pre-miRNA Information | |
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pre-miRNA | hsa-mir-4640 |
Genomic Coordinates | chr6: 30890883 - 30890972 |
Description | Homo sapiens miR-4640 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||||||||||||||
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Mature miRNA | hsa-miR-4640-5p | ||||||||||||||||||||||||
Sequence | 9| UGGGCCAGGGAGCAGCUGGUGGG |31 | ||||||||||||||||||||||||
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 |
Biomarker Information |
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Gene Information | |||||||||||||||||||||
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Gene Symbol | OSBPL5 | ||||||||||||||||||||
Synonyms | OBPH1, ORP5 | ||||||||||||||||||||
Description | oxysterol binding protein like 5 | ||||||||||||||||||||
Transcript | NM_001144063 | ||||||||||||||||||||
Other Transcripts | NM_020896 , NM_145638 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on OSBPL5 | |||||||||||||||||||||
3'UTR of OSBPL5 (miRNA target sites are highlighted) |
>OSBPL5|NM_001144063|3'UTR 1 GAGCCCTGAGGGCAGAGCTCCTGGCCGGTCCTGAGCCCTCCCTCCCAGGCACCCAGCACTTTAAGCCTGCTCCATGGAGG 81 CAGAGAGGCCCGGCAAGCACAGCCACTGTGACGGGGAGTCCAGGCGCAGGAGGGACCCGGGGCCACAAGGCGCTGCGGGC 161 CCAGGTGTGCTGGGCCCCTCTCAGGGGCACTGGCCTCTCTGCAGGGCCTTCCGCCCAGCGCTGGCCTTAATGCTAAAGCC 241 AAATGCAGCTTCTGCTGTGCGACGCACTCCTGGCCATCTTGCCGTGTCACCCCCTGTCCGGCCTCCACTTGCCATGGGGG 321 ATGGATGGATTTAGGGTGGGAGGGCCTGTGGGGGCCCTGGACAGTCACACCCCAGCAGCAGTGAGTGGGCAGGTTTGGAG 401 GAGCCCCGAGTGGCCCAGGAGTCCCCCCACACACAGATGCATAGGCCTGCCTTCCGGAGACCCTGTCCACATTGCCGGGA 481 CCACCCTGGTGGGGCCACTGGTGGGTGCCAGGGACAGGTTAGGGCCACTCTGGGGAAGGCATTTTGGTTTTTTATTCCAC 561 GCTGTGCTGTTTGGATGGGAGCCCCACAGAGGCAGGTCCTGGAACCACCCCACCCCCACACCTGGACGCTCGCTCTGGTG 641 GGGGCACACGCAGGTGGAGGTGGTTGTGGGTGCAGGTGTGTGCAGGGGTGTGGGGGGCGCAGGGGTGTGGCTTAGCTGGC 721 CCCGCACCCAGGCCGGGGAGGCTCAAGTTCGCCACTTTACTCAGACCGATGCACAGTCTTCCCATTTTACACTTTTTTAA 801 TAAACATAATTGCAATATTTTAGGTGGGCTGCGAGCTGCAGTCAGCCTTCACGTCTGGCCTCAGTCCCCGTGTCAGTGCC 881 GCTCTGCGTGTGCGTGTGCGCGTGTGTGAGCCTCTACACATATATATACGTACAGAGCCTTAAACCACATCGTGGCGGTG 961 CCGTCTGAGCTGTAGCGGGTGGCTTTGTTTCCAGTTTTTGTACCCGTGTCCTTGTCTCCCCTCCTCCCCCATCTGGGGAT 1041 GTGTCTGTGTTCCACACCTTGAAATAAACAGACACATACGTGTTCTCTTAAAAAAAAAAAAAAAAA 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 | hESCs (WA-09) | |||||||||
Disease | 114879.0 | |||||||||
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 SRR359787. RNA binding protein: AGO2. Condition:4-thiouridine
... - Lipchina I; Elkabetz Y; Hafner M; Sheridan et al., 2011, Genes & development. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Lipchina I; Elkabetz Y; Hafner M; Sheridan et al. - Genes & development, 2011
MicroRNAs are important regulators in many cellular processes, including stem cell self-renewal. Recent studies demonstrated their function as pluripotency factors with the capacity for somatic cell reprogramming. However, their role in human embryonic stem (ES) cells (hESCs) remains poorly understood, partially due to the lack of genome-wide strategies to identify their targets. Here, we performed comprehensive microRNA profiling in hESCs and in purified neural and mesenchymal derivatives. Using a combination of AGO cross-linking and microRNA perturbation experiments, together with computational prediction, we identified the targets of the miR-302/367 cluster, the most abundant microRNAs in hESCs. Functional studies identified novel roles of miR-302/367 in maintaining pluripotency and regulating hESC differentiation. We show that in addition to its role in TGF-beta signaling, miR-302/367 promotes bone morphogenetic protein (BMP) signaling by targeting BMP inhibitors TOB2, DAZAP2, and SLAIN1. This study broadens our understanding of microRNA function in hESCs and is a valuable resource for future studies in this area.
LinkOut: [PMID: 22012620]
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CLIP-seq Support 1 for dataset SRR359787 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | hESCs (WA-09) / 4-thiouridine, RNase T1 |
Location of target site | ENST00000478260.1 | 3UTR | UGUGGGGGGCGCAGGGGUGUGGCUUAGCUGG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 22012620 / SRX103431 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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87 hsa-miR-4640-5p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT100106 | ABT1 | activator of basal transcription 1 | ![]() |
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2 | 8 | ||||||
MIRT248144 | LMBR1L | limb development membrane protein 1 like | ![]() |
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2 | 2 | ||||||
MIRT327062 | KLHL15 | kelch like family member 15 | ![]() |
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2 | 2 | ||||||
MIRT347231 | GATAD2A | GATA zinc finger domain containing 2A | ![]() |
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2 | 2 | ||||||
MIRT450221 | CENPN | centromere protein N | ![]() |
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2 | 2 | ||||||
MIRT451264 | NDUFA11 | NADH:ubiquinone oxidoreductase subunit A11 | ![]() |
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2 | 2 | ||||||
MIRT452701 | C1orf226 | chromosome 1 open reading frame 226 | ![]() |
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2 | 2 | ||||||
MIRT453212 | CERS1 | ceramide synthase 1 | ![]() |
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2 | 2 | ||||||
MIRT454822 | POLR2J3 | RNA polymerase II subunit J3 | ![]() |
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2 | 2 | ||||||
MIRT454883 | RAD50 | RAD50 double strand break repair protein | ![]() |
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2 | 2 | ||||||
MIRT455783 | TAF8 | TATA-box binding protein associated factor 8 | ![]() |
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2 | 2 | ||||||
MIRT455858 | TMEM254 | transmembrane protein 254 | ![]() |
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2 | 2 | ||||||
MIRT457615 | UPK3BL | uroplakin 3B like 1 | ![]() |
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2 | 2 | ||||||
MIRT457822 | ITPRIP | inositol 1,4,5-trisphosphate receptor interacting protein | ![]() |
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2 | 4 | ||||||
MIRT458344 | NOC2L | NOC2 like nucleolar associated transcriptional repressor | ![]() |
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2 | 2 | ||||||
MIRT458376 | ITM2C | integral membrane protein 2C | ![]() |
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2 | 2 | ||||||
MIRT458928 | SAMD4B | sterile alpha motif domain containing 4B | ![]() |
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2 | 2 | ||||||
MIRT459066 | WFIKKN2 | WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT460138 | ASB16 | ankyrin repeat and SOCS box containing 16 | ![]() |
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2 | 2 | ||||||
MIRT460818 | FSTL4 | follistatin like 4 | ![]() |
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2 | 2 | ||||||
MIRT461285 | COX10 | COX10, heme A:farnesyltransferase cytochrome c oxidase assembly factor | ![]() |
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2 | 2 | ||||||
MIRT462738 | EFNB1 | ephrin B1 | ![]() |
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2 | 2 | ||||||
MIRT464556 | UBTF | upstream binding transcription factor, RNA polymerase I | ![]() |
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2 | 2 | ||||||
MIRT477910 | DUSP2 | dual specificity phosphatase 2 | ![]() |
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2 | 2 | ||||||
MIRT479073 | CNNM4 | cyclin and CBS domain divalent metal cation transport mediator 4 | ![]() |
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2 | 4 | ||||||
MIRT479534 | CDC5L | cell division cycle 5 like | ![]() |
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2 | 4 | ||||||
MIRT485628 | EEPD1 | endonuclease/exonuclease/phosphatase family domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT489896 | PPIC | peptidylprolyl isomerase C | ![]() |
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2 | 4 | ||||||
MIRT490737 | SRCIN1 | SRC kinase signaling inhibitor 1 | ![]() |
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2 | 2 | ||||||
MIRT491201 | MLLT1 | MLLT1, super elongation complex subunit | ![]() |
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2 | 4 | ||||||
MIRT492681 | PHYHIP | phytanoyl-CoA 2-hydroxylase interacting protein | ![]() |
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2 | 2 | ||||||
MIRT494593 | ATG7 | autophagy related 7 | ![]() |
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2 | 2 | ||||||
MIRT495061 | PADI3 | peptidyl arginine deiminase 3 | ![]() |
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2 | 4 | ||||||
MIRT496623 | TMEM67 | transmembrane protein 67 | ![]() |
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2 | 2 | ||||||
MIRT497177 | ZBTB40 | zinc finger and BTB domain containing 40 | ![]() |
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2 | 2 | ||||||
MIRT498217 | TLN2 | talin 2 | ![]() |
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2 | 2 | ||||||
MIRT498306 | BCL11B | B-cell CLL/lymphoma 11B | ![]() |
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2 | 2 | ||||||
MIRT499668 | NPHP3 | nephrocystin 3 | ![]() |
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2 | 2 | ||||||
MIRT508080 | ANKRD52 | ankyrin repeat domain 52 | ![]() |
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2 | 2 | ||||||
MIRT509707 | ANKRD23 | ankyrin repeat domain 23 | ![]() |
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2 | 2 | ||||||
MIRT509841 | FOS | Fos proto-oncogene, AP-1 transcription factor subunit | ![]() |
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2 | 2 | ||||||
MIRT512814 | ARRDC2 | arrestin domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT513353 | SLIT1 | slit guidance ligand 1 | ![]() |
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2 | 2 | ||||||
MIRT514293 | FXYD5 | FXYD domain containing ion transport regulator 5 | ![]() |
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2 | 2 | ||||||
MIRT516598 | FAM89A | family with sequence similarity 89 member A | ![]() |
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2 | 4 | ||||||
MIRT516616 | DARS2 | aspartyl-tRNA synthetase 2, mitochondrial | ![]() |
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2 | 2 | ||||||
MIRT518348 | CCL5 | C-C motif chemokine ligand 5 | ![]() |
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2 | 2 | ||||||
MIRT520130 | WSB1 | WD repeat and SOCS box containing 1 | ![]() |
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2 | 2 | ||||||
MIRT522072 | ORAI2 | ORAI calcium release-activated calcium modulator 2 | ![]() |
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2 | 2 | ||||||
MIRT526461 | OSBPL5 | oxysterol binding protein like 5 | ![]() |
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2 | 2 | ||||||
MIRT528278 | MBL2 | mannose binding lectin 2 | ![]() |
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2 | 2 | ||||||
MIRT534844 | RAB15 | RAB15, member RAS oncogene family | ![]() |
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2 | 4 | ||||||
MIRT542245 | HSPA4L | heat shock protein family A (Hsp70) member 4 like | ![]() |
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2 | 2 | ||||||
MIRT543299 | ZNF585B | zinc finger protein 585B | ![]() |
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2 | 2 | ||||||
MIRT552456 | ZNF410 | zinc finger protein 410 | ![]() |
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2 | 2 | ||||||
MIRT553641 | TJAP1 | tight junction associated protein 1 | ![]() |
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2 | 2 | ||||||
MIRT557103 | HOXA3 | homeobox A3 | ![]() |
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2 | 2 | ||||||
MIRT570782 | FANCA | Fanconi anemia complementation group A | ![]() |
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2 | 2 | ||||||
MIRT630912 | ZMAT2 | zinc finger matrin-type 2 | ![]() |
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2 | 2 | ||||||
MIRT631034 | ZNF878 | zinc finger protein 878 | ![]() |
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2 | 2 | ||||||
MIRT639017 | AAK1 | AP2 associated kinase 1 | ![]() |
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2 | 2 | ||||||
MIRT648596 | ZYG11B | zyg-11 family member B, cell cycle regulator | ![]() |
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2 | 2 | ||||||
MIRT648939 | ATP5A1 | ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle | ![]() |
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2 | 2 | ||||||
MIRT652834 | TACO1 | translational activator of cytochrome c oxidase I | ![]() |
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2 | 2 | ||||||
MIRT659347 | CSRP1 | cysteine and glycine rich protein 1 | ![]() |
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2 | 2 | ||||||
MIRT664163 | APOBEC3F | apolipoprotein B mRNA editing enzyme catalytic subunit 3F | ![]() |
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2 | 2 | ||||||
MIRT670511 | ZSCAN22 | zinc finger and SCAN domain containing 22 | ![]() |
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2 | 2 | ||||||
MIRT671246 | TMEM41B | transmembrane protein 41B | ![]() |
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2 | 2 | ||||||
MIRT672120 | ATP6V0A2 | ATPase H+ transporting V0 subunit a2 | ![]() |
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2 | 2 | ||||||
MIRT672313 | CD3D | CD3d molecule | ![]() |
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2 | 2 | ||||||
MIRT672543 | BRMS1L | breast cancer metastasis-suppressor 1 like | ![]() |
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2 | 2 | ||||||
MIRT673036 | SGPL1 | sphingosine-1-phosphate lyase 1 | ![]() |
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2 | 2 | ||||||
MIRT673814 | DARS | aspartyl-tRNA synthetase | ![]() |
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2 | 2 | ||||||
MIRT674858 | GINM1 | glycoprotein integral membrane 1 | ![]() |
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2 | 2 | ||||||
MIRT674970 | SH3BP2 | SH3 domain binding protein 2 | ![]() |
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2 | 2 | ||||||
MIRT675185 | KIF1C | kinesin family member 1C | ![]() |
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2 | 2 | ||||||
MIRT675219 | UGDH | UDP-glucose 6-dehydrogenase | ![]() |
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2 | 2 | ||||||
MIRT675558 | MED16 | mediator complex subunit 16 | ![]() |
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2 | 2 | ||||||
MIRT682566 | EIF4EBP1 | eukaryotic translation initiation factor 4E binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT684640 | PDE4C | phosphodiesterase 4C | ![]() |
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2 | 2 | ||||||
MIRT689722 | ATXN2 | ataxin 2 | ![]() |
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2 | 2 | ||||||
MIRT693594 | SLC39A1 | solute carrier family 39 member 1 | ![]() |
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2 | 2 | ||||||
MIRT704745 | CDKN2B | cyclin dependent kinase inhibitor 2B | ![]() |
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2 | 2 | ||||||
MIRT712779 | ZNF154 | zinc finger protein 154 | ![]() |
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2 | 2 | ||||||
MIRT718118 | OTOF | otoferlin | ![]() |
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2 | 2 | ||||||
MIRT720115 | SAMD4A | sterile alpha motif domain containing 4A | ![]() |
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2 | 2 | ||||||
MIRT720275 | EIF1AD | eukaryotic translation initiation factor 1A domain containing | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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