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    USP9X ubiquitin specific peptidase 9 X-linked [ Homo sapiens (human) ]

    Gene ID: 8239, updated on 3-Nov-2024

    Summary

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    Official Symbol
    USP9Xprovided by HGNC
    Official Full Name
    ubiquitin specific peptidase 9 X-linkedprovided by HGNC
    Primary source
    HGNC:HGNC:12632
    See related
    Ensembl:ENSG00000124486 MIM:300072; AllianceGenome:HGNC:12632
    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
    FAF; FAM; hFAM; DFFRX; FAF-X; MRX99; XLID99; MRXS99F
    Summary
    This gene is a member of the peptidase C19 family and encodes a protein that is similar to ubiquitin-specific proteases. Though this gene is located on the X chromosome, it escapes X-inactivation. Mutations in this gene have been associated with Turner syndrome. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 14.2), thyroid (RPKM 14.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See USP9X in Genome Data Viewer
    Location:
    Xp11.4
    Exon count:
    46
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (41085445..41236579)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (40487470..40638605)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (40944698..41095832)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:40809037-40809720 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:40809721-40810402 Neighboring gene ribosomal protein S2 pseudogene 55 Neighboring gene Sharpr-MPRA regulatory region 12561 Neighboring gene Sharpr-MPRA regulatory region 13807 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20771 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:40944771-40945308 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20772 Neighboring gene chloride intracellular channel 4 pseudogene 3 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:40973903-40974035 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29553 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:40991170-40991670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:41070375-41071092 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:41135078-41135578 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:41135579-41136079 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:41150473-41151037 Neighboring gene long intergenic non-protein coding RNA 2601 Neighboring gene RNA, 5S ribosomal pseudogene 502

    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. Novel USP9X variant associated with syndromic intellectual disability in a female: A case study and review. Meira JGC, et al. Am J Med Genet A, 2021 May. PMID 33638286
    2. Partial Loss of USP9X Function Leads to a Male Neurodevelopmental and Behavioral Disorder Converging on Transforming Growth Factor β Signaling. Johnson BV, et al. Biol Psychiatry, 2020 Jan 15. PMID 31443933, Free PMC Article
    3. Genetic disruption of USP9X sensitizes colorectal cancer cells to 5-fluorouracil. Harris DR, et al. Cancer Biol Ther, 2012 Nov. PMID 22895071, Free PMC Article
    4. Non-canonical regulation of homologous recombination DNA repair by the USP9X deubiquitylase. O'Dea R, et al. J Cell Sci, 2020 Feb 12. PMID 31964704
    5. Down-Regulation of Ubiquitin-Specific Peptidase 9X Inhibited Proliferation, Migration and Invasion of Osteosarcoma via ERK1/2 and PI3K/Akt Signaling Pathways. Zheng W, et al. Biol Pharm Bull, 2022. PMID 36047196

    See all (334) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. USP9X regulates the proliferation, survival, migration and invasion of gastric cancer cells by stabilizing MTH1.
      Title: USP9X regulates the proliferation, survival, migration and invasion of gastric cancer cells by stabilizing MTH1.
    2. USP9X deubiquitinates and stabilizes CDC123 to promote breast carcinogenesis through regulating cell cycle.
      Title: USP9X deubiquitinates and stabilizes CDC123 to promote breast carcinogenesis through regulating cell cycle.
    3. Deubiquitinase USP9X stabilizes RNA m[6]A demethylase ALKBH5 and promotes acute myeloid leukemia cell survival.
      Title: Deubiquitinase USP9X stabilizes RNA m(6)A demethylase ALKBH5 and promotes acute myeloid leukemia cell survival.
    4. Deubiquitinase USP9X loss sensitizes renal cancer cells to mTOR inhibition.
      Title: Deubiquitinase USP9X loss sensitizes renal cancer cells to mTOR inhibition.
    5. USP9X mediates an acute adaptive response to MAPK suppression in pancreatic cancer but creates multiple actionable therapeutic vulnerabilities.
      Title: USP9X mediates an acute adaptive response to MAPK suppression in pancreatic cancer but creates multiple actionable therapeutic vulnerabilities.
    6. KSHV Viral Protein Kinase Interacts with USP9X to Modulate the Viral Lifecycle.
      Title: KSHV Viral Protein Kinase Interacts with USP9X to Modulate the Viral Lifecycle.
    7. USP9X promotes lipopolysaccharide-stimulated acute lung injury by deubiquitination of NLRP3.
      Title: USP9X promotes lipopolysaccharide-stimulated acute lung injury by deubiquitination of NLRP3.
    8. Ablation of EWS-FLI1 by USP9X inhibition suppresses cancer cell growth in Ewing sarcoma.
      Title: Ablation of EWS-FLI1 by USP9X inhibition suppresses cancer cell growth in Ewing sarcoma.
    9. Down-Regulation of Ubiquitin-Specific Peptidase 9X Inhibited Proliferation, Migration and Invasion of Osteosarcoma via ERK1/2 and PI3K/Akt Signaling Pathways.
      Title: Down-Regulation of Ubiquitin-Specific Peptidase 9X Inhibited Proliferation, Migration and Invasion of Osteosarcoma via ERK1/2 and PI3K/Akt Signaling Pathways.
    10. Deubiquitinating enzyme USP9X regulates metastasis and chemoresistance in triple-negative breast cancer by stabilizing Snail1.
      Title: Deubiquitinating enzyme USP9X regulates metastasis and chemoresistance in triple-negative breast cancer by stabilizing Snail1.
    Submit: New GeneRIF Correction See all GeneRIFs (108)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Intellectual disability, X-linked 99
    MedGen: C3806746 OMIM: 300919 GeneReviews: Not available
    		Compare labs
    Intellectual disability, X-linked 99, syndromic, female-restricted
    MedGen: C4225416 OMIM: 300968 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2018-03-28)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2018-03-28)

    ClinGen Genome Curation PagePubMed

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables K11-linked deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables K48-linked deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables K63-linked deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables co-SMAD binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables cysteine-type deubiquitinase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables cysteine-type deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cysteine-type deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cysteine-type deubiquitinase activity TAS
    Traceable Author Statement
    more info
    		  
    enables cysteine-type endopeptidase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables cysteine-type peptidase activity TAS
    Traceable Author Statement
    more info
    		  
    enables deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables deubiquitinase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables molecular sequestering activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in BMP signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA alkylation repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in amyloid fibril formation TAS
    Traceable Author Statement
    more info
    		  
    involved_in axon extension IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromosome segregation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cilium assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cytosolic ciliogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in female gamete generation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in monoubiquitinated protein deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    		  
    involved_in neuron migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of TORC2 signaling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of protein binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein K63-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein deubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein deubiquitination TAS
    Traceable Author Statement
    more info
    		  
    involved_in protein deubiquitination involved in ubiquitin-dependent protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein import into peroxisome matrix, receptor recycling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein localization TAS
    Traceable Author Statement
    more info
    		  
    involved_in protein stabilization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein ubiquitination TAS
    Traceable Author Statement
    more info
    		  
    involved_in regulation of circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of protein stability IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in rhythmic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transforming growth factor beta receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cilium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in growth cone IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane HDA PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 9X
    Names
    Drosophila fat facets related, X-linked
    deubiquitinating enzyme FAF-X
    fat facets in mammals
    fat facets protein related, X-linked
    fat facets-like, X-linked
    probable ubiquitin carboxyl-terminal hydrolase FAF-X
    ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)
    ubiquitin thioesterase FAF-X
    ubiquitin thiolesterase FAF-X
    ubiquitin-specific processing protease FAF-X
    ubiquitin-specific protease 9, X chromosome
    NP_001034679.2
    NP_001034680.2
    NP_001397677.1
    NP_001397678.1
    XP_005272732.1
    XP_005272733.1
    XP_047298504.1
    XP_047298506.1
    XP_054183906.1
    XP_054183907.1
    XP_054183908.1
    XP_054183909.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_012547.1 RefSeqGene

      Range
      4811..155945
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001039590.3 → NP_001034679.2  ubiquitin carboxyl-terminal hydrolase 9X isoform 3

      See identical proteins and their annotated locations for NP_001034679.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longer transcript and encodes the longer isoform (3).
      Source sequence(s)
      AA261797, AF070645, AL109797, AL391259, AW183065, BC063645, BE925861, BX956755, CD619095, DA854185, X98296
      Consensus CDS
      CCDS43930.1
      UniProtKB/TrEMBL
      A0A994J4T3
      Related
      ENSP00000316357.6, ENST00000324545.9
      Conserved Domains (1) summary
      cd02659
      Location:1555 → 1958
      peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

    2. NM_001039591.3 → NP_001034680.2  ubiquitin carboxyl-terminal hydrolase 9X isoform 4

      See identical proteins and their annotated locations for NP_001034680.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice site at the 3' end of an exon compared to variant 3. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 3.
      Source sequence(s)
      AA261797, AL109797, AL391259, AW183065, BC046205, BC063645, BE925861, BX956755, CD619095, DA854185, X98296
      Consensus CDS
      CCDS55403.1
      UniProtKB/Swiss-Prot
      O75550, Q8WWT3, Q8WX12, Q93008
      UniProtKB/TrEMBL
      A0A994J4T3
      Related
      ENSP00000367558.2, ENST00000378308.7
      Conserved Domains (3) summary
      cd02659
      Location:1555 → 1958
      peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
      pfam12030
      Location:2097 → 2476
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:900 → 964
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold

    3. NM_001410748.1 → NP_001397677.1  ubiquitin carboxyl-terminal hydrolase 9X isoform 5

      Status: REVIEWED

      Source sequence(s)
      AL109797, AL391259
      Consensus CDS
      CCDS94594.1
      UniProtKB/TrEMBL
      A0A994J4R6

    4. NM_001410749.1 → NP_001397678.1  ubiquitin carboxyl-terminal hydrolase 9X isoform 6

      Status: REVIEWED

      Source sequence(s)
      AL109797, AL391259
      Consensus CDS
      CCDS94593.1
      UniProtKB/TrEMBL
      A0A994J6S4

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      41085445..41236579
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047442548.1 → XP_047298504.1  ubiquitin carboxyl-terminal hydrolase 9X isoform X2

    2. XM_047442550.1 → XP_047298506.1  ubiquitin carboxyl-terminal hydrolase 9X isoform X4

      UniProtKB/Swiss-Prot
      O75550, Q8WWT3, Q8WX12, Q93008

    3. XM_005272675.5 → XP_005272732.1  ubiquitin carboxyl-terminal hydrolase 9X isoform X1

      See identical proteins and their annotated locations for XP_005272732.1

      UniProtKB/TrEMBL
      A0A994J4R6, A0A994J4T3
      Related
      ENSP00000515604.1, ENST00000703987.1
      Conserved Domains (2) summary
      cd02659
      Location:1560 → 1963
      peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
      pfam00443
      Location:1562 → 1958
      UCH; Ubiquitin carboxyl-terminal hydrolase

    4. XM_005272676.5 → XP_005272733.1  ubiquitin carboxyl-terminal hydrolase 9X isoform X3

      See identical proteins and their annotated locations for XP_005272733.1

      UniProtKB/TrEMBL
      A0A994J4T3, A0A994J6S4
      Related
      ENSP00000515603.1, ENST00000703986.1
      Conserved Domains (2) summary
      cd02659
      Location:1560 → 1963
      peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
      pfam00443
      Location:1562 → 1958
      UCH; Ubiquitin carboxyl-terminal hydrolase

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      40487470..40638605
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327932.1 → XP_054183907.1  ubiquitin carboxyl-terminal hydrolase 9X isoform X2

    2. XM_054327934.1 → XP_054183909.1  ubiquitin carboxyl-terminal hydrolase 9X isoform X4

      UniProtKB/Swiss-Prot
      O75550, Q8WWT3, Q8WX12, Q93008

    3. XM_054327931.1 → XP_054183906.1  ubiquitin carboxyl-terminal hydrolase 9X isoform X1

      UniProtKB/TrEMBL
      A0A994J4R6

    4. XM_054327933.1 → XP_054183908.1  ubiquitin carboxyl-terminal hydrolase 9X isoform X3

      UniProtKB/TrEMBL
      A0A994J6S4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_004652.3: Suppressed sequence

      Description
      NM_004652.3: This RefSeq was temporarily suppressed because currently there is insufficient data to support this transcript.

    2. NM_021906.2: Suppressed sequence

      Description
      NM_021906.2: This RefSeq was temporarily suppressed because currently there is insufficient data to support this transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q93008.4 GenPept UniProtKB/Swiss-Prot:Q93008

    Gene LinkOut

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

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