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    PAX3 paired box 3 [ Homo sapiens (human) ]

    Gene ID: 5077, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PAX3provided by HGNC
    Official Full Name
    paired box 3provided by HGNC
    Primary source
    HGNC:HGNC:8617
    See related
    Ensembl:ENSG00000135903 MIM:606597; AllianceGenome:HGNC:8617
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    WS1; WS3; CDHS; HUP2; PAX-3
    Summary
    This gene is a member of the paired box (PAX) family of transcription factors. Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. These genes play critical roles during fetal development. Mutations in paired box gene 3 are associated with Waardenburg syndrome, craniofacial-deafness-hand syndrome, and alveolar rhabdomyosarcoma. The translocation t(2;13)(q35;q14), which represents a fusion between PAX3 and the forkhead gene, is a frequent finding in alveolar rhabdomyosarcoma. Alternative splicing results in transcripts encoding isoforms with different C-termini. [provided by RefSeq, Jul 2008]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See PAX3 in Genome Data Viewer
    Location:
    2q36.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (222199887..222298998, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (222684993..222784124, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (223064606..223163717, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:222849491-222850043 Neighboring gene heat shock protein family A (Hsp70) member 9 pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:222889616-222890602 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:222890603-222891589 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:222917569-222918330 Neighboring gene ribosomal protein L23a pseudogene 28 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:223072996-223073618 Neighboring gene uncharacterized LOC107985991 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:223084735-223085934 Neighboring gene NANOG hESC enhancer GRCh37_chr2:223137199-223137802 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:223154577-223155490 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:223155491-223156404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:223158467-223159003 Neighboring gene PAX3 promoter region Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223171419-223171954 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223171955-223172489 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223182883-223183478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12368 Neighboring gene CCDC140 long non-coding RNA Neighboring gene ring finger protein 228 Neighboring gene cancer/testis associated transcript 75 Neighboring gene NANOG hESC enhancer GRCh37_chr2:223258471-223259068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17166 Neighboring gene sphingosine-1-phosphate phosphatase 2 Neighboring gene Nanog homeobox pseudogene 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Mutations in PAX3 that cause Waardenburg syndrome type I: ten new mutations and review of the literature. Baldwin CT, et al. Am J Med Genet, 1995 Aug 28. PMID 8533800
    2. PAX3 in neuroblastoma: oncogenic potential, chemosensitivity and signalling pathways. Fang WH, et al. J Cell Mol Med, 2014 Jan. PMID 24188742, Free PMC Article
    3. Differentiation of human induced pluripotent stem cells into brown and white adipocytes: role of Pax3. Mohsen-Kanson T, et al. Stem Cells, 2014 Jun. PMID 24302443
    4. Identification of a novel mutation in the paired domain of PAX3 in an Iranian family with waardenburg syndrome type I. Sotirova VN, et al. Ophthalmic Genet, 2000 Mar. PMID 10779847
    5. Recurrent PAX3-MAML3 fusion in biphenotypic sinonasal sarcoma. Wang X, et al. Nat Genet, 2014 Jul. PMID 24859338, Free PMC Article

    See all (258) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Waardenburg syndrome type 1: a case report of a family with a intragenic PAX3 deletion with no hearing loss or heterochromia of iris.
      Title: Waardenburg syndrome type 1: a case report of a family with a intragenic PAX3 deletion with no hearing loss or heterochromia of iris.
    2. PAX3 mutation suppress otic progenitors proliferation and induce apoptosis by inhibiting WNT1/beta-catenin signaling pathway in WS1 patient iPSC-derived inner ear organoids.
      Title: PAX3 mutation suppress otic progenitors proliferation and induce apoptosis by inhibiting WNT1/β-catenin signaling pathway in WS1 patient iPSC-derived inner ear organoids.
    3. Comparative study on the expression of Pax3, Rad51 and VEGF-C in esophageal gastric junction adenocarcinoma and distal gastric adenocarcinoma.
      Title: Comparative study on the expression of Pax3, Rad51 and VEGF-C in esophageal gastric junction adenocarcinoma and distal gastric adenocarcinoma.
    4. PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors.
      Title: PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors.
    5. Identification of two variants in PAX3 and FBN1 in a Chinese family with Waardenburg and Marfan syndrome via whole exome sequencing.
      Title: Identification of two variants in PAX3 and FBN1 in a Chinese family with Waardenburg and Marfan syndrome via whole exome sequencing.
    6. Restoration of functional PAX3 transcriptional factor enhanced neuronal differentiation in PAX3b isoform-depleted neuroblastoma cells.
      Title: Restoration of functional PAX3 transcriptional factor enhanced neuronal differentiation in PAX3b isoform-depleted neuroblastoma cells.
    7. A Novel Variant in Paired Box 3 Gene-related with Waardenburg Syndrome Type-1 in an Afghan Family.
      Title: A Novel Variant in Paired Box 3 Gene-related with Waardenburg Syndrome Type-1 in an Afghan Family.
    8. Identification of nine novel variants across PAX3, SOX10, EDNRB, and MITF genes in Waardenburg syndrome with next-generation sequencing.
      Title: Identification of nine novel variants across PAX3, SOX10, EDNRB, and MITF genes in Waardenburg syndrome with next-generation sequencing.
    9. Downregulation of the paired box gene 3 inhibits the progression of skin cutaneous melanoma by inhibiting c-MET tyrosine kinase : PAX3 downregulation inhibits melanoma progression.
      Title: Downregulation of the paired box gene 3 inhibits the progression of skin cutaneous melanoma by inhibiting c-MET tyrosine kinase : PAX3 downregulation inhibits melanoma progression.
    10. Divergent transcriptional and transforming properties of PAX3-FOXO1 and PAX7-FOXO1 paralogs.
      Title: Divergent transcriptional and transforming properties of PAX3-FOXO1 and PAX7-FOXO1 paralogs.
    Submit: New GeneRIF Correction See all GeneRIFs (174)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Alveolar rhabdomyosarcoma
    MedGen: C0206655 OMIM: 268220 GeneReviews: Not available
    		Compare labs
    Craniofacial-deafness-hand syndrome
    MedGen: C1852510 OMIM: 122880 GeneReviews: Not available
    		Compare labs
    Waardenburg syndrome type 1
    MedGen: C1847800 OMIM: 193500 GeneReviews: Waardenburg Syndrome Type I
    		Compare labs
    Waardenburg syndrome type 3
    MedGen: C0079661 OMIM: 148820 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-05-27)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-05-27)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
    EBI GWAS Catalog
    Genome-wide association study of three-dimensional facial morphology identifies a variant in PAX3 associated with nasion position.
    EBI GWAS Catalog
    Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC120381, MGC120382, MGC120383, MGC120384, MGC134778

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables HMG box domain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in animal organ morphogenesis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in apoptotic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in muscle organ development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sensory perception of sound TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    paired box protein Pax-3
    Names
    paired box homeotic gene 3
    paired domain gene 3
    paired domain gene HuP2
    transcriptional factor PAX3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_011632.1 RefSeqGene

      Range
      4984..104095
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000438.6 → NP_000429.2  paired box protein Pax-3 isoform PAX3a

      See identical proteins and their annotated locations for NP_000429.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (PAX3A) differs in the 3' UTR, includes an alternate segment in the coding region, which causes a frameshift, and lacks several segments in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3a) has a shorter and distinct C-terminus, compared to isoform PAX3. Isoform PAX3a lacks the paired-type homeodomain.
      Source sequence(s)
      AC010980, BC101299, DA758804, S69369
      Consensus CDS
      CCDS46523.1
      UniProtKB/Swiss-Prot
      P23760
      Related
      ENSP00000386817.3, ENST00000409828.7
      Conserved Domains (1) summary
      pfam00292
      Location:34 → 159
      PAX; 'Paired box' domain

    2. NM_001127366.3 → NP_001120838.1  paired box protein Pax-3 isoform PAX3i

      See identical proteins and their annotated locations for NP_001120838.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (PAX3I) differs in the 3' UTR, uses an alternate in-frame splice site in the 5' coding region, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3i, also known as isoform PAX3dQ-) is longer and has a distinct C-terminus, compared to isoform PAX3.
      Source sequence(s)
      AC010980, AC012591, AI382779, BC101299, DA758804
      Consensus CDS
      CCDS46522.1
      UniProtKB/Swiss-Prot
      P23760
      Related
      ENSP00000386750.3, ENST00000409551.7
      Conserved Domains (3) summary
      smart00351
      Location:34 → 158
      PAX; Paired Box domain
      pfam00046
      Location:221 → 275
      Homeobox; Homeobox domain
      pfam12360
      Location:346 → 390
      Pax7; Paired box protein 7

    3. NM_013942.5 → NP_039230.1  paired box protein Pax-3 isoform PAX3b

      See identical proteins and their annotated locations for NP_039230.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (PAX3B) differs in the 3' UTR, includes an alternate segment in the coding region, which causes a frameshift, and lacks several segments in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3a) has a shorter and distinct C-terminus, compared to isoform PAX3. Isoform PAX3b lacks the paired-type homeodomain.
      Source sequence(s)
      AC010980, BC063547, BC101299, DA758804
      Consensus CDS
      CCDS2451.1
      UniProtKB/Swiss-Prot
      P23760
      Related
      ENSP00000258387.5, ENST00000258387.6
      Conserved Domains (1) summary
      pfam00292
      Location:34 → 159
      PAX; 'Paired box' domain

    4. NM_181457.4 → NP_852122.1  paired box protein Pax-3 isoform PAX3

      See identical proteins and their annotated locations for NP_852122.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (PAX3) encodes isoform PAX3 (also known as isoform PAX3c).
      Source sequence(s)
      AC010980, AC012591, BC101299, BC101301, DA758804
      Consensus CDS
      CCDS42826.1
      UniProtKB/Swiss-Prot
      G5E9C1, P23760, Q16448, Q494Z3, Q494Z4, Q53T90, Q6GSJ9, Q86UQ2, Q86UQ3
      Related
      ENSP00000343052.4, ENST00000350526.9
      Conserved Domains (4) summary
      pfam12360
      Location:347 → 391
      Pax7; Paired box protein 7
      pfam00046
      Location:222 → 275
      Homeobox; Homeobox domain
      pfam00292
      Location:34 → 159
      PAX; 'Paired box' domain
      pfam06991
      Location:163 → 286
      MFAP1; Microfibril-associated/Pre-mRNA processing

    5. NM_181458.4 → NP_852123.1  paired box protein Pax-3 isoform PAX3d

      See identical proteins and their annotated locations for NP_852123.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (PAX3D) differs in the 3' UTR, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3d) is longer and has a distinct C-terminus, compared to isoform PAX3.
      Source sequence(s)
      AC010980, AC012591, AI382779, AK291278, BC101299, BC101301
      Consensus CDS
      CCDS42825.1
      UniProtKB/Swiss-Prot
      P23760
      Related
      ENSP00000375922.3, ENST00000392070.7
      Conserved Domains (3) summary
      smart00351
      Location:34 → 159
      PAX; Paired Box domain
      pfam00046
      Location:222 → 276
      Homeobox; Homeobox domain
      pfam12360
      Location:347 → 391
      Pax7; Paired box protein 7

    6. NM_181459.4 → NP_852124.1  paired box protein Pax-3 isoform PAX3e

      See identical proteins and their annotated locations for NP_852124.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (PAX3E) differs in the 3' UTR, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3e) is longer and has a distinct C-terminus, compared to isoform PAX3.
      Source sequence(s)
      AC010980, AC012591, AI382779, BC101299, BC101301, DA758804
      Consensus CDS
      CCDS2448.1
      UniProtKB/Swiss-Prot
      P23760
      Related
      ENSP00000375921.2, ENST00000392069.6
      Conserved Domains (3) summary
      smart00351
      Location:34 → 159
      PAX; Paired Box domain
      pfam00046
      Location:222 → 276
      Homeobox; Homeobox domain
      pfam12360
      Location:347 → 391
      Pax7; Paired box protein 7

    7. NM_181460.4 → NP_852125.1  paired box protein Pax-3 isoform PAX3h

      See identical proteins and their annotated locations for NP_852125.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (PAX3H) differs in the 3' UTR, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3h) is shorter and has a distinct C-terminus, compared to variant PAX3.
      Source sequence(s)
      AC010980, AC012591, AI382779, BC101299, BC101301, DA758804
      Consensus CDS
      CCDS2449.1
      UniProtKB/Swiss-Prot
      P23760
      Related
      ENSP00000338767.5, ENST00000336840.11
      Conserved Domains (4) summary
      pfam12360
      Location:347 → 391
      Pax7; Paired box protein 7
      pfam00046
      Location:222 → 275
      Homeobox; Homeobox domain
      pfam00292
      Location:34 → 159
      PAX; 'Paired box' domain
      pfam06991
      Location:163 → 286
      MFAP1; Microfibril-associated/Pre-mRNA processing

    8. NM_181461.4 → NP_852126.1  paired box protein Pax-3 isoform PAX3g

      See identical proteins and their annotated locations for NP_852126.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (PAX3G) differs in the 3' UTR, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3g) is shorter and has a distinct C-terminus, compared to variant PAX3.
      Source sequence(s)
      AC010980, AC012591, AI382779, BC101299, BC101301, DA758804
      Consensus CDS
      CCDS2450.1
      UniProtKB/Swiss-Prot
      P23760
      Related
      ENSP00000342092.4, ENST00000344493.9
      Conserved Domains (3) summary
      pfam00046
      Location:222 → 275
      Homeobox; Homeobox domain
      pfam00292
      Location:34 → 159
      PAX; 'Paired box' domain
      pfam12360
      Location:347 → 391
      Pax7; Paired box protein 7

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      222199887..222298998 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      222684993..222784124 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P23760.2 GenPept UniProtKB/Swiss-Prot:P23760

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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