miRTarBase - #MIRT560380


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pre-miRNA Information
pre-miRNA hsa-mir-3675   
Genomic Coordinates chr1: 16858949 - 16859021
Description Homo sapiens miR-3675 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3675-5p
Sequence 12| UAUGGGGCUUCUGUAGAGAUUUC |34
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1229940041 1 dbSNP
rs1184422098 2 dbSNP
rs768029583 3 dbSNP
rs202014433 6 dbSNP
rs774834919 7 dbSNP
rs1484376029 8 dbSNP
rs771338088 8 dbSNP
rs749521347 10 dbSNP
rs773421450 12 dbSNP
rs1250672393 14 dbSNP
rs769780471 15 dbSNP
rs781028022 16 dbSNP
rs1315377622 17 dbSNP
rs754885466 18 dbSNP
rs746860289 20 dbSNP
rs1330333643 23 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol TIMM8A   
Synonyms DDP, DDP1, DFN1, MTS, TIM8
Description translocase of inner mitochondrial membrane 8A
Transcript NM_004085   
Other Transcripts NM_001145951   
Expression
Putative miRNA Targets on TIMM8A
3'UTR of TIMM8A
(miRNA target sites are highlighted)		 
>TIMM8A|NM_004085|3'UTR
   1 TCTCAGCATTACCTCTTTGGAAAAGGAAGGTAGTTCAAGAAATGAAGAGCTGTTGATGGGATGATTGAAGAAACAGCTAT
  81 GAGAGGATTGGCTCCCATCTTTTGTTACTCTTGGGACATCCTGTCATCTGAGAATGAACAAAGACCAATTTTTTGTGTGT
 161 GAAGCTTAAGGGTCATATGTTTGCTTGTATTTTTTAATGCTAATCTTGTGAAAATAATTGACAGGCGAAAGAAAACTCTA
 241 TTTAGATGCATATTACTGTACATGGGACTATGCTTTTCTCAAAGCCCCATTAACTGCTTCCTATAATTTTGATAGTGGGA
 321 CCACATACGTAAAAATCTCTCATTTGTGTGGAGTCATTTCTGATTTCAGGGGAGATCCTTGTGTTTATCAGAAAGGGCAG
 401 AAGTAGGGGAAGAATAATTTGGTATCCTTATCTAGTGTTTGATTGTCAATGCTGGAGAAAAATATCTGTAAGAGTGTTTA
 481 TACAGTACACTTCAGTTATCTTGATCTCCCTTTCCTATATGATGATTTGCTTAAATATCCATATTAAGTAAGTCTCAAGG
 561 TAGGGTAGGCAGCCTGAGAGTCTAGAGGCCTTTAGTTATAAAGGAATCTAGCCAGTGAACATAATTCTTATTACTAGACT
 641 GCCACAAGGAAGAAATTAACTTACCCTGTATATCAGGGTACAAAAAATTCAGTGATGTGCCTAAATAAGTTATAAAGATT
 721 TAGGCCAATCAGAAGCTAACAGCAGTTTCAGGTAGAGGTGCATGCCTAATGTTAGTTAGTGTAGATTCCATTTACTGCAT
 801 TCTTCTGATCACTGAAATAAAAGCTATATAAGATTCAACTCTGAAAAAAAAAAAAAAAAA
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' cuuuAGAGAUGUCUUCGGGGUAu 5'
              |:||| || ||||||||| 
Target 5' tgctTTTCT-CA-AAGCCCCATt 3'
 271 - 291 165.00 -17.60
2 
miRNA  3' cuuUAGAGA-UGUCUU---CG-GGGUAu 5'
             | || | | ||:|   || ||||| 
Target 5' aacAGCTATGAGAGGATTGGCTCCCATc 3'
 72 - 99 120.00 -12.50
3 
miRNA  3' cuUUAGAG--AUG--UC-UUCGGGGUau 5'
            ||| ||  ||:  || |||:|:||  
Target 5' taAATATCCATATTAAGTAAGTCTCAag 3'
 532 - 559 113.00 -8.40
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
21394 506 ClinVar
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs185711695 25 dbSNP
rs1402589367 26 dbSNP
rs782762708 29 dbSNP
rs782801850 30 dbSNP
rs782214090 43 dbSNP
rs1455861527 46 dbSNP
rs181919155 50 dbSNP
rs1383990084 72 dbSNP
rs1447690258 79 dbSNP
rs1283007618 95 dbSNP
rs2071224 97 dbSNP
rs782076826 121 dbSNP
rs1287134051 122 dbSNP
rs1326405745 128 dbSNP
rs1205209879 129 dbSNP
rs781800592 132 dbSNP
rs1263306666 158 dbSNP
rs1441688216 174 dbSNP
rs1207751757 189 dbSNP
rs1234568207 206 dbSNP
rs3027653 226 dbSNP
rs782638910 227 dbSNP
rs1411362514 240 dbSNP
rs1471610366 245 dbSNP
rs183928551 252 dbSNP
rs1178863987 257 dbSNP
rs1407100680 263 dbSNP
rs368774526 302 dbSNP
rs1414330287 323 dbSNP
rs1332577374 324 dbSNP
rs1356843757 325 dbSNP
rs782017070 328 dbSNP
rs1348092492 329 dbSNP
rs1224803088 343 dbSNP
rs782526107 355 dbSNP
rs1343812319 358 dbSNP
rs1217311681 368 dbSNP
rs1274881402 384 dbSNP
rs782704764 396 dbSNP
rs1249454810 398 dbSNP
rs1482150675 422 dbSNP
rs1201685177 432 dbSNP
rs1378471750 435 dbSNP
rs79564479 436 dbSNP
rs1170988349 437 dbSNP
rs1422135803 443 dbSNP
rs1430726047 447 dbSNP
rs1307975942 466 dbSNP
rs781892837 468 dbSNP
rs1406285231 469 dbSNP
rs1303203720 472 dbSNP
rs1329953369 473 dbSNP
rs782102842 477 dbSNP
rs1271505027 484 dbSNP
rs1339842505 489 dbSNP
rs879947933 493 dbSNP
rs1227373875 499 dbSNP
rs868979856 500 dbSNP
rs868969312 501 dbSNP
rs1331509900 506 dbSNP
rs4024308 506 dbSNP
rs782333734 506 dbSNP
rs868980473 507 dbSNP
rs1361470087 509 dbSNP
rs1224884886 519 dbSNP
rs3027654 521 dbSNP
rs1451070908 523 dbSNP
rs1197030405 529 dbSNP
rs1244003687 530 dbSNP
rs1450554035 535 dbSNP
rs1168319805 539 dbSNP
rs1388913096 581 dbSNP
rs1427133892 583 dbSNP
rs1164299270 590 dbSNP
rs1389392320 606 dbSNP
rs1384504054 617 dbSNP
rs1319941739 627 dbSNP
rs1326655611 630 dbSNP
rs782036530 641 dbSNP
rs1295103258 649 dbSNP
rs1246665825 665 dbSNP
rs1264722467 668 dbSNP
rs1355747684 682 dbSNP
rs1208124631 688 dbSNP
rs371672469 688 dbSNP
rs78682730 688 dbSNP
rs1188110178 703 dbSNP
rs1246605640 719 dbSNP
rs1446750692 724 dbSNP
rs1188866142 745 dbSNP
rs1368383619 752 dbSNP
rs1455988813 755 dbSNP
rs1159767129 760 dbSNP
rs1388990239 775 dbSNP
rs781979163 781 dbSNP
rs1318079187 795 dbSNP
rs1408037885 805 dbSNP
rs1396336725 813 dbSNP
rs375049891 828 dbSNP
rs1242761872 832 dbSNP
rs782301849 832 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 GSM545217. RNA binding protein: AGO2. Condition:miR-7 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' cuuuagagaugucuucGGGGUAu 5'
                          |||||| 
Target 5' ----------------CCCCAUu 3'
 		1 - 7
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_004085 | 3UTR | GGGACUAUGCUUUUCUCAAAGCCCCAUUAACUGCUUCCUAUAAUUUUGAUAGUGGGACCACAUACGUAAAAAUCUCUCAUUU
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_004085 | 3UTR | AAAACUCUAUUUAGAUGCAUAUUACUGUACAUGGGACUAUGCUUUUCUCAAAGCCCCAUUAACUGCUUCCUAUAAUUUUGAUAGUGGGACCACAUACGUAAAAAUCUCUCAUUU
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_004085 | 3UTR | UACAUGGGACUAUGCUUUUCUCAAAGCCCCAUUAACUGCUUCCUAUAAUUUUGAUAGUGGGACCACAUACGUAAAAAUCUCUCAUUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_004085 | 3UTR | UUUCUCAAAGCCCCAUUAACUGCUUCCUAUAAUUUUGAUAGUGGGACCACAUACGUAAAAAUCUCUCAUUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM545217
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-7 transfection
Location of target site ENST00000372902.3 | 3UTR | CCCCAUUAACUGCUUCCUAU
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
32 hsa-miR-3675-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT366903 NONO non-POU domain containing octamer binding 2 2
MIRT453894 DUSP18 dual specificity phosphatase 18 2 2
MIRT461725 ZNF426 zinc finger protein 426 2 2
MIRT464694 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 2
MIRT465957 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 2
MIRT466038 TMEM189 transmembrane protein 189 2 2
MIRT471546 PAX5 paired box 5 2 2
MIRT472813 MTMR12 myotubularin related protein 12 2 2
MIRT474099 LMBR1L limb development membrane protein 1 like 2 2
MIRT480205 CAD carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase 2 2
MIRT488268 HSP90AB1 heat shock protein 90 alpha family class B member 1 2 8
MIRT491222 MRPL34 mitochondrial ribosomal protein L34 2 2
MIRT494768 AP1G1 adaptor related protein complex 1 gamma 1 subunit 2 2
MIRT497228 MORC2 MORC family CW-type zinc finger 2 2 2
MIRT501676 PFN1 profilin 1 2 6
MIRT511831 H2AFX H2A histone family member X 2 4
MIRT513880 HNRNPUL1 heterogeneous nuclear ribonucleoprotein U like 1 2 4
MIRT519402 DNASE2 deoxyribonuclease 2, lysosomal 2 4
MIRT522627 MAP7D1 MAP7 domain containing 1 2 4
MIRT546998 PPP2CA protein phosphatase 2 catalytic subunit alpha 2 2
MIRT555119 PUM2 pumilio RNA binding family member 2 2 2
MIRT560380 TIMM8A translocase of inner mitochondrial membrane 8A 2 2
MIRT572188 CDADC1 cytidine and dCMP deaminase domain containing 1 2 2
MIRT634822 ASB6 ankyrin repeat and SOCS box containing 6 2 2
MIRT641149 DNMBP dynamin binding protein 2 2
MIRT647389 ZNF616 zinc finger protein 616 2 2
MIRT670851 SFT2D2 SFT2 domain containing 2 2 2
MIRT698600 TEX261 testis expressed 261 2 2
MIRT698691 TBPL1 TATA-box binding protein like 1 2 2
MIRT708725 PTPLAD2 3-hydroxyacyl-CoA dehydratase 4 1 1
MIRT718340 SYNDIG1L synapse differentiation inducing 1 like 2 2
MIRT725514 FBXO46 F-box protein 46 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-3675 Doxorubicin 31703 NSC123127 approved sensitive High Triple-Negative Breast Cancer cell line (MDA-MB-231, MDA-MB-468)
hsa-miR-3675-5p Cisplatin 5460033 NSC119875 approved resistant cell line (MGC-803)
hsa-miR-3675-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)

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