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

CCDC39 Gene

protein-coding   GIFtS: 45
GCID: GC03M180320

coiled-coil domain containing 39

 Explore 5 diseases affiliated with
CCDC39 via our new
 Human Malady Compendium 
Biological research products
for CCDC39
    

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

Aliases
Coiled-Coil Domain Containing 391 2
CILD141 2
FAP591 2
DKFZp434A1281
Coiled-Coil Domain-Containing Protein 392

External Ids:    HGNC: 252441   Entrez Gene: 3398292   Ensembl: ENSG000001450757   OMIM: 6137985   UniProtKB: Q9UFE43   

Export aliases for CCDC39 gene to outside databases

Previous GC identifers: GC03M181815 GC03M177736


(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 CCDC39:
The protein encoded by this gene is involved in the motility of cilia and flagella. The encoded protein is essential
for the assembly of dynein regulatory and inner dynein arm complexes, which regulate ciliary beat. Defects in this
gene are a cause of primary ciliary dyskinesia type 14 (CILD14). (provided by RefSeq, Jul 2011)

UniProtKB/Swiss-Prot: CCD39_HUMAN, Q9UFE4
Function: Required for assembly of dynein regulatory complex (DRC) and inner dynein arm complexes, which are
responsible for ciliary beat regulation, thereby playing a central role in motility in cilia and flagella. Not
required for outer dynein arm complexes assembly




(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_000003.11  NC_018914.1  NT_005612.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CCDC39 gene promoter:
         SRF   SRF (504 AA)   NF-AT   MEF-2A   NF-AT4   S8   NF-AT2   NF-AT3   aMEF-2   NF-AT1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for CCDC39

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CCDC39


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

Entrez Gene cytogenetic band: 3q26.33   Ensembl cytogenetic band:  3q26.33   HGNC cytogenetic band: 3q26.33

CCDC39 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC39 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M180320:  view genomic region     (about GC identifiers)

Start:
180,320,646 bp from pter      End:
180,588,793 bp from pter
Size:
268,148 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: CCD39_HUMAN, Q9UFE4 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 39  
Size: 941 amino acids; 109901 Da
Subcellular location: Cytoplasm, cytoskeleton, cilium axoneme. Note=CCDC40 is required for localization to axonemes
Secondary accessions: B4E2H1
Alternative splicing: 2 isoforms:  Q9UFE4-1   Q9UFE4-2   (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for CCDC39: NX_Q9UFE4

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9UFE4

  • CCDC39 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_852091.1  
    ENSEMBL proteins: 
     ENSP00000418482   ENSP00000420025   ENSP00000417960   ENSP00000405708   ENSP00000418702  
     ENSP00000273654  

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    Uscn Proteins for CCDC39

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm ----
    GO:0005856cytoskeleton IEA--
    GO:0035085cilium axoneme IDA--


    CCDC39 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

    ProtoNet protein and cluster: Q9UFE4

    UniProtKB/Swiss-Prot: CCD39_HUMAN, Q9UFE4
    Similarity: Belongs to the CCDC39 family


    (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: CCD39_HUMAN, Q9UFE4
    Function: Required for assembly of dynein regulatory complex (DRC) and inner dynein arm complexes, which are
    responsible for ciliary beat regulation, thereby playing a central role in motility in cilia and flagella. Not
    required for outer dynein arm complexes assembly

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC39

    2 GenomeRNAi human phenotypes for CCDC39:
     G0/1 arrest  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 CCDC39

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

    4 Interacting proteins for CCDC39 (ENSP000004057084) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    --ENSP000004135964STRING: ENSP00000413596
    --ENSP000004077374STRING: ENSP00000407737
    --ENSP000003908774STRING: ENSP00000390877
    --ENSP000003898944STRING: ENSP00000389894
    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:0060285ciliary cell motility IMP--
    GO:0060286flagellar cell motility IMP--
    GO:0060287epithelial cilium movement involved in determination of left/right asymmetry IMP--
    GO:0070286axonemal dynein complex assembly IMP--


    CCDC39 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 CCDC39
    Search CenterWatch for drugs/clinical trials and news about CCDC39 / CCD39 

    (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,
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    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 CCDC39 gene: 
    NM_181426.1  

    Unigene Clusters for CCDC39:

    Coiled-coil domain containing 39
    Hs.712820  [show with all ESTs], Hs.734668  [show with all ESTs]
    Unigene Representative Sequences: AL122120, BC047103
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000473854 ENST00000489868 ENST00000476379(uc010hxe.3 uc003fkn.3)
    ENST00000442201 ENST00000471307 ENST00000485055(uc003fko.3) ENST00000495817
    ENST00000273654

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    hsa-miR-498 hsa-miR-875-3p hsa-miR-599 hsa-miR-3148 hsa-miR-551b* hsa-miR-3147
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Additional cDNA sequence: 

    BC047103.1 BC094711.1 

    7 DOTS entries:

    DT.86858238  DT.86841139  DT.120924060  DT.91897989  DT.100682006  DT.70104335  DT.91676576 

    21 AceView cDNA sequences:

    AW571640 AL122120 CA448721 AI217488 BC047103 BF061321 AL045951 AW181942 
    AW571667 AI204288 BF574287 BU568081 CD244387 AA897385 BG530127 AW593125 
    BG205877 F34172 BU686455 BI559385 CD000948 

    GeneLoc Exon Structure


    (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

    CCDC39 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ATTACATTAA

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

    About this image

    CCDC39 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: 1 LifeMap Cell 
    NameCategory
    Posterior foregut-like cells (A scalable, suspensi...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See CCDC39 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CCDC39

    SOURCE GeneReport for Unigene clusters: Hs.712820 Hs.734668

    UniProtKB/Swiss-Prot: CCD39_HUMAN, Q9UFE4
    Tissue specificity: Mainly expressed in nasal brushings and, to a lesser extent, in lungs and testis

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    In Situ
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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 CCDC39 gene from 5/20 species (see all 20)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc391 , 5 coiled-coil domain containing 391, 5 78.48(n)1
    75.56(a)1
      3 (16.32 cM)5
    519381  NM_026222.21  NP_080498.11 
     338123625 
    chicken
    (Gallus gallus)
    Aves CCDC391 coiled-coil domain containing 39 66.27(n)
    58.06(a)
      424969  XM_422777.3  XP_422777.3 
    lizard
    (Anolis carolinensis)
    Reptilia CCDC396
    --
    54(a)
    1 ↔ 1
    3(1611945-1644826)
    zebrafish
    (Danio rerio)
    Actinopterygii ccdc391 coiled-coil domain containing 39 58.31(n)
    53.32(a)
      555319  XM_677617.5  XP_682709.5 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG173871 CG17387 37.71(n)
    23.45(a)
      40595  NM_141238.2  NP_649495.1 


    ENSEMBL Gene Tree for CCDC39 (if available)
    TreeFam Gene Tree for CCDC39 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (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

    10/1029 NCBI SNPs in CCDC39 are shown (see all 1029    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs285025651,2
    C,F,--177735869(+) CCTCTA/GCCTTC 1 -- int18Minor allele frequency- G:0.44NA WA CSA 249
    rs1145003101,2
    C,F,--177736343(+) TACTAC/TATTTG 1 -- ut311Minor allele frequency- T:0.03WA 118
    rs1858674481,2
    C,--177736483(+) ATCTTC/TAATGC 1 -- ut310--------
    rs793492851,2
    C,F,--177736568(+) TTGATA/GTACAG 1 -- ut311Minor allele frequency- G:0.03NA 120
    rs590163111,2
    C,--177736644(+) AAAAAT/GTATAG 1 -- ut313Minor allele frequency- G:0.06WA CSA 121
    rs738839021,2
    C,--177736818(+) AGATTG/ATTACA 1 -- ut311Minor allele frequency- A:0.50WA 2
    rs1136962481,2
    C,--177737010(+) TTTTTT/AAAAAC 1 -- ut312Minor allele frequency- A:0.21WA 120
    rs68077671,2
    C,F,H,--177737425(+) ATAGTG/ATTAAG 1 -- int16Minor allele frequency- A:0.12EA NS CSA WA NA 536
    rs1131076571,2
    --177737770(+) TAAATA/CTATAT 1 -- int12Minor allele frequency- C:0.02CSA WA 119
    rs769030921,2
    --177737883(+) AGGAAT/CAGTAA 1 -- int12Minor allele frequency- C:0.04CSA WA 119

    HapMap Linkage Disequilibrium report for CCDC39 (180320646 - 180570646 bp, first 250kb of CCDC39)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for CCDC39
         2 CNVs: 44093 98548
    Human Gene Mutation Database (HGMD): CCDC39

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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

    CCDC39 for disorders           About GeneDecksing

    OMIM gene information: 613798    OMIM disorders: --

    UniProtKB/Swiss-Prot: CCD39_HUMAN, Q9UFE4
  • Defects in CCDC39 are the cause of primary ciliary dyskinesia type 14 (CILD14) [MIM:613807]. A disorder
  • characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and
    bronchiectasis are recurrent, due to defects in the respiratory cilia; reduced fertility is often observed in male
    patients due to abnormalities of sperm tails. Half of the patients exhibit randomization of left-right body asymmetry
    and situs inversus, due to dysfunction of monocilia at the embryonic node. Primary ciliary dyskinesia associated with
    situs inversus is referred to as Kartagener syndrome

    5 diseases for CCDC39:    About MalaCards
    ciliary dyskinesia    primary ciliary dyskinesia    situs inversus    kartagener syndrome
    bronchiectasis

    2 diseases from the University of Copenhagen DISEASES database for CCDC39:
    Primary ciliary dyskinesia     Situs inversus
    Human Genome Epidemiology (HuGE) Navigator: CCDC39 (1 document)

    Export disorders for CCDC39 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 CCDC39 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with CCDC39)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. CCDC39 is required for assembly of inner dynein arms and the dynein regulatory complex and for normal ciliary motility in humans and dogs. (PubMed id 21131972)1, 2, 3 Merveille A.C....Amselem S. (2010)
    2. Delineation of CCDC39/CCDC40 mutation spectrum and ass ociated phenotypes in primary ciliary dyskinesia. (PubMed id 22693285)1 Blanchon S....Amselem S. (2012)
    3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    4. The coiled-coil domain containing protein CCDC40 is e ssential for motile cilia function and left-right axis formation. (PubMed id 21131974)2 Becker-Heck A....Burdine R.D. (2010)
    5. Dynamics of cullin-RING ubiquitin ligase network revea led by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (2010)
    6. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    7. The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)2 Muzny D.M....Gibbs R.A. (2006)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    9. 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)
    10. Creation of genome-wide protein expression libraries using random activation of gene expression. (PubMed id 11329013)1 Harrington J.J.... Ducar M. (2001)

    (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, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 339829 HGNC: 25244 AceView: DKFZp434A128 Ensembl:ENSG00000145075 euGenes: HUgn339829
    ECgene: CCDC39 H-InvDB: CCDC39

    (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 CCDC39 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 CCDC39 gene:
    Search GeneIP for patents involving CCDC39

    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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