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GPC3 Gene

protein-coding   GIFtS: 60

GC0XM132497
glypican 3
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: SDYS)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
DGSX 1, 2
GTR2-2 3
MXR7 3
OCI-5 1, 2
OCI5 3
OTTHUMP00000024058 2
OTTHUMP00000062492 2
SDYS 2, 5
SGB 1, 2
SGBS 1, 2
SGBS1 1, 2, 5
Descriptions
Intestinal protein OCI-5 3
glypican 3 2
glypican proteoglycan 3 2
External Ids
HGNC: 44511
Entrez Gene: 27192
UniProtKB: P516543
Ensembl: ENSG000001472577
Search outside databases for aliases for GPC3 gene

Previous GC identifers: GC0XM127315 GC0XM129515 GC0XM130614 GC0XM131375 GC0XM132395

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

EntrezGene summary for GPC3:
Cell surface heparan sulfate proteoglycans are composed of a membrane-associated protein core
substituted with a variable number of heparan sulfate chains. Members of the glypican-related
integral membrane proteoglycan family (GRIPS) contain a core protein anchored to the cytoplasmic
membrane via a glycosyl phosphatidylinositol linkage. These proteins may play a role in the
control of cell division and growth regulation. Deletion mutations in this gene are associated
with Simpson-Golabi-Behmel syndrome. [provided by RefSeq]

UniProtKB/Swiss-Prot: GPC3_HUMAN, P51654
Function: Cell surface proteoglycan that bears heparan sulfate. May be involved in the
suppression/modulation of growth in the predominantly mesodermal tissues and organs. May play a
role in the modulation of IGF2 interactions with its receptor and thereby modulate its function.
May regulate growth and tumor predisposition

Gene Wiki entry for GPC3 (Glypican_3)

(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 GPC3 gene  

Entrez Gene cytogenetic band: Xq26.1   Ensembl cytogenetic band:  Xq26.2   HGNC cytogenetic band: Xq26

GPC3 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 X         GeneLoc Exon Structure

GeneLoc location for GC0XM132497:     (about GC identifiers)

Start:
132,497,439 bp from pter
End:
132,947,332 bp from pter
Size:
449,894 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000023.9  NT_011786.15  
(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)
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UniProtKB/Swiss-Prot: GPC3_HUMAN, P51654 (See protein sequence)
Recommended Name: Glypican-3 precursor  
Size: 580 amino acids; 65563 Da
Subcellular location: Cell membrane; Lipid-anchor, GPI-anchor; Extracellular side (By similarity)
Subcellular location: Secreted glypican-3: Secreted, extracellular space (By similarity)

REFSEQ proteins: NP_004475.1  

ENSEMBL proteins: 
ENSP00000377836 ENSP00000359854 ENSP00000385307 


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 GPC3 (Glypican 3)
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (Glypican 3)
Human Recombinant Proteins from Abnova (GPC3)
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

5/7 Gene Ontology (GO) cellular component terms (links to tree view) (see all 7 ):

GO IDQualified GO termEvidencePubMed IDs
GO:0005576 extracellular region IEA--
GO:0005578 proteinaceous extracellular matrix IEA--
GO:0005737 cytoplasm IDA18029348
GO:0005794 Golgi apparatus IDA18029348
GO:0005886 plasma membrane IEA--
About this table

Antibodies for GPC3: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Sigma-Aldrich Antibodies for GPC3
R&D Systems Antibodies for GPC3 (Glypican 3)
Antibodies from Abcam (Glypican 3), each with their AbpromiseSM
Monoclonal and Polyclonal Antibodies from Abnova (GPC3)
Novus Biologicals Antibody for GPC3

Assays for GPC3: 
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

3 InterPro domains/families:
 IPR019803 Glypican_CS
 IPR001863 Glypican
 IPR015501 Glypican-3


   GeneDecks  GPC3 for the domains selected above  
About GeneDecksing

Graphical View of Domain Structure for InterPro Entry P51654

ProtoNet protein and cluster: P51654

1 Blocks protein family: IPB001863 Glypican

UniProtKB/Swiss-Prot: GPC3_HUMAN, P51654
Similarity: Belongs to the glypican family

(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.)
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Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (GPC3)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_004484

              Applied Biosystems Silencer® siRNAs for GPC3

              Sigma-Aldrich siRNA and siRNA Panels for GPC3  
                     Sigma-Aldrich shRNA Panels and shRNA for GPC3  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Invitrogen Clones for GPC3
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_004484
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_004484
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_004484 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_004484

UniProtKB/Swiss-Prot: GPC3_HUMAN, P51654
Function: Cell surface proteoglycan that bears heparan sulfate. May be involved in the
suppression/modulation of growth in the predominantly mesodermal tissues and organs. May play a
role in the modulation of IGF2 interactions with its receptor and thereby modulate its function.
May regulate growth and tumor predisposition

Genatlas biochemistry entry for GPC3:
glypican 3,60kDa,putative extracellular proteoglycan,involved in growth control in embryonic
mesodermal tissues,complexing with and putative modulator of IGF2,juxtaposed to GPC4,with tumor
suppression activity

15/17 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Gpc3) (see all 17 ):

cellularcraniofacialdigestive/alimentaryembryogenesisgrowth/size
hematopoietic systemhomeostasis/metabolismimmune systemlethality-postnatallethality-prenatal/perinatal
limbs/digits/tailpigmentationrenal/urinary systemreproductive systemrespiratory system

(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


 Gene Network CentralTM Interacting Genes and Proteins Network for  GPC3 


5/17 Interacting proteins for GPC3 (ENSP000003598543) via UniProtKB, MINT, and/or STRING (see all 17 )
InteractantInteraction Details
GeneCardExternal ID(s)
PTCH1ENSP000003323533STRING (score=.934)
FURINENSP000002681713STRING (score=.92)
SHHENSP000002972613STRING (score=.917)
FGF2ENSP000002644983STRING (score=.908)
NUDT6ENSP000003060703STRING (score=.908)
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1 Gene Ontology (GO) biological process term (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0009653 anatomical structure morphogenesis TAS8589713
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 GPC3
3 Novoseek chemical compound relationships for GPC3 gene
Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
heparan sulfate 50.64 3 18477453 (1), 10814714 (1), 15537637 (1)
oligonucleotide 0.00 1 12478660 (1)
lipid 0.00 1 15620688 (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 (GPC3)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_004484

              Sigma-Aldrich siRNA and siRNA Panels for GPC3  
                     Sigma-Aldrich shRNA Panels and shRNA for GPC3  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_004484  

REFSEQ mRNAs for GPC3 gene: 

NM_004484.2   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_004484  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_004484
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_004484
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_004484 

Additional cDNA sequence: 

AK222761.1 AK222766.1 AK300168.1 AK310196.1 AK310689.1 BC035972.1 CR593041.1 CR594389.1 
CR600770.1 CR611970.1 CR620091.1 CR624507.1 DQ349136.1 DQ349137.1 DQ349138.1 L47125.1 
L47176.1 U50410.1 Z37987.1 

15 DOTS entries:

DT.452188  DT.100884054  DT.100884058  DT.121306095  DT.95311297  DT.100026089  DT.91768760  DT.91768767 
DT.95227507  DT.100697690  DT.100884069  DT.119635  DT.95311282  DT.100884067  DT.91768761 

24/452 AceView cDNA sequences (see all 452 ):

NM_004484 BQ643589 AU131321 AI052443 AI076178 BM974181 AV686384 BI793159 
AA971113 CR620091 BQ647204 L47176 BP374031 BX438697 BC035972 AA340731 
Z37987 BU844616 AU117929 AU118103 CR600770 AA953049 CR611970 BI822082 

highest scoring ESTs for GPC3:

U50410 AU117929 AU118103 AU118820 AU131321 AU135370 AU136239 AU137963 AU138269 AV750925 

Unigene Cluster for GPC3:

Glypican 3
Hs.644108  [show with all ESTs]
Unigene Representative Sequence: NM_004484


GeneLoc Exon Structure

3 Ensembl transcripts including schematic representations:
ENST00000394299  ENST00000370818  ENST00000406757  
(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

GPC3 expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for GPC3

1 / 2 / 3

6 probe-sets matching GPC3 gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
39350_at2, 3 U95-A 1 1.00 1.00 0.97 1.01 U50410 1.00 0.90 0.95 1
79192_i_at*2, 3 U95-D 1 -- -- 0.64 1.01 R07953 0.20 1.00 0.72 1

209220_at2, 3 U133-A 1 1.00 1.00 -- -- L47125 0.80 0.88 0.84 1

243243_at*2, 3 U133-B NULL 0.00 0.00 -- -- R07953 0.20 1.00 0.72 1

209220_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

243243_at*2 U133Plus2 NULL 0.00 0.00 -- -- -- -- -- -- --
GeneDecks  GPC3 for binary patterns associated with the probe-sets selected above  
About GeneDecksing
About this table    
Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: GATTTCTTTG

SOURCE GeneReport for Unigene cluster: Hs.644108

Expression variation in blood from EXPOLDB for GPC3

UniProtKB/Swiss-Prot: GPC3_HUMAN, P51654
Tissue specificity: Highly expressed in lung, liver and kidney

(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 GPC3 gene from 5/6 species (see all 6 )
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
GPC31   -- glypican 3 92.18(n)
95.52(a)
481056  XM_538178.2  XP_538178.2 
cow
(Bos taurus)
GPC31   -- glypican 3 93.28(n)
95.69(a)
615239  NM_001035463.1  NP_001030540.1 
rat
(Rattus norvegicus)
Gpc31   -- glypican 3 90.78(n)
94.09(a)
25236  NM_012774.1  NP_036906.1 
mouse
(Mus musculus)
Gpc31, 5 X5
glypican 31, 5 90.73(n)1
94.13(a)1
147341  NM_016697.21  NP_057906.21 
 AF1856145  AK0779425  (see all 17)
chicken
(Gallus gallus)
GPC31   -- glypican 3 69.84(n)
68.66(a)
770863  XM_001232891.1  XP_001232892.1 
About this table        Species with no ortholog for GPC3

ENSEMBL Gene Tree for GPC3
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for GPC3 gene
GPC52  GPC22  

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


10/1006 NCBI SNPs in GPC3 are shown (see all 1006 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 234)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr X posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs22675311,2
A,C,F132947926(+) TCCCGC/GGAACC 1 -- ng312Minor allele frequency- G:0.35NA 182
--
rs128332761,2
H132715336(+) AATCTC/TCACCA 1 E/K mis14Minor allele frequency- T:0.00EU EA WA 418
rs128332921,2
H132715339(+) CTCCAC/ACACAC 1 L/V mis14Minor allele frequency- A:0.00EU EA WA 418
rs23142981,2
C,F,H132558207(-) GGTGAT/CGATGA 1 D/D syn15Minor allele frequency- C:0.08EU EA WA NA 488
rs12643831,2
A,C,F,H,O132914376(+) CATGTG/ATCCCA 1 -- int17Minor allele frequency- A:0.04EU EA WA NA 517
rs12643791,2
A,C,F,H,O132893432(+) GGACTA/GAGCCC 1 -- int111Minor allele frequency- G:0.24EU EA WA NA 884
rs22675191,2
A,C,F,H,O132843934(+) TAACCA/GGTGCC 1 -- int116Minor allele frequency- G:0.35EU EA WA NA 1023
rs22675271,2
A,C,F,H,O132930377(+) GTCACA/GCTAGT 1 -- int18Minor allele frequency- G:0.34EU EA WA 733
rs9262281,2
A,C,F,H,O132550050(+) ATAGGT/ACCTAA 1 -- int17Minor allele frequency- A:0.46NA EA EU WA 668
rs12643821,2
A,C,F,H,O132907845(+) TTTTTA/TAATTA 1 -- int111Minor allele frequency- T:0.43EU EA WA NA 881
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HapMap Linkage Disequilibrium images for GPC3 (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: 300037   disorders: 312870  194070  

UniProtKB/Swiss-Prot: GPC3_HUMAN, P51654

  • Defects in GPC3 are the cause of Simpson-Golabi-Behmel syndrome (SGBS) [MIM:312870]; also
    known as Simpson dysmorphia syndrome (SDYS). SGBS is a condition characterized by pre- and
    postnatal overgrowth (gigantism) with visceral and skeletal anomalies
  • 10/39 Novoseek disease relationships for GPC3 gene (see all 39 )

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    perlman syndrome 89.13 2 11477610 (1), 10814714 (1)
    embryonal tumor 78.39 4 11008203 (2), 7909248 (1), 16158429 (1)
    beckwith-wiedemann syndrome 74.32 5 12949968 (1), 11477610 (1), 10814714 (1)
    gigantism 69.23 3 7909248 (1), 9339360 (1), 10814714 (1)
    hepatocellular carcinoma 68.41 47 15920546 (5), 15623647 (3), 16024626 (2), 16698587 (2) (see all 24)
    sotos syndrome 66.70 1 11477610 (1)
    nipples, supernumerary 64.27 1 11477610 (1)
    wilms tumor 60.51 16 12949968 (5), 11878776 (3), 11008203 (2), 17350117 (1) (see all 6)
    adenoma hepatocellular 60.41 5 18976006 (2), 16949914 (1), 15920546 (1), 9371521 (1)
    mesothelioma 60.28 8 11320054 (1), 18404367 (1), 15537637 (1), 11704870 (1) (see all 5)
    About this table

    GeneTests: GPC3
    Simpson-Golabi-Behmel Syndrome

    Human Gene Mutation Database: GPC3

    (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

    10/129 PubMed articles for GPC3 gene (see all 129 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     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, and/or H-InvDB)
    About This Section

    Entrez Gene: 2719 HGNC: 4451 AceView: GPC3 Ensembl:ENSG00000147257 euGenes: HUgn2719
    ECgene: GPC3 H-InvDB: GPC3
    (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 GPC3 Genetics and Cytogenetics in Oncology and Haematology
    GeneReviewshttp://www.genetests.org/query?gene=GPC3
    (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 GPC3:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for GPC3 Antibodies for GPC3
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for GPC3 Browse small molecules at Sigma-Aldrich
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