cDNA sequences (see all 102):

    AA626438 BM478119 BE397286 AA456423 BE312243 BQ721347 AW291735 BQ064934 
    BC003103 BU930896 NM_014747 AU120066 AI346380 BI820965 AY326956 BU681931 
    BM053119 D87074 AI274884 BE261795 CR619233 BU848876 BP362770 BU156647 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for RIMS3    About this scheme

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


    ECgene alternative splicing isoforms for RIMS3

    (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

    RIMS3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ATTAAAGTCA

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

    About this image

    RIMS3 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: 4 LifeMap Cells 
    NameCategory
    PureStem™ progenitor E68 (Embryonic Progenitor Cell)
    PureStem™ progenitor T42 (Embryonic Progenitor Cell)
    PureStem™ progenitor E69 (Embryonic Progenitor Cell)
    PureStem™ progenitor Z1 (Embryonic Progenitor Cell)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See RIMS3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RIMS3

    SOURCE GeneReport for Unigene cluster: Hs.654808
        SABiosciences Custom PCR Arrays for RIMS3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RIMS3

    (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 RIMS3 gene from 5/19 species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves RIMS31 regulating synaptic membrane exocytosis 3 79.61(n)
    81.91(a)
      428226  XM_425785.2  XP_425785.2 
    lizard
    (Anolis carolinensis)
    Reptilia RIMS36
    --
    80(a)
    1 ↔ 1
    GL343308.1(133429-151923)
    zebrafish
    (Danio rerio)
    Actinopterygii rims31 regulating synaptic membrane exocytosis 3 74.02(n)
    79.93(a)
      563414  NM_001100009.2  NP_001093479.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Rim6
    Rim
    4(a)
    1 → many
    3R(13698470-13742300)
    worm
    (Caenorhabditis elegans)
    Secernentea unc-106
    Rab-3-interacting molecule unc-10
    7(a)
    1 → many
    X(7272279-7280275)


    ENSEMBL Gene Tree for RIMS3 (if available)
    TreeFam Gene Tree for RIMS3 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RIMS3 gene
    RIMS12  RIMS22  RIMS42  
    3 SIMAP similar genes for RIMS3 using alignment to 2 protein entries:     RIMS3_HUMAN (see all proteins):
    RIMS2    RIMS4    RIMS1

    RIMS3 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

    10/765 NCBI SNPs in RIMS3 are shown (see all 765    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs120593051,2
    C,F,H,--41085926(+) ATCAGG/ATGTGG 1 -- ds500117Minor allele frequency- A:0.12NS EA NA CSA WA 2222
    rs1821517071,2
    --41085937(+) CTGCAA/GTAAGC 1 -- ds50010--------
    rs1116140241,2
    C,--41085967(+) GAGCTA/GCTGGA 1 -- ds50010--------
    rs1868313121,2
    --41086014(+) AGCTGC/TGGCCT 1 -- ds50010--------
    rs1379511231,2
    --41086045(+) CTGTCA/GTTGGA 1 -- ds50010--------
    rs1492057891,2
    --41086077(+) AAGTAG/TAAGGC 1 -- ds50010--------
    rs1379700631,2
    --41086116(+) GAGAC-/AGAGCC 1 -- ds50010--------
    rs121257241,2
    C,F,A,H,--41086224(+) ATGCTC/TTTTTT 1 -- ds500133Minor allele frequency- T:0.48NS EA NA WA CSA 3376
    rs1160963481,2
    C,F,--41086396(+) ATACTG/TTACAT 1 -- ut311Minor allele frequency- T:0.04WA 118
    rs1174729151,2
    --41086527(+) TGCTGC/TACATA 1 -- ut311Minor allele frequency- T:0.01EA 120

    HapMap Linkage Disequilibrium report for RIMS3 (41086351 - 41131329 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for RIMS3: --
    Human Gene Mutation Database (HGMD): RIMS3

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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

    RIMS3 for disorders           About GeneDecksing

    OMIM gene information: 611600    OMIM disorders: --

    2 diseases for RIMS3:    About MalaCards
    schizophrenia    neuronitis

    Human Genome Epidemiology (HuGE) Navigator: RIMS3 (1 document)

    Export disorders for RIMS3 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 RIMS3 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with RIMS3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Genomic definition of RIM proteins: evolutionary amplification of a family of synaptic regulatory proteins. (PubMed id 12620390)1, 2, 3 Wang Y. and Suedhof T.C. (2003)
    2. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
    3. 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)
    4. The RIM/NIM family of neuronal C2 domain proteins. Interactions with Rab3 and a new class of Src homology 3 domain proteins. (PubMed id 10748113)1, 3 Wang Y....Sudhof T.C. (2000)
    5. Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain. (PubMed id 9039502)1, 2 Nagase T....Nomura N. (1996)
    6. A de novo 1p34.2 microdeletion identifies the synapti c vesicle gene RIMS3 as a novel candidate for autism. (PubMed id 19546099)1 Kumar R.A....Dobyns W.B. (2010)
    7. Investigation of the expression of genes affecting cytomatrix active zone function in the amygdala in schizophrenia: effects of antipsychotic drugs. (PubMed id 18490030)1 Weidenhofer J....Tooney P.A. (2009)
    8. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. (PubMed id 17525332)2 Matsuoka S.... Elledge S.J. (2007)
    9. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1 Olsen J.V....Mann M. (2006)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
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    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: 9783 HGNC: 21292 AceView: RIMS3 Ensembl:ENSG00000117016 euGenes: HUgn9783
    ECgene: RIMS3 H-InvDB: RIMS3

    (According to HUGE)
    About This Section
    HUGE: KIAA0137 KIAA0237

    (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 RIMS3 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 RIMS3 gene:
    Search GeneIP for patents involving RIMS3

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
    In Situ Hybridization Assays from
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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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