pre-miRNA Information
pre-miRNA hsa-mir-2115   
Genomic Coordinates chr3: 48316360 - 48316459
Description Homo sapiens miR-2115 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-2115-3p
Sequence 58| CAUCAGAAUUCAUGGAGGCUAG |79
Evidence Experimental
Experiments 454
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN31490809 22 COSMIC
COSN31579735 22 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs543123304 18 dbSNP
rs1450988157 21 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol CCDC58   
Synonyms -
Description coiled-coil domain containing 58
Transcript NM_001017928   
Expression
Putative miRNA Targets on CCDC58
3'UTR of CCDC58
(miRNA target sites are highlighted)
>CCDC58|NM_001017928|3'UTR
   1 AGAGAGATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAGGACTGGGTCATCTCATAAGAGCTAAGCATGACAGATATC
  81 AACAGGGCGGGCTTTCTAGGATGATTTCTGAGCCAACAGTCCAAGACCTTTTGTTGATTTCAGCCCCACTTAGCCAAGAC
 161 CTCAAGTATAAATAATTCTGATAATTATGGAGAAATCAACTGCTATTTTATACTGATTCTGTAAAAAAAAAAAAAAAAAA
 241 TTTTTGTAACTATTAAAATAATTTTCTGACTCAGTGTAAAAAAAAAAA
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
miRNA-target interactions
(Predicted by miRanda)
ID Duplex structure Position Score MFE
1
miRNA  3' gaUCGGAGGUACUUAAGACUAc 5'
            ||: |  || ||||||||| 
Target 5' caAGTATAAAT-AATTCTGATa 3'
163 - 183 159.00 -8.40
2
miRNA  3' gaUCGGAGG----UACUUAAGACUac 5'
            :||:|:|    |||| ||||||  
Target 5' cgGGCTTTCTAGGATGATTTCTGAgc 3'
88 - 113 146.00 -14.40
3
miRNA  3' gaUCGGAGGU-ACUUAAGACUAc 5'
            | |: |:| |  || ||||| 
Target 5' tcAACTGCTATTTTATACTGATt 3'
196 - 218 120.00 -6.50
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30128014 8 COSMIC
COSN20066740 10 COSMIC
COSN32051228 10 COSMIC
COSN30112883 59 COSMIC
COSN26585190 73 COSMIC
COSN31553104 88 COSMIC
COSN31531215 105 COSMIC
COSN26669044 110 COSMIC
COSN20098958 223 COSMIC
COSN20098957 241 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs767673899 2 dbSNP
rs558878834 3 dbSNP
rs1196440111 4 dbSNP
rs1316937410 5 dbSNP
rs752513128 6 dbSNP
rs765123169 7 dbSNP
rs759478209 8 dbSNP
rs766309142 8 dbSNP
rs1246388034 9 dbSNP
rs776066248 10 dbSNP
rs13096094 11 dbSNP
rs369604831 11 dbSNP
rs71136568 11 dbSNP
rs773263545 13 dbSNP
rs765593355 15 dbSNP
rs1378186399 16 dbSNP
rs1333804607 17 dbSNP
rs760519903 19 dbSNP
rs775497571 20 dbSNP
rs866260514 20 dbSNP
rs772000589 21 dbSNP
rs745737302 22 dbSNP
rs774370494 23 dbSNP
rs1459556804 24 dbSNP
rs1366618728 27 dbSNP
rs765903865 29 dbSNP
rs1164082345 30 dbSNP
rs1266467301 31 dbSNP
rs1440065217 32 dbSNP
rs888076701 33 dbSNP
rs1176552461 34 dbSNP
rs1457010349 35 dbSNP
rs1267640927 36 dbSNP
rs1211075851 37 dbSNP
rs111604414 38 dbSNP
rs1162721860 39 dbSNP
rs1175590264 39 dbSNP
rs1225436716 39 dbSNP
rs1241294166 39 dbSNP
rs1266563867 39 dbSNP
rs1274487618 39 dbSNP
rs1291554663 39 dbSNP
rs1308641981 39 dbSNP
rs1336003592 39 dbSNP
rs1357914123 39 dbSNP
rs1363616193 39 dbSNP
rs1365767126 39 dbSNP
rs1426518600 39 dbSNP
rs1454087721 39 dbSNP
rs1480314089 39 dbSNP
rs527562300 39 dbSNP
rs748507581 39 dbSNP
rs755822160 39 dbSNP
rs777166037 39 dbSNP
rs777269009 39 dbSNP
rs1227147827 40 dbSNP
rs1231091587 40 dbSNP
rs755348367 41 dbSNP
rs993710307 44 dbSNP
rs566554770 46 dbSNP
rs1314017785 47 dbSNP
rs1434825354 48 dbSNP
rs897961829 55 dbSNP
rs748647859 56 dbSNP
rs1202501868 68 dbSNP
rs1253189325 72 dbSNP
rs571685599 76 dbSNP
rs950101002 79 dbSNP
rs1241535810 82 dbSNP
rs1274355533 85 dbSNP
rs546731949 88 dbSNP
rs894554206 89 dbSNP
rs1418676404 91 dbSNP
rs12638966 108 dbSNP
rs985799460 123 dbSNP
rs1294728217 125 dbSNP
rs1055760152 136 dbSNP
rs536225925 167 dbSNP
rs936288719 179 dbSNP
rs781780787 187 dbSNP
rs1334214336 192 dbSNP
rs1372303533 194 dbSNP
rs1296197484 203 dbSNP
rs766982775 205 dbSNP
rs567273851 209 dbSNP
rs1361834410 211 dbSNP
rs1297797140 213 dbSNP
rs1354980421 219 dbSNP
rs1325145886 221 dbSNP
rs1354381926 222 dbSNP
rs1318629147 223 dbSNP
rs1223017300 236 dbSNP
rs977602733 240 dbSNP
rs1462861724 241 dbSNP
rs1491587774 241 dbSNP
rs73855768 241 dbSNP
rs879005909 241 dbSNP
rs967537223 241 dbSNP
rs1173667728 242 dbSNP
rs139441254 242 dbSNP
rs1491432197 242 dbSNP
rs866877447 242 dbSNP
rs1291103226 246 dbSNP
rs1491029658 246 dbSNP
rs759993941 246 dbSNP
rs763958005 246 dbSNP
rs1341702021 247 dbSNP
rs1404388912 249 dbSNP
rs925251028 252 dbSNP
rs550809143 254 dbSNP
rs755542896 255 dbSNP
rs866417839 272 dbSNP
rs1325917360 275 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 131076.0
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 ...

- Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' gaucggaggUACUUAAGACUAc 5'
                   || ||||||||| 
Target 5' ----uauaaAU-AAUUCUGAUa 3'
1 - 17
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]
CLIP-seq Support 1 for dataset GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000291458.5 | 3UTR | UAUAAAUAAUUCUGAUAAUUAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
LUSC 0.548 0.02 0.596 0.01 15 Click to see details
BLCA -0.517 0.15 -0.486 0.16 6 Click to see details
HNSC -0.13 0.33 -0.099 0.37 14 Click to see details
STAD 0.468 0.34 0.500 0.33 3 Click to see details
LIHC 0.135 0.43 0.200 0.4 4 Click to see details
BRCA 0.028 0.44 0.011 0.48 31 Click to see details
BRCA 0.028 0.44 0.011 0.48 31 Click to see details
BRCA 0.028 0.44 0.011 0.48 31 Click to see details
BRCA 0.028 0.44 0.011 0.48 31 Click to see details
BRCA 0.028 0.44 0.011 0.48 31 Click to see details
BRCA 0.028 0.44 0.011 0.48 31 Click to see details
BRCA 0.028 0.44 0.011 0.48 31 Click to see details
UCEC 1 0.5 1.000 0.5 3 Click to see details
80 hsa-miR-2115-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT057089 DDIT4 DNA damage inducible transcript 4 2 2
MIRT071216 FCF1 FCF1, rRNA-processing protein 2 2
MIRT226901 RAD23B RAD23 homolog B, nucleotide excision repair protein 2 2
MIRT235961 BACH1 BTB domain and CNC homolog 1 2 2
MIRT294569 ZNF460 zinc finger protein 460 2 4
MIRT321046 RAC1 Rac family small GTPase 1 2 4
MIRT359666 NUS1 NUS1 dehydrodolichyl diphosphate synthase subunit 2 8
MIRT366451 KLHL15 kelch like family member 15 2 2
MIRT405375 ZBTB18 zinc finger and BTB domain containing 18 2 2
MIRT441794 TCEAL5 transcription elongation factor A like 5 2 2
MIRT443295 TCEAL3 transcription elongation factor A like 3 2 2
MIRT455275 DDX39B DExD-box helicase 39B 2 2
MIRT458523 C5orf22 chromosome 5 open reading frame 22 2 2
MIRT464960 TWIST1 twist family bHLH transcription factor 1 2 2
MIRT466848 STX6 syntaxin 6 2 2
MIRT469252 RHOB ras homolog family member B 2 2
MIRT469825 RAB14 RAB14, member RAS oncogene family 2 4
MIRT470047 PTGFRN prostaglandin F2 receptor inhibitor 2 2
MIRT471420 PDP2 pyruvate dehyrogenase phosphatase catalytic subunit 2 2 2
MIRT472024 NPM1 nucleophosmin 1 2 2
MIRT484156 CENPN centromere protein N 2 2
MIRT485490 HMGN2 high mobility group nucleosomal binding domain 2 2 2
MIRT490462 PROSER2 proline and serine rich 2 2 2
MIRT493069 MTCH1 mitochondrial carrier 1 2 2
MIRT493573 HSP90AA1 heat shock protein 90 alpha family class A member 1 2 8
MIRT494919 NDUFC2-KCTD14 NDUFC2-KCTD14 readthrough 2 2
MIRT500439 ZMAT3 zinc finger matrin-type 3 2 2
MIRT500931 SRPR SRP receptor alpha subunit 2 4
MIRT501551 POC1B-GALNT4 POC1B-GALNT4 readthrough 2 2
MIRT501809 NEURL1B neuralized E3 ubiquitin protein ligase 1B 2 2
MIRT502415 GALNT4 polypeptide N-acetylgalactosaminyltransferase 4 2 2
MIRT506504 MSANTD4 Myb/SANT DNA binding domain containing 4 with coiled-coils 2 2
MIRT507861 CCNE2 cyclin E2 2 2
MIRT510511 YOD1 YOD1 deubiquitinase 2 6
MIRT516073 RAB42 RAB42, member RAS oncogene family 2 2
MIRT519030 KYNU kynureninase 2 6
MIRT521762 PPIL1 peptidylprolyl isomerase like 1 2 4
MIRT522898 KCNJ3 potassium voltage-gated channel subfamily J member 3 2 4
MIRT527370 MGARP mitochondria localized glutamic acid rich protein 2 2
MIRT530691 C8orf46 chromosome 8 open reading frame 46 2 2
MIRT530867 TRUB1 TruB pseudouridine synthase family member 1 2 2
MIRT531832 MTPAP mitochondrial poly(A) polymerase 2 4
MIRT533035 ZBTB5 zinc finger and BTB domain containing 5 2 2
MIRT533165 WIPF2 WAS/WASL interacting protein family member 2 2 2
MIRT533464 TRIM71 tripartite motif containing 71 2 2
MIRT534331 SHCBP1 SHC binding and spindle associated 1 2 2
MIRT539372 ADSS adenylosuccinate synthase 2 6
MIRT545951 ZBTB10 zinc finger and BTB domain containing 10 2 2
MIRT553283 TSR1 TSR1, ribosome maturation factor 2 2
MIRT553532 TMEM185B transmembrane protein 185B 2 4
MIRT556480 LIPA lipase A, lysosomal acid type 2 2
MIRT556975 HSPA4L heat shock protein family A (Hsp70) member 4 like 2 2
MIRT557697 GATA6 GATA binding protein 6 2 2
MIRT558901 CCDC58 coiled-coil domain containing 58 2 2
MIRT559224 BLMH bleomycin hydrolase 2 2
MIRT559827 SLPI secretory leukocyte peptidase inhibitor 2 2
MIRT563435 SLC3A2 solute carrier family 3 member 2 2 2
MIRT569270 PCDH11X protocadherin 11 X-linked 2 2
MIRT571386 JKAMP JNK1/MAPK8-associated membrane protein 2 2
MIRT572567 AFF1 AF4/FMR2 family member 1 2 2
MIRT610400 AR androgen receptor 2 2
MIRT611058 ZNF621 zinc finger protein 621 2 2
MIRT635118 TMEM233 transmembrane protein 233 2 2
MIRT641617 DEFB118 defensin beta 118 2 2
MIRT642146 CHORDC1 cysteine and histidine rich domain containing 1 2 2
MIRT647295 C8orf33 chromosome 8 open reading frame 33 2 2
MIRT648155 MPLKIP M-phase specific PLK1 interacting protein 2 2
MIRT652780 TENM3 teneurin transmembrane protein 3 2 2
MIRT657356 HNRNPA2B1 heterogeneous nuclear ribonucleoprotein A2/B1 2 2
MIRT658718 ELN elastin 2 2
MIRT662441 RALGAPA1 Ral GTPase activating protein catalytic alpha subunit 1 2 2
MIRT665302 ZBTB38 zinc finger and BTB domain containing 38 2 2
MIRT699898 RUNX1 runt related transcription factor 1 2 2
MIRT700921 PDS5A PDS5 cohesin associated factor A 2 2
MIRT700992 PDE3A phosphodiesterase 3A 2 2
MIRT707397 DCAF4L1 DDB1 and CUL4 associated factor 4 like 1 2 2
MIRT711895 INSIG2 insulin induced gene 2 2 2
MIRT712072 XRCC5 X-ray repair cross complementing 5 2 2
MIRT716121 PTPLAD2 3-hydroxyacyl-CoA dehydratase 4 1 1
MIRT724470 SMAD2 SMAD family member 2 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-2115 Docetaxel+Cisplatin+5-Fluorouracil sensitive tissue (hypopharyngeal squamous cell carcinoma)
hsa-mir-2115 Decitabine 451668 approved sensitive tissue (esopheageal cancer)
hsa-miR-2115-3p Imatinib 5291 NSC743414 approved resistant High Chronic Myelogenous Leukemia cell line (K562)
hsa-miR-2115-3p Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-2115-3p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-2115-3p Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-miR-2115-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-2115-3p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-2115-3p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (100 ng/ml)

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