pre-miRNA Information
pre-miRNA hsa-mir-3120   
Genomic Coordinates chr1: 172138808 - 172138888
Description Homo sapiens miR-3120 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3120-5p
Sequence 13| CCUGUCUGUGCCUGCUGUACA |33
Evidence Experimental
Experiments Illumina
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 19 1 + 172138838 26449202, 27587585 MiREDiBase
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN26637643 8 COSMIC
COSN31603497 11 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs750386761 8 dbSNP
rs760725207 9 dbSNP
rs766486759 10 dbSNP
rs754055278 12 dbSNP
rs755288536 19 dbSNP
rs754726014 21 dbSNP
Putative Targets

Gene Information
Gene Symbol NPVF   
Synonyms C7orf9, RFRP
Description neuropeptide VF precursor
Transcript NM_022150   
Expression
Putative miRNA Targets on NPVF
3'UTR of NPVF
(miRNA target sites are highlighted)
>NPVF|NM_022150|3'UTR
   1 GAAACCTGGAGCCTGTCCCTAAAGCTGTGGCCTGTAATCTACAAATGGCTCTATAGCGAAGACCACACGGAAGAGTAGCT
  81 ACATACACTTCATCAGCTATGGATCATCAACGGCAATTTTTCCTTGTCAGTACAGCTATAATAGTATCTTGAAAGTTGTA
 161 AAAAAATTAAAGCATATTTGTTACGTAAAGTTAAAATGATTTTTGTCTGAATAAAAAAAAAGCATTGCAAATGCTTTAGA
 241 AATCTCTGATAATGGAGAGAGAGACAGAGGACCCTCCTCACTACCCTATATAAAAATCATTGGCACAGTTACACTTAATA
 321 AAAAAAATTAAACAGAAGAGCACCCTGAAAAACATTATGATGGAAATTAAATAGTATGCCAGAATAACATGGTTGACAAA
 401 TAAGTGAACAAGGATTAAAAATCACTTACAAACGTGTTTCTGTACACCCTTTCTATCGTGTCAAATGTTAATGAATCTGT
 481 GATCAATTGAAATGTAAATGTCTGTGTAAAACTACAAAATAAAAACTCTTAGACTTTAGGGAGAAAAGAAAA
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' acAUGUCGUCCGUGUCUGUCc 5'
            ||  | ||  | |||||| 
Target 5' gaTAATGGAGAGAGAGACAGa 3'
248 - 268 123.00 -9.10
2
miRNA  3' acaUGUCGUCCGUGUCUGUcc 5'
             | ||:|| :||| |||  
Target 5' ggaAGAGTAGCTACATACAct 3'
69 - 89 114.00 -9.40
3
miRNA  3' acaugucguccguGUC-UGUCc 5'
                       ||| |||| 
Target 5' aatttttccttgtCAGTACAGc 3'
115 - 136 108.00 -8.85
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30497924 4 COSMIC
COSN31540679 7 COSMIC
COSN31553619 13 COSMIC
COSN28821011 25 COSMIC
COSN30152087 25 COSMIC
COSN26986906 39 COSMIC
COSN30165814 46 COSMIC
COSN30193437 49 COSMIC
COSN213171 52 COSMIC
COSN31526186 57 COSMIC
COSN28630142 68 COSMIC
COSN30171775 70 COSMIC
COSN30184227 80 COSMIC
COSN30496419 85 COSMIC
COSN30104172 108 COSMIC
COSN28201507 111 COSMIC
COSN31510228 114 COSMIC
COSN31593096 121 COSMIC
COSN30104145 123 COSMIC
COSN30187168 126 COSMIC
COSN30510927 137 COSMIC
COSN30510926 138 COSMIC
COSN31562273 160 COSMIC
COSN17579551 184 COSMIC
COSN31561445 212 COSMIC
COSN20070268 213 COSMIC
COSN5654823 271 COSMIC
COSN30115329 298 COSMIC
COSN1347692 325 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs770824027 1 dbSNP
rs760648180 4 dbSNP
rs574022279 5 dbSNP
rs1195797956 7 dbSNP
rs917462177 14 dbSNP
rs374104557 15 dbSNP
rs1262775242 17 dbSNP
rs1223437204 18 dbSNP
rs1361827263 19 dbSNP
rs748391029 24 dbSNP
rs779065510 25 dbSNP
rs768891973 27 dbSNP
rs1397726571 29 dbSNP
rs749375890 30 dbSNP
rs780165660 32 dbSNP
rs1338102585 34 dbSNP
rs992268803 35 dbSNP
rs553747268 46 dbSNP
rs199708914 48 dbSNP
rs907576296 49 dbSNP
rs983161434 54 dbSNP
rs1254470721 55 dbSNP
rs1229702941 56 dbSNP
rs1297526666 58 dbSNP
rs368412736 68 dbSNP
rs375749118 69 dbSNP
rs1289861281 73 dbSNP
rs974952263 75 dbSNP
rs1212762562 76 dbSNP
rs1250529550 82 dbSNP
rs968034564 83 dbSNP
rs577626545 84 dbSNP
rs1019258957 93 dbSNP
rs371337473 100 dbSNP
rs1164755691 104 dbSNP
rs1414327539 106 dbSNP
rs113811642 111 dbSNP
rs1030217162 112 dbSNP
rs997296554 117 dbSNP
rs537977348 125 dbSNP
rs1325177944 129 dbSNP
rs901563606 132 dbSNP
rs1450892479 134 dbSNP
rs1035996015 139 dbSNP
rs1309681684 146 dbSNP
rs1410202182 156 dbSNP
rs1330559516 158 dbSNP
rs1000201414 165 dbSNP
rs940398666 166 dbSNP
rs1161298136 167 dbSNP
rs1260489472 167 dbSNP
rs569800310 173 dbSNP
rs183197226 180 dbSNP
rs142505821 184 dbSNP
rs978095 185 dbSNP
rs1162993388 190 dbSNP
rs940316109 192 dbSNP
rs55789252 198 dbSNP
rs139084893 200 dbSNP
rs939423292 213 dbSNP
rs1490291098 214 dbSNP
rs571264391 215 dbSNP
rs924055382 216 dbSNP
rs974541504 217 dbSNP
rs1452367630 221 dbSNP
rs200857217 222 dbSNP
rs964885969 222 dbSNP
rs1228686684 223 dbSNP
rs1283709297 224 dbSNP
rs1259620171 226 dbSNP
rs1347928491 230 dbSNP
rs1202051903 236 dbSNP
rs1279271230 241 dbSNP
rs1222127173 243 dbSNP
rs1185503690 247 dbSNP
rs1253782542 249 dbSNP
rs987385038 252 dbSNP
rs73691518 253 dbSNP
rs1031602325 261 dbSNP
rs1000170313 265 dbSNP
rs1173634320 265 dbSNP
rs774332658 265 dbSNP
rs1375342709 267 dbSNP
rs531321971 268 dbSNP
rs118032448 276 dbSNP
rs968767898 281 dbSNP
rs1391538042 282 dbSNP
rs968065788 285 dbSNP
rs1305869146 286 dbSNP
rs1290140738 290 dbSNP
rs1022705211 296 dbSNP
rs985744076 297 dbSNP
rs1344659893 300 dbSNP
rs1276428799 302 dbSNP
rs954419884 307 dbSNP
rs1029835232 312 dbSNP
rs146193251 315 dbSNP
rs1248726469 322 dbSNP
rs1013031984 324 dbSNP
rs1199641028 328 dbSNP
rs895965496 328 dbSNP
rs570579661 330 dbSNP
rs1453109617 338 dbSNP
rs1350087691 340 dbSNP
rs1171035647 341 dbSNP
rs1317096097 343 dbSNP
rs1398450265 344 dbSNP
rs1413447037 345 dbSNP
rs763961194 347 dbSNP
rs190652058 348 dbSNP
rs1461815886 350 dbSNP
rs1297207676 354 dbSNP
rs60142768 355 dbSNP
rs1388212649 357 dbSNP
rs1325992150 358 dbSNP
rs1004346402 368 dbSNP
rs560374051 369 dbSNP
rs6956128 374 dbSNP
rs930285174 377 dbSNP
rs752743360 378 dbSNP
rs765199553 381 dbSNP
rs1193260734 382 dbSNP
rs920301302 389 dbSNP
rs947999794 390 dbSNP
rs1210730904 392 dbSNP
rs1252376185 396 dbSNP
rs895020190 399 dbSNP
rs577588940 401 dbSNP
rs527894206 404 dbSNP
rs1191005355 412 dbSNP
rs1391358231 428 dbSNP
rs776711965 429 dbSNP
rs557885232 433 dbSNP
rs1268796959 434 dbSNP
rs11976166 436 dbSNP
rs978200536 440 dbSNP
rs771099754 448 dbSNP
rs1393036620 453 dbSNP
rs1298987145 455 dbSNP
rs1438124701 455 dbSNP
rs915266640 457 dbSNP
rs183343764 458 dbSNP
rs1293169086 492 dbSNP
rs985827936 493 dbSNP
rs374011047 496 dbSNP
rs922882057 501 dbSNP
rs1272812206 504 dbSNP
rs1332714602 505 dbSNP
rs1210633699 515 dbSNP
rs1248776319 526 dbSNP
rs1269236609 527 dbSNP
rs976952801 528 dbSNP
rs1432372328 529 dbSNP
rs568599483 532 dbSNP
rs1015683348 533 dbSNP
rs1004605436 539 dbSNP
rs1023000297 549 dbSNP
rs1320599770 550 dbSNP
rs536488836 553 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HeLa
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 Chi_ControlA_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell Control A ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' acaugucguccgugUCUGUCc 5'
                        |||||| 
Target 5' -------gagagagAGACAGa 3'
1 - 14
Article - Chi SW; Zang JB; Mele A; Darnell RB
- Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
CLIP-seq Support 1 for dataset Chi_ControlA_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell Control A
Location of target site ENST00000222674.2 | 3UTR | GAGAGAGAGACAGAGGACCCUCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
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
134 hsa-miR-3120-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT096972 BDP1 B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB 2 2
MIRT442624 LOX lysyl oxidase 2 2
MIRT473438 MDM4 MDM4, p53 regulator 2 2
MIRT490011 KIFC2 kinesin family member C2 2 2
MIRT496449 N6AMT1 N-6 adenine-specific DNA methyltransferase 1 2 2
MIRT496752 TGIF2 TGFB induced factor homeobox 2 2 2
MIRT497721 CYP1A1 cytochrome P450 family 1 subfamily A member 1 2 2
MIRT498287 PADI3 peptidyl arginine deiminase 3 2 2
MIRT503195 ACVR1B activin A receptor type 1B 2 4
MIRT504760 TEP1 telomerase associated protein 1 2 4
MIRT517810 UGDH UDP-glucose 6-dehydrogenase 2 6
MIRT519686 ZNF622 zinc finger protein 622 2 4
MIRT520263 URGCP upregulator of cell proliferation 2 2
MIRT523051 ICMT isoprenylcysteine carboxyl methyltransferase 2 2
MIRT525601 OLR1 oxidized low density lipoprotein receptor 1 2 4
MIRT526995 ARL8B ADP ribosylation factor like GTPase 8B 2 2
MIRT528699 TRAF3IP2 TRAF3 interacting protein 2 2 4
MIRT533142 WNT10A Wnt family member 10A 2 2
MIRT537618 ERI1 exoribonuclease 1 2 2
MIRT539707 EIF3H eukaryotic translation initiation factor 3 subunit H 2 2
MIRT539752 CNBP CCHC-type zinc finger nucleic acid binding protein 2 2
MIRT539808 GAPVD1 GTPase activating protein and VPS9 domains 1 2 2
MIRT539941 IFNAR2 interferon alpha and beta receptor subunit 2 2 2
MIRT540424 FAM83F family with sequence similarity 83 member F 2 2
MIRT540509 CXCL10 C-X-C motif chemokine ligand 10 2 2
MIRT540720 GUF1 GUF1 homolog, GTPase 2 2
MIRT541630 PARP2 poly(ADP-ribose) polymerase 2 2 2
MIRT542286 POLR3K RNA polymerase III subunit K 2 2
MIRT542456 AKR7A2 aldo-keto reductase family 7 member A2 2 2
MIRT542550 MRPS10 mitochondrial ribosomal protein S10 2 2
MIRT542771 PPAP2B phospholipid phosphatase 3 2 2
MIRT550085 TRAPPC2 trafficking protein particle complex 2 2 2
MIRT551458 CARKD NAD(P)HX dehydratase 2 2
MIRT555622 PHLPP2 PH domain and leucine rich repeat protein phosphatase 2 2 2
MIRT569136 KATNAL1 katanin catalytic subunit A1 like 1 2 2
MIRT572328 HSPB6 heat shock protein family B (small) member 6 2 2
MIRT574607 LZIC leucine zipper and CTNNBIP1 domain containing 2 2
MIRT575583 Mcm8 minichromosome maintenance 8 homologous recombination repair factor 2 4
MIRT576125 Hrk harakiri, BCL2 interacting protein (contains only BH3 domain) 2 5
MIRT576657 Fam216a family with sequence similarity 216, member A 2 2
MIRT607222 ACSM2A acyl-CoA synthetase medium chain family member 2A 2 4
MIRT607292 CD300E CD300e molecule 2 6
MIRT607746 ANGPT4 angiopoietin 4 2 2
MIRT607905 SPRYD4 SPRY domain containing 4 2 2
MIRT608159 HRK harakiri, BCL2 interacting protein 2 7
MIRT608657 ABCF3 ATP binding cassette subfamily F member 3 2 4
MIRT609115 ZNF703 zinc finger protein 703 2 6
MIRT610231 ACOT9 acyl-CoA thioesterase 9 2 2
MIRT610870 NUDCD3 NudC domain containing 3 2 2
MIRT611217 MC2R melanocortin 2 receptor 2 2
MIRT614858 PLEKHA6 pleckstrin homology domain containing A6 2 2
MIRT616966 LMX1A LIM homeobox transcription factor 1 alpha 2 2
MIRT617258 GLIPR1L2 GLI pathogenesis related 1 like 2 2 2
MIRT618009 SLC9A3R2 SLC9A3 regulator 2 2 2
MIRT619067 BSND barttin CLCNK type accessory beta subunit 2 4
MIRT619295 FAM26E calcium homeostasis modulator family member 5 2 2
MIRT619348 GINM1 glycoprotein integral membrane 1 2 2
MIRT619362 CFHR5 complement factor H related 5 2 2
MIRT619541 PIWIL2 piwi like RNA-mediated gene silencing 2 2 2
MIRT619782 NRIP2 nuclear receptor interacting protein 2 2 2
MIRT619994 NPAP1 nuclear pore associated protein 1 2 2
MIRT621030 CDC14B cell division cycle 14B 2 2
MIRT622033 STAT5A signal transducer and activator of transcription 5A 2 2
MIRT622728 PITPNM3 PITPNM family member 3 2 2
MIRT623144 NAV2 neuron navigator 2 2 2
MIRT623600 IPO9 importin 9 2 2
MIRT624608 B3GALT5 beta-1,3-galactosyltransferase 5 2 2
MIRT624905 CTCFL CCCTC-binding factor like 2 2
MIRT625030 SPC24 SPC24, NDC80 kinetochore complex component 2 2
MIRT625688 MCM8 minichromosome maintenance 8 homologous recombination repair factor 2 5
MIRT626531 EMCN endomucin 2 2
MIRT627204 ZDHHC20 zinc finger DHHC-type containing 20 2 2
MIRT628033 LSAMP limbic system-associated membrane protein 2 2
MIRT628203 FREM2 FRAS1 related extracellular matrix protein 2 2 2
MIRT631012 LINS lines homolog 1 2 2
MIRT633195 HSPE1-MOB4 HSPE1-MOB4 readthrough 2 2
MIRT633890 CACNG8 calcium voltage-gated channel auxiliary subunit gamma 8 2 2
MIRT634023 MOB4 MOB family member 4, phocein 2 2
MIRT634416 PLCXD3 phosphatidylinositol specific phospholipase C X domain containing 3 2 2
MIRT636866 ARSE arylsulfatase E (chondrodysplasia punctata 1) 2 2
MIRT642527 ANKRD9 ankyrin repeat domain 9 2 2
MIRT645408 FAM110A family with sequence similarity 110 member A 2 2
MIRT645635 SYTL4 synaptotagmin like 4 2 2
MIRT646013 TNFAIP8L2 TNF alpha induced protein 8 like 2 2 2
MIRT646686 ASGR2 asialoglycoprotein receptor 2 2 2
MIRT652838 TACO1 translational activator of cytochrome c oxidase I 2 2
MIRT655156 PHF21B PHD finger protein 21B 2 2
MIRT658491 EXOC7 exocyst complex component 7 2 2
MIRT659398 CORO2A coronin 2A 2 2
MIRT666825 PRCP prolylcarboxypeptidase 2 2
MIRT666866 POU2F2 POU class 2 homeobox 2 2 2
MIRT668224 GABRA1 gamma-aminobutyric acid type A receptor alpha1 subunit 2 2
MIRT673288 PDE3A phosphodiesterase 3A 2 2
MIRT673878 KLF2 Kruppel like factor 2 2 2
MIRT681721 KCNE4 potassium voltage-gated channel subfamily E regulatory subunit 4 2 2
MIRT682406 PARD6B par-6 family cell polarity regulator beta 2 2
MIRT684109 MCM10 minichromosome maintenance 10 replication initiation factor 2 2
MIRT684423 TUFT1 tuftelin 1 2 2
MIRT684684 OR7D2 olfactory receptor family 7 subfamily D member 2 2 2
MIRT686638 TMEM184C transmembrane protein 184C 2 2
MIRT689457 NXN nucleoredoxin 2 2
MIRT689627 NAA30 N(alpha)-acetyltransferase 30, NatC catalytic subunit 2 2
MIRT690773 PLA2G2C phospholipase A2 group IIC 2 2
MIRT690822 SGSM2 small G protein signaling modulator 2 2 2
MIRT693669 MXRA7 matrix remodeling associated 7 2 2
MIRT695553 CLPB ClpB homolog, mitochondrial AAA ATPase chaperonin 2 2
MIRT695872 C19orf52 translocase of inner mitochondrial membrane 29 2 2
MIRT698160 TNFRSF13C TNF receptor superfamily member 13C 2 2
MIRT699933 RUFY2 RUN and FYVE domain containing 2 2 2
MIRT708639 UBE2W ubiquitin conjugating enzyme E2 W 2 2
MIRT710816 RAB11FIP4 RAB11 family interacting protein 4 2 2
MIRT711242 TRAT1 T-cell receptor associated transmembrane adaptor 1 2 2
MIRT711542 MSH3 mutS homolog 3 2 2
MIRT711749 DTX1 deltex E3 ubiquitin ligase 1 2 2
MIRT712303 PGM2L1 phosphoglucomutase 2 like 1 2 2
MIRT712922 RPF2 ribosome production factor 2 homolog 2 2
MIRT714027 SYDE2 synapse defective Rho GTPase homolog 2 2 2
MIRT714768 TERF1 telomeric repeat binding factor 1 2 2
MIRT714844 ADAMTS17 ADAM metallopeptidase with thrombospondin type 1 motif 17 2 2
MIRT715223 NPVF neuropeptide VF precursor 2 2
MIRT716110 GMPS guanine monophosphate synthase 2 2
MIRT716174 FAM71F2 family with sequence similarity 71 member F2 2 2
MIRT716383 C6orf223 chromosome 6 open reading frame 223 2 2
MIRT716527 KSR2 kinase suppressor of ras 2 2 2
MIRT716962 P2RY6 pyrimidinergic receptor P2Y6 2 2
MIRT717605 DSTYK dual serine/threonine and tyrosine protein kinase 2 2
MIRT717696 PTGS1 prostaglandin-endoperoxide synthase 1 2 2
MIRT721360 ENTHD1 ENTH domain containing 1 2 2
MIRT721381 MACC1 MACC1, MET transcriptional regulator 2 2
MIRT721935 RASSF2 Ras association domain family member 2 2 2
MIRT722094 SUSD1 sushi domain containing 1 2 2
MIRT722837 C17orf102 chromosome 17 open reading frame 102 2 2
MIRT722990 TOR1A torsin family 1 member A 2 2
MIRT724174 ABCF2 ATP binding cassette subfamily F member 2 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3120-5p Cisplatin 5460033 NSC119875 approved sensitive cell line
hsa-miR-3120-5p Prednisone/Azathioprine/Methotrexate/Cyclophosphamide/Mycophenolate mofetil sensitive tissue (myasthenia gravis)
hsa-miR-3120-5p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)

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