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 GIGYF1   
Synonyms GYF1, PERQ1
Description GRB10 interacting GYF protein 1
Transcript NM_022574   
Expression
Putative miRNA Targets on GIGYF1
3'UTR of GIGYF1
(miRNA target sites are highlighted)
>GIGYF1|NM_022574|3'UTR
   1 CCAGCCCGGACCCCCAGCCCCTGGGCTGTAGGCCAGGGCAGCCACAGCGGCGTGGACCGAGGGTCCCAGCCTGCAGGCTC
  81 CCCGCAGAGAGCACAGGAAGAGGCAGGGGCGGGGTCCCCAGCACTTGTTACAAACACACGATGCACCTTAACTCACCCAC
 161 CACGAGGCACTTTACAGACTGGGGGAGGGGGTTTTTCTTTTTATTTTTTTTTTTAATTTTAAACGACTGAAGAAAACATT
 241 AGGAGAGGCAAAAATATTGTTAAAAACTAGACTCTAAACACCCCTTCCTGCTGTGAGGATAGTGGGTGTGACAATGGAAG
 321 GTCCACAGAGGTTTTTGTTTTTTGGTTTTTTTTTTTTTTTTAAGAAAAAAAGATGAAAAATGAAAAAAAAAATGGTTAGG
 401 AGGCTGAAAGAAAAAACACACTGTTATTTTGGGGCAGTGGGGACACAGGCCCCGTGGACCTGTCCTGCCTGGCCCCCAAG
 481 GCCATACTTACCCCCCAGAAGGCGGGCCATGGGGTAACTGGAAGCTGGGGGCCAGCAGTTTGCACAGGAGGCCTGTCTGA
 561 GCCCCACCCGCCAGACCTGTTGTGAGCAGCTCCTGTCACTGAGGCTGGCTGAGGTGTCCGGGGTGGGGCCAAAGTAGCCC
 641 CTTGGCTTCGCTGCTTTGGGGGACAGTTGCACAAATTGGACGAGTGGCCCCAGCTCTCTGGCTGCCATCTTGTGCTGGCC
 721 GAGTAGACGGGAGGGGCCAAGCCGTGCCAACCTCTCTGGCTGGCAGGGTGGGGCAGCAGGACTCTGGTTCTGGTGAGGGG
 801 CGTCTCCCACTGCTGCCATTTTGGGGGACACCCTGGGTTTGAACCTGAAAGCCCCAGCTCTCTGCCTTGCCACGTGAATG
 881 TATTCTTTGGGCCACAAGCCCCCGCCTCACCCCTGCCTGAGCTGCCTCACCCCTGTGAGCGGCGGGGGTGGATGATTGCT
 961 CCAGAGGCTGCAGAGAGAAGGCTGAGCTGTTTCTCCAGTGAAGGGGGCAGGAGGAGGGGCCTCAAAGGCAAGGAGTGGGT
1041 GGCTTTGGGCTTAGGGTTGCAGTAGAGGGGCTGCCGCCCGGGGCCCCAACCTGTAGCCAGCTCGTAAGATGTGGACCACC
1121 CAGCTCTGCACCTGACCCTTCCGCTGACCAAATGGGAGAGGAGCAGGTGGCCTTCCGGGTCTGATATGATGCGCTTTTTA
1201 CCGTTGGGTAAGGTTGGGGTGAAGAGAAGTGTGCGGCTCCTGGGTCAGAGGAGGCTGCCCCTTCTATTGCTCACCCACTT
1281 CTTATTCCCGGTCCCCTACTTGGGTTCGTCTCCGCCCATTTTGGGTTTTGTAACAGTTTTGTCTTTTGGGTTTCTCATCC
1361 AGCTCCTCCCATTGACCTCATTGCTCAGAGTGCAGTATTAGGGCAAGGCTTCGCCACTGCCTCCCTCCATGAATGTATTT
1441 CTCCCTCCTGCCCTGGGGACATGGGGAGTGGCCCGTTTCTTTCCCCATCTAGTCCCAGAAAGATGGTGTTTGGTTTTCTG
1521 TTGTTGGATTTTTTTTTTTTTTTTTTTTTTTTTGCACCAAAGTGGCAACTAGGTCAGTGTTGGGGGATCAAGCTGGCCTC
1601 GGGGTGGGGGGCCCCCACCTGCCTCTCCCTGGTTCCCACAGTGTTAGCGTCCCTGAAAAGACAATATTCTCTCTAAAGCA
1681 ATAAGGGGTGACGGGCCGGGGGGAGTGTTTGCTGCTGCTGGCCCCCAGCTCCCCTTCCCTCTTGCCAGGTGTGGGGGAGA
1761 CTCCTGTTGTGACTGAATGTAACCCCCCCACCCCTGCCGCAGCCAATGCAGGGGAAGGGGGACACTCTTCCTGTCTCTTC
1841 TCCCCAGCTAAAGAGACTTTGGACTTAGGGGGCCCATGAGCCTGGAGAGGCCTTAACCCTGTGAGGAAGTATAGGGGGAG
1921 CCCTCTCCCACCCCCATCCCCTTCTGAGAGTGGTCAATGTTTACAAGCCCCTGAGCCCCCCTGCCCAGGGACTCAGACCC
2001 TGTTGCTGTCCTTCCCCGGCCCCGGTCTTCCTGGGCCCTCGCTGCTCCCCTGCCCTTCCTGGGGTTGGGGTGGGTGCAGG
2081 GGTCACCGTGTTCCCTGTCTGCCTTGTACCCACAGTCTCCCCGCCCCCTCTCCACCCTGTGTGACTTCCCTCTCTTTTAC
2161 CTGCTCCTGTAAATACTCCCTTCTCCCAATAAAACTTGGTGTGTGTTCTCCCGAAAAAAAAAAAAAAAAA
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' cuaaUUUGU--UAAGAGAc 5'
              |:|||  ||||||| 
Target 5' gaaaAGACAATATTCTCTc 3'
1655 - 1673 151.00 -8.00
2
miRNA  3' cuaAUUUGU-UAAGAGAc 5'
             |:||:: |||||:| 
Target 5' acgTGAATGTATTCTTTg 3'
872 - 889 134.00 -6.90
3
miRNA  3' cuAAUUU----GUUAAGAGAc 5'
            | |||    ||: ||||| 
Target 5' ccTGAAAGCCCCAGCTCTCTg 3'
844 - 864 105.00 -10.90
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 64599.0
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 GSM714645. 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' cuaauuUGU--UAAGAGAc 5'
                |||  ||||||| 
Target 5' ------ACAAUAUUCUCUc 3'
1 - 13
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 GSM714645
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repB
Location of target site ENST00000275732.5 | 3UTR | ACAAUAUUCUCUCUAAAGCAAUAAG
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
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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