pre-miRNA Information | |
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pre-miRNA | hsa-mir-3911 |
Genomic Coordinates | chr9: 127690687 - 127690795 |
Description | Homo sapiens miR-3911 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-3911 | |||||||||||||||||||||||||||
Sequence | 12| UGUGUGGAUCCUGGAGGAGGCA |33 | |||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||
Experiments | Illumina | DRVs in miRNA |
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SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | ZNF548 | ||||||||||||||||||||
Synonyms | - | ||||||||||||||||||||
Description | zinc finger protein 548 | ||||||||||||||||||||
Transcript | NM_001172773 | ||||||||||||||||||||
Other Transcripts | NM_152909 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on ZNF548 | |||||||||||||||||||||
3'UTR of ZNF548 (miRNA target sites are highlighted) |
>ZNF548|NM_001172773|3'UTR 1 CTATTGTAATTGGGTAGTAATGTTATATAAATTCCACATTTTTATGCAACTAATCTCCAGAACATTTTTCCTCTTACCAA 81 GAAGTAAAATGCTGTACCCATTAACAACAACTCATTCCCCTTCCCTACTTCCCCAGAAATGTCTCAACTATATTTCTATA 161 CTCTATGGTACTTATATGAGGTACCAATAGATATCTATGAATTTGATATATATTTGTACCTCATATAAGTGGATTCTACA 241 GTATTTATCTTTTGAGACTGGCTTATTTCACTTAGGATAAGGTCTTCACGGTTCACCCATGTTGTATAATGTGTCAGAAT 321 ATCCTTCCTTTTTAGGTGAAATAATATTCTATGGTATTTATATACCACATTTATTTATCCATTCATCTGTTAGTGGATAC 401 TTGGGCTACTTCCACCTTTTGCCTATTGAAATAATGCTGCTATGAAGATGAGTGTACAAGTGTCTATTCAAGATTCTACT 481 TTCAATTCTTATAGGGTATATACTCAGAAATGGTGGTGCTGGATCATATAGGATTTCTATTTTTTTTTTTTGTTTGTTTT 561 TGAGACAGAGTCTTGCTCTGTCACCCAGGCTGGAGTGCAGTGCTGTGATCTTGGCTCACTGCAAGCTCCGCCTCCCAGGT 641 TCATGCCATTCTCCTGCCTCACCCTCCCGAGTAGCTGGGACTACAGGTGCCTGCCACCACGCCTGGCTAATTTTTTTGTA 721 TTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCCTGATCTCCTGACCTTGTGATCTGCCTGCCTTGGCCT 801 CTCAAAGTGCTGGGATTACGGGCGTGAGCCACCGCGCCTGGCCAGGATTTCTATTTTTAATATTTTTGGGAAAATTTTTC 881 CATAGTACCTGTGCCATTTTACATTCCCACCAGCAGTGCACAAGGATTGCAATCTATATACATCCTCACCAACATTGTTC 961 ATTTTCTATTTCTGTTTTTGGGGTTTTTTGTAGTGCCTTTTGTTTTGGATAGCAGCTATCTTGTTGGATGTGAGGTGGAA 1041 TCTATAGTGTCTTTCATTTTTATTTTGTGAATGATTGATGATGTTGAGGATCTTTTCATGTGCTTGTTAGGCATTTGTGT 1121 ATCTGGAAAAATATTCAAGTCTTTTTTTTCCATTTTTAATGGGACTATTTGCTTTTTGTTGTTGAGTTGTAGTTCTTTAT 1201 ACATTCTGGATATTAACTCCTTACCAAATATATGCTTTTTACATATTACCTCCCAGTCCATAGGTTGCTTTTTCGCTCTG 1281 TTGATTGTGTCCTTTGATGAAATTTTAAGTTTTGATGTACTGTTGACTCTTTCTGTCTGTGGGTTCTGTATTCATGGATC 1361 GAAGCAACCATGGATCAAAAGTATTTGGAGCATCCATGGATTGCAGTGATCATTAATCAAAAATATTTGGAAAACAAAAA 1441 GGGTAGTTGCATCTGTACTAAACATGAACAGACATTTTTTCTTGTCATTATTCCCTAAACTATATAGTATAATAAATATT 1521 TACATAGCATTTACATTGTATTAGAAGTTATAAATAACCTAATGATAATCTATATAGGAAGATGTGTGTAGGTTATATTC 1601 AAACACTATGCCTTTTTATGTGAGGGACCTCTTGAGCATCAGATGATTTTGGTATCCACAAGGGGTCCTGGAATCAGTCC 1681 CCCACAGACACCAAGGGATGACTGTAGTGCATTTTATCTATTTTTACTTCTGTTACCTGGGCTTTTGATGTTATATATTA 1761 AAAAAAATTAGTATCAAATCCAATGCCAAGCATTTTCCCTATGCTTTATTCTAAGAATTTTATATTTGAAGGTCTTACAT 1841 TTAGGTCTTTTTTTTTTTTTTCTTTTGGAGGCAGAGTCTTGCTCTGTCACCCAGCCTGGAGTGCAGTAGTGGAATCTCAG 1921 CTCACTACAACCTCCGCCTCCTGGGTTCGAGCCATCACCCCACCTCAGCCTCCCAAGTAGCTTGGATTACAAGTGTACAC 2001 CACCACACCTGGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTTGCCATGTTGGCCAGGCTGGTCTTAAACTTCTGGC 2081 CTTAAGTGATCCCCCTGCCTCGGCCTCCCAAATTGCTGAGATTACAGGCAGGAGTTGTAATGCACTGTGCCTGGCTACAT 2161 TTAGATCTTTAATCTACTTGGGGTTCATTTTTGCATATGGTTTAAGGCAAAAGTCCACTTTATGTGGCTATCCAGTTTTC 2241 CAAGCACCATTTTTTGAAAAGAGCATCTTTCCTCTGTTGAGTAGTCTTGGCACACTTGTCAAAATCATTTGTCCATATAT 2321 GCCATGGTTTATATGTGGATTCTCTATTTTATTGGTCATATGTCTGTCTTTATGTCAGTACCACACATTTTAGGTGTGTG 2401 TGTGTGAGACTCAGTGTTGAGGACAAGGCTAGTGGGCTTTCACACTCCAGACTGCTGTATTCCAGCCCAAATTACTCAAA 2481 TTAGCCAATCCATGGGGAACATGGAAAACGTAGCTAATGCAATCCGCTTGCCTTACCTAAGTTGTCCCCTGCAGCCTCAG 2561 GTTGCTGTTACTGTGTTTCAGATGCAACCCTCTGTGGGACCCTACCCAAGTTCTCTCATTCTTAGCTATAGGTAATAAAT 2641 TGTTCTGATTTTGTGTATCCAAAAAAAAAAAAAAAAA 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 | HEK293S |
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 GSM1084077. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep1_SigmaAb
... - Karginov FV; Hannon GJ, 2013, Genes & development. |
Article |
- Karginov FV; Hannon GJ - Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
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CLIP-seq Support 1 for dataset GSM1084077 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_hippuristanol_rep1_SigmaAb |
Location of target site | ENST00000366197.5 | 3UTR | AUUUUAGGUGUGUGUGUGUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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70 hsa-miR-3911 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT207399 | MAT2A | methionine adenosyltransferase 2A | ![]() |
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2 | 6 | ||||||
MIRT284537 | PDP2 | pyruvate dehyrogenase phosphatase catalytic subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT291946 | TPM4 | tropomyosin 4 | ![]() |
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2 | 2 | ||||||
MIRT293609 | PVR | poliovirus receptor | ![]() |
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2 | 2 | ||||||
MIRT357688 | PAIP2 | poly(A) binding protein interacting protein 2 | ![]() |
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2 | 2 | ||||||
MIRT451607 | MEIS3P1 | Meis homeobox 3 pseudogene 1 | ![]() |
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2 | 2 | ||||||
MIRT452110 | IFITM1 | interferon induced transmembrane protein 1 | ![]() |
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2 | 2 | ||||||
MIRT457804 | KLHL25 | kelch like family member 25 | ![]() |
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2 | 2 | ||||||
MIRT462730 | EFNB1 | ephrin B1 | ![]() |
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2 | 2 | ||||||
MIRT463219 | ZNF131 | zinc finger protein 131 | ![]() |
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2 | 2 | ||||||
MIRT464141 | VPS28 | VPS28, ESCRT-I subunit | ![]() |
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2 | 2 | ||||||
MIRT467582 | SLC7A5 | solute carrier family 7 member 5 | ![]() |
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2 | 6 | ||||||
MIRT470824 | PLXND1 | plexin D1 | ![]() |
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2 | 2 | ||||||
MIRT474230 | LCLAT1 | lysocardiolipin acyltransferase 1 | ![]() |
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2 | 2 | ||||||
MIRT478989 | COLGALT1 | collagen beta(1-O)galactosyltransferase 1 | ![]() |
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2 | 2 | ||||||
MIRT479462 | CDK6 | cyclin dependent kinase 6 | ![]() |
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2 | 2 | ||||||
MIRT483558 | SYT2 | synaptotagmin 2 | ![]() |
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2 | 2 | ||||||
MIRT484483 | SLC9A1 | solute carrier family 9 member A1 | ![]() |
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2 | 2 | ||||||
MIRT485224 | PRICKLE1 | prickle planar cell polarity protein 1 | ![]() |
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2 | 2 | ||||||
MIRT490356 | DPYSL5 | dihydropyrimidinase like 5 | ![]() |
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2 | 4 | ||||||
MIRT493177 | MKNK2 | MAP kinase interacting serine/threonine kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT509802 | CHAF1B | chromatin assembly factor 1 subunit B | ![]() |
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2 | 4 | ||||||
MIRT511815 | HDGF | heparin binding growth factor | ![]() |
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2 | 2 | ||||||
MIRT512254 | ARPP19 | cAMP regulated phosphoprotein 19 | ![]() |
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2 | 6 | ||||||
MIRT513025 | GPT2 | glutamic--pyruvic transaminase 2 | ![]() |
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2 | 2 | ||||||
MIRT519640 | ZNF772 | zinc finger protein 772 | ![]() |
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2 | 4 | ||||||
MIRT531178 | SIGLEC12 | sialic acid binding Ig like lectin 12 (gene/pseudogene) | ![]() |
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2 | 2 | ||||||
MIRT537870 | EDA2R | ectodysplasin A2 receptor | ![]() |
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2 | 2 | ||||||
MIRT551914 | IGLON5 | IgLON family member 5 | ![]() |
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2 | 2 | ||||||
MIRT558359 | DMTF1 | cyclin D binding myb like transcription factor 1 | ![]() |
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2 | 2 | ||||||
MIRT559771 | URGCP-MRPS24 | URGCP-MRPS24 readthrough | ![]() |
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2 | 4 | ||||||
MIRT559813 | ZNF83 | zinc finger protein 83 | ![]() |
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2 | 2 | ||||||
MIRT561999 | LPP | LIM domain containing preferred translocation partner in lipoma | ![]() |
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2 | 2 | ||||||
MIRT565754 | SERTAD2 | SERTA domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT569423 | DCAF8 | DDB1 and CUL4 associated factor 8 | ![]() |
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2 | 2 | ||||||
MIRT569845 | RGS5 | regulator of G protein signaling 5 | ![]() |
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2 | 2 | ||||||
MIRT606928 | CDK15 | cyclin dependent kinase 15 | ![]() |
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2 | 2 | ||||||
MIRT607616 | TMEM130 | transmembrane protein 130 | ![]() |
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2 | 4 | ||||||
MIRT607629 | TRIOBP | TRIO and F-actin binding protein | ![]() |
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2 | 2 | ||||||
MIRT607885 | SATB1 | SATB homeobox 1 | ![]() |
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2 | 2 | ||||||
MIRT607942 | SSX2 | SSX family member 2 | ![]() |
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2 | 4 | ||||||
MIRT608017 | CARNS1 | carnosine synthase 1 | ![]() |
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2 | 4 | ||||||
MIRT608036 | UBLCP1 | ubiquitin like domain containing CTD phosphatase 1 | ![]() |
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2 | 2 | ||||||
MIRT608063 | SSX2B | SSX family member 2B | ![]() |
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2 | 4 | ||||||
MIRT608558 | SBK1 | SH3 domain binding kinase 1 | ![]() |
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2 | 6 | ||||||
MIRT608915 | NCDN | neurochondrin | ![]() |
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2 | 6 | ||||||
MIRT615876 | HIF1AN | hypoxia inducible factor 1 alpha subunit inhibitor | ![]() |
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2 | 4 | ||||||
MIRT618023 | ELFN1 | extracellular leucine rich repeat and fibronectin type III domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT620505 | SNRPD1 | small nuclear ribonucleoprotein D1 polypeptide | ![]() |
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2 | 2 | ||||||
MIRT628101 | IL1RAPL1 | interleukin 1 receptor accessory protein like 1 | ![]() |
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2 | 2 | ||||||
MIRT628700 | ZNF548 | zinc finger protein 548 | ![]() |
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2 | 2 | ||||||
MIRT630658 | POU2F1 | POU class 2 homeobox 1 | ![]() |
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2 | 2 | ||||||
MIRT643508 | ZNF28 | zinc finger protein 28 | ![]() |
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2 | 2 | ||||||
MIRT646379 | SLC22A6 | solute carrier family 22 member 6 | ![]() |
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2 | 2 | ||||||
MIRT660041 | C15orf61 | chromosome 15 open reading frame 61 | ![]() |
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2 | 2 | ||||||
MIRT687700 | KRR1 | KRR1, small subunit processome component homolog | ![]() |
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2 | 2 | ||||||
MIRT688858 | CAMKK2 | calcium/calmodulin dependent protein kinase kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT690443 | REPIN1 | replication initiator 1 | ![]() |
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2 | 2 | ||||||
MIRT690456 | ZNF33A | zinc finger protein 33A | ![]() |
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2 | 2 | ||||||
MIRT693796 | RHOG | ras homolog family member G | ![]() |
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2 | 2 | ||||||
MIRT694274 | ZNF529 | zinc finger protein 529 | ![]() |
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2 | 4 | ||||||
MIRT697697 | WAC | WW domain containing adaptor with coiled-coil | ![]() |
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2 | 2 | ||||||
MIRT700242 | RCC2 | regulator of chromosome condensation 2 | ![]() |
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2 | 2 | ||||||
MIRT701836 | MRPL37 | mitochondrial ribosomal protein L37 | ![]() |
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2 | 2 | ||||||
MIRT704255 | DHCR24 | 24-dehydrocholesterol reductase | ![]() |
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2 | 2 | ||||||
MIRT707203 | SDK2 | sidekick cell adhesion molecule 2 | ![]() |
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2 | 2 | ||||||
MIRT710365 | CREB5 | cAMP responsive element binding protein 5 | ![]() |
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2 | 2 | ||||||
MIRT711943 | WDFY1 | WD repeat and FYVE domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT715496 | MAZ | MYC associated zinc finger protein | ![]() |
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2 | 2 | ||||||
MIRT719250 | MS4A1 | membrane spanning 4-domains A1 | ![]() |
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2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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