miRTarBase - #MIRT563103


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pre-miRNA Information
pre-miRNA hsa-mir-3915   
Genomic Coordinates chrX: 32583656 - 32583752
Description Homo sapiens miR-3915 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3915
Sequence 21| UUGAGGAAAAGAUGGUCUUAUU |42
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs997323565 10 dbSNP
rs1192161547 15 dbSNP
rs1255075246 19 dbSNP
rs1452812574 20 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol IFRD2   
Synonyms IFNRP, SKMc15, SM15
Description interferon related developmental regulator 2
Transcript NM_006764   
Expression
Putative miRNA Targets on IFRD2
3'UTR of IFRD2
(miRNA target sites are highlighted)		 
>IFRD2|NM_006764|3'UTR
   1 AGCAGGACCTGCTGAAGAGGAGACTTTCTATGCCCTTGGTCCGTATTTTTAACAGAAGACAGTGCAACAACTGGTCTCCA
  81 CCAGTATTTGTCACTTTATTTTTTTTAATGACAAAACCAAAAACAGACATGGGGTGGGTAGCTGGGGGCCCGGACACTTG
 161 GGACCCTGACCCCTTTGTCCCTGCACTCAGCCCTGTGGCCCCTTCCTGTCCTGTCTCAGGCCAGGCTAAATATGTGCCTT
 241 CCTCAGGGCTGTGGGGCAGGCACTAGGGGGCCTTTCCCTTCCTTTCCTTTCTCAGGCCTTGCTCCCCCAGGATGACCCAC
 321 TCTTAGGGGGGTGGTGGCATCTGGACAAATGCCACCACAGCAGGTGGGGTGGCAAAGCTACCTGGAATGGATTTGTGTGC
 401 TGATTTTTAAGGATTATTACAGATAATTAAACAGAACGGTCAGCCTTCTGTGGTCTTAAAAAAAAAAAAAAAAAAAAAA
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' uuAUUCUGGUAGAAAAGGAGUu 5'
            |||   ::|   ||||||| 
Target 5' gcTAAATATGTGCCTTCCTCAg 3'
 225 - 246 144.00 -9.70
2 
miRNA  3' uuauucuGGUAGAAAAGGAGUu 5'
                 || |:  ||:|||| 
Target 5' ttcccttCCTTTCCTTTCTCAg 3'
 274 - 295 131.00 -8.36
3 
miRNA  3' uuAUUCUGG-UA---GAAAAGGAguu 5'
            | || || :|   |  |||||   
Target 5' acTCAGCCCTGTGGCCCCTTCCTgtc 3'
 185 - 210 104.00 -5.22
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31497408 14 COSMIC
COSN19750846 58 COSMIC
COSN31488171 92 COSMIC
COSN30118814 98 COSMIC
COSN30586162 99 COSMIC
COSN21509451 202 COSMIC
COSN29150335 260 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1206161123 3 dbSNP
rs988109377 4 dbSNP
rs374857927 6 dbSNP
rs1186333587 7 dbSNP
rs1233107144 8 dbSNP
rs1471017762 10 dbSNP
rs782239618 20 dbSNP
rs781963978 22 dbSNP
rs1175290540 23 dbSNP
rs1411024281 27 dbSNP
rs782329301 30 dbSNP
rs782176634 36 dbSNP
rs781815893 39 dbSNP
rs1178570630 40 dbSNP
rs782533487 42 dbSNP
rs185959790 43 dbSNP
rs782613859 46 dbSNP
rs782366952 48 dbSNP
rs1440350419 53 dbSNP
rs1279302671 54 dbSNP
rs1346608471 61 dbSNP
rs1225878505 72 dbSNP
rs181671415 74 dbSNP
rs1320719689 78 dbSNP
rs1199422204 80 dbSNP
rs1273212624 87 dbSNP
rs1439173563 90 dbSNP
rs1202056160 98 dbSNP
rs1480648114 101 dbSNP
rs1201411534 103 dbSNP
rs200386050 107 dbSNP
rs782322172 107 dbSNP
rs1168543646 111 dbSNP
rs1025125129 143 dbSNP
rs1013811585 151 dbSNP
rs962242504 152 dbSNP
rs1408419267 155 dbSNP
rs1307725876 171 dbSNP
rs1366525287 176 dbSNP
rs1407155086 181 dbSNP
rs1281888918 186 dbSNP
rs1345461528 194 dbSNP
rs1014553062 195 dbSNP
rs1270240930 205 dbSNP
rs782511063 207 dbSNP
rs1340947105 213 dbSNP
rs887442363 226 dbSNP
rs587689836 234 dbSNP
rs995925808 237 dbSNP
rs1193658667 242 dbSNP
rs781900138 249 dbSNP
rs901697364 253 dbSNP
rs1490440610 256 dbSNP
rs587632448 262 dbSNP
rs945958905 266 dbSNP
rs1224469848 271 dbSNP
rs3204447 291 dbSNP
rs913117928 303 dbSNP
rs1450929137 305 dbSNP
rs1193891311 308 dbSNP
rs587757661 310 dbSNP
rs1474478084 314 dbSNP
rs1168127381 316 dbSNP
rs1386130729 320 dbSNP
rs1426894446 326 dbSNP
rs936692994 327 dbSNP
rs1390518843 328 dbSNP
rs1383266367 332 dbSNP
rs925296755 334 dbSNP
rs1327608993 343 dbSNP
rs1225584534 366 dbSNP
rs1296352533 369 dbSNP
rs981290329 370 dbSNP
rs782796364 372 dbSNP
rs1247765018 380 dbSNP
rs1289312014 394 dbSNP
rs1205591806 397 dbSNP
rs1263773001 404 dbSNP
rs1445316379 409 dbSNP
rs1188034580 414 dbSNP
rs1243878414 417 dbSNP
rs1446640072 422 dbSNP
rs1161974367 425 dbSNP
rs1368241679 431 dbSNP
rs1454634869 431 dbSNP
rs748027229 437 dbSNP
rs918094156 438 dbSNP
rs1435072699 441 dbSNP
rs1319262459 450 dbSNP
rs992252949 455 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
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 GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection ...

- Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' uuAUUCUGGUAGAAAAGGAGUu 5'
            |||   ::|   ||||||| 
Target 5' -cUAAAUAUGUGCCUUCCUCAg 3'
 		1 - 21
Article - Hafner M; Landthaler M; Burger L; Khorshid et al.
- Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
CLIP-seq Support 1 for dataset GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_006764 | 3UTR | GGCCCGGACACUUGGGACCCUGACCCCUUUGUCCCUGCACUCAGCCCUGUGGCCCCUUCCUGUCCUGUCUCAGGCCAGGCUAAAUAUGUGCCUUCCUCAGGGCUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903834
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_b
Location of target site NM_006764 | 3UTR | UAAAUAUGUGCCUUCCUCAGGGCUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903835
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_c
Location of target site NM_006764 | 3UTR | GACAUGGGGUGGGUAGCUGGGGGCCCGGACACUUGGGACCCUGACCCCUUUGUCCCUGCACUCAGCCCUGUGGCCCCUUCCUGUCCUGUCUCAGGCCAGGCUAAAUAUGUGCCUUCCUCAGGGCUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4903836
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_a
Location of target site NM_006764 | 3UTR | GGCCAGGCUAAAUAUGUGCCUUCCUCAGGGCUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM4903837
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_b
Location of target site NM_006764 | 3UTR | AAACAGACAUGGGGUGGGUAGCUGGGGGCCCGGACACUUGGGACCCUGACCCCUUUGUCCCUGCACUCAGCCCUGUGGCCCCUUCCUGUCCUGUCUCAGGCCAGGCUAAAUAUGUGCCUUCCUCAGGGCUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_006764 | 3UTR | AGCUGGGGGCCCGGACACUUGGGACCCUGACCCCUUUGUCCCUGCACUCAGCCCUGUGGCCCCUUCCUGUCCUGUCUCAGGCCAGGCUAAAUAUGUGCCUUCCUCAGGGCUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000417626.2 | 3UTR | CUAAAUAUGUGCCUUCCUCAGGGCUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
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
111 hsa-miR-3915 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT059544 PIP5K1A phosphatidylinositol-4-phosphate 5-kinase type 1 alpha 2 2
MIRT081703 ZNF507 zinc finger protein 507 2 2
MIRT083311 ZCCHC3 zinc finger CCHC-type containing 3 2 6
MIRT119046 SFT2D3 SFT2 domain containing 3 2 2
MIRT189381 TXLNA taxilin alpha 2 4
MIRT195895 C16ORF72 chromosome 16 open reading frame 72 2 6
MIRT223807 OXR1 oxidation resistance 1 2 2
MIRT292954 ZNF146 zinc finger protein 146 2 4
MIRT293949 RPL13A ribosomal protein L13a 2 6
MIRT300900 KREMEN1 kringle containing transmembrane protein 1 2 2
MIRT339332 SESN2 sestrin 2 2 2
MIRT349304 ZNF317 zinc finger protein 317 2 2
MIRT364736 TOR1B torsin family 1 member B 2 2
MIRT366233 VMA21 VMA21, vacuolar ATPase assembly factor 2 2
MIRT384605 CLIC4 chloride intracellular channel 4 2 2
MIRT401745 HLA-DRA major histocompatibility complex, class II, DR alpha 2 2
MIRT443169 UBL3 ubiquitin like 3 2 2
MIRT444215 METTL12 methyltransferase like 12 2 2
MIRT444375 SH3TC2 SH3 domain and tetratricopeptide repeats 2 2 2
MIRT445340 TCEANC transcription elongation factor A N-terminal and central domain containing 2 2
MIRT445474 KDM6A lysine demethylase 6A 2 2
MIRT445598 CAMK2N1 calcium/calmodulin dependent protein kinase II inhibitor 1 2 2
MIRT445630 TMEM50A transmembrane protein 50A 2 2
MIRT446012 VNN1 vanin 1 2 2
MIRT446115 ASTN1 astrotactin 1 2 2
MIRT446248 ELP2 elongator acetyltransferase complex subunit 2 2 2
MIRT446382 SYNCRIP synaptotagmin binding cytoplasmic RNA interacting protein 2 2
MIRT446940 ZMAT3 zinc finger matrin-type 3 2 2
MIRT446967 SLCO4C1 solute carrier organic anion transporter family member 4C1 2 2
MIRT447178 PGRMC2 progesterone receptor membrane component 2 2 2
MIRT447209 APBB2 amyloid beta precursor protein binding family B member 2 2 2
MIRT447237 IHH indian hedgehog 2 2
MIRT447807 EMX1 empty spiracles homeobox 1 2 2
MIRT447853 RRP8 ribosomal RNA processing 8 2 4
MIRT448054 MMP15 matrix metallopeptidase 15 2 2
MIRT448094 RASD2 RASD family member 2 2 2
MIRT448704 KLHL11 kelch like family member 11 2 2
MIRT448851 FEM1C fem-1 homolog C 2 2
MIRT449488 ZBTB4 zinc finger and BTB domain containing 4 2 2
MIRT449785 C1orf109 chromosome 1 open reading frame 109 2 2
MIRT450774 PDE3A phosphodiesterase 3A 2 2
MIRT451124 ZNF99 zinc finger protein 99 2 2
MIRT452676 GPR156 G protein-coupled receptor 156 2 2
MIRT452888 PSD4 pleckstrin and Sec7 domain containing 4 2 2
MIRT453188 ACSF2 acyl-CoA synthetase family member 2 2 2
MIRT453353 ZNF3 zinc finger protein 3 2 2
MIRT454502 ZFYVE27 zinc finger FYVE-type containing 27 2 2
MIRT454629 FAM83H family with sequence similarity 83 member H 2 2
MIRT455183 AGTRAP angiotensin II receptor associated protein 2 2
MIRT458204 FOXL2 forkhead box L2 2 2
MIRT458723 CES2 carboxylesterase 2 2 2
MIRT458942 SAMD4B sterile alpha motif domain containing 4B 2 2
MIRT460304 FLCN folliculin 2 2
MIRT460989 SYT7 synaptotagmin 7 2 2
MIRT461697 ZNF426 zinc finger protein 426 2 2
MIRT461903 NECAB3 N-terminal EF-hand calcium binding protein 3 2 2
MIRT462193 NDUFS1 NADH:ubiquinone oxidoreductase core subunit S1 2 2
MIRT462290 PPM1H protein phosphatase, Mg2+/Mn2+ dependent 1H 2 2
MIRT463795 XPOT exportin for tRNA 2 2
MIRT464649 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 4
MIRT465911 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 4
MIRT465992 TMEM189 transmembrane protein 189 2 4
MIRT466302 TIMM22 translocase of inner mitochondrial membrane 22 2 2
MIRT466575 TBC1D2B TBC1 domain family member 2B 2 2
MIRT470558 POU2F1 POU class 2 homeobox 1 2 2
MIRT471333 PERP PERP, TP53 apoptosis effector 2 2
MIRT471659 PALM2 paralemmin 2 2 2
MIRT472363 TSPAN1 tetraspanin 1 2 2
MIRT473468 MCFD2 multiple coagulation factor deficiency 2 2 2
MIRT474702 KIF3A kinesin family member 3A 2 2
MIRT476067 GRIN2A glutamate ionotropic receptor NMDA type subunit 2A 2 2
MIRT476077 GRB2 growth factor receptor bound protein 2 2 2
MIRT476423 GBA2 glucosylceramidase beta 2 2 2
MIRT476463 GATAD2B GATA zinc finger domain containing 2B 2 2
MIRT477877 DYNLL2 dynein light chain LC8-type 2 2 2
MIRT478240 DDX3X DEAD-box helicase 3, X-linked 2 4
MIRT479460 CDK6 cyclin dependent kinase 6 2 2
MIRT481030 BAZ2A bromodomain adjacent to zinc finger domain 2A 2 2
MIRT491496 HLA-DOA major histocompatibility complex, class II, DO alpha 2 2
MIRT497585 SLC23A1 solute carrier family 23 member 1 2 2
MIRT498542 TMEM30B transmembrane protein 30B 2 2
MIRT499263 NBPF11 NBPF member 11 2 2
MIRT504698 ZNF117 zinc finger protein 117 2 2
MIRT511288 KLHL15 kelch like family member 15 2 4
MIRT523121 HSP90B1 heat shock protein 90 beta family member 1 2 4
MIRT529601 H1F0 H1 histone family member 0 2 2
MIRT533481 TRIM71 tripartite motif containing 71 2 2
MIRT535571 NUP37 nucleoporin 37 2 4
MIRT537869 EDA2R ectodysplasin A2 receptor 2 2
MIRT538010 DNAJC10 DnaJ heat shock protein family (Hsp40) member C10 2 2
MIRT552681 YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta 2 4
MIRT554986 RAB39B RAB39B, member RAS oncogene family 2 2
MIRT556659 KMT2D lysine methyltransferase 2D 2 4
MIRT557437 GTPBP2 GTP binding protein 2 2 2
MIRT560813 CRTAP cartilage associated protein 2 2
MIRT562115 IGFBP5 insulin like growth factor binding protein 5 2 2
MIRT563103 IFRD2 interferon related developmental regulator 2 2 2
MIRT574199 LMNB1 lamin B1 2 2
MIRT623920 FMNL3 formin like 3 2 2
MIRT626551 NMNAT2 nicotinamide nucleotide adenylyltransferase 2 2 2
MIRT645458 ANKS6 ankyrin repeat and sterile alpha motif domain containing 6 2 2
MIRT649082 CACNA1B calcium voltage-gated channel subunit alpha1 B 2 2
MIRT659477 CLDN1 claudin 1 2 2
MIRT667950 HMGCS1 3-hydroxy-3-methylglutaryl-CoA synthase 1 2 2
MIRT701981 MIER3 MIER family member 3 2 2
MIRT708694 TFDP2 transcription factor Dp-2 2 2
MIRT709649 DFFB DNA fragmentation factor subunit beta 2 2
MIRT710090 FAM229B family with sequence similarity 229 member B 2 2
MIRT718396 ALDH1A3 aldehyde dehydrogenase 1 family member A3 2 2
MIRT724972 TNS1 tensin 1 2 2
MIRT756050 HRH4 histamine receptor H4 2 1
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3915 Paclitaxel 36314 NSC125973 approved resistant High Prostate Cancer cell line (DU-145, PC-3)
hsa-miR-3915 Cisplatin + Decitabine sensitive High Non-Small Cell Lung Cancer cell line (A549)
hsa-mir-3915 Cisplatin 5460033 NSC119875 approved sensitive cell line (BxPC3)
hsa-miR-3915 Tripterygium wilfordii Hook F sensitive tissue
hsa-miR-3915 Cisplatin 5460033 NSC119875 approved resistant cell line (A549)
hsa-miR-3915 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3915 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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