pre-miRNA Information | |
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pre-miRNA | hsa-mir-4316 |
Genomic Coordinates | chr17: 77396984 - 77397054 |
Description | Homo sapiens miR-4316 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||
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Mature miRNA | hsa-miR-4316 | |||||||||
Sequence | 11| GGUGAGGCUAGCUGGUG |27 | |||||||||
Evidence | Experimental | |||||||||
Experiments | SOLiD | |||||||||
SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | EIF2S3 | ||||||||||||||||||||
Synonyms | EIF2, EIF2G, EIF2gamma, MRXSBRK, eIF-2gA | ||||||||||||||||||||
Description | eukaryotic translation initiation factor 2 subunit gamma | ||||||||||||||||||||
Transcript | NM_001415 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on EIF2S3 | |||||||||||||||||||||
3'UTR of EIF2S3 (miRNA target sites are highlighted) |
>EIF2S3|NM_001415|3'UTR 1 AGAATACCAGTTAAATAATACATTCGGATGGATTTGGAAGTTGGAATTCCTCTTAACAACCAAGGGGTTTATTTTCAAAG 81 CAATATTGGGGAATTGATTTCACAGTTCGTTACCTTAGTAGGTAACGGTAAGGTTATTCTCTTTTTTTTTTTTTTTTTTT 161 TTGGTTATGAAAACTTAGGGACTAAAATTAATATAAAAATTGGCATAATGTTGGATTGAATCTACATTTTGGCAGAAGTT 241 AAACATTCCCACATAATGTCAAAATTATACATCATGCAGTTCTGTTTTTTTGTTTGTTTTATTTTGTTTTGTTTTTGAGT 321 CTGGCTCTGTCACCCAGGCTGGAGTGCAGTGGCGTGATCTGCAACCTCTGCCCCCCGGGTTCAAGCGATTCTCCTGCCTC 401 AGCCTCCCGAGTAGCTGAGATTACAGGTGCGCGCCACCACACTTGGCTAATTTTTGTATTATTAGTAGAGACGGGGTTTC 481 AGCATGTTGGCTAGGCCGGTCTCTCCTGACCTCAGGGTGATCAGCCCACCTCGGCCTCACAAAGTGCTGGGATTACAGGC 561 GTGAGCCACCTTGCCCAGCCCACATCATACAGTTTGAAATGAAACTTTGCCACAACCAGCCTTTGCTGTAGCACACACAT 641 ATATCACTGAACCTGTTTGAAATAAAGTTTTTTTTCTTTTTCATGATTCGTCTTTGAGTACCTCCAGGCTGAAAGACTGT 721 TGTACCAGTAAAAACTTAAAGGCACAAATTCTCCTTGAAGACCTTCTCCCTTTTATGTGGCCCCATATTTTATGTTGCTT 801 TATCTTTGAAATTTTGCATGAAAAGGAAATGAATGGATTCGAATGAAATTGTCCTTTAGAGCATGATTACTTGTTCCCAT 881 GGACAAATATTTTTCTCCCCTTGCTCTTCCTGGCCTGAAACACGGGAAACCAGAGTCAAAAGTTATCTCCCTCTCCCTGT 961 GATGCCTTGAGATTTTTTTCTGCGTTGTTTAATGCCTGAAATCCAAGTCTTCCTCCATGGGAAAATACTGTTATACCAAA 1041 TAATTCTAGATGAGTAACAAAGATCTTTTTAGGCCTTCATTTTATGTTTTTTCTTAACTGTTATATTATGATTGTGACAT 1121 AGATTATACTACTACTAATTTTTGGATGTTTCAAAAGGTCAAGAAGTAAAAGATGTTAGAAAGCAATGAGTGAGTCCTTT 1201 TGATTTTTAACTTATTCCCCATGTCCCTATACTTCGTGTGCTTTTCCTTTTTTTTTTTGAGACGGAGGCTCACTCCGTCA 1281 CCTAGGCTAGAGTACAGTGGCACGATCTTGGCTCGCTGCAACCTCTGCCTCCCTGATTCAAGTGATTCTCGTGCTTCAGC 1361 CTCCCATGTAGCTGATATTACAGGCACTTGCCACCATACCCGGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACC 1441 ATGTTGCCCAGGCTGGTCTTGAACTCCTAACCTCAGGTGATCCGCCCGCCTCTGCCTTCCAAAGTGCTGGGATTACAGGC 1521 GTGAGCCACTCTGCCCGGCTTATTTTTCTTTATGTTTTTGCTTCGTAAGAGGTTCTGTTGAGCAGTGATTTGCAACTCTT 1601 GCTGACGTTGCTGGGGAAGCTTTAAAAAAAAAAAAGATGCCCCACAGAGATTCTGATTTTAATTGTTCTGATTTAATTGG 1681 CTTGGAGTAGAATTCAGGCATTGATATCTTTAAAAACTCCCCAGTGTTGAGAAACAAATTTAGAGAGTTGAGAAGTAGGT 1761 ATATTAAATTACAGAATCTTACTGAGTTTTGGTAGACTGATAATACAATTTGCTTTGCTTTTCTTAAATTTGCATTGAGA 1841 TGGGATTTGAAGCATATTGTGCTCTTGTGAATGTTGAAGTTGCATTGTAGAAGTTTAGAAGCTCTGGCTATGGGTTGCCT 1921 AAATTGATGTTTTGAGGAAGCATATTAATGTTATAAACTTCGCTGACTTTGAAGGTTGTGTTGTAGCATGAGGAACACAA 2001 ATAAAACAATTCTAAATCAAACTAAAAAAAAAAAAAAAAAAAAAAA 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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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 GSM1084047. RNA binding protein: AGO2. Condition:CLIP_arsenite_rep4
HITS-CLIP data was present in GSM1084068. RNA binding protein: AGO2. Condition:CLIP_noemetine_SigmaAb
HITS-CLIP data was present in GSM1084073. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep1_AbnovaAb
... - 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 GSM4903829 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Human neurons / CTLTD_shCTL_a |
Location of target site | NM_001415 | 3UTR | CUCGGCCUCACAAAGUGCUGGGAUUACAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161238 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM4903830 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Human neurons / CTLTD_shCTL_b |
Location of target site | NM_001415 | 3UTR | CGGCCUCACAAAGUGCUGGGAUUACAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161238 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset GSM4903832 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Human neurons / 124TD_shELAVL3_b |
Location of target site | NM_001415 | 3UTR | ACAAAGUGCUGGGAUUACAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161238 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 for dataset GSM4903833 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_a |
Location of target site | NM_001415 | 3UTR | CACCCAGGCUGGAGUGCAGUGGCGUGAUCUGCAACCUCUGCCCCCCGGGUUCAAGCGAUUCUCCUGCCUCAGCCUCCCGAGUAGCUGAGAUUACAGGUGCGCGCCACCACACUUGGCUAAUUUUUGUAUUAUUAGUAGAGACGGGGUUUCAGCAUGUUGGCUAGGCCGGUCUCUCCUGACCUCAGGGUGAUCAGCCCACCUCGGCCUCACAAAGUGCUGGGAUUACAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 5 for dataset GSM4903834 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_b |
Location of target site | NM_001415 | 3UTR | CCCACCUCGGCCUCACAAAGUGCUGGGAUUACAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 6 for dataset GSM4903835 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_c |
Location of target site | NM_001415 | 3UTR | CACCCAGGCUGGAGUGCAGUGGCGUGAUCUGCAACCUCUGCCCCCCGGGUUCAAGCGAUUCUCCUGCCUCAGCCUCCCGAGUAGCUGAGAUUACAGGUGCGCGCCACCACACUUGGCUAAUUUUUGUAUUAUUAGUAGAGACGGGGUUUCAGCAUGUUGGCUAGGCCGGUCUCUCCUGACCUCAGGGUGAUCAGCCCACCUCGGCCUCACAAAGUGCUGGGAUUACAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 7 for dataset GSM4903836 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_a |
Location of target site | NM_001415 | 3UTR | CCUCGGCCUCACAAAGUGCUGGGAUUACAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 8 for dataset GSM4903837 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_b |
Location of target site | NM_001415 | 3UTR | GGCCUCACAAAGUGCUGGGAUUACAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 9 for dataset GSM4903838 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_c |
Location of target site | NM_001415 | 3UTR | CGGCCUCACAAAGUGCUGGGAUUACAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 10 for dataset GSM1084047 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_arsenite_rep4 |
Location of target site | ENST00000253039.4 | 3UTR | ACAAAGUGCUGGGAUUACAGGCGUGAGCC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 11 for dataset GSM1084068 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_noemetine_SigmaAb |
Location of target site | ENST00000253039.4 | 3UTR | ACAAAGUGCUGGGAUUACAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 12 for dataset GSM1084073 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_hippuristanol_rep1_AbnovaAb |
Location of target site | ENST00000253039.4 | 3UTR | CACAAAGUGCUGGGAUUACAGGCGUGAGCCACC |
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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74 hsa-miR-4316 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT080624 | PMAIP1 | phorbol-12-myristate-13-acetate-induced protein 1 | ![]() |
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2 | 2 | ||||||
MIRT095088 | SEC24A | SEC24 homolog A, COPII coat complex component | ![]() |
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2 | 4 | ||||||
MIRT123331 | CALU | calumenin | ![]() |
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2 | 2 | ||||||
MIRT154964 | RRM2 | ribonucleotide reductase regulatory subunit M2 | ![]() |
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2 | 2 | ||||||
MIRT370850 | TGFBR2 | transforming growth factor beta receptor 2 | ![]() |
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2 | 2 | ||||||
MIRT442955 | SGCD | sarcoglycan delta | ![]() |
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2 | 2 | ||||||
MIRT448240 | ZNF774 | zinc finger protein 774 | ![]() |
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2 | 2 | ||||||
MIRT451710 | OLR1 | oxidized low density lipoprotein receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT452072 | ATP6V0B | ATPase H+ transporting V0 subunit b | ![]() |
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2 | 2 | ||||||
MIRT455665 | GLO1 | glyoxalase I | ![]() |
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2 | 2 | ||||||
MIRT460354 | TXNDC16 | thioredoxin domain containing 16 | ![]() |
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2 | 2 | ||||||
MIRT461908 | NECAB3 | N-terminal EF-hand calcium binding protein 3 | ![]() |
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2 | 2 | ||||||
MIRT462047 | HOXC13 | homeobox C13 | ![]() |
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2 | 2 | ||||||
MIRT462735 | EFNB1 | ephrin B1 | ![]() |
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2 | 2 | ||||||
MIRT463409 | ZC3HAV1L | zinc finger CCCH-type containing, antiviral 1 like | ![]() |
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2 | 2 | ||||||
MIRT464952 | TWIST1 | twist family bHLH transcription factor 1 | ![]() |
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2 | 2 | ||||||
MIRT465052 | TSR1 | TSR1, ribosome maturation factor | ![]() |
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2 | 2 | ||||||
MIRT467549 | SMARCD1 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 | ![]() |
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2 | 4 | ||||||
MIRT470226 | PRRC2A | proline rich coiled-coil 2A | ![]() |
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2 | 2 | ||||||
MIRT474081 | LMBR1L | limb development membrane protein 1 like | ![]() |
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2 | 2 | ||||||
MIRT474481 | KLHDC8B | kelch domain containing 8B | ![]() |
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2 | 2 | ||||||
MIRT474704 | KIF3A | kinesin family member 3A | ![]() |
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2 | 2 | ||||||
MIRT474897 | KCTD21 | potassium channel tetramerization domain containing 21 | ![]() |
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2 | 2 | ||||||
MIRT475203 | IL2RB | interleukin 2 receptor subunit beta | ![]() |
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2 | 2 | ||||||
MIRT477664 | EFHD2 | EF-hand domain family member D2 | ![]() |
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2 | 2 | ||||||
MIRT477775 | E2F3 | E2F transcription factor 3 | ![]() |
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2 | 2 | ||||||
MIRT477940 | DPM2 | dolichyl-phosphate mannosyltransferase subunit 2, regulatory | ![]() |
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2 | 2 | ||||||
MIRT478224 | DDX52 | DExD-box helicase 52 | ![]() |
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2 | 2 | ||||||
MIRT479904 | CCDC117 | coiled-coil domain containing 117 | ![]() |
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2 | 2 | ||||||
MIRT480639 | BSCL2 | BSCL2, seipin lipid droplet biogenesis associated | ![]() |
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2 | 2 | ||||||
MIRT482435 | ADM | adrenomedullin | ![]() |
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2 | 10 | ||||||
MIRT483908 | GNB1L | G protein subunit beta 1 like | ![]() |
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2 | 2 | ||||||
MIRT484161 | FAM71B | family with sequence similarity 71 member B | ![]() |
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2 | 2 | ||||||
MIRT484405 | SNX19 | sorting nexin 19 | ![]() |
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2 | 2 | ||||||
MIRT485426 | LASP1 | LIM and SH3 protein 1 | ![]() |
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2 | 2 | ||||||
MIRT489788 | KRT80 | keratin 80 | ![]() |
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2 | 4 | ||||||
MIRT490813 | ASB1 | ankyrin repeat and SOCS box containing 1 | ![]() |
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2 | 4 | ||||||
MIRT491176 | LAMA5 | laminin subunit alpha 5 | ![]() |
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2 | 2 | ||||||
MIRT491573 | HSDL1 | hydroxysteroid dehydrogenase like 1 | ![]() |
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2 | 2 | ||||||
MIRT492633 | PLXNA1 | plexin A1 | ![]() |
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2 | 2 | ||||||
MIRT492984 | NAV1 | neuron navigator 1 | ![]() |
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2 | 2 | ||||||
MIRT496441 | RAB11FIP4 | RAB11 family interacting protein 4 | ![]() |
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2 | 2 | ||||||
MIRT501829 | NCOA3 | nuclear receptor coactivator 3 | ![]() |
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2 | 2 | ||||||
MIRT502165 | KIAA0195 | transmembrane protein 94 | ![]() |
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2 | 2 | ||||||
MIRT508652 | DIABLO | diablo IAP-binding mitochondrial protein | ![]() |
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2 | 4 | ||||||
MIRT509554 | ACTG1 | actin gamma 1 | ![]() |
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2 | 4 | ||||||
MIRT520033 | YOD1 | YOD1 deubiquitinase | ![]() |
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2 | 6 | ||||||
MIRT523969 | DVL3 | dishevelled segment polarity protein 3 | ![]() |
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2 | 2 | ||||||
MIRT526150 | KIAA1456 | KIAA1456 | ![]() |
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2 | 2 | ||||||
MIRT530330 | ARHGAP1 | Rho GTPase activating protein 1 | ![]() |
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2 | 2 | ||||||
MIRT539985 | SLC24A4 | solute carrier family 24 member 4 | ![]() |
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2 | 4 | ||||||
MIRT540851 | NUP155 | nucleoporin 155 | ![]() |
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2 | 2 | ||||||
MIRT542326 | LIMD1 | LIM domains containing 1 | ![]() |
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2 | 2 | ||||||
MIRT558908 | CBX5 | chromobox 5 | ![]() |
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2 | 2 | ||||||
MIRT563663 | SMC4 | structural maintenance of chromosomes 4 | ![]() |
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2 | 2 | ||||||
MIRT565433 | SURF4 | surfeit 4 | ![]() |
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2 | 2 | ||||||
MIRT567773 | DGAT2 | diacylglycerol O-acyltransferase 2 | ![]() |
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2 | 2 | ||||||
MIRT615573 | NCS1 | neuronal calcium sensor 1 | ![]() |
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2 | 2 | ||||||
MIRT627336 | TTLL7 | tubulin tyrosine ligase like 7 | ![]() |
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2 | 2 | ||||||
MIRT632965 | EIF2S3 | eukaryotic translation initiation factor 2 subunit gamma | ![]() |
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2 | 2 | ||||||
MIRT634307 | SNTN | sentan, cilia apical structure protein | ![]() |
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2 | 2 | ||||||
MIRT641569 | RAX | retina and anterior neural fold homeobox | ![]() |
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2 | 2 | ||||||
MIRT660509 | ARL5A | ADP ribosylation factor like GTPase 5A | ![]() |
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2 | 2 | ||||||
MIRT662703 | C10orf111 | chromosome 10 open reading frame 111 | ![]() |
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2 | 4 | ||||||
MIRT663214 | ZNF277 | zinc finger protein 277 | ![]() |
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2 | 2 | ||||||
MIRT665318 | YIPF4 | Yip1 domain family member 4 | ![]() |
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2 | 2 | ||||||
MIRT695264 | CD209 | CD209 molecule | ![]() |
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2 | 2 | ||||||
MIRT696231 | LIN9 | lin-9 DREAM MuvB core complex component | ![]() |
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2 | 2 | ||||||
MIRT698867 | SRPR | SRP receptor alpha subunit | ![]() |
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2 | 2 | ||||||
MIRT702700 | IPO9 | importin 9 | ![]() |
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2 | 2 | ||||||
MIRT704236 | DHDDS | dehydrodolichyl diphosphate synthase subunit | ![]() |
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2 | 2 | ||||||
MIRT704935 | CCDC120 | coiled-coil domain containing 120 | ![]() |
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2 | 2 | ||||||
MIRT724285 | KCNMB1 | potassium calcium-activated channel subfamily M regulatory beta subunit 1 | ![]() |
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2 | 2 | ||||||
MIRT735579 | VEGFA | vascular endothelial growth factor A | ![]() |
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3 | 0 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||
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