pre-miRNA Information | |
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pre-miRNA | mmu-mir-494 |
Genomic Coordinates | chr12: 109715318 - 109715402 |
Synonyms | Mirn494, mmu-mir-494, Mir494 |
Description | Mus musculus miR-494 stem-loop |
Comment | The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies . |
RNA Secondary Structure |
Mature miRNA Information | |
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Mature miRNA | mmu-miR-494-3p |
Sequence | 50| UGAAACAUACACGGGAAACCUC |71 |
Evidence | Experimental |
Experiments | Cloned |
Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | Gmeb1 | ||||||||||||||||||||
Synonyms | 1110050A04Rik, AI256615, AI481278 | ||||||||||||||||||||
Description | glucocorticoid modulatory element binding protein 1 | ||||||||||||||||||||
Transcript | NM_001122992 | ||||||||||||||||||||
Other Transcripts | NM_020273 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on Gmeb1 | |||||||||||||||||||||
3'UTR of Gmeb1 (miRNA target sites are highlighted) |
>Gmeb1|NM_001122992|3'UTR 1 TTGGGGACAGGGCCAAGAGCTGTGTTTTGGTTTGGAATTTTAATTATGTTTATTTTTATCATTGTCCCGCTCATTTCCAC 81 ATAGAACTTTTTTTAAAAAAAAAACAAAAACAAACAAAAAAAAACCAAACTACAAAATCTCGTTGTAACTGCAAATGTTG 161 GGTTCCTCCTACTTCCTCATTGACAACTGGACAGAACAAGCTGCCTTTCCAGAAGTTAGAAACAGGGCACCCAGGGTCTG 241 AACCATCTTTCCCCAAGGAAGGTAATTGCTTTTAGGGGAAGTGTCAAAATATCCAGGAATCCTTTCCAGAATAGTCTGTC 321 TGTGTATACACGCATGGTCTCACTCTTGTAAAGACGCATTGACCAGACCCTGGAACACAGATCTGACTCCAGAAGATGAC 401 CAGCTCTGCTGTGGATACAGAAGCACGCTTGCCTCTGTGTCCTGGATATGATGGCCTCAGATGCTGGTGTGCAAAACTGA 481 AAGAACAGGAGGTTGGCTCTGCTTAGGGTGGAAAGTAGTGTGATCAGCAGCTCATAGGGGGAGCCCTTTGACAGGGAGGG 561 GCCGAGGAATGGTCTTCCAGAGGTGCATCTGATGCCCCTTGCGCTCTCTGAGGGTTGGGTACCATTTTCAATTTCAGAAG 641 AGGACAGAGATTATAGAAAGACACAAAGCAATCAAAAGATTGTCACAGCTGTGCTTTTGGGATAGCTCACCTTGCCCCCA 721 GCCTTGTCAAAGCCCTCACCCTCCTCGCCCAGGACTATCAGTCCATTCCTTTGCAGACTGTGATGTGGTATAAATTGTTC 801 TAATTCTTGGACTGTGGCTGTCATGGAGGTGGGGCTCCAAGGCCATCATTTTTCGTTTCTTGACTCCAGGAATGGCAGAG 881 TCCCTCGTGCAGACCAGCTGCTATTTTTGGTGGAGCCCTGCACGTAAGCATGCAAGTGTGTGTGTGTGTGTGTGTATGTG 961 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTACATGTTTCGGGTTTGGAACCAAAAGCAGTCATTTCCCTGGTGCTTCCTTT 1041 TCTTTTCCTTCCGTCTGCTGGACCCCATGCTCAGTAGCTTTTTGGCAGACAGCAGTGACAGGTGCCTGCCTGCCTTCATT 1121 CTCTTTGCCATTCTCCTCTTCTGATACCACAGATGTTTCTGTGAGATACCGAACTCATAAAATGGCTTAGGCTTGGCAGG 1201 GACAACTGGTAACACCTTTCCTGAGGTGTGGACTAGATGGCTCCTGAGTGAGCTGCACTTTCTGGGAAAGGGACATTGTA 1281 TTTGACATTGTAAGAAGTATGACAGGAGTGTCAGTAACGTCCAGGCGTGGGGCTTCTTCCTAAATGCTGTTTGTACATTC 1361 GGTACTACTAGGTCACTCTTTCTGCTGTGATCCCATGTCGTTGATTCTCTTCAGCGTTTGGGGGAGAGTAAGCAGTTTCT 1441 GGTTTCTTTAATTATATTGTTTACTATGTTAGGGAAAATATAGAGACTCTCGAGGTGACTTTATAGGTCAAAAAAGCATA 1521 CAGCTTAGGAGCTGGAGGATTTATTATTATTATTAAAAGTAAAATTTTGGCTTTTGTTTAAAAAAAAAAAATAGAGAAGG 1601 ATGCCTGTCTAAATCTGTCTTCCTGCCTGCAGGTTTTGAAAACCCTGTAAGCAACCAAAAGTTGCACCTTCCATCTCTTA 1681 GACGGCCATGTGTCACCAGGGAAGCAAGCCCTCAGGGATCACTCTGAAGACCCTGAAGAGTGCGGCTTCTGAACTCTATT 1761 CAGATTTGTTTCAGCTTTAAAACTGGACTTTTCTTTTCAGACTCTTTAGTTAGGCTGGGGACAGAACTGAATTGGTAAAG 1841 TGGTCACCTAGCGTTCATGAAACCCTGGGCTCAGTCTCCAGCCAGAAGTAAACTGGGCATGGGGCCACATATCTGATCCT 1921 AACACTTGGGAAATAGAGACGGGAGACTTAGAAATTCAAGGTCATACATACCAAGTTCAAGACCAACCTGGGATATATGA 2001 AATAGTGTCTCAAAAAATTTTTGTTTAGGACAAGCTTTTGGTGAAAGAAGGAATTTATTCCTGCCTTCCTTACACTTTGT 2081 TAATACATAGGAATTTTTATTACATTTATTTATCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGATGGTG 2161 AGCTTGCTACGGTATGTATGTGAAGATCAGAGAACAACCTGCAGGAGTCTGTTCTCGCCTTCCACCATGTGGGTCCTGGG 2241 AATTGAACTCAGGTTGCCAGGCTTGGTGGTAAGCACCCTCATCCATTGAGCCATCTTGCCTGCTCTAAAAGTTTCGGTCT 2321 TCAGACCAAAACTGTTACTTGAACCTAGAAAGCCACATCGCATCCCTGTTGTGTCCTTTAGGTCATTTCTCTTTTCCAGA 2401 GATGGGCAGACCAATTCAGGACACGGGAGGCACCCTAGAGAATAGAGGCAGGCTCCTTCAGGTCCTGCCTTTTTGCTCTT 2481 CACAGCTGTTGTGTCATTAAAGGTTGTGTGAGCAGCATGCTTCCAAAGTCAGATTTCCTTCTTGAGACAGAGCCTGTTTA 2561 CTTAAAACAGATTACATGAGCTTTGCTGTTTTCCTGGTCTTCCAATTGCTGTCATTGCTAGCTGCAGTGGTACTTGGAGA 2641 GATGAGATCTCTCACAGACCTGGTCTAGATTATTTTAGGTGGGGTGATACACATGCAAGCTTCTGATGTGTGAATAGGCA 2721 GTTGCAATGAAATTACTCCTCAGGCTGACTTGATGGTAGCTATCTTTTCTCTAGCCATTCATTAAATAAACATTTGTAAG 2801 TACTGTCTATGTATAAGTACTAAACGCCAACTGATTGCGTCACCTAAGCCCCAGTAAGTACCATGAAGATGCAGGTTTTG 2881 TGCTAGACACTGATCTTGCAGACAAGACAATTCCTGTTCTTAAGAAGTTCATACCCAGACATCTTTGCAGTTAACCACAC 2961 TTTTTGTTTGTTTGGTTTGTTTTTTGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCTCACTATGTAGCC 3041 AGGCTGACTGGAACTCACAGAGATCTGTTTGCCTCTGTCTTCCAAGTGCTGGGATTAAAGGTGTGCACCACCACTGCCAT 3121 AGTGAATAGTCAACCGTATTTTAATGTCATTGGTTTCTTTTGTGATCCTGTTTTATCTTAAATATTGGGAAGGACTCTGA 3201 GTCTTTAGTTCCTAGGTTTCAACAGGCAAAGTCACAGAGGTGAAGCCACCCCTGGTGAGATTTTACCTTAGGTTGAGGTG 3281 ACTGTAGCTATGGTCTTTTTTTTTTTTTTTAAAGATTTATTTATTTATTATATGTAAGTACACTGTAGCTGTCTTCAGAC 3361 ACTCCAGAAGAGGGAGTCAGATCTTGTTACAGATGGCTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCTGGACCTT 3441 CGGAAGAACAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCCAGCTATGGTCTTTTGGCCTGGAGTTAAGCAC 3521 AAAAGATCAAGCACTTACTCAGCTTGGGGTCTGAATGGCTTCCGCTAATCTGAGGCAGTTCTCTGCATACCCTAGTTGCC 3601 CTTGAACTTGGCTATGTAGAGTAGCCTGGCTTTGAGCTCATAAAGGTCCATCTGCCTCTGCCTCCTAAGCATTGGGATTA 3681 AAGCTATCACACTTGGCTCTTGCTACTCCTCAGTTTCTAGGCTTCCAAAGAGTGGTGCTGCATGCGTGCCTGGGGCCCCG 3761 GCCCCAGAGGGCAGGGGCAAGAAGAGAGAAAGCTTCAAGATCCTGTCTCACAAACCAGAAATTTAGGCTTCCACATCCCA 3841 AACCCAAAGTTACTCTACTTTTGTTTGTGTCGCTCCCCCCTCCCCCATGGACAATAGACATTCAAGATTCAAACCCACTT 3921 TGGTGTGTCGTTCCCTCACCTGCCATAGCAGGAGAGAGAACTAATATAGATGAATAGCAGGTGATTCTTTTAATGTTGCT 4001 GGTTTGTCCCATTTCATGAGAGACACTATAGATAAGTATATATGGGGAGTACTGATTTTATTTACAAAAAAAAAAAATGT 4081 ACATTTAGTGTGCTTGTGTGTGTGTGGCATGCCGGAGTACATGGTGTCTTTATCAATGAACAGCTTTCAGGATTCAGTTC 4161 TCGCCTTCCACTGTGTGGGTCCCAGGGGTCAAATTCAGTTTGCCAGGCTTGGCAAGCAAGCACCTCTACTCACTGAGCTA 4241 TCTTGCTGGCCCAATGAGATTTTTTCTTTTTCATGTATTTATTTTAGTTTATAATTGTTCTTGCAAGTATGTATGTGCAC 4321 CTCACCTCTCACGCATGCCTGGTATCTGACGTGGTTGGTCGGAGAACATTTCTGATCCCCTGGAACTGGTGTTAGAGATG 4401 GTGTCTGCTACCATGTGGGCGCTGGAAATCCAACCCAGGTTCTCTGAATGAATACATGCTCTCAACTGAGCTGTCTCTTC 4481 GGGTGATATTATAAATAACAAAACTGTTGTGAAATATGGAGTCATTGAGTCAGAACTGACCCATAATGGAGGACTATCTA 4561 GGAGATGGAAAAGAATCCTTCCCTCAACCCTCCCCAAAAAAGGTTGAATTCTGAAATTAAGCACAAAGTGGTGGTGGCAC 4641 ACATCTTTGATCCCAGCACGTAGGAGCCAGTTGGATCTCTGAGTTCAAGGCCAGACTTGTCTCGAGGACAGCCAAGGCTA 4721 CACAGAGAAATCACATCTTG 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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Experimental Support 1 for Functional miRNA-Target Interaction | |||||||
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miRNA:Target | ---- | ||||||
Validation Method |
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Conditions | Brain (Mouse neocortex) | ||||||
Location of target site | 3'UTR | ||||||
Tools used in this research | TargetScan , miRTarCLIP , Piranha | ||||||
Original Description (Extracted from the article) |
...
HITS-CLIP data was present in Chi_BrainB_130_50. RNA binding protein: AGO. Condition:Brain B 2A8 P13 130 KD
HITS-CLIP data was present in Chi_BrainC_130_50. RNA binding protein: AGO. Condition:Brain C 2A8 P13 130 KD
... - Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Chi SW; Zang JB; Mele A; Darnell RB - Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
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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 | Liver |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
...
HITS-CLIP data was present in ERR266281. RNA binding protein: AGO2. Condition:A_Liver partial hapatectomy 48h
HITS-CLIP data was present in ERR266286. RNA binding protein: AGO2. Condition:A_Liver partial hapatectomy 1h
HITS-CLIP data was present in ERR266287. RNA binding protein: AGO2. Condition:B_Liver partial hapatectomy 36h
HITS-CLIP data was present in ERR266292. RNA binding protein: AGO2. Condition:B_Liver partial hapatectomy 48h
HITS-CLIP data was present in ERR266293. RNA binding protein: AGO2. Condition:A_Liver partial hapatectomy 36h
HITS-CLIP data was present in ERR266295. RNA binding protein: AGO2. Condition:B_Liver partial hapatectomy 1h
HITS-CLIP data was present in ERR266298. RNA binding protein: AGO2. Condition:A_Untreated
HITS-CLIP data was present in ERR266300. RNA binding protein: AGO2. Condition:B_Untreated
... - Schug J; McKenna LB; Walton G; Hand N; et al., 2013, BMC genomics. |
Article |
- Schug J; McKenna LB; Walton G; Hand N; et al. - BMC genomics, 2013
BACKGROUND: Validation of physiologic miRNA targets has been met with significant challenges. We employed HITS-CLIP to identify which miRNAs participate in liver regeneration, and to identify their target mRNAs. RESULTS: miRNA recruitment to the RISC is highly dynamic, changing more than five-fold for several miRNAs. miRNA recruitment to the RISC did not correlate with changes in overall miRNA expression for these dynamically recruited miRNAs, emphasizing the necessity to determine miRNA recruitment to the RISC in order to fully assess the impact of miRNA regulation. We incorporated RNA-seq quantification of total mRNA to identify expression-weighted Ago footprints, and developed a microRNA regulatory element (MRE) prediction algorithm that represents a greater than 20-fold refinement over computational methods alone. These high confidence MREs were used to generate candidate 'competing endogenous RNA' (ceRNA) networks. CONCLUSION: HITS-CLIP analysis provide novel insights into global miRNA:mRNA relationships in the regenerating liver.
LinkOut: [PMID: 23597149]
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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 | C2C12 |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
...
HITS-CLIP data was present in GSM1385342. RNA binding protein: 聽AGO2. Condition:C2C12_GM_Ago2_CLIP-Seq_myoblast
HITS-CLIP data was present in GSM1385343. RNA binding protein: 聽AGO2. Condition:C2C12_DM_Ago2_CLIP-Seq_myotubes
... - Zhang X; Zuo X; Yang B; Li Z; Xue Y; Zhou et al., 2014, Cell. |
Article |
- Zhang X; Zuo X; Yang B; Li Z; Xue Y; Zhou et al. - Cell, 2014
MicroRNAs are well known to mediate translational repression and mRNA degradation in the cytoplasm. Various microRNAs have also been detected in membrane-compartmentalized organelles, but the functional significance has remained elusive. Here, we report that miR-1, a microRNA specifically induced during myogenesis, efficiently enters the mitochondria where it unexpectedly stimulates, rather than represses, the translation of specific mitochondrial genome-encoded transcripts. We show that this positive effect requires specific miR:mRNA base-pairing and Ago2, but not its functional partner GW182, which is excluded from the mitochondria. We provide evidence for the direct action of Ago2 in mitochondrial translation by crosslinking immunoprecipitation coupled with deep sequencing (CLIP-seq), functional rescue with mitochondria-targeted Ago2, and selective inhibition of the microRNA machinery in the cytoplasm. These findings unveil a positive function of microRNA in mitochondrial translation and suggest a highly coordinated myogenic program via miR-1-mediated translational stimulation in the mitochondria and repression in the cytoplasm.
LinkOut: [PMID: 25083871]
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42 mmu-miR-494-3p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT005687 | Hsf2 | heat shock factor 2 | 1 | 1 | ||||||||
MIRT006622 | Pten | phosphatase and tensin homolog | 1 | 1 | ||||||||
MIRT006623 | Rock1 | Rho-associated coiled-coil containing protein kinase 1 | 1 | 1 | ||||||||
MIRT006624 | Camk2b | calcium/calmodulin-dependent protein kinase II beta | 1 | 1 | ||||||||
MIRT006625 | Fgfr2 | fibroblast growth factor receptor 2 | 1 | 1 | ||||||||
MIRT006626 | Lif | LIF, interleukin 6 family cytokine | 1 | 1 | ||||||||
MIRT578347 | Lsm12 | LSM12 homolog | 1 | 2 | ||||||||
MIRT578906 | Ephx3 | epoxide hydrolase 3 | 1 | 3 | ||||||||
MIRT579711 | Zhx2 | zinc fingers and homeoboxes 2 | 1 | 1 | ||||||||
MIRT580333 | Tnfaip1 | tumor necrosis factor, alpha-induced protein 1 (endothelial) | 1 | 1 | ||||||||
MIRT582377 | Msrb3 | methionine sulfoxide reductase B3 | 1 | 2 | ||||||||
MIRT582618 | Lrch1 | leucine-rich repeats and calponin homology (CH) domain containing 1 | 1 | 1 | ||||||||
MIRT583235 | Gopc | golgi associated PDZ and coiled-coil motif containing | 1 | 1 | ||||||||
MIRT583267 | Gmeb1 | glucocorticoid modulatory element binding protein 1 | 1 | 3 | ||||||||
MIRT583415 | Fyttd1 | forty-two-three domain containing 1 | 1 | 1 | ||||||||
MIRT583463 | Foxk1 | forkhead box K1 | 1 | 1 | ||||||||
MIRT583788 | Elovl5 | ELOVL family member 5, elongation of long chain fatty acids (yeast) | 1 | 1 | ||||||||
MIRT583876 | Dusp7 | dual specificity phosphatase 7 | 1 | 1 | ||||||||
MIRT584114 | Csmd1 | CUB and Sushi multiple domains 1 | 1 | 3 | ||||||||
MIRT584936 | Ado | 2-aminoethanethiol (cysteamine) dioxygenase | 1 | 1 | ||||||||
MIRT585324 | Zdbf2 | zinc finger, DBF-type containing 2 | 1 | 1 | ||||||||
MIRT585542 | Tpte | transmembrane phosphatase with tensin homology | 1 | 1 | ||||||||
MIRT586337 | Pex13 | peroxisomal biogenesis factor 13 | 1 | 2 | ||||||||
MIRT587029 | Gmip | Gem-interacting protein | 1 | 2 | ||||||||
MIRT588763 | Stxbp5 | syntaxin binding protein 5 (tomosyn) | 1 | 2 | ||||||||
MIRT589348 | Ostf1 | osteoclast stimulating factor 1 | 1 | 1 | ||||||||
MIRT589540 | Mkrn3 | makorin, ring finger protein, 3 | 1 | 1 | ||||||||
MIRT590075 | Faf1 | Fas-associated factor 1 | 1 | 1 | ||||||||
MIRT590633 | Arl5a | ADP-ribosylation factor-like 5A | 1 | 1 | ||||||||
MIRT592898 | Otx1 | orthodenticle homeobox 1 | 1 | 2 | ||||||||
MIRT595129 | Magee2 | melanoma antigen, family E, 2 | 1 | 1 | ||||||||
MIRT595134 | Lrrc4c | leucine rich repeat containing 4C | 1 | 1 | ||||||||
MIRT595443 | 9030617O03Rik | D-glutamate cyclase | 1 | 1 | ||||||||
MIRT595554 | Ubr3 | ubiquitin protein ligase E3 component n-recognin 3 | 1 | 1 | ||||||||
MIRT595634 | Atrn | attractin | 1 | 1 | ||||||||
MIRT595916 | Syne2 | spectrin repeat containing, nuclear envelope 2 | 1 | 1 | ||||||||
MIRT597960 | Olig3 | oligodendrocyte transcription factor 3 | 1 | 1 | ||||||||
MIRT604095 | Dpm1 | dolichol-phosphate (beta-D) mannosyltransferase 1 | 1 | 1 | ||||||||
MIRT605674 | Itsn1 | intersectin 1 (SH3 domain protein 1A) | 1 | 1 | ||||||||
MIRT731455 | Fgfr2 | fibroblast growth factor receptor 2 | 4 | 1 | ||||||||
MIRT731456 | Rock1 | Rho-associated coiled-coil containing protein kinase 1 | 4 | 1 | ||||||||
MIRT736998 | Rnf41 | ring finger protein 41 | 3 | 0 |
miRNA-Drug Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||
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