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 FAM110A   
Synonyms C20orf55, F10, bA371L19.3
Description family with sequence similarity 110 member A
Transcript NM_001042353   
Other Transcripts NM_031424 , NM_207121   
Expression
Putative miRNA Targets on FAM110A
3'UTR of FAM110A
(miRNA target sites are highlighted)
>FAM110A|NM_001042353|3'UTR
   1 GCGCCACTGGGCCTGGAATTCGCCACAGGACGGATCTTACAGAGGCAAGTGGTCCCTGGACCTCTCTTGCATCCATTCTC
  81 TAGACGGCCGTGTCAGAGGCTCCACCCTGTTGTGAACTTGGTATGGAGGCAAAGGCTTAGAGGCTGGACCAGCATTGTTG
 161 GGCAAGGACTGACTCTCCAAGGGTTTTGTTCTTGGCTTTGGACACCTGAGAACCCCCTCCTCCCCTCCCCCAATACAAGG
 241 TTTTTGACATGAGTGTACTCCTGCTTAGTTCCTCTTGTGGGGCTGCATTTGCGGTGCTTTGCCCTCCCCACTGTGAGTGA
 321 GGGGCCAAGGGATCTCCTCAATCCTGTCTCCCCAGCGGCTCTGTTTCCTCCTTCCTTCCTTGGCCTCTGTCCTTTGCTGA
 401 CTTCCTCTTCCTTACCCAGCAGAACTCACCCTGGGGTCGGGGCAGTGGGGAGGGGCCTATCCACTGCTCTTCCTAGTCCT
 481 TGGCAGCTGGCCTAGGTGGGCAGACTATAGGAGGGACTGGTTAGGAGTCTGCATTGCTTTGACTTCCCTCTCCTTGGTTA
 561 ATAAACACAAATGCTTGTTTCTCAAGG
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' acaUGUCGUCCG--------UGUCUGucc 5'
             :|||| |||        :|||||   
Target 5' ttgGCAGCTGGCCTAGGTGGGCAGACtat 3'
480 - 508 112.00 -21.26
2
miRNA  3' acAUGU-CGUCCG-UGUCUGUCc 5'
            |:||  ||  |  :||||:| 
Target 5' ctTGCATCCATTCTCTAGACGGc 3'
66 - 88 111.00 -7.90
3
miRNA  3' acaugucguCCGUGU-CUGUCc 5'
                   | |||| |||:| 
Target 5' ctggaattcGCCACAGGACGGa 3'
13 - 34 104.00 -11.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN18716864 17 COSMIC
COSN30479994 22 COSMIC
COSN30108343 23 COSMIC
COSN24633184 32 COSMIC
COSN31509010 33 COSMIC
COSN30169821 47 COSMIC
COSN30140081 90 COSMIC
COSN30156035 97 COSMIC
COSN31555590 104 COSMIC
COSN20079823 144 COSMIC
COSN28744677 158 COSMIC
COSN28652449 179 COSMIC
COSN31541358 189 COSMIC
COSN15623958 220 COSMIC
COSN31489699 227 COSMIC
COSN31522977 242 COSMIC
COSN30116770 294 COSMIC
COSN28631895 332 COSMIC
COSN28754953 376 COSMIC
COSN30540413 412 COSMIC
COSN15623960 421 COSMIC
COSN26671534 490 COSMIC
COSN15623961 525 COSMIC
COSN30132444 538 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs372778762 3 dbSNP
rs375915338 6 dbSNP
rs535040807 9 dbSNP
rs1399250676 10 dbSNP
rs754955051 15 dbSNP
rs762408732 17 dbSNP
rs150839256 22 dbSNP
rs201672012 23 dbSNP
rs772872188 24 dbSNP
rs746529741 32 dbSNP
rs1219350157 35 dbSNP
rs1268108895 37 dbSNP
rs770513776 39 dbSNP
rs775979407 46 dbSNP
rs1019995642 47 dbSNP
rs768145575 49 dbSNP
rs955164752 49 dbSNP
rs760091575 51 dbSNP
rs1421239719 64 dbSNP
rs1157185465 69 dbSNP
rs1235299937 76 dbSNP
rs759072121 82 dbSNP
rs1461713061 86 dbSNP
rs77193875 87 dbSNP
rs943609985 90 dbSNP
rs1196550720 91 dbSNP
rs975412443 92 dbSNP
rs920559350 100 dbSNP
rs556992798 101 dbSNP
rs1215429674 105 dbSNP
rs1378703747 107 dbSNP
rs1468882743 118 dbSNP
rs1336845814 121 dbSNP
rs1384855487 122 dbSNP
rs946617226 129 dbSNP
rs1047798163 130 dbSNP
rs1042429118 136 dbSNP
rs1331209460 153 dbSNP
rs2282050 158 dbSNP
rs933958003 159 dbSNP
rs558953126 163 dbSNP
rs118050140 167 dbSNP
rs1045553423 177 dbSNP
rs2282051 179 dbSNP
rs1444658653 199 dbSNP
rs1007089538 202 dbSNP
rs139279615 204 dbSNP
rs1032901132 205 dbSNP
rs1263863209 207 dbSNP
rs892765724 216 dbSNP
rs898788280 218 dbSNP
rs994830984 222 dbSNP
rs1177325522 226 dbSNP
rs180704472 234 dbSNP
rs565208585 236 dbSNP
rs1178559018 249 dbSNP
rs1248294185 250 dbSNP
rs1360209516 256 dbSNP
rs1308590853 258 dbSNP
rs1422563416 258 dbSNP
rs1390221071 260 dbSNP
rs955112698 261 dbSNP
rs1299101565 269 dbSNP
rs1034791671 270 dbSNP
rs959370029 275 dbSNP
rs530689891 276 dbSNP
rs1379207851 279 dbSNP
rs1156290083 282 dbSNP
rs1420879715 283 dbSNP
rs1408538745 287 dbSNP
rs544352256 288 dbSNP
rs967868484 293 dbSNP
rs751333903 294 dbSNP
rs1490569748 295 dbSNP
rs1328174315 310 dbSNP
rs1354866754 315 dbSNP
rs1285478179 325 dbSNP
rs986973804 329 dbSNP
rs1045410 332 dbSNP
rs934010404 333 dbSNP
rs1219037373 335 dbSNP
rs1272877824 337 dbSNP
rs1365701876 339 dbSNP
rs560919994 342 dbSNP
rs529863442 346 dbSNP
rs1405240421 349 dbSNP
rs920842371 353 dbSNP
rs1295817406 356 dbSNP
rs1223137151 357 dbSNP
rs546559323 364 dbSNP
rs1283938799 371 dbSNP
rs1325839599 374 dbSNP
rs1045412 376 dbSNP
rs1431341066 379 dbSNP
rs1431231444 390 dbSNP
rs907896717 395 dbSNP
rs1038418885 398 dbSNP
rs1438926134 405 dbSNP
rs950142255 406 dbSNP
rs1203487245 418 dbSNP
rs1046248907 421 dbSNP
rs1261351260 431 dbSNP
rs1210089552 437 dbSNP
rs1322018687 439 dbSNP
rs994319403 440 dbSNP
rs905663906 441 dbSNP
rs1245349499 442 dbSNP
rs1292939975 444 dbSNP
rs1047363850 446 dbSNP
rs937175924 453 dbSNP
rs145340716 462 dbSNP
rs893048208 466 dbSNP
rs1408210493 473 dbSNP
rs1176901267 474 dbSNP
rs745845404 479 dbSNP
rs1019884083 494 dbSNP
rs890799479 497 dbSNP
rs1423216592 503 dbSNP
rs1191350343 506 dbSNP
rs756189835 507 dbSNP
rs1262586892 508 dbSNP
rs1034676277 510 dbSNP
rs1476576506 514 dbSNP
rs551750664 516 dbSNP
rs557888487 522 dbSNP
rs963866530 540 dbSNP
rs1265482547 554 dbSNP
rs571614157 558 dbSNP
rs1204738677 560 dbSNP
rs559276698 566 dbSNP
rs185323311 569 dbSNP
rs1229218909 571 dbSNP
rs753090682 578 dbSNP
rs1321256562 585 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
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 GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb ...

- 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]
CLIP-seq Support 1 for dataset GSM1084064
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_AbnovaAb
Location of target site ENST00000375551.3 | 3UTR | ACAGGGAGAGGGAGAGAGAGAGGAGACAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1084065
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_AbnovaAb
Location of target site ENST00000375551.3 | 3UTR | GACAGGGAGAGGGAGAGAGAGAGGAGAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
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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