pre-miRNA Information | |
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pre-miRNA | hsa-mir-3123 |
Genomic Coordinates | chr1: 241132272 - 241132346 |
Description | Homo sapiens miR-3123 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||||
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Mature miRNA | hsa-miR-3123 | ||||||||||||||
Sequence | 49| CAGAGAAUUGUUUAAUC |65 | ||||||||||||||
Evidence | Experimental | ||||||||||||||
Experiments | Illumina | ||||||||||||||
Editing Events in miRNAs |
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SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | ZWILCH | ||||||||||||||||||||
Synonyms | KNTC1AP, hZwilch | ||||||||||||||||||||
Description | zwilch kinetochore protein | ||||||||||||||||||||
Transcript | NM_017975 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on ZWILCH | |||||||||||||||||||||
3'UTR of ZWILCH (miRNA target sites are highlighted) |
>ZWILCH|NM_017975|3'UTR 1 AGTGTGCTGATGAAGTCCTCTATAAGCACAAGCCAAAAAGAGAAAGAGAAAAAAAGGTAATTATTGTAGAACCTGAAAAC 81 AGCAATGTATGGAAACCCTCAAAGCAGAAAAGGGAGGAAGATCCTGAAGATTCTCTTATGAAGCTCCAAAATTGATAATC 161 CTGTCTCAGCTCTGCCTCCTCAGGAGGAGCATTAGTAGAACAGCAGTGATGAGGACACAGAGGGAGCAGACAGTGGGTAC 241 CACGATCTCCGTAACCATTTGCATGTGACTTAGCAAGGGCTCTGAAATGACAAAGAGAACGAGCACCACAAATGAGAACA 321 GGATCATTTTAGTAAATACAGCTTTATCCCAAAAGCTTTAACTGTATTGGGAAAACTTAAAAAATAGCATCCTCAAATTT 401 TCTGATTCTTATTTGCCATGAAATAGAACTTAGTAAATTAAATGTTATTTGAAAATGTTATAAGAGCTTTGTAAATATTT 481 CAGAAAATATGGGATAAATGCCTGAATTTGGTTCTTCTACAGGTGCTATAATAAAGTCCATCTCTCAATACTTATACTTT 561 CTAAATTCATCTCAGAATATTAGCAGCCATATTCCACAGTTCCTATAATTTTTACTGGGGGGGATTTGTGATAGGAAAGT 641 CCTTGGGAAACATTTCCAATCTTTCAAAATATTATTGTGTATCTTAAGAAGTATAGGAACTTGTATGTTGAAATGTTGTA 721 TGGTAGTTCTTGTATAGTTAAATAATAATCTTTTTAAGAGTTAATGATAAGCATATGTTATGTGCATTATTAATAAAATA 801 GTGGCCACTTAGGTAATACCCACTTTTATCTTGTGTGCTGGGTACTCTGGTTACTGAGATAAATAAGGCACTGGACATCC 881 TCACGTGGAGTTCACAGGCTCATCAGTGAATTCTGTACCACATTTCAACCTTGTTTATTTTAGTTTAATGGAATATACAT 961 TCTTAGTATTGCCTGATTATTTAAATTTGTTGAGGGGGATTGCATGTTGCTTTATTGGCCTGTAAAAATAGCTAGTTTGG 1041 TAAGATTTGGTCTCGCACCTTCCATCTTTGCTACCACATTAAAGATGAGCTTGTTAAAAAGGAAAGCATATTTCTCTGAT 1121 TGCCCTTATGGAGAAATAAAGATAAAATTCAAAGAAACAAAAAAAAAAAAAA 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 GSM1084064. RNA binding protein: AGO2. Condition:CLIP_noemetine_AbnovaAb
HITS-CLIP data was present in GSM1084068. RNA binding protein: AGO2. Condition:CLIP_noemetine_SigmaAb
HITS-CLIP data was present in GSM1084069. RNA binding protein: AGO2. Condition:CLIP_emetine_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 GSM4903829 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Human neurons / CTLTD_shCTL_a |
Location of target site | NM_017975 | 3UTR | ACCCUCAAAGCAGAAAAGGGAGGAAGAUCCUGAAGAUUCUCUUAUGAAGCUCCAAAAUUGAUAAUCCU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161238 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM4903831 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Human neurons / 124TD_shELAVL3_a |
Location of target site | NM_017975 | 3UTR | CAGAAAAGGGAGGAAGAUCCUGAAGAUUCUCUUAUGAAGCUCCAAAAUUGAUAAUCCU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161238 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 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_017975 | 3UTR | AAUUAUUGUAGAACCUGAAAACAGCAAUGUAUGGAAACCCUCAAAGCAGAAAAGGGAGGAAGAUCCUGAAGAUUCUCUUAUGAAGCUCCAAAAUUGAUAAUCCUGUCuca |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 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_017975 | 3UTR | UAAUUAUUGUAGAACCUGAAAACAGCAAUGUAUGGAAACCCUCAAAGCAGAAAAGGGAGGAAGAUCCUGAAGAUUCUCUUAUGAAGCUCCAAAAUUGAUAAUCCU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 5 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_017975 | 3UTR | UCUUAUGAAGCUCCAAAAUUGAUAAUCCUGUCuca |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 6 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_017975 | 3UTR | UCUCUUAUGAAGCUCCAAAAUUGAUAAUCCUGUCuc |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 7 for dataset GSM1084064 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_noemetine_AbnovaAb |
Location of target site | ENST00000307897.5 | 3UTR | AGCAGAAAAGGGAGGAAGAUCCUGAAGA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 8 for dataset GSM1084068 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_noemetine_SigmaAb |
Location of target site | ENST00000307897.5 | 3UTR | AGAAAAGGGAGGAAGAUCCUGAAGAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 9 for dataset GSM1084069 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_emetine_SigmaAb |
Location of target site | ENST00000307897.5 | 3UTR | GAAAAGGGAGGAAGAUCCUGAAGAU |
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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113 hsa-miR-3123 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT058369 | TBCEL | tubulin folding cofactor E like | ![]() |
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2 | 4 | ||||||
MIRT059816 | EFNA1 | ephrin A1 | ![]() |
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2 | 2 | ||||||
MIRT066850 | TMEM19 | transmembrane protein 19 | ![]() |
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2 | 2 | ||||||
MIRT071503 | CALM1 | calmodulin 1 | ![]() |
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2 | 6 | ||||||
MIRT073758 | NUBP1 | nucleotide binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT074324 | TNRC6A | trinucleotide repeat containing 6A | ![]() |
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2 | 10 | ||||||
MIRT094805 | LMNB1 | lamin B1 | ![]() |
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2 | 2 | ||||||
MIRT099173 | MAP3K4 | mitogen-activated protein kinase kinase kinase 4 | ![]() |
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2 | 2 | ||||||
MIRT099545 | ID4 | inhibitor of DNA binding 4, HLH protein | ![]() |
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2 | 2 | ||||||
MIRT122643 | E2F3 | E2F transcription factor 3 | ![]() |
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2 | 2 | ||||||
MIRT180918 | RPRD2 | regulation of nuclear pre-mRNA domain containing 2 | ![]() |
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2 | 8 | ||||||
MIRT192844 | BLOC1S6 | biogenesis of lysosomal organelles complex 1 subunit 6 | ![]() |
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2 | 2 | ||||||
MIRT224984 | BAG4 | BCL2 associated athanogene 4 | ![]() |
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2 | 2 | ||||||
MIRT246065 | NRAS | NRAS proto-oncogene, GTPase | ![]() |
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2 | 2 | ||||||
MIRT357085 | PRRC1 | proline rich coiled-coil 1 | ![]() |
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2 | 2 | ||||||
MIRT378170 | C5ORF51 | chromosome 5 open reading frame 51 | ![]() |
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2 | 2 | ||||||
MIRT441636 | KDM5A | lysine demethylase 5A | ![]() |
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2 | 2 | ||||||
MIRT441802 | BCAS1 | breast carcinoma amplified sequence 1 | ![]() |
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2 | 2 | ||||||
MIRT443019 | C21orf91 | chromosome 21 open reading frame 91 | ![]() |
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2 | 2 | ||||||
MIRT443445 | SERPINB4 | serpin family B member 4 | ![]() |
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2 | 2 | ||||||
MIRT443661 | SERPINB3 | serpin family B member 3 | ![]() |
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2 | 2 | ||||||
MIRT443776 | STS | steroid sulfatase | ![]() |
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2 | 2 | ||||||
MIRT444663 | TSPAN14 | tetraspanin 14 | ![]() |
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2 | 2 | ||||||
MIRT444924 | KIAA1522 | KIAA1522 | ![]() |
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2 | 2 | ||||||
MIRT445378 | FOXO1 | forkhead box O1 | ![]() |
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2 | 2 | ||||||
MIRT447920 | PAIP2B | poly(A) binding protein interacting protein 2B | ![]() |
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2 | 2 | ||||||
MIRT449202 | PTPLAD2 | 3-hydroxyacyl-CoA dehydratase 4 | ![]() |
1 | 1 | |||||||
MIRT449713 | TSPYL1 | TSPY like 1 | ![]() |
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2 | 2 | ||||||
MIRT450403 | TMEM47 | transmembrane protein 47 | ![]() |
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2 | 2 | ||||||
MIRT450787 | PAPOLG | poly(A) polymerase gamma | ![]() |
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2 | 2 | ||||||
MIRT451381 | C19orf43 | telomerase RNA component interacting RNase | ![]() |
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2 | 2 | ||||||
MIRT452507 | WDR1 | WD repeat domain 1 | ![]() |
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2 | 2 | ||||||
MIRT453264 | PARP11 | poly(ADP-ribose) polymerase family member 11 | ![]() |
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2 | 2 | ||||||
MIRT454642 | FAM83H | family with sequence similarity 83 member H | ![]() |
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2 | 2 | ||||||
MIRT455513 | C6orf106 | chromosome 6 open reading frame 106 | ![]() |
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2 | 2 | ||||||
MIRT456709 | LDB1 | LIM domain binding 1 | ![]() |
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2 | 2 | ||||||
MIRT457231 | AP3D1 | adaptor related protein complex 3 delta 1 subunit | ![]() |
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2 | 2 | ||||||
MIRT459235 | MRPS21 | mitochondrial ribosomal protein S21 | ![]() |
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2 | 2 | ||||||
MIRT460553 | IFNAR1 | interferon alpha and beta receptor subunit 1 | ![]() |
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2 | 4 | ||||||
MIRT461424 | CTSL2 | cathepsin V | ![]() |
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2 | 3 | ||||||
MIRT462869 | CYP51A1 | cytochrome P450 family 51 subfamily A member 1 | ![]() |
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2 | 2 | ||||||
MIRT467178 | SPTY2D1 | SPT2 chromatin protein domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT469233 | RHOBTB3 | Rho related BTB domain containing 3 | ![]() |
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2 | 2 | ||||||
MIRT474125 | LIPC | lipase C, hepatic type | ![]() |
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2 | 2 | ||||||
MIRT475509 | HSP90B1 | heat shock protein 90 beta family member 1 | ![]() |
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2 | 4 | ||||||
MIRT478134 | DHX36 | DEAH-box helicase 36 | ![]() |
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2 | 2 | ||||||
MIRT481326 | ATP5A1 | ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle | ![]() |
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2 | 2 | ||||||
MIRT482003 | AMOTL2 | angiomotin like 2 | ![]() |
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2 | 2 | ||||||
MIRT482230 | AHCYL2 | adenosylhomocysteinase like 2 | ![]() |
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2 | 2 | ||||||
MIRT483436 | RHOXF2B | Rhox homeobox family member 2B | ![]() |
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2 | 2 | ||||||
MIRT483824 | ZC3H12B | zinc finger CCCH-type containing 12B | ![]() |
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2 | 2 | ||||||
MIRT492051 | TNFSF9 | TNF superfamily member 9 | ![]() |
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2 | 2 | ||||||
MIRT494114 | DLX6 | distal-less homeobox 6 | ![]() |
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2 | 2 | ||||||
MIRT498882 | ZNF12 | zinc finger protein 12 | ![]() |
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2 | 10 | ||||||
MIRT499674 | NPHP3 | nephrocystin 3 | ![]() |
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2 | 2 | ||||||
MIRT506932 | IGDCC4 | immunoglobulin superfamily DCC subclass member 4 | ![]() |
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2 | 6 | ||||||
MIRT509461 | ZNF587 | zinc finger protein 587 | ![]() |
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2 | 6 | ||||||
MIRT510048 | AKR1B10 | aldo-keto reductase family 1 member B10 | ![]() |
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2 | 4 | ||||||
MIRT514807 | NWD1 | NACHT and WD repeat domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT515217 | CRCP | CGRP receptor component | ![]() |
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2 | 2 | ||||||
MIRT515486 | INCENP | inner centromere protein | ![]() |
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2 | 4 | ||||||
MIRT517765 | ZNF366 | zinc finger protein 366 | ![]() |
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2 | 4 | ||||||
MIRT518216 | TRMT10B | tRNA methyltransferase 10B | ![]() |
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2 | 2 | ||||||
MIRT519602 | ZNF805 | zinc finger protein 805 | ![]() |
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2 | 2 | ||||||
MIRT523570 | GGCX | gamma-glutamyl carboxylase | ![]() |
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2 | 4 | ||||||
MIRT525795 | SOD2 | superoxide dismutase 2 | ![]() |
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2 | 2 | ||||||
MIRT533055 | ZBTB37 | zinc finger and BTB domain containing 37 | ![]() |
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2 | 2 | ||||||
MIRT534218 | SLC37A3 | solute carrier family 37 member 3 | ![]() |
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2 | 4 | ||||||
MIRT535633 | NR2E1 | nuclear receptor subfamily 2 group E member 1 | ![]() |
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2 | 2 | ||||||
MIRT535863 | MRPL17 | mitochondrial ribosomal protein L17 | ![]() |
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2 | 2 | ||||||
MIRT536344 | LEFTY1 | left-right determination factor 1 | ![]() |
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2 | 2 | ||||||
MIRT537923 | DSTYK | dual serine/threonine and tyrosine protein kinase | ![]() |
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2 | 2 | ||||||
MIRT543114 | SKA2 | spindle and kinetochore associated complex subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT544717 | ZNF529 | zinc finger protein 529 | ![]() |
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2 | 2 | ||||||
MIRT544847 | BASP1 | brain abundant membrane attached signal protein 1 | ![]() |
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2 | 4 | ||||||
MIRT545536 | ARF3 | ADP ribosylation factor 3 | ![]() |
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2 | 2 | ||||||
MIRT547124 | PHLPP2 | PH domain and leucine rich repeat protein phosphatase 2 | ![]() |
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2 | 2 | ||||||
MIRT548070 | GIGYF1 | GRB10 interacting GYF protein 1 | ![]() |
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2 | 2 | ||||||
MIRT548446 | EIF1AX | eukaryotic translation initiation factor 1A, X-linked | ![]() |
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2 | 2 | ||||||
MIRT548626 | DAZAP1 | DAZ associated protein 1 | ![]() |
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2 | 4 | ||||||
MIRT550259 | FAM120AOS | family with sequence similarity 120A opposite strand | ![]() |
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2 | 2 | ||||||
MIRT551940 | AKAP8 | A-kinase anchoring protein 8 | ![]() |
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2 | 4 | ||||||
MIRT552511 | ZIK1 | zinc finger protein interacting with K protein 1 | ![]() |
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2 | 4 | ||||||
MIRT554015 | SPIRE1 | spire type actin nucleation factor 1 | ![]() |
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2 | 2 | ||||||
MIRT556647 | KPNA2 | karyopherin subunit alpha 2 | ![]() |
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2 | 4 | ||||||
MIRT559744 | ACOX1 | acyl-CoA oxidase 1 | ![]() |
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2 | 2 | ||||||
MIRT560393 | TMEM254 | transmembrane protein 254 | ![]() |
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2 | 2 | ||||||
MIRT562234 | HMGB2 | high mobility group box 2 | ![]() |
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2 | 2 | ||||||
MIRT563325 | ORC4 | origin recognition complex subunit 4 | ![]() |
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2 | 2 | ||||||
MIRT563697 | RPS26 | ribosomal protein S26 | ![]() |
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2 | 2 | ||||||
MIRT565066 | USP25 | ubiquitin specific peptidase 25 | ![]() |
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2 | 2 | ||||||
MIRT565349 | TMED2 | transmembrane p24 trafficking protein 2 | ![]() |
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2 | 2 | ||||||
MIRT565624 | SLC31A1 | solute carrier family 31 member 1 | ![]() |
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2 | 2 | ||||||
MIRT566379 | PNISR | PNN interacting serine and arginine rich protein | ![]() |
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2 | 2 | ||||||
MIRT567575 | FEM1C | fem-1 homolog C | ![]() |
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2 | 2 | ||||||
MIRT569383 | DDX20 | DEAD-box helicase 20 | ![]() |
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2 | 2 | ||||||
MIRT570037 | FAM228A | family with sequence similarity 228 member A | ![]() |
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2 | 2 | ||||||
MIRT573269 | DCAF10 | DDB1 and CUL4 associated factor 10 | ![]() |
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2 | 2 | ||||||
MIRT573912 | PARP1 | poly(ADP-ribose) polymerase 1 | ![]() |
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2 | 2 | ||||||
MIRT620034 | ST6GALNAC3 | ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 | ![]() |
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2 | 2 | ||||||
MIRT635606 | ZWILCH | zwilch kinetochore protein | ![]() |
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2 | 2 | ||||||
MIRT644413 | FRMD6 | FERM domain containing 6 | ![]() |
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2 | 2 | ||||||
MIRT652528 | TM9SF4 | transmembrane 9 superfamily member 4 | ![]() |
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2 | 2 | ||||||
MIRT656238 | MFSD6 | major facilitator superfamily domain containing 6 | ![]() |
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2 | 2 | ||||||
MIRT661373 | DYRK4 | dual specificity tyrosine phosphorylation regulated kinase 4 | ![]() |
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2 | 2 | ||||||
MIRT662530 | PNPLA4 | patatin like phospholipase domain containing 4 | ![]() |
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2 | 2 | ||||||
MIRT675551 | MALL | mal, T-cell differentiation protein like | ![]() |
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2 | 2 | ||||||
MIRT693650 | ACBD7 | acyl-CoA binding domain containing 7 | ![]() |
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2 | 2 | ||||||
MIRT696348 | SLC35D2 | solute carrier family 35 member D2 | ![]() |
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2 | 2 | ||||||
MIRT705815 | AKNA | AT-hook transcription factor | ![]() |
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2 | 2 | ||||||
MIRT707632 | TARDBP | TAR DNA binding protein | ![]() |
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2 | 2 | ||||||
MIRT717902 | COPS8 | COP9 signalosome subunit 8 | ![]() |
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2 | 2 | ||||||
MIRT723626 | SOBP | sine oculis binding protein homolog | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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