pre-miRNA Information
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
Mature miRNA hsa-miR-3123
Sequence 49| CAGAGAAUUGUUUAAUC |65
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 4 1 + 241132323 29233923 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1453759221 1 dbSNP
rs968575171 5 dbSNP
rs979407933 9 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol LEFTY1   
Synonyms LEFTB, LEFTYB
Description left-right determination factor 1
Transcript NM_020997   
Expression
Putative miRNA Targets on LEFTY1
3'UTR of LEFTY1
(miRNA target sites are highlighted)
>LEFTY1|NM_020997|3'UTR
   1 GCGCCTAGTGTAGCCATCGAGGGACTTGACTTGTGTGTGTTTCTGAAGTGTTCGAGGGTACCAGGAGAGCTGGCGATGAC
  81 TGAACTGCTGATGGACAAATGCTCTGTGCTCTCTAGTGAGCCCTGAATTTGCTTCCTCTGACAAGTTACCTCACCTAATT
 161 TTTGCTTCTCAGGAATGAGAATCTTTGGCCACTGGAGAGCCCTTGCTCAGTTTTCTCTATTCTTATTATTCACTGCACTA
 241 TATTCTAAGCACTTACATGTGGAGATACTGTAACCTGAGGGCAGAAAGCCCAATGTGTCATTGTTTACTTGTCCTGTCAC
 321 TGGATCTGGGCTAAAGTCCTCCACCACCACTCTGGACCTAAGACCTGGGGTTAAGTGTGGGTTGTGCATCCCCAATCCAG
 401 ATAATAAAGACTTTGTAAAACATGAATAAAACACATTTTATTCTAAAAAAAAAAAAAAAAAAA
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' cuAAUUUGUUAAGAGAc 5'
            ||:  ||:||:||| 
Target 5' ccTTGCTCAGTTTTCTc 3'
201 - 217 123.00 -6.80
2
miRNA  3' cuaAUUUG-UUAAGAGAc 5'
             |::|| ||| |||| 
Target 5' tgaTGGACAAATGCTCTg 3'
89 - 106 122.00 -11.10
3
miRNA  3' cuaaUUUG--UUAAGAGAC- 5'
              :||:  :| |||:|| 
Target 5' tcagGAATGAGAATCTTTGG 3'
169 - 188 87.00 -6.30
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN1079812 1 COSMIC
COSN31512519 2 COSMIC
COSN30516174 25 COSMIC
COSN30138288 37 COSMIC
COSN31580845 53 COSMIC
COSN19624593 54 COSMIC
COSN30490485 56 COSMIC
COSN30457302 57 COSMIC
COSN20073409 74 COSMIC
COSN30501143 77 COSMIC
COSN31479596 123 COSMIC
COSN30518203 125 COSMIC
COSN31496154 135 COSMIC
COSN13520852 138 COSMIC
COSN28196132 150 COSMIC
COSN30530801 150 COSMIC
COSN29463041 164 COSMIC
COSN24298585 192 COSMIC
COSN30159377 222 COSMIC
COSN22901269 254 COSMIC
COSN7206273 275 COSMIC
COSN31538827 296 COSMIC
COSN30172980 326 COSMIC
COSN1434065 378 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs375605718 3 dbSNP
rs780764463 4 dbSNP
rs56769658 5 dbSNP
rs770359521 7 dbSNP
rs1202549647 8 dbSNP
rs746514621 13 dbSNP
rs1458787967 18 dbSNP
rs777456113 19 dbSNP
rs985781819 21 dbSNP
rs200925389 22 dbSNP
rs374502992 23 dbSNP
rs778534702 26 dbSNP
rs754967971 36 dbSNP
rs753662154 37 dbSNP
rs923004195 41 dbSNP
rs766574031 50 dbSNP
rs544009880 53 dbSNP
rs3766941 54 dbSNP
rs553573225 62 dbSNP
rs967361255 63 dbSNP
rs764915714 65 dbSNP
rs535363908 74 dbSNP
rs761009550 75 dbSNP
rs41315436 79 dbSNP
rs1311326039 82 dbSNP
rs1372432944 84 dbSNP
rs1392050497 85 dbSNP
rs76469045 90 dbSNP
rs558921203 91 dbSNP
rs752392778 97 dbSNP
rs189294996 104 dbSNP
rs41315438 106 dbSNP
rs1001832197 107 dbSNP
rs548421154 110 dbSNP
rs754477787 113 dbSNP
rs1024338532 119 dbSNP
rs142585586 138 dbSNP
rs1025677804 145 dbSNP
rs994571827 147 dbSNP
rs148425461 155 dbSNP
rs1041334350 165 dbSNP
rs1200694967 177 dbSNP
rs936511417 179 dbSNP
rs774942341 183 dbSNP
rs185315202 186 dbSNP
rs528818276 191 dbSNP
rs1171947581 196 dbSNP
rs889982153 199 dbSNP
rs1392261404 204 dbSNP
rs528371524 212 dbSNP
rs1053947872 219 dbSNP
rs1297741888 226 dbSNP
rs563996491 232 dbSNP
rs762171279 239 dbSNP
rs1327206155 243 dbSNP
rs180867518 264 dbSNP
rs1370659460 268 dbSNP
rs371592461 271 dbSNP
rs925692931 282 dbSNP
rs1308947394 284 dbSNP
rs922917783 300 dbSNP
rs1417941301 313 dbSNP
rs1041428726 315 dbSNP
rs41307698 316 dbSNP
rs1336916814 320 dbSNP
rs940421641 329 dbSNP
rs1253562029 330 dbSNP
rs916892464 331 dbSNP
rs907636601 336 dbSNP
rs200851219 337 dbSNP
rs1250121704 341 dbSNP
rs992719944 349 dbSNP
rs1429391657 352 dbSNP
rs1169792442 367 dbSNP
rs1440032788 369 dbSNP
rs1459535204 370 dbSNP
rs958595309 371 dbSNP
rs1166193746 374 dbSNP
rs766297726 377 dbSNP
rs1439138635 387 dbSNP
rs1323021370 390 dbSNP
rs952309094 400 dbSNP
rs983910664 406 dbSNP
rs1034547169 410 dbSNP
rs980746281 415 dbSNP
rs775833106 429 dbSNP
rs559952913 440 dbSNP
rs971683608 440 dbSNP
rs1273735600 442 dbSNP
rs1434604700 444 dbSNP
rs1024286228 446 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions hESCs (WA-09)
Disease 10637.0
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 SRR359787. RNA binding protein: AGO2. Condition:4-thiouridine ...

- Lipchina I; Elkabetz Y; Hafner M; Sheridan et al., 2011, Genes & development.

Article - Lipchina I; Elkabetz Y; Hafner M; Sheridan et al.
- Genes & development, 2011
MicroRNAs are important regulators in many cellular processes, including stem cell self-renewal. Recent studies demonstrated their function as pluripotency factors with the capacity for somatic cell reprogramming. However, their role in human embryonic stem (ES) cells (hESCs) remains poorly understood, partially due to the lack of genome-wide strategies to identify their targets. Here, we performed comprehensive microRNA profiling in hESCs and in purified neural and mesenchymal derivatives. Using a combination of AGO cross-linking and microRNA perturbation experiments, together with computational prediction, we identified the targets of the miR-302/367 cluster, the most abundant microRNAs in hESCs. Functional studies identified novel roles of miR-302/367 in maintaining pluripotency and regulating hESC differentiation. We show that in addition to its role in TGF-beta signaling, miR-302/367 promotes bone morphogenetic protein (BMP) signaling by targeting BMP inhibitors TOB2, DAZAP2, and SLAIN1. This study broadens our understanding of microRNA function in hESCs and is a valuable resource for future studies in this area.
LinkOut: [PMID: 22012620]
CLIP-seq Support 1 for dataset SRR359787
Method / RBP PAR-CLIP / AGO2
Cell line / Condition hESCs (WA-09) / 4-thiouridine, RNase T1
Location of target site ENST00000272134.5 | 3UTR | CUCAGUUUUCUCUAUUCUUAUUAUUCACUGCACUAUAUUCUAAGCACUUACAUGUGGAGAUACUGUAACCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22012620 / SRX103431
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
113 hsa-miR-3123 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT058369 TBCEL tubulin folding cofactor E like 2 4
MIRT059816 EFNA1 ephrin A1 2 2
MIRT066850 TMEM19 transmembrane protein 19 2 2
MIRT071503 CALM1 calmodulin 1 2 6
MIRT073758 NUBP1 nucleotide binding protein 1 2 2
MIRT074324 TNRC6A trinucleotide repeat containing 6A 2 10
MIRT094805 LMNB1 lamin B1 2 2
MIRT099173 MAP3K4 mitogen-activated protein kinase kinase kinase 4 2 2
MIRT099545 ID4 inhibitor of DNA binding 4, HLH protein 2 2
MIRT122643 E2F3 E2F transcription factor 3 2 2
MIRT180918 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 8
MIRT192844 BLOC1S6 biogenesis of lysosomal organelles complex 1 subunit 6 2 2
MIRT224984 BAG4 BCL2 associated athanogene 4 2 2
MIRT246065 NRAS NRAS proto-oncogene, GTPase 2 2
MIRT357085 PRRC1 proline rich coiled-coil 1 2 2
MIRT378170 C5ORF51 chromosome 5 open reading frame 51 2 2
MIRT441636 KDM5A lysine demethylase 5A 2 2
MIRT441802 BCAS1 breast carcinoma amplified sequence 1 2 2
MIRT443019 C21orf91 chromosome 21 open reading frame 91 2 2
MIRT443445 SERPINB4 serpin family B member 4 2 2
MIRT443661 SERPINB3 serpin family B member 3 2 2
MIRT443776 STS steroid sulfatase 2 2
MIRT444663 TSPAN14 tetraspanin 14 2 2
MIRT444924 KIAA1522 KIAA1522 2 2
MIRT445378 FOXO1 forkhead box O1 2 2
MIRT447920 PAIP2B poly(A) binding protein interacting protein 2B 2 2
MIRT449202 PTPLAD2 3-hydroxyacyl-CoA dehydratase 4 1 1
MIRT449713 TSPYL1 TSPY like 1 2 2
MIRT450403 TMEM47 transmembrane protein 47 2 2
MIRT450787 PAPOLG poly(A) polymerase gamma 2 2
MIRT451381 C19orf43 telomerase RNA component interacting RNase 2 2
MIRT452507 WDR1 WD repeat domain 1 2 2
MIRT453264 PARP11 poly(ADP-ribose) polymerase family member 11 2 2
MIRT454642 FAM83H family with sequence similarity 83 member H 2 2
MIRT455513 C6orf106 chromosome 6 open reading frame 106 2 2
MIRT456709 LDB1 LIM domain binding 1 2 2
MIRT457231 AP3D1 adaptor related protein complex 3 delta 1 subunit 2 2
MIRT459235 MRPS21 mitochondrial ribosomal protein S21 2 2
MIRT460553 IFNAR1 interferon alpha and beta receptor subunit 1 2 4
MIRT461424 CTSL2 cathepsin V 2 3
MIRT462869 CYP51A1 cytochrome P450 family 51 subfamily A member 1 2 2
MIRT467178 SPTY2D1 SPT2 chromatin protein domain containing 1 2 2
MIRT469233 RHOBTB3 Rho related BTB domain containing 3 2 2
MIRT474125 LIPC lipase C, hepatic type 2 2
MIRT475509 HSP90B1 heat shock protein 90 beta family member 1 2 4
MIRT478134 DHX36 DEAH-box helicase 36 2 2
MIRT481326 ATP5A1 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle 2 2
MIRT482003 AMOTL2 angiomotin like 2 2 2
MIRT482230 AHCYL2 adenosylhomocysteinase like 2 2 2
MIRT483436 RHOXF2B Rhox homeobox family member 2B 2 2
MIRT483824 ZC3H12B zinc finger CCCH-type containing 12B 2 2
MIRT492051 TNFSF9 TNF superfamily member 9 2 2
MIRT494114 DLX6 distal-less homeobox 6 2 2
MIRT498882 ZNF12 zinc finger protein 12 2 10
MIRT499674 NPHP3 nephrocystin 3 2 2
MIRT506932 IGDCC4 immunoglobulin superfamily DCC subclass member 4 2 6
MIRT509461 ZNF587 zinc finger protein 587 2 6
MIRT510048 AKR1B10 aldo-keto reductase family 1 member B10 2 4
MIRT514807 NWD1 NACHT and WD repeat domain containing 1 2 2
MIRT515217 CRCP CGRP receptor component 2 2
MIRT515486 INCENP inner centromere protein 2 4
MIRT517765 ZNF366 zinc finger protein 366 2 4
MIRT518216 TRMT10B tRNA methyltransferase 10B 2 2
MIRT519602 ZNF805 zinc finger protein 805 2 2
MIRT523570 GGCX gamma-glutamyl carboxylase 2 4
MIRT525795 SOD2 superoxide dismutase 2 2 2
MIRT533055 ZBTB37 zinc finger and BTB domain containing 37 2 2
MIRT534218 SLC37A3 solute carrier family 37 member 3 2 4
MIRT535633 NR2E1 nuclear receptor subfamily 2 group E member 1 2 2
MIRT535863 MRPL17 mitochondrial ribosomal protein L17 2 2
MIRT536344 LEFTY1 left-right determination factor 1 2 2
MIRT537923 DSTYK dual serine/threonine and tyrosine protein kinase 2 2
MIRT543114 SKA2 spindle and kinetochore associated complex subunit 2 2 2
MIRT544717 ZNF529 zinc finger protein 529 2 2
MIRT544847 BASP1 brain abundant membrane attached signal protein 1 2 4
MIRT545536 ARF3 ADP ribosylation factor 3 2 2
MIRT547124 PHLPP2 PH domain and leucine rich repeat protein phosphatase 2 2 2
MIRT548070 GIGYF1 GRB10 interacting GYF protein 1 2 2
MIRT548446 EIF1AX eukaryotic translation initiation factor 1A, X-linked 2 2
MIRT548626 DAZAP1 DAZ associated protein 1 2 4
MIRT550259 FAM120AOS family with sequence similarity 120A opposite strand 2 2
MIRT551940 AKAP8 A-kinase anchoring protein 8 2 4
MIRT552511 ZIK1 zinc finger protein interacting with K protein 1 2 4
MIRT554015 SPIRE1 spire type actin nucleation factor 1 2 2
MIRT556647 KPNA2 karyopherin subunit alpha 2 2 4
MIRT559744 ACOX1 acyl-CoA oxidase 1 2 2
MIRT560393 TMEM254 transmembrane protein 254 2 2
MIRT562234 HMGB2 high mobility group box 2 2 2
MIRT563325 ORC4 origin recognition complex subunit 4 2 2
MIRT563697 RPS26 ribosomal protein S26 2 2
MIRT565066 USP25 ubiquitin specific peptidase 25 2 2
MIRT565349 TMED2 transmembrane p24 trafficking protein 2 2 2
MIRT565624 SLC31A1 solute carrier family 31 member 1 2 2
MIRT566379 PNISR PNN interacting serine and arginine rich protein 2 2
MIRT567575 FEM1C fem-1 homolog C 2 2
MIRT569383 DDX20 DEAD-box helicase 20 2 2
MIRT570037 FAM228A family with sequence similarity 228 member A 2 2
MIRT573269 DCAF10 DDB1 and CUL4 associated factor 10 2 2
MIRT573912 PARP1 poly(ADP-ribose) polymerase 1 2 2
MIRT620034 ST6GALNAC3 ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 2 2
MIRT635606 ZWILCH zwilch kinetochore protein 2 2
MIRT644413 FRMD6 FERM domain containing 6 2 2
MIRT652528 TM9SF4 transmembrane 9 superfamily member 4 2 2
MIRT656238 MFSD6 major facilitator superfamily domain containing 6 2 2
MIRT661373 DYRK4 dual specificity tyrosine phosphorylation regulated kinase 4 2 2
MIRT662530 PNPLA4 patatin like phospholipase domain containing 4 2 2
MIRT675551 MALL mal, T-cell differentiation protein like 2 2
MIRT693650 ACBD7 acyl-CoA binding domain containing 7 2 2
MIRT696348 SLC35D2 solute carrier family 35 member D2 2 2
MIRT705815 AKNA AT-hook transcription factor 2 2
MIRT707632 TARDBP TAR DNA binding protein 2 2
MIRT717902 COPS8 COP9 signalosome subunit 8 2 2
MIRT723626 SOBP sine oculis binding protein homolog 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3123 Doxorubicin 31703 NSC123127 approved sensitive High Triple-Negative Breast Cancer cell line (MDA-MB-231, MDA-MB-468)
hsa-mir-3123 Cisplatin 5460033 NSC119875 approved sensitive cell line (BxPC3)
hsa-miR-3123 Osimertinib 71496458 NSC779217 approved sensitive cell line (PC9)
hsa-miR-3123 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3123 Vemurafenib 42611257 NSC761431 approved resistant cell line (LM16)

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