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Aliases for USP9X Gene

Aliases for USP9X Gene

  • Ubiquitin Specific Peptidase 9, X-Linked 2 3 5
  • Ubiquitin Specific Protease 9, X Chromosome (Fat Facets-Like Drosophila) 2 3
  • Ubiquitin-Specific Protease 9, X Chromosome 3 4
  • Deubiquitinating Enzyme FAF-X 3 4
  • Ubiquitin Thioesterase FAF-X 3 4
  • Fat Facets In Mammals 3 4
  • DFFRX 3 4
  • HFAM 3 4
  • FAM 3 4
  • Ubiquitin Specific Peptidase 9, X-Linked (Fat Facets-Like, Drosophila) 2
  • Ubiquitin Specific Protease 9, X-Linked (Fat Facets-Like, Drosophila) 2
  • Probable Ubiquitin Carboxyl-Terminal Hydrolase FAF-X 3
  • Ubiquitin-Specific Processing Protease FAF-X 3
  • Ubiquitin-Specific-Processing Protease FAF-X 4
  • Drosophila Fat Facets Related, X-Linked 3
  • Fat Facets Protein Related, X-Linked 3
  • Fat Facets Protein-Related, X-Linked 4
  • Ubiquitin Thiolesterase FAF-X 3
  • EC 3.4.19.12 4
  • EC 3.1.2.15 61
  • MRXS99F 3
  • MRX99 3
  • USP9 4
  • FAF 3

External Ids for USP9X Gene

Previous GeneCards Identifiers for USP9X Gene

  • GC0XP039009
  • GC0XP039231
  • GC0XP039827
  • GC0XP040013
  • GC0XP040739
  • GC0XP040829
  • GC0XP040944
  • GC0XP038676

Summaries for USP9X Gene

Entrez Gene Summary for USP9X Gene

  • 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]

GeneCards Summary for USP9X Gene

USP9X (Ubiquitin Specific Peptidase 9, X-Linked) is a Protein Coding gene. Diseases associated with USP9X include Mental Retardation, X-Linked 99 and Mental Retsrdation, X-Linked Syndromic, Female Restricted. Among its related pathways are Transcriptional activity of SMAD2/SMAD3-SMAD4 heterotrimer and Gene Expression. GO annotations related to this gene include binding and cysteine-type peptidase activity. An important paralog of this gene is USP9Y.

UniProtKB/Swiss-Prot for USP9X Gene

  • Deubiquitinase involved both in the processing of ubiquitin precursors and of ubiquitinated proteins. May therefore play an important regulatory role at the level of protein turnover by preventing degradation of proteins through the removal of conjugated ubiquitin. Essential component of TGF-beta/BMP signaling cascade. Regulates chromosome alignment and segregation in mitosis by regulating the localization of BIRC5/survivin to mitotic centromeres. Specifically hydrolyzes both Lys-29- and Lys-33-linked polyubiquitins chains. Specifically deubiquitinates monoubiquitinated SMAD4, opposing the activity of E3 ubiquitin-protein ligase TRIM33. Involved in axonal growth and neuronal cell migration.

Gene Wiki entry for USP9X Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USP9X Gene

Genomics for USP9X Gene

Regulatory Elements for USP9X Gene

Enhancers for USP9X Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XF040577 1.3 Ensembl ENCODE 26.6 -505.4 -505365 4.8 PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 FOS ZNF263 CEBPZ SP3 DDX3X CASK-AS1 USP9X MED14 ATP6AP2 GC0XM040583
GH0XF041491 1.1 Ensembl ENCODE 27.5 +406.2 406170 1.7 TBP SIN3A FEZF1 BMI1 CBX5 FOS ZNF263 PAF1 ZNF362 SMAD5 CASK-AS1 DDX3X USP9X MED14 NYX GPR34 LOC100506654
GH0XF041329 1.6 FANTOM5 ENCODE 17.9 +248.0 248041 7.3 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A YBX1 FEZF1 DMAP1 DDX3X CASK-AS1 CXorf38 USP9X MED14 NYX PIR48586
GH0XF041473 1.4 Ensembl ENCODE 20.1 +390.1 390092 3.9 HDGF PKNOX1 ARNT CREB3L1 ARID4B SIN3A FEZF1 DMAP1 YBX1 ZNF2 CASK-AS1 DDX3X USP9X ENSG00000233103 LOC100132831 MPC1L CXorf38 LOC100506654
GH0XF041083 1.6 FANTOM5 ENCODE 14 +1.1 1091 6.1 HDGF PKNOX1 CREB3L1 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 CASK-AS1 LOC100132831 MPC1L IMPDH1P2 ENSG00000233103 DDX3X USP9X MED14 CXorf38 GC0XP041123
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around USP9X on UCSC Golden Path with GeneCards custom track

Promoters for USP9X Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000477648 1967 7201 CREB3L1 MLX ZFP64 FEZF1 DMAP1 YY1 ZNF143 ZNF548 ZNF263 SP3

Genomic Location for USP9X Gene

Chromosome:
X
Start:
41,085,433 bp from pter
End:
41,236,579 bp from pter
Size:
151,147 bases
Orientation:
Plus strand

Genomic View for USP9X Gene

Genes around USP9X on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP9X Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP9X Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP9X Gene

Proteins for USP9X Gene

  • Protein details for USP9X Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q93008-USP9X_HUMAN
    Recommended name:
    Probable ubiquitin carboxyl-terminal hydrolase FAF-X
    Protein Accession:
    Q93008
    Secondary Accessions:
    • O75550
    • Q8WWT3
    • Q8WX12

    Protein attributes for USP9X Gene

    Size:
    2570 amino acids
    Molecular mass:
    292280 Da
    Quaternary structure:
    • Interacts with SMAD4, MARK4, NUAK1 and BIRC5/survivin. Interacts with DCX.
    Miscellaneous:
    • Escapes X-inactivation.
    SequenceCaution:
    • Sequence=CAD13527.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAD18900.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for USP9X Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP9X Gene

Selected DME Specific Peptides for USP9X Gene

Q93008:
  • GLKNAGATCYMNSV
  • FLLKDGQLWLCA
  • INKDFFE
  • AQAGKHEAIVKNVHDLLAKLAWDF
  • GEPVNLREQ
  • FRLKMILRLLQ
  • HYQKRAYQ
  • PRWVVPVLP
  • IQQLYMIP
  • CAIKFNDYFEFPR
  • LLELIRRLAEDDK
  • YRRQKRWWNAY
  • PFGQCYE
  • KCFERFFKAVN
  • DSLHQPQYVEKLEKI
  • KILDYSCSQ

Post-translational modifications for USP9X Gene

  • Ubiquitination at Lys 329, Lys 1045, Lys 1370, Lys 1627, Lys 1632, Lys 1712, Lys 1798, Lys 1862, and Lys 2301
  • Modification sites at PhosphoSitePlus

Other Protein References for USP9X Gene

Domains & Families for USP9X Gene

Graphical View of Domain Structure for InterPro Entry

Q93008

UniProtKB/Swiss-Prot:

USP9X_HUMAN :
  • Contains 1 USP domain.
  • Belongs to the peptidase C19 family.
Domain:
  • Contains 1 USP domain.
Family:
  • Belongs to the peptidase C19 family.
genes like me logo Genes that share domains with USP9X: view

Function for USP9X Gene

Molecular function for USP9X Gene

GENATLAS Biochemistry:
ubiquitin specific protease 9,X chromosome,Drosophila developmental gene fat facets related on the X,Dres14 mouse homolog,ubiquitously expressed at low levels in embryo,escaping inactivation,widely expressed,deubiquitin enzyme family
UniProtKB/Swiss-Prot CatalyticActivity:
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
UniProtKB/Swiss-Prot Function:
Deubiquitinase involved both in the processing of ubiquitin precursors and of ubiquitinated proteins. May therefore play an important regulatory role at the level of protein turnover by preventing degradation of proteins through the removal of conjugated ubiquitin. Essential component of TGF-beta/BMP signaling cascade. Regulates chromosome alignment and segregation in mitosis by regulating the localization of BIRC5/survivin to mitotic centromeres. Specifically hydrolyzes both Lys-29- and Lys-33-linked polyubiquitins chains. Specifically deubiquitinates monoubiquitinated SMAD4, opposing the activity of E3 ubiquitin-protein ligase TRIM33. Involved in axonal growth and neuronal cell migration.

Enzyme Numbers (IUBMB) for USP9X Gene

Gene Ontology (GO) - Molecular Function for USP9X Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004197 cysteine-type endopeptidase activity TAS 9827704
GO:0004843 thiol-dependent ubiquitin-specific protease activity TAS --
GO:0005515 protein binding IPI 16322459
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity TAS --
genes like me logo Genes that share ontologies with USP9X: view
genes like me logo Genes that share phenotypes with USP9X: view

Human Phenotype Ontology for USP9X Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for USP9X Gene

Localization for USP9X Gene

Subcellular locations from UniProtKB/Swiss-Prot for USP9X Gene

Cytoplasm. Cell projection, growth cone.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for USP9X gene
Compartment Confidence
cytosol 5
plasma membrane 3
cytoskeleton 1
endosome 1

Gene Ontology (GO) - Cellular Components for USP9X Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IDA 19135894
GO:0005829 cytosol TAS --
GO:0016020 membrane IDA 19946888
GO:0030426 growth cone IEA,IDA 24607389
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with USP9X: view

Pathways & Interactions for USP9X Gene

genes like me logo Genes that share pathways with USP9X: view

Pathways by source for USP9X Gene

1 R&D Systems pathway for USP9X Gene
1 Qiagen pathway for USP9X Gene

SIGNOR curated interactions for USP9X Gene

Activates:

Gene Ontology (GO) - Biological Process for USP9X Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter TAS --
GO:0001764 neuron migration IMP 24607389
GO:0006508 proteolysis IEA --
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
GO:0007049 cell cycle IEA --
genes like me logo Genes that share ontologies with USP9X: view

Drugs & Compounds for USP9X Gene

(2) Drugs for USP9X Gene - From: ApexBio and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
WP1130 Pharma Deubiquitinase (DUB) inhibitor, Cell permeable 0

(1) ApexBio Compounds for USP9X Gene

Compound Action Cas Number
WP1130 Deubiquitinase (DUB) inhibitor, Cell permeable 856243-80-6
genes like me logo Genes that share compounds with USP9X: view

Transcripts for USP9X Gene

Unigene Clusters for USP9X Gene

Ubiquitin specific peptidase 9, X-linked:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for USP9X Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^
SP1:
SP2:
SP3:
SP4:
SP5:
SP6: -
SP7:
SP8:
SP9: -
SP10:
SP11: -
SP12:
SP13:

ExUns: 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24 ^ 25a · 25b ^ 26a · 26b · 26c ^ 27a · 27b ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33a · 33b ^ 34 ^ 35 ^ 36 ^ 37a · 37b ^ 38 ^
SP1: - -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10: -
SP11:
SP12:
SP13:

ExUns: 39a · 39b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for USP9X Gene

GeneLoc Exon Structure for
USP9X
ECgene alternative splicing isoforms for
USP9X

Expression for USP9X Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for USP9X Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for USP9X Gene

This gene is overexpressed in Bone (16.1) and Peripheral blood mononuclear cells (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for USP9X Gene



Protein tissue co-expression partners for USP9X Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of USP9X Gene:

USP9X

SOURCE GeneReport for Unigene cluster for USP9X Gene:

Hs.77578

mRNA Expression by UniProt/SwissProt for USP9X Gene:

Q93008-USP9X_HUMAN
Tissue specificity: Widely expressed in embryonic and adult tissues.
genes like me logo Genes that share expression patterns with USP9X: view

Primer Products

No data available for mRNA differential expression in normal tissues for USP9X Gene

Orthologs for USP9X Gene

This gene was present in the common ancestor of animals.

Orthologs for USP9X Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia USP9Y 35
  • 99 (a)
OneToOne
USP9X 34
  • 94.4 (n)
dog
(Canis familiaris)
Mammalia -- 35
  • 99 (a)
OneToMany
-- 35
  • 99 (a)
OneToMany
chimpanzee
(Pan troglodytes)
Mammalia USP9X 34
  • 98.96 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 96 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 95 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Usp9x 34
  • 92.9 (n)
mouse
(Mus musculus)
Mammalia Usp9x 34 16 35
  • 92.85 (n)
chicken
(Gallus gallus)
Aves -- 35
  • 95 (a)
OneToMany
USP9X 34
  • 85.94 (n)
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 95 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.19925 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.4490 34
zebrafish
(Danio rerio)
Actinopterygii usp9 34 35
  • 76.27 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10083 34
fruit fly
(Drosophila melanogaster)
Insecta faf 36 34 35
  • 53.8 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010088 34
  • 41.3 (n)
worm
(Caenorhabditis elegans)
Secernentea F37B12.4 36
  • 30 (a)
T24B8.7 35
  • 15 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5270 35
  • 56 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13972 34
Species where no ortholog for USP9X was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for USP9X Gene

ENSEMBL:
Gene Tree for USP9X (if available)
TreeFam:
Gene Tree for USP9X (if available)

Paralogs for USP9X Gene

Paralogs for USP9X Gene

(2) SIMAP similar genes for USP9X Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with USP9X: view

Variants for USP9X Gene

Sequence variations from dbSNP and Humsavar for USP9X Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs587777317 Mental retardation, X-linked 99 (MRX99) [MIM:300919], Pathogenic 41,218,440(+) CGTCC(A/T)TTTTA reference, missense
rs587777318 Pathogenic 41,230,595(+) TCAAC(-/A)GGTAA reference, frameshift-variant
rs869025588 Pathogenic 41,168,136(+) TGGTT(C/T)GAGTA reference, stop-gained
rs869025589 Pathogenic 41,171,836(+) ATTCT(A/G)GATAA splice-acceptor-variant
rs869025590 Pathogenic 41,170,002(+) ATTCC(-/A)GCGGT reference, frameshift-variant

Structural Variations from Database of Genomic Variants (DGV) for USP9X Gene

Variant ID Type Subtype PubMed ID
nsv6874 CNV insertion 18451855
esv3558815 CNV deletion 23714750
esv33720 CNV loss 17666407
esv2740112 CNV deletion 23290073
esv2740111 CNV deletion 23290073
esv2740110 CNV deletion 23290073
esv2675527 CNV deletion 23128226
dgv512n21 CNV gain 19592680

Variation tolerance for USP9X Gene

Residual Variation Intolerance Score: 0.296% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.08; 21.99% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for USP9X Gene

Human Gene Mutation Database (HGMD)
USP9X
SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP9X

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP9X Gene

Disorders for USP9X Gene

MalaCards: The human disease database

(4) MalaCards diseases for USP9X Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search USP9X in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

USP9X_HUMAN
  • Mental retardation, X-linked 99 (MRX99) [MIM:300919]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Intellectual deficiency is the only primary symptom of non-syndromic X-linked mental retardation, while syndromic mental retardation presents with associated physical, neurological and/or psychiatric manifestations. {ECO:0000269 PubMed:24607389}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for USP9X

Genetic Association Database (GAD)
USP9X
Human Genome Epidemiology (HuGE) Navigator
USP9X
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
USP9X
genes like me logo Genes that share disorders with USP9X: view

No data available for Genatlas for USP9X Gene

Publications for USP9X Gene

  1. The Drosophila developmental gene fat facets has a human homologue in Xp11.4 which escapes X-inactivation and has related sequences on Yq11.2. (PMID: 8922996) Jones M.H. … Affara N.A. (Hum. Mol. Genet. 1996) 2 3 4 64
  2. Mutations in USP9X are associated with X-linked intellectual disability and disrupt neuronal cell migration and growth. (PMID: 24607389) Homan C.C. … Jolly L.A. (Am. J. Hum. Genet. 2014) 3 4 64
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 64
  4. FAM/USP9x, a deubiquitinating enzyme essential for TGFbeta signaling, controls Smad4 monoubiquitination. (PMID: 19135894) Dupont S. … Piccolo S. (Cell 2009) 3 4 64
  5. Genome-wide association study in premature ovarian failure patients suggests ADAMTS19 as a possible candidate gene. (PMID: 19508998) Knauff E.A. … Fauser B.C. (Hum. Reprod. 2009) 3 46 64

Products for USP9X Gene

Sources for USP9X Gene

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