pre-miRNA Information | |
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pre-miRNA | hsa-mir-134 |
Genomic Coordinates | chr14: 101054687 - 101054759 |
Description | Homo sapiens miR-134 stem-loop |
Comment | miR-134 was first identified by cloning studies in mouse . |
RNA Secondary Structure | |
Associated Diseases |
Mature miRNA Information | ||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-134-3p | |||||||||||||||||||||||||||
Sequence | 46| CCUGUGGGCCACCUAGUCACCAA |68 | |||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||
Experiments | Illumina | |||||||||||||||||||||||||||
Editing Events in miRNAs |
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SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | PAICS | ||||||||||||||||||||
Synonyms | ADE2, ADE2H1, AIRC, PAIS | ||||||||||||||||||||
Description | phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthase | ||||||||||||||||||||
Transcript | NM_001079524 | ||||||||||||||||||||
Other Transcripts | NM_001079525 , NM_006452 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on PAICS | |||||||||||||||||||||
3'UTR of PAICS (miRNA target sites are highlighted) |
>PAICS|NM_001079524|3'UTR 1 GAAAGAATGCCATTGAATTTTTTAGGGGAAAAACTACAAATTTCTAATTTAGCTGAAGGAAAATCAAGCAAGATGAAAAG 81 GTAATTTTAAATTAGAGAACACAAATAAAATGTATTAGTGAATAAATGCTTCTCTAGATCCATATTAATAAACATGAGCA 161 TCTAACCCCTCCTTTCTTAGGCTAGACACCAAGATATTTCAGCCAGCCTTTATCATTCCTCTTACTTTATCCTTTTTCCT 241 TAAGTATTGGTGGTCACTACTATTGAGTTTCTTCCTTAACACTGATTAAATGATCTTAACTCCCTCAGCTAAAACTGGCA 321 TTACTGACTCCCAGCTATATTTCTCCAGACTTGCATTTTTTTTTTTTTTTTTGAGACAGGGTCTCACTGTCGCCCAGGCT 401 GGAGTGCAGTGGCGTGATCTCAGTTCACTGCTGCTTTCCCTCCTGGGCTCAAGCAGTTCTCCCACCTCAGCCTCTCGACT 481 AACAGGGACTATAATCTTGCAGCACCATGCCGAGCTAATTTTATTTTTTGTAGAGATGAGCTCTCACTATGTCACCCAGG 561 TTCGTCTCAAACTCCTGAACCCTAGTAATTCTCCTATCTCAGCCTCCCAAAGTGCTAGGGTTACAGACATGAGCCACTGT 641 GCCTGTCTAGACTTGTACTTTCAACTGTCCATTTCTCCCTGTCTGTCCCATGGGCACTCATGAAAAAACAGAATGCTCCC 721 AACTTTATTCATCTTCCAAGCCTGTAGCTCTTGGTATACTCACTGTTGCAAGTCAGAAGCTTGATTTCATCATTGATGTT 801 TTTCTCACGTTTCACATCTCACTCATCACCAAGTCATGTTGGTGTTAATTTCTGATTAACCCTTGAATTTACCGTCTTCT 881 CATCCTCTGTACAAAAGCCTCAAGTGAGGGTCAAATTCAACATTATCCTGATCTAGACAGCCCCCATTCTCAATCCACCC 961 TTTTCCAAGTTGATTGCCCAAGGACTTCTAACAATAAACTCTCTTTTGCACCACAGACTTCTTTGAAAATATACATGCTG 1041 TTGACCCTCTCTGTAGAAAACCGCACACATAAAACTTACCAACAGATTTCATTGGTTCTTGGGTTCTCCCGAAGCCTATC 1121 CATGGTTTATAGATTAAGAATTGATGAGGTAGCTGGGCACAGTGGCTCACACCTACGATCACAGCACTTCGGGAGGCTGA 1201 AGCAAGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCTGTCTCTACTAAAAATACAA 1281 AAAGTAGCCAGCCGTGATGACAGGCACCTGTAATCCCAGCTACTCGGGAGGCTGAGGCATGAGAATTGCTTGAACCCGGG 1361 AGGCGGAGGTTGCAGTGAGCCTAGATCATGCCACTGCACTCCAACCTGGGCAGCAGAGCAAGACTCTGTCTCAAAAGGGG 1441 AAAAAAAAAATTGCTGATGTGACCCATGAAGGGAACTCATTTTCCTCGTAATTTTGGACTGCCACACATTGGTACCTTTA 1521 GTTCTCTGAAGGCCCACGTTTTTATCATTAAGACCTATTTGTTAGCTAGTAGAGCTTTATGTTCGCTGTCCATGAAACCT 1601 TCTGTAACCACAGTGACTACAAGTAGTTCTTTCTCTATTGAATTATTAGGTCCAGAATAGAAGATGTCATTGTACACTTT 1681 ATTTCCCTCACACTGTGTTATGCTCTGATGTGCTATGCTTAGCTATCTGTCAGAGATTAGTAAATTATAAAACTCATGTG 1761 TACTACTTAAGTTTATATCTTATGCTAGTTTATAAGAACAATTAAAAGGACTTAGAAGATTAACTTTGGTAAAAAAAAAA 1841 A Target sites
Provided by authors
Predicted by miRanda
DRVs
SNPs
DRVs & SNPs
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miRNA-target interactions (Predicted by miRanda) |
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DRVs in gene 3'UTRs | |||||||||||||||||||||
SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |||||||
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miRNA:Target | ---- | ||||||
Validation Method |
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Conditions | HEK293 | ||||||
Location of target site | 3'UTR | ||||||
Tools used in this research | TargetScan , miRTarCLIP , Piranha | ||||||
Original Description (Extracted from the article) |
...
PAR-CLIP data was present in GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection
... - Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Hafner M; Landthaler M; Burger L; Khorshid et al. - Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
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Experimental Support 2 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | HEK293 |
Disease | 10606.0 |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
...
"PAR-CLIP data was present in GSM714644. RNA binding protein: AGO2. Condition:completeT1
"PAR-CLIP data was present in GSM714645. RNA binding protein: AGO2. Condition:completeT1
... - Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods. |
Article |
- Kishore S; Jaskiewicz L; Burger L; Hausser et al. - Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
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Experimental Support 3 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | HCT116 |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
...
PAR-CLIP data was present in ERX177599. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_2_1
PAR-CLIP data was present in ERX177623. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_4_1
PAR-CLIP data was present in ERX177611. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_3_1
... - Krell J; Stebbing J; Carissimi C; Dabrowska et al., 2016, Genome research. |
Article |
- Krell J; Stebbing J; Carissimi C; Dabrowska et al. - Genome research, 2016
DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.
LinkOut: [PMID: 26701625]
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Experimental Support 4 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | Prostate Tissue |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
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PAR-CLIP data was present in SRX1760638. RNA binding protein: AGO2. Condition:AGO-CLIP-PC3-miR148
... - Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al., 2016, Neoplasia (New York, N.Y.). |
Article |
- Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al. - Neoplasia (New York, N.Y.), 2016
MicroRNA (miRNA) deregulation in prostate cancer (PCa) contributes to PCa initiation and metastatic progression. To comprehensively define the cancer-associated changes in miRNA targeting and function in commonly studied models of PCa, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the Argonaute protein in a panel of PCa cell lines modeling different stages of PCa progression. Using this comprehensive catalogue of miRNA targets, we analyzed miRNA targeting on known drivers of PCa and examined tissue-specific and stage-specific pathway targeting by miRNAs. We found that androgen receptor is the most frequently targeted PCa oncogene and that miR-148a targets the largest number of known PCa drivers. Globally, tissue-specific and stage-specific changes in miRNA targeting are driven by homeostatic response to active oncogenic pathways. Our findings indicate that, even in advanced PCa, the miRNA pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. These findings are important because they are the first to globally characterize miRNA changes in PCa and demonstrate how the miRNA target spectrum responds to staged tumorigenesis.
LinkOut: [PMID: 27292025]
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CLIP-seq Support 1 for dataset GSM545216 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / miR-124 transfection |
Location of target site | ENST00000264221.2 | 3UTR | ACUUCUAACAAUAAACUCUCUUUUGCACCACA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 20371350 / GSE21578 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM714644 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repA |
Location of target site | ENST00000264221.2 | 3UTR | ACUUCUAACAAUAAACUCUCUUUUGCACCACAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 21572407 / GSE28865 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset GSM714645 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repB |
Location of target site | ENST00000264221.2 | 3UTR | ACUUCUAACAAUAAACUCUCUUUUGCACCACAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 21572407 / GSE28865 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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64 hsa-miR-134-3p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT082376 | HNRNPUL1 | heterogeneous nuclear ribonucleoprotein U like 1 | 2 | 6 | ||||||||
MIRT091883 | ACVR2B | activin A receptor type 2B | 2 | 4 | ||||||||
MIRT094089 | PAICS | phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthase | 2 | 4 | ||||||||
MIRT316375 | PPP1R14C | protein phosphatase 1 regulatory inhibitor subunit 14C | 2 | 2 | ||||||||
MIRT368317 | E2F2 | E2F transcription factor 2 | 2 | 2 | ||||||||
MIRT446160 | RPL12 | ribosomal protein L12 | 2 | 2 | ||||||||
MIRT458223 | SHMT2 | serine hydroxymethyltransferase 2 | 2 | 2 | ||||||||
MIRT483575 | SYT2 | synaptotagmin 2 | 2 | 2 | ||||||||
MIRT486251 | FASTK | Fas activated serine/threonine kinase | 2 | 2 | ||||||||
MIRT487556 | TM6SF2 | transmembrane 6 superfamily member 2 | 2 | 4 | ||||||||
MIRT488952 | CYP2W1 | cytochrome P450 family 2 subfamily W member 1 | 2 | 2 | ||||||||
MIRT489232 | ASCL2 | achaete-scute family bHLH transcription factor 2 | 2 | 4 | ||||||||
MIRT491923 | WNK2 | WNK lysine deficient protein kinase 2 | 2 | 2 | ||||||||
MIRT504191 | FAM127B | retrotransposon Gag like 8A | 2 | 2 | ||||||||
MIRT517340 | ZNF529 | zinc finger protein 529 | 2 | 4 | ||||||||
MIRT528964 | FAM19A3 | family with sequence similarity 19 member A3, C-C motif chemokine like | 2 | 2 | ||||||||
MIRT530497 | FADS6 | fatty acid desaturase 6 | 2 | 2 | ||||||||
MIRT539575 | UPP2 | uridine phosphorylase 2 | 2 | 2 | ||||||||
MIRT549348 | ARC | activity regulated cytoskeleton associated protein | 2 | 2 | ||||||||
MIRT554316 | SHMT1 | serine hydroxymethyltransferase 1 | 2 | 2 | ||||||||
MIRT555311 | PPP2R5C | protein phosphatase 2 regulatory subunit B'gamma | 2 | 2 | ||||||||
MIRT558029 | EXT1 | exostosin glycosyltransferase 1 | 2 | 2 | ||||||||
MIRT564075 | KIAA1191 | KIAA1191 | 2 | 2 | ||||||||
MIRT569986 | TMEM184A | transmembrane protein 184A | 2 | 2 | ||||||||
MIRT570669 | INSIG1 | insulin induced gene 1 | 2 | 2 | ||||||||
MIRT571911 | LSM14A | LSM14A, mRNA processing body assembly factor | 2 | 4 | ||||||||
MIRT574042 | PEX26 | peroxisomal biogenesis factor 26 | 2 | 2 | ||||||||
MIRT574076 | RNF152 | ring finger protein 152 | 2 | 2 | ||||||||
MIRT575774 | Tnfrsf10b | tumor necrosis factor receptor superfamily, member 10b | 2 | 2 | ||||||||
MIRT576510 | Slc35e2 | solute carrier family 35, member E2 | 2 | 2 | ||||||||
MIRT609004 | PYGO1 | pygopus family PHD finger 1 | 2 | 2 | ||||||||
MIRT619992 | NPAP1 | nuclear pore associated protein 1 | 2 | 2 | ||||||||
MIRT630308 | PDP2 | pyruvate dehyrogenase phosphatase catalytic subunit 2 | 2 | 2 | ||||||||
MIRT636261 | RRAGC | Ras related GTP binding C | 2 | 2 | ||||||||
MIRT638834 | CRTAP | cartilage associated protein | 2 | 2 | ||||||||
MIRT639813 | TMED8 | transmembrane p24 trafficking protein family member 8 | 2 | 2 | ||||||||
MIRT641938 | SCOC | short coiled-coil protein | 2 | 2 | ||||||||
MIRT644770 | TXNRD3NB | thioredoxin reductase 3 neighbor | 2 | 2 | ||||||||
MIRT650082 | MTL5 | testis expressed metallothionein like protein | 2 | 2 | ||||||||
MIRT651539 | WNK1 | WNK lysine deficient protein kinase 1 | 2 | 2 | ||||||||
MIRT653695 | SLC25A33 | solute carrier family 25 member 33 | 2 | 2 | ||||||||
MIRT654579 | PXMP4 | peroxisomal membrane protein 4 | 2 | 2 | ||||||||
MIRT655804 | NOVA2 | NOVA alternative splicing regulator 2 | 2 | 2 | ||||||||
MIRT662741 | LRRC3C | leucine rich repeat containing 3C | 2 | 2 | ||||||||
MIRT667588 | LONRF2 | LON peptidase N-terminal domain and ring finger 2 | 2 | 2 | ||||||||
MIRT667730 | KIAA1456 | KIAA1456 | 2 | 2 | ||||||||
MIRT667909 | ING1 | inhibitor of growth family member 1 | 2 | 2 | ||||||||
MIRT675875 | ATP1B4 | ATPase Na+/K+ transporting family member beta 4 | 2 | 2 | ||||||||
MIRT684043 | FOLR1 | folate receptor 1 | 2 | 2 | ||||||||
MIRT686239 | ZMIZ1 | zinc finger MIZ-type containing 1 | 2 | 2 | ||||||||
MIRT710043 | POLL | DNA polymerase lambda | 2 | 2 | ||||||||
MIRT711988 | EXTL3 | exostosin like glycosyltransferase 3 | 2 | 2 | ||||||||
MIRT714061 | VHLL | VHL like | 2 | 2 | ||||||||
MIRT715879 | ACIN1 | apoptotic chromatin condensation inducer 1 | 2 | 2 | ||||||||
MIRT716779 | C1orf229 | chromosome 1 open reading frame 229 | 2 | 2 | ||||||||
MIRT717104 | PXDC1 | PX domain containing 1 | 2 | 2 | ||||||||
MIRT723567 | ZBTB34 | zinc finger and BTB domain containing 34 | 2 | 2 | ||||||||
MIRT725668 | ABI2 | abl interactor 2 | 2 | 2 | ||||||||
MIRT735690 | SYT11 | synaptotagmin 11 | 1 | 0 | ||||||||
MIRT736843 | CCND1 | cyclin D1 | 2 | 0 | ||||||||
MIRT736981 | MLH1 | mutL homolog 1 | 1 | 0 | ||||||||
MIRT737413 | FOXM1 | forkhead box M1 | 3 | 0 | ||||||||
MIRT756143 | GPR137 | G protein-coupled receptor 137 | 3 | 1 | ||||||||
MIRT756411 | SOX9 | SRY-box 9 | 3 | 1 |
miRNA-Drug Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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