pre-miRNA Information | |
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pre-miRNA | hsa-mir-520a |
Genomic Coordinates | chr19: 53690881 - 53690965 |
Description | Homo sapiens miR-520a stem-loop |
Comment | None |
RNA Secondary Structure | |
Associated Diseases |
Mature miRNA Information | |||||||||||||||||||||||||
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Mature miRNA | hsa-miR-520a-5p | ||||||||||||||||||||||||
Sequence | 15| CUCCAGAGGGAAGUACUUUCU |35 | ||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||
Experiments | Array-cloned | ||||||||||||||||||||||||
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 | CALCR | ||||||||||||||||||||
Synonyms | CRT, CT-R, CTR, CTR1 | ||||||||||||||||||||
Description | calcitonin receptor | ||||||||||||||||||||
Transcript | NM_001164737 | ||||||||||||||||||||
Other Transcripts | NM_001164738 , NM_001742 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on CALCR | |||||||||||||||||||||
3'UTR of CALCR (miRNA target sites are highlighted) |
>CALCR|NM_001164737|3'UTR 1 ATGTGAAGCAAACACAGCATCGTGATCACTGAGCCATCATTTCCTGGGAGAAAGACCATGCATTTAAAGTATTCTCCATC 81 CTCCCAGGAACCGAACATATCATTTGTGAAGAATTATTCAGTGAATTTGTCCATTGTAAATCTGAAGAAAGTTATTCTTG 161 GTACTGTTGCTTTGGGAGACAGTCTAGGAATGGAGTCTCCCACTGCAACTTGTGAACTCCATCATTCATCCAGGACTGAG 241 ATGCAAATGTCACAGTAATGCAAGCAAAGTATCAAAGAAAAACAATGAAATTGACCTAGTTCAGATACAGGGTGCTCCTT 321 GTCAATACTGAGCCATTTATACCTTTGAAATATTAAAATCACTGTCAATATTTTTATTTTTAACTCTGGATTTTGAATTA 401 GATTATTTCTGTATTTGGCTATGGATCTGATTTTTAATTTTTTTAAATTTCAGTCAATTCTGATGTTACTGAGATGTTTT 481 ACCATCCTTACAATGTAAACCACATGAACTACGTGACCTCTGCAAGACAAAGCGGCTTTCTAATAGAGAGATTAGTAAAT 561 ATGTGAAGAAAAAGACCTGCATTTGGCAGGAAGATGTATGCTTTGAATGCAAAAGAAATTTAGAGTCAATTTGCTGAAAA 641 CATTACATGCTCAGCTTGGTTTTGGACAAGCCTGTCCATTGGGCAGGACCTAGCTGTTGTAAAGAATTGGTCTTAATGTT 721 GAATGTATTTTGGTTGCTGATGTTTATAAACTGAGAGGTCACAAAGAATCTATCACTAAAAATTTTTACAAAACTGCCAA 801 AAATATAATTCTTAGTGGAAGACAATACTCCCTTTAAAGAGAGTTTGCCACTCCCCTAAACTCCAGGATTTATAAAGCAA 881 ATTACTCCAAGGTTTATAAAGCAGATTACCTCTTGCCCTTGGGTGCTATCTAGCAGTAAAAGATAAATTTGTTGAATATT 961 GGTAATTAAAAGACTCCACATAAGTCCATTAACTGCTTTCCACCCAGCTTCAAAGCTTAAAAAGAGCTCAGGCTTTTCCA 1041 GGAAGATCCAGGAGGGCTAATTAGAAATCAACTTGTGGTTGACCGCTTGTTTCTTGTTATTACCAAAACAGGAGGGGAAA 1121 AAATTAACTGCTCCAAATTTAACCATAAATCAATTCATGTTTAACGTTTCTCATTAAAATCCAGTATTATATTATCATAT 1201 CTCTCTTTACTTCCCAGTATAAGATTTTTGAAAATCCTGAATAAACCAGTATCGTTACTGGCACCTGAAATTAATTTGTG 1281 AATTTGCAACAGTAATCAGAGTTACCATTATTTAATTTGTATGCTAAATGAGGAGGTACATTGAAACCCTCCAAATCTCC 1361 AGTCTCATCTATGTCATATTTTGCCACTGCCTTTCAGAAGTGATTTAGTTGTGGAAAGATAATAAATTGATTTGTTATGG 1441 TTACATATTTAGCGCACCCAGAGAAAATTAATTATATTTCTACAGAGAAAATGAATTTGGGATACTAAAGTAGTTTAAGT 1521 CTCCTTTACTGAATGTAAGGGGGGGATCGAAAAGAAGGTATTTTTCCAATCACAGTGTTATGTAGTATTGTTCTATTTTT 1601 GTTTACAAACATGGAAAACAGAGTATTTCTGGCAGCTGTGGTACAAATGTGATAATATATTGCTAAAATATTTTAGATGT 1681 TATTATGCTAATATAGTAGGGGTTGAAGAAAACAAAATAGCTTATTATAGAATTGCACATAGTTCTGCCCAAATTATGTG 1761 AAATGCTTATGCTTGTGTATATGTATAAATTAATACAGAGTACGTTAAAAGCAAAAAGATGTATATTTGCATATTTTTCT 1841 AAAGAAATATATTATTCATCTTTTCATTC 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 | TZM-bl | ||||||
Location of target site | 3'UTR | ||||||
Tools used in this research | TargetScan , miRTarCLIP , Piranha | ||||||
Original Description (Extracted from the article) |
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PAR-CLIP data was present in GSM1462573. RNA binding protein: AGO2. Condition:TZM-bl BaL
... - Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Whisnant AW; Bogerd HP; Flores O; Ho P; et al. - mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
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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 | Prostate Tissue | ||||||
Location of target site | 3'UTR | ||||||
Tools used in this research | TargetScan , miRTarCLIP , Piranha | ||||||
Original Description (Extracted from the article) |
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PAR-CLIP data was present in SRX1760639. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP-MDV_A
... - Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al., 2016, Neoplasia (New York, N.Y.). |
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miRNA-target interactions (Provided by authors) |
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Article |
- Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al. - Neoplasia (New York, N.Y.), 2016
MicroRNA (miRNA) deregulation in prostate cancer (PCa) contributes to PCa initiation and metastatic progression. To comprehensively define the cancer-associated changes in miRNA targeting and function in commonly studied models of PCa, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the Argonaute protein in a panel of PCa cell lines modeling different stages of PCa progression. Using this comprehensive catalogue of miRNA targets, we analyzed miRNA targeting on known drivers of PCa and examined tissue-specific and stage-specific pathway targeting by miRNAs. We found that androgen receptor is the most frequently targeted PCa oncogene and that miR-148a targets the largest number of known PCa drivers. Globally, tissue-specific and stage-specific changes in miRNA targeting are driven by homeostatic response to active oncogenic pathways. Our findings indicate that, even in advanced PCa, the miRNA pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. These findings are important because they are the first to globally characterize miRNA changes in PCa and demonstrate how the miRNA target spectrum responds to staged tumorigenesis.
LinkOut: [PMID: 27292025]
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CLIP-seq Support 1 for dataset GSM1462573 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | TZM-bl / TZM-bl BaL |
Location of target site | ENST00000359558.2 | 3UTR | AACUCUGGAUUUUGAA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23592263 / GSE59944 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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MiRNA-Target Expression Profile (TCGA) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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115 hsa-miR-520a-5p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT092732 | SETD5 | SET domain containing 5 | 2 | 4 | ||||||||
MIRT168595 | HMGA1 | high mobility group AT-hook 1 | 2 | 4 | ||||||||
MIRT232084 | CCSAP | centriole, cilia and spindle associated protein | 2 | 2 | ||||||||
MIRT252430 | MIDN | midnolin | 2 | 4 | ||||||||
MIRT294600 | ZNF460 | zinc finger protein 460 | 2 | 2 | ||||||||
MIRT343114 | IGF1R | insulin like growth factor 1 receptor | 2 | 2 | ||||||||
MIRT441904 | SEPN1 | selenoprotein N | 2 | 2 | ||||||||
MIRT443233 | ALG8 | ALG8, alpha-1,3-glucosyltransferase | 2 | 2 | ||||||||
MIRT446250 | ELP2 | elongator acetyltransferase complex subunit 2 | 2 | 2 | ||||||||
MIRT448001 | GPR63 | G protein-coupled receptor 63 | 2 | 2 | ||||||||
MIRT451560 | CIAPIN1 | cytokine induced apoptosis inhibitor 1 | 2 | 2 | ||||||||
MIRT455285 | BCL2L1 | BCL2 like 1 | 2 | 2 | ||||||||
MIRT456170 | ZDHHC6 | zinc finger DHHC-type containing 6 | 2 | 2 | ||||||||
MIRT456679 | LDB1 | LIM domain binding 1 | 2 | 2 | ||||||||
MIRT458206 | FOXL2 | forkhead box L2 | 2 | 2 | ||||||||
MIRT461267 | COX10 | COX10, heme A:farnesyltransferase cytochrome c oxidase assembly factor | 2 | 2 | ||||||||
MIRT461683 | ZNF426 | zinc finger protein 426 | 2 | 2 | ||||||||
MIRT462656 | HMOX1 | heme oxygenase 1 | 2 | 4 | ||||||||
MIRT464368 | URM1 | ubiquitin related modifier 1 | 2 | 2 | ||||||||
MIRT468138 | SH3BP4 | SH3 domain binding protein 4 | 2 | 2 | ||||||||
MIRT468234 | SGK1 | serum/glucocorticoid regulated kinase 1 | 2 | 2 | ||||||||
MIRT470357 | PPP2R5E | protein phosphatase 2 regulatory subunit B'epsilon | 2 | 2 | ||||||||
MIRT472039 | NPAT | nuclear protein, coactivator of histone transcription | 2 | 2 | ||||||||
MIRT475941 | GXYLT1 | glucoside xylosyltransferase 1 | 2 | 2 | ||||||||
MIRT477880 | DYNLL2 | dynein light chain LC8-type 2 | 2 | 2 | ||||||||
MIRT480419 | C17orf85 | nuclear cap binding subunit 3 | 2 | 2 | ||||||||
MIRT482642 | RPL18A | ribosomal protein L18a | 2 | 2 | ||||||||
MIRT485666 | CDC25B | cell division cycle 25B | 2 | 2 | ||||||||
MIRT485740 | CALCR | calcitonin receptor | 2 | 2 | ||||||||
MIRT488906 | TSTD2 | thiosulfate sulfurtransferase like domain containing 2 | 2 | 6 | ||||||||
MIRT490412 | NRXN3 | neurexin 3 | 2 | 2 | ||||||||
MIRT494726 | ARHGAP1 | Rho GTPase activating protein 1 | 2 | 6 | ||||||||
MIRT495957 | TBC1D19 | TBC1 domain family member 19 | 2 | 2 | ||||||||
MIRT498087 | SEMA7A | semaphorin 7A (John Milton Hagen blood group) | 2 | 2 | ||||||||
MIRT507449 | EIF6 | eukaryotic translation initiation factor 6 | 2 | 2 | ||||||||
MIRT522992 | INPP4A | inositol polyphosphate-4-phosphatase type I A | 2 | 4 | ||||||||
MIRT526008 | RBM4B | RNA binding motif protein 4B | 2 | 2 | ||||||||
MIRT527693 | IL17REL | interleukin 17 receptor E like | 2 | 2 | ||||||||
MIRT528202 | NELFE | negative elongation factor complex member E | 2 | 2 | ||||||||
MIRT529123 | HOMEZ | homeobox and leucine zipper encoding | 2 | 2 | ||||||||
MIRT529484 | TPD52L3 | tumor protein D52 like 3 | 2 | 2 | ||||||||
MIRT530760 | ZNF582 | zinc finger protein 582 | 2 | 2 | ||||||||
MIRT531930 | IL12RB2 | interleukin 12 receptor subunit beta 2 | 2 | 2 | ||||||||
MIRT532347 | PLEK | pleckstrin | 2 | 2 | ||||||||
MIRT532819 | ZNF827 | zinc finger protein 827 | 2 | 2 | ||||||||
MIRT533262 | VAV3 | vav guanine nucleotide exchange factor 3 | 2 | 4 | ||||||||
MIRT533518 | TRIM13 | tripartite motif containing 13 | 2 | 2 | ||||||||
MIRT534279 | SLC12A7 | solute carrier family 12 member 7 | 2 | 2 | ||||||||
MIRT534483 | SAR1B | secretion associated Ras related GTPase 1B | 2 | 2 | ||||||||
MIRT538555 | CELF1 | CUGBP Elav-like family member 1 | 2 | 4 | ||||||||
MIRT538801 | C2CD5 | C2 calcium dependent domain containing 5 | 2 | 2 | ||||||||
MIRT553759 | TAOK1 | TAO kinase 1 | 2 | 2 | ||||||||
MIRT556035 | MXD1 | MAX dimerization protein 1 | 2 | 2 | ||||||||
MIRT557541 | GOSR1 | golgi SNAP receptor complex member 1 | 2 | 2 | ||||||||
MIRT562451 | CSDE1 | cold shock domain containing E1 | 2 | 2 | ||||||||
MIRT563686 | RPS26 | ribosomal protein S26 | 2 | 2 | ||||||||
MIRT568249 | BTF3L4 | basic transcription factor 3 like 4 | 2 | 2 | ||||||||
MIRT568422 | ATF7IP | activating transcription factor 7 interacting protein | 2 | 2 | ||||||||
MIRT574053 | PROSC | pyridoxal phosphate binding protein | 2 | 2 | ||||||||
MIRT606825 | APBB2 | amyloid beta precursor protein binding family B member 2 | 2 | 2 | ||||||||
MIRT609585 | GPM6B | glycoprotein M6B | 2 | 2 | ||||||||
MIRT609680 | TMEM213 | transmembrane protein 213 | 2 | 2 | ||||||||
MIRT611223 | ZNF274 | zinc finger protein 274 | 2 | 2 | ||||||||
MIRT612585 | SYNGAP1 | synaptic Ras GTPase activating protein 1 | 2 | 4 | ||||||||
MIRT613585 | MDGA2 | MAM domain containing glycosylphosphatidylinositol anchor 2 | 2 | 2 | ||||||||
MIRT614396 | C11orf45 | chromosome 11 open reading frame 45 | 2 | 2 | ||||||||
MIRT615562 | JPH2 | junctophilin 2 | 2 | 2 | ||||||||
MIRT615852 | RASGRP1 | RAS guanyl releasing protein 1 | 2 | 2 | ||||||||
MIRT615934 | MAP1LC3B | microtubule associated protein 1 light chain 3 beta | 2 | 2 | ||||||||
MIRT617635 | RXRA | retinoid X receptor alpha | 2 | 2 | ||||||||
MIRT618058 | PCDH19 | protocadherin 19 | 2 | 2 | ||||||||
MIRT618747 | CNNM3 | cyclin and CBS domain divalent metal cation transport mediator 3 | 2 | 2 | ||||||||
MIRT623739 | GRIN2B | glutamate ionotropic receptor NMDA type subunit 2B | 2 | 2 | ||||||||
MIRT629609 | NOL10 | nucleolar protein 10 | 2 | 2 | ||||||||
MIRT635219 | CD59 | CD59 molecule (CD59 blood group) | 2 | 2 | ||||||||
MIRT638035 | SHPK | sedoheptulokinase | 2 | 2 | ||||||||
MIRT638545 | KIAA1549 | KIAA1549 | 2 | 2 | ||||||||
MIRT645853 | AFF2 | AF4/FMR2 family member 2 | 2 | 2 | ||||||||
MIRT646023 | S100A7A | S100 calcium binding protein A7A | 2 | 2 | ||||||||
MIRT646562 | ALDH5A1 | aldehyde dehydrogenase 5 family member A1 | 2 | 2 | ||||||||
MIRT646735 | FADS1 | fatty acid desaturase 1 | 2 | 2 | ||||||||
MIRT652853 | TACC1 | transforming acidic coiled-coil containing protein 1 | 2 | 2 | ||||||||
MIRT654754 | PRKCB | protein kinase C beta | 2 | 2 | ||||||||
MIRT655238 | PEX26 | peroxisomal biogenesis factor 26 | 2 | 2 | ||||||||
MIRT655627 | ONECUT1 | one cut homeobox 1 | 2 | 2 | ||||||||
MIRT655892 | NEK9 | NIMA related kinase 9 | 2 | 2 | ||||||||
MIRT656184 | MON1B | MON1 homolog B, secretory trafficking associated | 2 | 2 | ||||||||
MIRT656551 | LZIC | leucine zipper and CTNNBIP1 domain containing | 2 | 2 | ||||||||
MIRT657743 | GNG12 | G protein subunit gamma 12 | 2 | 2 | ||||||||
MIRT659981 | C2CD2L | C2CD2 like | 2 | 2 | ||||||||
MIRT660824 | AGO3 | argonaute 3, RISC catalytic component | 2 | 2 | ||||||||
MIRT663511 | AGMO | alkylglycerol monooxygenase | 2 | 2 | ||||||||
MIRT666613 | REEP2 | receptor accessory protein 2 | 2 | 2 | ||||||||
MIRT668266 | FOXO3 | forkhead box O3 | 2 | 2 | ||||||||
MIRT669395 | BACE2 | beta-site APP-cleaving enzyme 2 | 2 | 2 | ||||||||
MIRT669512 | ARHGAP26 | Rho GTPase activating protein 26 | 2 | 2 | ||||||||
MIRT678895 | TTLL12 | tubulin tyrosine ligase like 12 | 2 | 2 | ||||||||
MIRT685122 | ADAT1 | adenosine deaminase, tRNA specific 1 | 2 | 2 | ||||||||
MIRT685674 | PSMB7 | proteasome subunit beta 7 | 2 | 2 | ||||||||
MIRT690647 | RPF2 | ribosome production factor 2 homolog | 2 | 2 | ||||||||
MIRT697114 | OTUD5 | OTU deubiquitinase 5 | 2 | 2 | ||||||||
MIRT697742 | USP5 | ubiquitin specific peptidase 5 | 2 | 2 | ||||||||
MIRT698584 | TEX261 | testis expressed 261 | 2 | 2 | ||||||||
MIRT700075 | RNF38 | ring finger protein 38 | 2 | 2 | ||||||||
MIRT709340 | ZNF35 | zinc finger protein 35 | 2 | 2 | ||||||||
MIRT711071 | NLGN2 | neuroligin 2 | 2 | 2 | ||||||||
MIRT714634 | TM4SF18 | transmembrane 4 L six family member 18 | 2 | 2 | ||||||||
MIRT715421 | SPOPL | speckle type BTB/POZ protein like | 2 | 2 | ||||||||
MIRT718663 | HNF4A | hepatocyte nuclear factor 4 alpha | 2 | 2 | ||||||||
MIRT718931 | TRIM66 | tripartite motif containing 66 | 2 | 2 | ||||||||
MIRT720640 | ELF5 | E74 like ETS transcription factor 5 | 2 | 2 | ||||||||
MIRT720788 | PRKRIP1 | PRKR interacting protein 1 | 2 | 2 | ||||||||
MIRT721289 | TRABD2A | TraB domain containing 2A | 2 | 2 | ||||||||
MIRT722893 | LRRC20 | leucine rich repeat containing 20 | 2 | 2 | ||||||||
MIRT724307 | KCNH1 | potassium voltage-gated channel subfamily H member 1 | 2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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