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 | NCDN | ||||||||||||||||||||
Synonyms | - | ||||||||||||||||||||
Description | neurochondrin | ||||||||||||||||||||
Transcript | NM_001014839 | ||||||||||||||||||||
Other Transcripts | NM_001014841 , NM_014284 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on NCDN | |||||||||||||||||||||
3'UTR of NCDN (miRNA target sites are highlighted) |
>NCDN|NM_001014839|3'UTR 1 GGGGTGTCCACCGGGGACAGACCCAGGGGCGGGCAGAGAGGGAAGGAGGGAGGAGGCATCTTCCCTGAAGCCCCCAATCT 81 GGCCCCCCCCTCCCCAGACTTCCTCCCCAAAACACCCCAGCTTTCTGGCTTTTCTGAGGGCAAGGGCATGGTGCCCACCC 161 CTCAAGTGTAAGGAACTGCGTTCCGCCCCTCAGGCCCCCATGGGGGCAGGGATCGGCTTGGAAATCAACGTGGTTGTCCC 241 CGCCAGGCCGGGGAAGGTTGGAGCAGCCCCCAGGGAGGGGGGCACTAGGTGTCATTGTGCCCGATGTCTGGCTCCCCTGC 321 AGGAGGGAGGCTCCAGGGTAAGACAGGGCTGGCAGGAGCAGACTGCCTCAGCCCATGTGCCCTGCCGGCCAGGGCGTGGG 401 CTCCCCTCGGCTGTGGTGCCTCCTCTGGCCCCCCAGGTCCACGTCCTTTAAATTGGCCCTTTGGCTCTTGCCCTTGGCTC 481 CCTTGGGCAGACAGCAGGCTTAGGCCATTGATATCGCAGTTCTTCCTATCAGCTTCAGTGACCCAGGGTCTGAACTGCCT 561 CCATCCTAGGGCAACCTGGGGCAGACAGGCCTGGTGGGGGGTGGGGAAACCTCCTTCCACCTGAGCTTGCTTGAAGGGAC 641 CCAGAGTCTTTGGGCCCAGATCTTTAAACCTTTGTGTCGTGTTGCAGCAGAGTGACGATGGGGGTTGGGGGGTTATTTAT 721 TTTGCCTGTCCTTATCCCTGCTTGGACACCTGAGCATCTGATTCCTGTCCCCCTGGTGCCATCTGGCCTGGCTGGAGCCA 801 GGAACAGGAGGGACACTTCCCCAGAATCCGCATGTTTCCCCAGTGATTACACTCCACTGCCACCGTGGTGCCTGGCTTTA 881 ACTCCCACCCCTGCTATGACTCCTCTCTGCAGAGACGCGACTGGCGGCTCCAGCAGGGACTACCTTTCTTATAAACCCAG 961 GGGGACCACACACACACACACACACACACACACACACACACACACACACACACACACTCTTGATCCCTTGCTTCCCTCCC 1041 CCAGTGCGTTCTGTGATCGCCAAGTTCAAAGCTGTGCACATGTGGACACTCAATAAATGTTCATTGGTGACGAGAAAAAA 1121 AAAAAAAAA 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 | Hela | ||||||
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 GSM1048188. RNA binding protein: AGO2. Condition:Hela_AGO2_CLIP_ptb_knockdown
... - Xue Y; Ouyang K; Huang J; Zhou Y; Ouyang H; et al., 2013, Cell. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Xue Y; Ouyang K; Huang J; Zhou Y; Ouyang H; et al. - Cell, 2013
The induction of pluripotency or trans-differentiation of one cell type to another can be accomplished with cell-lineage-specific transcription factors. Here, we report that repression of a single RNA binding polypyrimidine-tract-binding (PTB) protein, which occurs during normal brain development via the action of miR-124, is sufficient to induce trans-differentiation of fibroblasts into functional neurons. Besides its traditional role in regulated splicing, we show that PTB has a previously undocumented function in the regulation of microRNA functions, suppressing or enhancing microRNA targeting by competitive binding on target mRNA or altering local RNA secondary structure. A key event during neuronal induction is the relief of PTB-mediated blockage of microRNA action on multiple components of the REST complex, thereby derepressing a large array of neuronal genes, including miR-124 and multiple neuronal-specific transcription factors, in nonneuronal cells. This converts a negative feedback loop to a positive one to elicit cellular reprogramming to the neuronal lineage.
LinkOut: [PMID: 23313552]
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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 | 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 GSM1084064. RNA binding protein: AGO2. Condition:CLIP_noemetine_AbnovaAb
... - Karginov FV; Hannon GJ, 2013, Genes & development. |
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miRNA-target interactions (Provided by authors) |
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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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Experimental Support 3 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | MCF7 |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
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HITS-CLIP data was present in GSM1395164. RNA binding protein: AGO. Condition:MCF7 AGO HITS-CLIP Replicate 2
... - Pillai MM; Gillen AE; Yamamoto TM; Kline E; et al., 2014, Breast cancer research and treatment. |
Article |
- Pillai MM; Gillen AE; Yamamoto TM; Kline E; et al. - Breast cancer research and treatment, 2014
miRNAs regulate the expression of genes in both normal physiology and disease. While miRNAs have been demonstrated to play a pivotal role in aspects of cancer biology, these reports have generally focused on the regulation of single genes. Such single-gene approaches have significant limitations, relying on miRNA expression levels and heuristic predictions of mRNA-binding sites. This results in only circumstantial evidence of miRNA-target interaction and typically leads to large numbers of false positive predictions. Here, we used a genome-wide approach (high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation, HITS-CLIP) to define direct miRNA-mRNA interactions in three breast cancer subtypes (estrogen receptor positive, Her2 amplified, and triple negative). Focusing on steroid receptor signaling, we identified two novel regulators of the ER pathway (miR-9-5p and miR-193a/b-3p), which together target multiple genes involved in ER signaling. Moreover, this approach enabled the definition of miR-9-5p as a global regulator of steroid receptor signaling in breast cancer. We show that miRNA targets and networks defined by HITS-CLIP under physiologic conditions are predictive of patient outcomes and provide global insight into miRNA regulation in breast cancer.
LinkOut: [PMID: 24906430]
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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 | Cardiac Tissues |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
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HITS-CLIP data was present in GSM2202480. RNA binding protein: AGO2. Condition:S5_LV_36yo_Male_AGO2_bound_RNA
HITS-CLIP data was present in GSM2202477. RNA binding protein: AGO2. Condition:S2_LV_25yo_Male_AGO2_bound_RNA
... - Spengler RM; Zhang X; Cheng C; McLendon JM; et al., 2016, Nucleic acids research. |
Article |
Elucidation of transcriptome-wide microRNA binding sites in human cardiac tissues by Ago2 HITS-CLIP.
- Spengler RM; Zhang X; Cheng C; McLendon JM; et al.- Nucleic acids research, 2016
MicroRNAs (miRs) have emerged as key biological effectors in human health and disease. These small noncoding RNAs are incorporated into Argonaute (Ago) proteins, where they direct post-transcriptional gene silencing via base-pairing with target transcripts. Although miRs have become intriguing biological entities and attractive therapeutic targets, the translational impacts of miR research remain limited by a paucity of empirical miR targeting data, particularly in human primary tissues. Here, to improve our understanding of the diverse roles miRs play in cardiovascular function and disease, we applied high-throughput methods to globally profile miR:target interactions in human heart tissues. We deciphered Ago2:RNA interactions using crosslinking immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to generate the first transcriptome-wide map of miR targeting events in human myocardium, detecting 4000 cardiac Ago2 binding sites across >2200 target transcripts. Our initial exploration of this interactome revealed an abundance of miR target sites in gene coding regions, including several sites pointing to new miR-29 functions in regulating cardiomyocyte calcium, growth and metabolism. Also, we uncovered several clinically-relevant interactions involving common genetic variants that alter miR targeting events in cardiomyopathy-associated genes. Overall, these data provide a critical resource for bolstering translational miR research in heart, and likely beyond.
LinkOut: [PMID: 27418678]
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CLIP-seq Support 1 for dataset GSM1048188 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | Hela / Hela_AGO2_CLIP_ptb_knockdown |
Location of target site | ENST00000356090.4 | 3UTR | GGACCACACACACACACACACACA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23313552 / GSE42701 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM1084064 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_noemetine_AbnovaAb |
Location of target site | ENST00000356090.4 | 3UTR | GGACCACACACACACACACACAC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset GSM1395164 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | MCF7 / MCF7 AGO HITS-CLIP Replicate 2 |
Location of target site | ENST00000356090.4 | 3UTR | GGACCACACACACACACACACACACACACACACACACACACACACACACA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 24906430 / GSE57855 |
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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