pre-miRNA Information | |
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pre-miRNA | hsa-mir-3678 |
Genomic Coordinates | chr17: 75406069 - 75406162 |
Description | Homo sapiens miR-3678 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-3678-3p | ||||||||||||||||||||||||||||||
Sequence | 69| CUGCAGAGUUUGUACGGACCGG |90 | ||||||||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||||||||
Experiments | Illumina | ||||||||||||||||||||||||||||||
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 | EPS15L1 | ||||||||||||||||||||
Synonyms | EPS15R | ||||||||||||||||||||
Description | epidermal growth factor receptor pathway substrate 15 like 1 | ||||||||||||||||||||
Transcript | NM_021235 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on EPS15L1 | |||||||||||||||||||||
3'UTR of EPS15L1 (miRNA target sites are highlighted) |
>EPS15L1|NM_021235|3'UTR 1 GTCCTCCGCCTCCGGGCCACCCCACTCCCTTCCGCTTGCAGCTTCCCTGGGATTTTTGTCTCCTTTTAAAGGCAAACCTC 81 CCAGCTTCTTTAGCCTCTTGGTACCTCACACTCTCTGTCCCTCGCGTTATTTATTCTACACTGCCACTTCTGTAAGAAAA 161 ACAGTTTCTCAATAAAAAAAAAAAGAGCCGCA 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 | 58513.0 |
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 | HEK293 |
Disease | 58513.0 |
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 GSM1065667. RNA binding protein: AGO1. Condition:4-thiouridine
... - Memczak S; Jens M; Elefsinioti A; Torti F; et al., 2013, Nature. |
Article |
- Memczak S; Jens M; Elefsinioti A; Torti F; et al. - Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
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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 | ENST00000602009.1 | 3UTR | UUUAAAAACCUCUGCACUUUACUCU |
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 | ENST00000602009.1 | 3UTR | UUAUGUUUAAAAACCUCUGCACUUUACUCUGAC |
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 | ENST00000602009.1 | 3UTR | UUUAAAAACCUCUGCACUUUACUCUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 21572407 / GSE28865 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 for dataset GSM1065667 | |
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Method / RBP | PAR-CLIP / AGO1 |
Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_6 |
Location of target site | ENST00000602009.1 | 3UTR | UUUAAAAACCUCUGCACUUUACUCU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23446348 / GSE43573 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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86 hsa-miR-3678-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT074327 | TNRC6A | trinucleotide repeat containing 6A | ![]() |
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2 | 10 | ||||||
MIRT107705 | CLTA | clathrin light chain A | ![]() |
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2 | 2 | ||||||
MIRT114113 | AGO1 | argonaute 1, RISC catalytic component | ![]() |
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2 | 2 | ||||||
MIRT155293 | IFNAR2 | interferon alpha and beta receptor subunit 2 | ![]() |
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2 | 4 | ||||||
MIRT159171 | NRBP1 | nuclear receptor binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT185795 | ZNF678 | zinc finger protein 678 | ![]() |
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2 | 2 | ||||||
MIRT282672 | SYNM | synemin | ![]() |
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2 | 2 | ||||||
MIRT294386 | ZNF264 | zinc finger protein 264 | ![]() |
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2 | 2 | ||||||
MIRT295818 | CHMP4B | charged multivesicular body protein 4B | ![]() |
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2 | 2 | ||||||
MIRT332777 | CAPRIN1 | cell cycle associated protein 1 | ![]() |
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2 | 4 | ||||||
MIRT334112 | PPP6R3 | protein phosphatase 6 regulatory subunit 3 | ![]() |
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2 | 2 | ||||||
MIRT340971 | IPO5 | importin 5 | ![]() |
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2 | 2 | ||||||
MIRT354679 | CDV3 | CDV3 homolog | ![]() |
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2 | 2 | ||||||
MIRT366662 | PLP2 | proteolipid protein 2 | ![]() |
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2 | 2 | ||||||
MIRT404272 | PLEKHA8 | pleckstrin homology domain containing A8 | ![]() |
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2 | 2 | ||||||
MIRT447536 | RNF165 | ring finger protein 165 | ![]() |
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2 | 2 | ||||||
MIRT449139 | UQCRB | ubiquinol-cytochrome c reductase binding protein | ![]() |
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2 | 2 | ||||||
MIRT451301 | LGALS3BP | galectin 3 binding protein | ![]() |
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2 | 2 | ||||||
MIRT451488 | FOPNL | FGFR1OP N-terminal like | ![]() |
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2 | 2 | ||||||
MIRT455198 | GNL1 | G protein nucleolar 1 (putative) | ![]() |
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2 | 2 | ||||||
MIRT459215 | MRPS21 | mitochondrial ribosomal protein S21 | ![]() |
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2 | 2 | ||||||
MIRT461764 | MPDU1 | mannose-P-dolichol utilization defect 1 | ![]() |
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2 | 2 | ||||||
MIRT463273 | ZFX | zinc finger protein, X-linked | ![]() |
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2 | 2 | ||||||
MIRT464862 | UBB | ubiquitin B | ![]() |
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2 | 8 | ||||||
MIRT464950 | TWIST1 | twist family bHLH transcription factor 1 | ![]() |
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2 | 2 | ||||||
MIRT467378 | SON | SON DNA binding protein | ![]() |
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2 | 4 | ||||||
MIRT469282 | RHOA | ras homolog family member A | ![]() |
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2 | 2 | ||||||
MIRT470293 | PPTC7 | PTC7 protein phosphatase homolog | ![]() |
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2 | 2 | ||||||
MIRT470639 | POM121C | POM121 transmembrane nucleoporin C | ![]() |
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2 | 2 | ||||||
MIRT477163 | FABP3 | fatty acid binding protein 3 | ![]() |
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2 | 2 | ||||||
MIRT477686 | EFHD2 | EF-hand domain family member D2 | ![]() |
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2 | 2 | ||||||
MIRT479725 | CCNF | cyclin F | ![]() |
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2 | 2 | ||||||
MIRT481726 | APH1A | aph-1 homolog A, gamma-secretase subunit | ![]() |
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2 | 2 | ||||||
MIRT485673 | CCDC64 | BICD family like cargo adaptor 1 | ![]() |
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2 | 2 | ||||||
MIRT498280 | PADI2 | peptidyl arginine deiminase 2 | ![]() |
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2 | 2 | ||||||
MIRT499921 | GPX8 | glutathione peroxidase 8 (putative) | ![]() |
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2 | 2 | ||||||
MIRT503616 | SLC25A36 | solute carrier family 25 member 36 | ![]() |
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2 | 4 | ||||||
MIRT506927 | IGDCC4 | immunoglobulin superfamily DCC subclass member 4 | ![]() |
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2 | 6 | ||||||
MIRT507348 | FAM129A | family with sequence similarity 129 member A | ![]() |
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2 | 6 | ||||||
MIRT508265 | DYNLL2 | dynein light chain LC8-type 2 | ![]() |
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2 | 4 | ||||||
MIRT508284 | YES1 | YES proto-oncogene 1, Src family tyrosine kinase | ![]() |
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2 | 4 | ||||||
MIRT509353 | COPS8 | COP9 signalosome subunit 8 | ![]() |
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2 | 2 | ||||||
MIRT510892 | RAB1A | RAB1A, member RAS oncogene family | ![]() |
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2 | 4 | ||||||
MIRT511882 | GAS1 | growth arrest specific 1 | ![]() |
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2 | 6 | ||||||
MIRT511990 | E2F1 | E2F transcription factor 1 | ![]() |
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2 | 4 | ||||||
MIRT512239 | ARPP19 | cAMP regulated phosphoprotein 19 | ![]() |
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2 | 4 | ||||||
MIRT512392 | BUB1 | BUB1 mitotic checkpoint serine/threonine kinase | ![]() |
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2 | 4 | ||||||
MIRT514086 | EPS15L1 | epidermal growth factor receptor pathway substrate 15 like 1 | ![]() |
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2 | 6 | ||||||
MIRT514358 | UBBP4 | ubiquitin B pseudogene 4 | ![]() |
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2 | 6 | ||||||
MIRT523149 | HNRNPU | heterogeneous nuclear ribonucleoprotein U | ![]() |
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2 | 2 | ||||||
MIRT525511 | FSIP2 | fibrous sheath interacting protein 2 | ![]() |
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2 | 2 | ||||||
MIRT526333 | SH3TC2 | SH3 domain and tetratricopeptide repeats 2 | ![]() |
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2 | 2 | ||||||
MIRT529962 | ZNF71 | zinc finger protein 71 | ![]() |
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2 | 2 | ||||||
MIRT530337 | GABRB3 | gamma-aminobutyric acid type A receptor beta3 subunit | ![]() |
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2 | 2 | ||||||
MIRT530884 | PHOX2A | paired like homeobox 2a | ![]() |
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2 | 2 | ||||||
MIRT533097 | YOD1 | YOD1 deubiquitinase | ![]() |
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2 | 2 | ||||||
MIRT533250 | VCAM1 | vascular cell adhesion molecule 1 | ![]() |
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2 | 2 | ||||||
MIRT534786 | RAB8B | RAB8B, member RAS oncogene family | ![]() |
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2 | 2 | ||||||
MIRT537917 | DSTYK | dual serine/threonine and tyrosine protein kinase | ![]() |
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2 | 2 | ||||||
MIRT547799 | JARID2 | jumonji and AT-rich interaction domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT548714 | CRK | CRK proto-oncogene, adaptor protein | ![]() |
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2 | 2 | ||||||
MIRT555509 | PMEPA1 | prostate transmembrane protein, androgen induced 1 | ![]() |
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2 | 2 | ||||||
MIRT555984 | NFYB | nuclear transcription factor Y subunit beta | ![]() |
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2 | 2 | ||||||
MIRT557942 | FAM222B | family with sequence similarity 222 member B | ![]() |
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2 | 2 | ||||||
MIRT560830 | ZNF786 | zinc finger protein 786 | ![]() |
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2 | 2 | ||||||
MIRT562720 | ZNF714 | zinc finger protein 714 | ![]() |
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2 | 2 | ||||||
MIRT565337 | TMEM104 | transmembrane protein 104 | ![]() |
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2 | 2 | ||||||
MIRT614453 | REL | REL proto-oncogene, NF-kB subunit | ![]() |
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2 | 2 | ||||||
MIRT639474 | SLC6A4 | solute carrier family 6 member 4 | ![]() |
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2 | 2 | ||||||
MIRT644056 | IQCE | IQ motif containing E | ![]() |
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2 | 2 | ||||||
MIRT651652 | VWA1 | von Willebrand factor A domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT651866 | UNC119B | unc-119 lipid binding chaperone B | ![]() |
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2 | 2 | ||||||
MIRT653490 | SLC43A2 | solute carrier family 43 member 2 | ![]() |
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2 | 2 | ||||||
MIRT657039 | KCNJ6 | potassium voltage-gated channel subfamily J member 6 | ![]() |
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2 | 2 | ||||||
MIRT657985 | GAN | gigaxonin | ![]() |
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2 | 2 | ||||||
MIRT672117 | ATP6V0A2 | ATPase H+ transporting V0 subunit a2 | ![]() |
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2 | 2 | ||||||
MIRT683583 | GSTCD | glutathione S-transferase C-terminal domain containing | ![]() |
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2 | 2 | ||||||
MIRT688689 | CPS1 | carbamoyl-phosphate synthase 1 | ![]() |
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2 | 2 | ||||||
MIRT695375 | NSA2 | NSA2, ribosome biogenesis homolog | ![]() |
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2 | 2 | ||||||
MIRT696351 | EIF2S3 | eukaryotic translation initiation factor 2 subunit gamma | ![]() |
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2 | 2 | ||||||
MIRT700614 | PRKAA2 | protein kinase AMP-activated catalytic subunit alpha 2 | ![]() |
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2 | 2 | ||||||
MIRT703512 | FKBP15 | FK506 binding protein 15 | ![]() |
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2 | 2 | ||||||
MIRT705051 | C5orf15 | chromosome 5 open reading frame 15 | ![]() |
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2 | 2 | ||||||
MIRT705180 | BTG1 | BTG anti-proliferation factor 1 | ![]() |
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2 | 2 | ||||||
MIRT709409 | FBXL20 | F-box and leucine rich repeat protein 20 | ![]() |
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2 | 2 | ||||||
MIRT721053 | DCC | DCC netrin 1 receptor | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||
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