Affinage

RNF10

E3 ubiquitin-protein ligase RNF10 · UniProt Q8N5U6

Length
811 aa
Mass
89.9 kDa
Annotated
2026-06-10
38 papers in source corpus 18 papers cited in narrative 18 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RNF10 is a RING-domain E3 ubiquitin ligase that serves as the central sensor and effector of ribosome surveillance at the small (40S) subunit (PMID:34469731, PMID:34348161). It site-specifically monoubiquitinates the 40S ribosomal proteins uS3/RPS3 and uS5/RPS2 on ribosomes compromised during translation, acting both downstream of ZNF598-dependent sensing of collided ribosomes and independently upon impairment of translation initiation or elongation; this modification is reversed by the deubiquitylase USP10 (PMID:34469731, PMID:34348161). Prolonged ubiquitylation drives selective degradation of the 40S subunit and its 18S rRNA via a quality-control pathway termed initiation RQC (iRQC), with RIOK3 recognizing ubiquitylated 40S subunits through a ubiquitin-interacting motif and executing progressive 3'-to-5' 18S rRNA decay (PMID:34469731, PMID:39947183). This GCN2–RNF10–RIOK3 axis is triggered by physiological cues including amino-acid starvation, disrupted 60S:40S stoichiometry, and nonfunctional 18S rRNA, and RNF10 abundance is itself coupled to 40S levels through proteasomal turnover and feedforward induction (PMID:39947182, PMID:39609413, PMID:40022732). Independently of its ligase activity, RNF10 acts as a transcriptional regulator: in hippocampal neurons it is a synaptonuclear messenger that associates with GluN2A-containing NMDA receptors, detaches following PKC-dependent Ser31 phosphorylation, and translocates importin-dependently to the nucleus to support LTP maintenance and dendritic spine architecture (PMID:26977767, PMID:31069631). In other contexts it controls gene expression programs—activating the MAG gene in Schwann cells during myelination, driving p21-dependent neuronal differentiation and cell-cycle exit, and repressing Rbpjk during vascular calcification—and negatively regulates NF-κB/IRF3 innate immune signaling in macrophages (PMID:18941509, PMID:23526782, PMID:41988714, PMID:33249776).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 2005 Medium

    Before any catalytic role was assigned, RNF10 was placed in a transcriptional context by identifying a direct partner, establishing it as more than an orphan RING protein.

    Evidence Yeast two-hybrid, reciprocal pull-down/co-IP, deletion mapping and p21WAF1 reporter showing RNF10 binds MEOX2 and enhances p21 promoter activation

    PMID:16335786

    Open questions at the time
    • Did not establish whether the interaction depends on RNF10 catalytic activity
    • No in vivo relevance demonstrated
  2. 2008 Medium

    Extended the transcriptional role by showing RNF10 directly drives a tissue-specific gene program, demonstrating sequence-specific promoter engagement.

    Evidence Yeast one-hybrid, luciferase reporter, siRNA knockdown, and Schwann cell–DRG myelination co-culture showing RNF10 activates the MAG gene via an upstream cis-element

    PMID:18941509

    Open questions at the time
    • Mechanism of DNA-element recognition unresolved
    • Whether RNF10 binds DNA directly or via cofactors unclear
  3. 2013 Medium

    Connected RNF10 to cell-fate decisions by placing it upstream of a cyclin-dependent kinase inhibitor, defining a differentiation pathway.

    Evidence siRNA knockdown, BrdU/flow cytometry, and p21 rescue in retinoic acid-treated P19 cells showing RNF10 drives differentiation and G1 arrest via p21

    PMID:23526782

    Open questions at the time
    • Mechanism of p21 upregulation (direct vs indirect) not defined
    • Restricted to one carcinoma model
  4. 2016 High

    Revealed an unanticipated synaptonuclear signaling role, showing RNF10 carries activity-dependent information from synapse to nucleus.

    Evidence Reciprocal co-IP, live-cell imaging with importin inhibition, LTP electrophysiology, and spine morphology in hippocampal neurons

    PMID:26977767

    Open questions at the time
    • Nuclear transcriptional targets in neurons not identified
    • Whether ligase activity is needed for synaptonuclear function unresolved
  5. 2019 Medium

    Defined the molecular switch governing RNF10 nuclear trafficking, identifying the post-translational trigger for receptor detachment.

    Evidence Phospho-specific antibodies, Ser31 phosphomimetic/phospho-dead mutants, spine density and CREB reporter assays

    PMID:31069631

    Open questions at the time
    • Which PKC isoform phosphorylates Ser31 not specified
    • Nuclear effectors downstream of CREB not mapped
  6. 2021 High

    Established the defining catalytic function: RNF10 is the E3 ligase that site-specifically monoubiquitinates 40S proteins to mark stalled small subunits for degradation, opposed by USP10.

    Evidence Two companion studies using genetic screens, RNF10/USP10 knockout/knockdown, ribosome fractionation, PAR-CLIP, and ZNF598 epistasis defining iRQC

    PMID:34348161 PMID:34469731

    Open questions at the time
    • Downstream degradation machinery not yet identified in these studies
    • Determinants of uS3/uS5 site selectivity unresolved
  7. 2021 Medium

    Showed RNF10 acts as a brake on innate immunity, extending its functional repertoire to inflammation and aging.

    Evidence siRNA knockdown in primary macrophages with NF-κB/IRF3 signaling, cytokine, and Listeria clearance readouts

    PMID:33249776

    Open questions at the time
    • Molecular substrate/mechanism of NF-κB/IRF3 suppression not defined
    • Link to its ribosomal or transcriptional activities unclear
  8. 2025 High

    Resolved the executioner of RNF10-tagged ribosomes, defining the GCN2–RNF10–RIOK3 axis and the structural basis of 18S rRNA decay.

    Evidence Genome-wide CRISPR interaction screens, ribosome profiling, and cryo-EM of degradation intermediates showing RIOK3 recognizes ubiquitylated 40S and degrades 18S rRNA from the 3' end

    PMID:39947182 PMID:39947183

    Open questions at the time
    • Nuclease responsible for 18S cleavage not fully defined
    • How GCN2 activation is coupled to RNF10 recruitment incompletely resolved
  9. 2025 High

    Clarified the physiological triggers and homeostatic regulation of iRQC, including RNF10's coupling to 40S abundance and a feedforward loop.

    Evidence Polysome/half-mer analysis, eIF4A1 depletion, RPS/RPL knockdown, and ubiquitylation assays across multiple studies

    PMID:39609413 PMID:40022732

    Open questions at the time
    • Sensing mechanism linking 60S:40S imbalance to RNF10 activation not fully defined
    • Physiological consequences of half-mer resolution in vivo unclear
  10. 2025 Medium

    Demonstrated regulatory crosstalk among RQC ligases, showing RNF10 levels are controlled by a second E3 ligase.

    Evidence Knockout mouse/human cell lines and LTN1 RING-domain mutant analysis showing LTN1 suppresses RNF10 expression

    PMID:41451945

    Open questions at the time
    • Whether LTN1 directly ubiquitinates RNF10 not established
    • Mechanism of RING-dependent suppression undefined
  11. 2025 Medium

    Extended the ligase-independent transcriptional role to vascular disease, showing RNF10 represses an osteogenic transcription factor.

    Evidence RNA-seq, ChIP-seq/qPCR, luciferase reporters, RNF10 knock-in rats, and siRNA in VSMCs showing proteasome-independent repression of Rbpjk

    PMID:41988714

    Open questions at the time
    • How nuclear RNF10 represses Rbpjk transcription mechanistically unresolved
    • Relationship to synaptonuclear nuclear function unexplored
  12. 2024 Medium

    Tested conservation and pathway architecture of 40S quality control in an invertebrate model, placing RNF10 in a ligase–DUB circuit.

    Evidence Co-IP, ubiquitinated-protein enrichment, and genetic epistasis in Drosophila showing CNOT4/RNF10 act upstream of OTUD6 on the free 40S

    PMID:39127721

    Open questions at the time
    • Whether mammalian RNF10 acts in the same OTUD6 circuit unknown
    • RPS7 as a mammalian RNF10 substrate not confirmed

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unresolved how RNF10's distinct activities—40S ubiquitylation in the cytoplasm versus ligase-independent transcriptional regulation in the nucleus—are coordinated within a single cell or whether they share regulatory inputs.
  • No unified model linking cytoplasmic ligase and nuclear transcriptional roles
  • Tissue-specific determinants of which RNF10 function dominates unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016740 transferase activity 3 GO:0140096 catalytic activity, acting on a protein 3 GO:0140110 transcription regulator activity 3 GO:0016874 ligase activity 2 GO:0003723 RNA binding 1
Localization
GO:0005634 nucleus 3 GO:0005840 ribosome 3 GO:0005829 cytosol 2
Pathway
R-HSA-8953854 Metabolism of RNA 4 R-HSA-74160 Gene expression (Transcription) 3 R-HSA-112316 Neuronal System 2 R-HSA-392499 Metabolism of proteins 2 R-HSA-168256 Immune System 1

Evidence

Reading pass · 18 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2021 RNF10 is the E3 ubiquitin ligase responsible for site-specific monoubiquitylation of 40S ribosomal proteins uS3 (RPS3) and uS5 (RPS2) during ribosome-associated quality control (RQC); USP10 is the opposing deubiquitylase. Prolonged uS3/uS5 ubiquitylation leads to selective 40S (but not 60S) ribosomal protein degradation independent of canonical autophagy. This pathway, termed initiation RQC (iRQC), is triggered by blockade of scanning or elongating ribosomes at the start codon. Genetic screen with ubiquitylation assays, ribosome fractionation, RNF10/USP10 knockout/knockdown, autophagy inhibitors Cell reports High 34469731
2021 RNF10 is the RING-domain E3 ligase that specifically monoubiquitinates RPS2/uS5 and RPS3/uS3 on ribosomes compromised in translation. RNF10-mediated ubiquitination occurs both downstream of ZNF598-dependent sensing of collided ribosomes and independently upon ZNF598-independent impairment of translation initiation and elongation. PAR-CLIP showed RNF10 crosslinks to mRNAs, tRNAs, and 18S rRNA, indicating physical recruitment to stalled ribosomes. Overexpression of RNF10 increases 40S subunit degradation similarly to USP10 knockout. Overexpression/knockout, ribosome sedimentation, PAR-CLIP, ubiquitylation assays, ZNF598 genetic epistasis Cell reports High 34348161
2025 Mammalian 18S nonfunctional rRNA decay (18S NRD) is initiated through the integrated stress response via GCN2. GCN2 activation limits translation initiation, attenuating collisions between scanning 43S preinitiation complexes and stalled nonfunctional ribosomes. RNF10-mediated ubiquitination of 40S ribosomal proteins promotes 18S NRD and 40S ribosomal protein turnover. RIOK3 subsequently binds ubiquitylated 40S subunits to facilitate 18S rRNA decay, establishing a GCN2–RNF10–RIOK3 axis for ribosome surveillance at translation initiation. Genome-wide CRISPR genetic interaction screens, ribosome profiling, biochemical fractionation, ubiquitylation assays Molecular cell High 39947182
2025 Starvation induces selective depletion of 40S ribosomes through RNF10-mediated ubiquitylation. RIOK3 specifically recognizes ubiquitylated 40S ribosomes via a unique ubiquitin-interacting motif (visualized by cryo-EM). RIOK3 then induces progressive 18S rRNA degradation beginning at the 3' end, as revealed by cryo-EM structures of degradation intermediates. cryo-EM structure determination, ubiquitylation assays, ribosome fractionation, RIOK3 mutant analysis Molecular cell High 39947183
2025 RNF10-mediated RPS3/uS3 monoubiquitination antagonizes ribosomal half-mer formation by promoting dissociation of 40S subunits stalled during translation elongation and aberrant translation initiation. RNF10 protein levels are tightly coupled to 40S subunit abundance: knockdown of RPS proteins leads to proteasomal degradation of RNF10, whereas knockdown of RPL proteins increases 40S stalling, elevates RNF10 levels, and enhances RPS3 monoubiquitination. Polysome/half-mer analysis, RNF10 knockdown/overexpression, ribosome fractionation, immunoblotting Nature communications High 39609413
2025 Disruption of 60S biogenesis (altered 60S:40S stoichiometry) triggers iRQC activation and RNF10-dependent 40S decay. Depletion of the scanning helicase eIF4A1 impairs 40S ubiquitylation and degradation, indicating that mRNA engagement is required for iRQC. Amino acid starvation also stimulates iRQC-dependent 40S decay. RIOK3 is required for iRQC and interacts with ubiquitylated 40S subunits. RNF10 and RIOK3 protein levels increase upon iRQC activation, establishing a feedforward mechanism. Genetic knockdown/knockout, ribosome fractionation, ubiquitylation assays, eIF4A1 depletion Cell reports High 40022732
2025 The E3 ubiquitin ligase LTN1 suppresses RNF10 expression in a manner dependent on the RING domain of LTN1, revealing regulatory crosstalk between ribosome quality control E3 ligases. Knockout mouse and human cell lines, immunoblotting, LTN1 RING domain mutant analysis FEBS letters Medium 41451945
2025 RNF10 negatively regulates Rbpjk expression during vascular calcification in a transcriptional (non-ubiquitin ligase) capacity. Nuclear RNF10 expression increases in calcified VSMCs; pharmacological inhibition of the ubiquitin-proteasome system did not impair RNF10's anticalcific activity. Rbpjk overexpression partially reversed the protective effects of RNF10, and Rbpjk knockdown reduced osteogenic marker expression. RNA-seq, ChIP-seq, ChIP-qPCR, luciferase reporter assays, RNF10 knock-in rats, siRNA knockdown, gain/loss-of-function in vivo and in vitro Arteriosclerosis, thrombosis, and vascular biology Medium 41988714
2016 RNF10 functions as a synaptonuclear protein messenger in hippocampal neurons. It associates with the GluN2A subunit of NMDA receptors at excitatory synapses and translocates from dendritic spines to the nucleus in an importin-dependent manner upon activation of synaptic GluN2A-containing NMDARs and LTP induction. RNF10 silencing prevents LTP maintenance and LTP-dependent structural modifications of dendritic spines. Co-immunoprecipitation, live-cell imaging, importin inhibition, siRNA knockdown, LTP electrophysiology, spine morphology analysis eLife High 26977767
2019 PKC-dependent phosphorylation of RNF10 at Ser31 is required for RNF10 detachment from the NMDA receptor GluN2A subunit and subsequent nuclear translocation. Preventing Ser31 phosphorylation decreases spine density, neuronal branching, and CREB signaling; mimicking stable Ser31 phosphorylation produces opposite effects. Phospho-specific antibodies, phosphomimetic and phospho-dead mutants, spine density quantification, CREB reporter assays, imaging Molecular neurobiology Medium 31069631
2008 RNF10 acts as a transcriptional activator of the myelin-associated glycoprotein (MAG) gene in Schwann cells by binding a cis-acting element 160 bp upstream of the MAG transcription start site. RNF10 overexpression enhanced MAG promoter activity; RNF10 siRNA knockdown reduced MAG mRNA and protein expression and inhibited myelin formation in Schwann cell–DRG neuron co-cultures. Yeast one-hybrid screen, luciferase reporter assay, siRNA knockdown, retroviral expression, Schwann cell–DRG co-culture myelination assay PloS one Medium 18941509
2005 RNF10 physically binds to the transcription factor MEOX2. In vitro pull-down and co-immunoprecipitation in mammalian cells confirmed the interaction. The minimal MEOX2 binding region maps to amino acids 101–185 (between the HQ-rich domain and homeodomain), while the N-terminal RING finger domain of RNF10 is not required for MEOX2 binding. RNF10 co-expression enhanced MEOX2 activation of the p21WAF1 promoter. Yeast two-hybrid, in vitro pull-down, co-immunoprecipitation, deletion mapping, p21WAF1 luciferase reporter assay Molecular and cellular biochemistry Medium 16335786
2013 RNF10 is required for retinoic acid-induced neuronal differentiation and cell cycle exit in P19 embryonic carcinoma cells. Rnf10 knockdown impairs neuronal marker expression and prevents G1 arrest after RA treatment. RNF10 acts via upregulation of the cyclin-dependent kinase inhibitor p21 (but not p27 or p57); ectopic p21 expression partially rescues the differentiation defect caused by Rnf10 depletion. siRNA knockdown, BrdU incorporation, flow cytometry, immunoblotting, p21/p27/p57 protein analysis, p21 rescue experiment Journal of cellular biochemistry Medium 23526782
2013 RNF10 is one of eight E3 ubiquitin ligases identified as substrates for S-nitrosylation, suggesting that nitric oxide modulates RNF10 activity via S-nitrosylation of cysteine residues. High-density protein microarray (16,368 proteins), affinity capture of S-nitrosylated proteins, mass spectrometry identification of modified cysteine residues Molecular & cellular proteomics : MCP Low 24105792
2021 RNF10 expression is reduced in aged mouse macrophages. Knockdown of RNF10 in macrophages enhances both NF-κB and IRF3 signaling pathways, increasing proinflammatory cytokines and type I interferons and promoting Listeria monocytogenes clearance, indicating that RNF10 negatively regulates innate immune signaling in macrophages. siRNA knockdown in primary macrophages, NF-κB/IRF3 reporter/signaling assays, cytokine measurement, bacterial clearance assay FEBS open bio Medium 33249776
2024 In Drosophila, the E3 ligases CNOT4 and RNF10 function upstream of the deubiquitinase OTUD6 to regulate RPS7 ubiquitination and alkylation stress response on the free 40S ribosome. OTUD6 acts on the free 40S (not on 43S/48S or translating ribosomes), and its loss results in RPS7 hyperubiquitination. Co-immunoprecipitation, enrichment of monoubiquitinated proteins from catalytically inactive OTUD6 flies, genetic epistasis in Drosophila Nature communications Medium 39127721
2007 RNF10 interacts with the tumor suppressor RASSF1C in a nuclear protein interactome; the interaction was confirmed in vitro by pull-down of bacterially expressed proteins. Yeast two-hybrid screen, in vitro pull-down with bacterially expressed proteins Biochemical and biophysical research communications Low 17335777
2024 Mammalian 18S NRD acts through GCN2 and RNF10-mediated ribosomal protein ubiquitination. CRISPR genetic interaction screens identified RNF10 as essential for nonfunctional 18S rRNA and 40S ribosomal protein turnover, with ribosome profiling showing translational arrest at start sites as the initiating event. (Preprint version of PMID:39947182.) Genome-wide CRISPR genetic interaction screens, selective ribosome profiling, biochemical fractionation bioRxivpreprint Medium 39211161

Source papers

Stage 0 corpus · 38 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2021 iRQC, a surveillance pathway for 40S ribosomal quality control during mRNA translation initiation. Cell reports 59 34469731
2020 Putative regulators for the continuum of erythroid differentiation revealed by single-cell transcriptome of human BM and UCB cells. Proceedings of the National Academy of Sciences of the United States of America 52 32457162
2013 Protein microarray characterization of the S-nitrosoproteome. Molecular & cellular proteomics : MCP 50 24105792
2021 The E3 ubiquitin ligase RNF10 modifies 40S ribosomal subunits of ribosomes compromised in translation. Cell reports 48 34348161
2016 Ring finger protein 10 is a novel synaptonuclear messenger encoding activation of NMDA receptors in hippocampus. eLife 39 26977767
2010 Genomics and proteomics approaches to the study of cancer-stroma interactions. BMC medical genomics 34 20441585
2018 Synapse-to-nucleus communication: from developmental disorders to Alzheimer's disease. Current opinion in neurobiology 33 29316492
2005 Characterization of Mesenchyme Homeobox 2 (MEOX2) transcription factor binding to RING finger protein 10. Molecular and cellular biochemistry 23 16335786
2023 A deep transcriptome meta-analysis reveals sex differences in multiple sclerosis. Neurobiology of disease 20 37023829
2008 A novel function of RING finger protein 10 in transcriptional regulation of the myelin-associated glycoprotein gene and myelin formation in Schwann cells. PloS one 20 18941509
2025 The integrated stress response regulates 18S nonfunctional rRNA decay in mammals. Molecular cell 19 39947182
2025 RIOK3 mediates the degradation of 40S ribosomes. Molecular cell 18 39947183
2013 RING finger protein 10 regulates retinoic acid-induced neuronal differentiation and the cell cycle exit of P19 embryonic carcinoma cells. Journal of cellular biochemistry 18 23526782
2019 The Synaptonuclear Messenger RNF10 Acts as an Architect of Neuronal Morphology. Molecular neurobiology 15 31069631
2007 Characterization of hampin/MSL1 as a node in the nuclear interactome. Biochemical and biophysical research communications 15 17335777
2025 RNF10 and RIOK3 facilitate 40S ribosomal subunit degradation upon 60S biogenesis disruption or amino acid starvation. Cell reports 13 40022732
2024 E3 ubiquitin ligase RNF10 promotes dissociation of stalled ribosomes and responds to ribosomal subunit imbalance. Nature communications 12 39609413
2018 RING finger protein 10 attenuates vascular restenosis by inhibiting vascular smooth muscle cell hyperproliferation in vivo and vitro. IUBMB life 10 30597731
2025 An in-silico pan-cancer bulk and single-cell profiling of transcription factors in protein autoubiquitination. Discover oncology 8 40591126
2019 RING finger protein 10 is a potential drug target for diabetic vascular complications. Molecular medicine reports 8 31173254
2011 Host cell targets of tegument protein VP22 of herpes simplex virus 1. Archives of virology 8 21424732
2023 An epitope encoded by uORF of RNF10 elicits a therapeutic anti-tumor immune response. Molecular therapy oncolytics 7 38020063
2018 RING finger protein 10 prevents neointimal hyperplasia by promoting apoptosis in vitro and in vivo. Life sciences 7 29723537
2024 OTUD6 deubiquitination of RPS7/eS7 on the free 40 S ribosome regulates global protein translation and stress. Nature communications 4 39127721
2021 Reduced RING finger protein 10 expression in macrophages is associated with aging-related inflammation. FEBS open bio 4 33249776
2024 The integrated stress response regulates 18S nonfunctional rRNA decay in mammals. bioRxiv : the preprint server for biology 3 39211161
2023 RING Finger Protein 10 Regulates AP-1/Meox2 to Mediate Pirarubicin-Induced Cardiomyocyte Apoptosis. Oxidative medicine and cellular longevity 3 36713029
2005 A new mutation in the timing of autogamy in Paramecium tetraurelia. Mechanisms of ageing and development 3 15888330
2025 Employing Expression-Matched Controls Enables High-Confidence Proximity-Based Interactome Classification. Molecular & cellular proteomics : MCP 2 40441440
2025 Genomic Exploration of Selection Signatures Linked to Reproductive Traits in Locally Adapted Indicine, Taurine and Crossbred Cattle of India. Reproduction in domestic animals = Zuchthygiene 2 40631534
2023 Ring finger protein 10 improves pirarubicin-induced cardiac inflammation by regulating the AP-1/Meox2 signaling pathway. Toxicology and applied pharmacology 2 36740146
2023 Screening the optimal housekeeping genes (HKGs) of placenta tissues by RNA-sequence and qRT-PCR throughout gestation in goat (Capra Hircus). Gene 2 37972698
2022 CircRNA RNF10 inhibits tumorigenicity by targeting miR-942-5p/GOLIM4 axis in breast cancer. Environmental and molecular mutagenesis 2 36054164
2026 E3 Ubiquitin Ligase RNF10 Negatively Regulates Rbpjk Expression During Vascular Calcification in Chronic Kidney Disease. Arteriosclerosis, thrombosis, and vascular biology 0 41988714
2025 Genomic scan of selective sweeps in an alpaca population subjected to directional selection for fibre quality traits. Animal : an international journal of animal bioscience 0 41161070
2025 Ring finger protein 10 is atherosclerosis protective and modulates macrophage polarization. Experimental animals 0 41339005
2025 Crosstalk between the ribosome quality control-associated E3 ubiquitin ligases LTN1 and RNF10. FEBS letters 0 41451945
2006 [Cloning to rule out 10 candidate genes located in chromosome 12q24 for Charcot-Marie-Tooth disease type 2L]. Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics 0 16604494

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