pre-miRNA Information
pre-miRNA hsa-mir-569   
Genomic Coordinates chr3: 171106664 - 171106759
Synonyms MIRN569, hsa-mir-569, MIR569
Description Homo sapiens miR-569 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-569
Sequence 61| AGUUAAUGAAUCCUGGAAAGU |81
Evidence Experimental
Experiments SAGE
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN23021417 4 COSMIC
COSN1083370 8 COSMIC
COSN30455038 12 COSMIC
COSN24300323 13 COSMIC
COSN32068274 16 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs752673293 5 dbSNP
rs1218920077 8 dbSNP
rs745722313 12 dbSNP
rs1368837885 14 dbSNP
Putative Targets

Gene Information
Gene Symbol ZFP36   
Synonyms G0S24, GOS24, NUP475, RNF162A, TIS11, TTP, zfp-36
Description ZFP36 ring finger protein
Transcript NM_003407   
Expression
Putative miRNA Targets on ZFP36
3'UTR of ZFP36
(miRNA target sites are highlighted)
>ZFP36|NM_003407|3'UTR
   1 CAAAGTGACTGCCCGGTCAGATCAGCTGGATCTCAGCGGGGAGCCACGTCTCTTGCACTGTGGTCTCTGCATGGACCCCA
  81 GGGCTGTGGGGACTTGGGGGACAGTAATCAAGTAATCCCCTTTTCCAGAATGCATTAACCCACTCCCCTGACCTCACGCT
 161 GGGGCAGGTCCCCAAGTGTGCAAGCTCAGTATTCATGATGGTGGGGGATGGAGTGTCTTCCGAGGTTCTTGGGGGAAAAA
 241 AAATTGTAGCATATTTAAGGGAGGCAATGAACCCTCTCCCCCACCTCTTCCCTGCCCAAATCTGTCTCCTAGAATCTTAT
 321 GTGCTGTGAATAATAGGCCTTCACTGCCCCTCCAGTTTTTATAGACCTGAGGTTCCAGTGTCTCCTGGTAACTGGAACCT
 401 CTCCTGAGGGGGAATCCTGGTGCTCAAATTACCCTCCAAAAGCAAGTAGCCAAAGCCGTTGCCAAACCCCACCCATAAAT
 481 CAATGGGCCCTTTATTTATGACGACTTTATTTATTCTAATATGATTTTATAGTATTTATATATATTGGGTCGTCTGCTTC
 561 CCTTGTATTTTTCTTCCTTTTTTTGTAATATTGAAAACGACGATATAATTATTATAAGTAGACTATAATATATTTAGTAA
 641 TATATATTATTACCTTAAAAGTCTATTTTTGTGTTTTGGGCATTTTTAAATAAACAATCTGAGTGTAAGCTGG
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' ugAAAGGUCCUAAGUAAUUGa 5'
            ||||||| || ||||||| 
Target 5' ctTTTCCAGAATGCATTAACc 3'
120 - 140 179.00 -15.60
2
miRNA  3' ugaaAGGUCCUAAGUAAUUGa 5'
              |||||  ||:|| :|| 
Target 5' ccccTCCAGTTTTTATAGACc 3'
347 - 367 105.00 -9.00
3
miRNA  3' ugaAAGGUCCUA-AGUA--AUUGa 5'
             |||||| :| || |  |||| 
Target 5' aggTTCCAGTGTCTCCTGGTAACt 3'
370 - 393 98.00 -10.50
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30528416 5 COSMIC
COSN30193745 10 COSMIC
COSN30162007 12 COSMIC
COSN30761080 14 COSMIC
COSN27005677 16 COSMIC
COSN30148469 21 COSMIC
COSN30447571 43 COSMIC
COSN30535334 45 COSMIC
COSN18742938 47 COSMIC
COSN31502727 53 COSMIC
COSN1768048 67 COSMIC
COSN30455358 80 COSMIC
COSN27005679 90 COSMIC
COSN20877747 115 COSMIC
COSN23652883 198 COSMIC
COSN31527987 225 COSMIC
COSN28847090 244 COSMIC
COSN9850172 291 COSMIC
COSN20079547 348 COSMIC
COSN31483825 413 COSMIC
COSN21103995 490 COSMIC
COSN1768050 504 COSMIC
COSN31530258 528 COSMIC
COSN7126729 603 COSMIC
COSN25211470 614 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1360882099 6 dbSNP
rs767742260 9 dbSNP
rs1368882909 10 dbSNP
rs768521688 15 dbSNP
rs568030711 16 dbSNP
rs552419216 19 dbSNP
rs993119243 19 dbSNP
rs147603931 26 dbSNP
rs4446003 27 dbSNP
rs4458127 28 dbSNP
rs1193452061 31 dbSNP
rs1335992619 38 dbSNP
rs770209296 39 dbSNP
rs754745061 44 dbSNP
rs778759973 48 dbSNP
rs1204841108 49 dbSNP
rs948552383 61 dbSNP
rs1488839794 62 dbSNP
rs1244146864 63 dbSNP
rs889188594 64 dbSNP
rs1011780955 70 dbSNP
rs980851601 73 dbSNP
rs968075071 78 dbSNP
rs1325291299 82 dbSNP
rs1310655967 88 dbSNP
rs780456422 89 dbSNP
rs550434688 94 dbSNP
rs936735238 103 dbSNP
rs1217578563 109 dbSNP
rs569019234 118 dbSNP
rs1238430715 120 dbSNP
rs1290342396 122 dbSNP
rs1445815392 125 dbSNP
rs1031091454 142 dbSNP
rs892430220 154 dbSNP
rs1470980922 168 dbSNP
rs991887744 171 dbSNP
rs539288952 172 dbSNP
rs1170264291 173 dbSNP
rs1478238646 176 dbSNP
rs945684958 181 dbSNP
rs916354453 189 dbSNP
rs1180477533 202 dbSNP
rs557628710 203 dbSNP
rs867688512 211 dbSNP
rs768904023 213 dbSNP
rs1206078807 215 dbSNP
rs1462284866 216 dbSNP
rs1255533410 217 dbSNP
rs890655152 218 dbSNP
rs1007718211 229 dbSNP
rs1307710182 231 dbSNP
rs1297532352 233 dbSNP
rs1226380711 236 dbSNP
rs75936692 236 dbSNP
rs1315682528 237 dbSNP
rs1454467758 238 dbSNP
rs1398223311 242 dbSNP
rs1460948362 243 dbSNP
rs1179115647 244 dbSNP
rs1017755370 245 dbSNP
rs909042225 253 dbSNP
rs940604540 254 dbSNP
rs1437591836 261 dbSNP
rs1414909836 270 dbSNP
rs1185978735 273 dbSNP
rs1036254802 274 dbSNP
rs901861084 277 dbSNP
rs1197442987 280 dbSNP
rs1480783808 283 dbSNP
rs1252671488 285 dbSNP
rs1218876170 287 dbSNP
rs1320914433 295 dbSNP
rs898931507 299 dbSNP
rs1292163488 300 dbSNP
rs1248090354 302 dbSNP
rs376787756 309 dbSNP
rs1377824285 310 dbSNP
rs1308697500 312 dbSNP
rs1050406299 313 dbSNP
rs1392004071 321 dbSNP
rs1292021512 325 dbSNP
rs889239185 325 dbSNP
rs1025987306 327 dbSNP
rs1803662 343 dbSNP
rs1366587410 344 dbSNP
rs1170476579 345 dbSNP
rs1165856320 349 dbSNP
rs1418469201 355 dbSNP
rs1380205489 365 dbSNP
rs1177512453 372 dbSNP
rs1419185979 378 dbSNP
rs1251988977 379 dbSNP
rs1189115314 382 dbSNP
rs1011666331 383 dbSNP
rs566433333 397 dbSNP
rs950426691 398 dbSNP
rs527987908 399 dbSNP
rs1269421464 408 dbSNP
rs1465698607 408 dbSNP
rs534664726 409 dbSNP
rs1332552603 415 dbSNP
rs903317928 417 dbSNP
rs1285258133 423 dbSNP
rs1239615822 428 dbSNP
rs1403169918 437 dbSNP
rs1445007272 440 dbSNP
rs1386489739 448 dbSNP
rs1306796335 453 dbSNP
rs992797960 456 dbSNP
rs1305389475 457 dbSNP
rs1288597181 458 dbSNP
rs1332074847 459 dbSNP
rs1024623862 473 dbSNP
rs1398511065 485 dbSNP
rs553351861 488 dbSNP
rs557102559 500 dbSNP
rs34202355 514 dbSNP
rs1159679141 524 dbSNP
rs1455753307 529 dbSNP
rs574767381 533 dbSNP
rs1322830121 537 dbSNP
rs1173343520 542 dbSNP
rs17881999 545 dbSNP
rs960262766 558 dbSNP
rs577113687 570 dbSNP
rs991812489 570 dbSNP
rs969148245 571 dbSNP
rs1486804385 575 dbSNP
rs1254398007 578 dbSNP
rs17879933 578 dbSNP
rs386545043 578 dbSNP
rs557212592 584 dbSNP
rs14860 586 dbSNP
rs1324589045 597 dbSNP
rs979924765 608 dbSNP
rs1194985314 616 dbSNP
rs575903007 630 dbSNP
rs1216977164 632 dbSNP
rs909053352 640 dbSNP
rs925750623 643 dbSNP
rs1319319609 645 dbSNP
rs936768071 664 dbSNP
rs989965984 665 dbSNP
rs972292666 666 dbSNP
rs1300622097 667 dbSNP
rs1196232423 668 dbSNP
rs1343075214 669 dbSNP
rs1222589003 670 dbSNP
rs923214672 674 dbSNP
rs913945208 678 dbSNP
rs1178154375 679 dbSNP
rs1268369796 682 dbSNP
rs1318283691 683 dbSNP
rs1476595943 688 dbSNP
rs1172265076 692 dbSNP
rs1193614288 697 dbSNP
rs945352531 698 dbSNP
rs1199768299 705 dbSNP
rs1253956700 705 dbSNP
rs1052050446 708 dbSNP
rs912160280 709 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions C8166
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 GSM1462572. RNA binding protein: AGO2. Condition:C8166 NL4-3 ...

- Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' ugaaagguccUAAGUAAUUGa 5'
                    || ||||||| 
Target 5' ----------AUGCAUUAACc 3'
1 - 11
Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
CLIP-seq Support 1 for dataset GSM1462572
Method / RBP PAR-CLIP / AGO2
Cell line / Condition C8166 / C8166 NL4-3
Location of target site ENST00000597629.1 | 3UTR | AUGCAUUAACCCACUCCCCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
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
GSE28544 Breast cancer 0.462 1.2e-2 0.507 5.7e-3 24 Click to see details
GSE38974 Chronic obstructive pulmonary disease 0.408 2.1e-2 0.458 1.1e-2 25 Click to see details
GSE42095 Differentiated embryonic stem cells 0.205 1.7e-1 0.184 2.0e-1 23 Click to see details
GSE17306 Multiple myeloma -0.12 2.1e-1 0.425 1.2e-3 49 Click to see details
GSE14794 Lymphoblastoid cells -0.078 2.3e-1 -0.092 1.9e-1 90 Click to see details
GSE17498 Multiple myeloma -0.114 2.4e-1 0.015 4.6e-1 40 Click to see details
GSE26953 Aortic valvular endothelial cells -0.144 2.5e-1 0.006 4.9e-1 24 Click to see details
GSE38226 Liver fibrosis -0.14 2.7e-1 -0.077 3.7e-1 21 Click to see details
GSE32688 Pancreatic cancer -0.079 3.3e-1 -0.051 3.9e-1 32 Click to see details
GSE28260 Renal cortex and medulla 0.105 3.7e-1 0.022 4.7e-1 13 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis 0.068 3.9e-1 -0.126 3.0e-1 20 Click to see details
GSE27834 Pluripotent stem cells 0.07 4.0e-1 0.097 3.6e-1 16 Click to see details
GSE21687 Ependynoma primary tumors -0.014 4.6e-1 -0.083 2.6e-1 64 Click to see details
GSE21849 B cell lymphoma 0.003 4.9e-1 0.007 4.9e-1 29 Click to see details
GSE21849 B cell lymphoma 0.003 4.9e-1 0.007 4.9e-1 29 Click to see details
GSE21849 B cell lymphoma 0.003 4.9e-1 0.007 4.9e-1 29 Click to see details
GSE21849 B cell lymphoma 0.003 4.9e-1 0.007 4.9e-1 29 Click to see details
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
58 hsa-miR-569 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT004827 SPI1 Spi-1 proto-oncogene 2 1
MIRT086537 HSPE1-MOB4 HSPE1-MOB4 readthrough 2 2
MIRT086545 MOB4 MOB family member 4, phocein 2 2
MIRT154349 PARD6B par-6 family cell polarity regulator beta 2 4
MIRT182174 POU2F1 POU class 2 homeobox 1 2 2
MIRT190452 EIF5 eukaryotic translation initiation factor 5 2 2
MIRT191410 NAA30 N(alpha)-acetyltransferase 30, NatC catalytic subunit 2 2
MIRT199846 CSNK1G2 casein kinase 1 gamma 2 2 2
MIRT208376 SLC25A36 solute carrier family 25 member 36 2 2
MIRT275677 CARKD NAD(P)HX dehydratase 2 2
MIRT275764 TFDP1 transcription factor Dp-1 2 2
MIRT280470 UBR7 ubiquitin protein ligase E3 component n-recognin 7 (putative) 2 2
MIRT296592 FAM217B family with sequence similarity 217 member B 2 4
MIRT306847 FYTTD1 forty-two-three domain containing 1 2 2
MIRT443764 HLF HLF, PAR bZIP transcription factor 2 2
MIRT448026 GSR glutathione-disulfide reductase 2 2
MIRT448659 NCALD neurocalcin delta 2 2
MIRT449142 UQCRB ubiquinol-cytochrome c reductase binding protein 2 2
MIRT449225 RAD51B RAD51 paralog B 2 2
MIRT462421 TWISTNB TWIST neighbor 2 2
MIRT468478 SESN3 sestrin 3 2 4
MIRT478170 DENND5B DENN domain containing 5B 2 2
MIRT478577 VSIG2 V-set and immunoglobulin domain containing 2 2 2
MIRT481300 ATP5G3 ATP synthase, H+ transporting, mitochondrial Fo complex subunit C3 (subunit 9) 2 16
MIRT485894 ZFP36 ZFP36 ring finger protein 2 2
MIRT497242 FITM2 fat storage inducing transmembrane protein 2 2 2
MIRT500282 ZNF703 zinc finger protein 703 2 8
MIRT509536 RSBN1L round spermatid basic protein 1 like 2 4
MIRT511835 GPATCH8 G-patch domain containing 8 2 4
MIRT522437 MON1B MON1 homolog B, secretory trafficking associated 2 2
MIRT523538 GLO1 glyoxalase I 2 4
MIRT527631 MYBPC1 myosin binding protein C, slow type 2 4
MIRT528059 OLAH oleoyl-ACP hydrolase 2 2
MIRT532549 TXNL1 thioredoxin like 1 2 2
MIRT545503 NAP1L1 nucleosome assembly protein 1 like 1 2 2
MIRT546724 RNF6 ring finger protein 6 2 2
MIRT546737 RNF141 ring finger protein 141 2 2
MIRT550889 ACTA1 actin, alpha 1, skeletal muscle 2 2
MIRT554180 SLC35E2B solute carrier family 35 member E2B 2 2
MIRT555878 PAFAH1B2 platelet activating factor acetylhydrolase 1b catalytic subunit 2 2 2
MIRT558458 DCUN1D1 defective in cullin neddylation 1 domain containing 1 2 2
MIRT560375 TIMM8A translocase of inner mitochondrial membrane 8A 2 2
MIRT562672 AKT3 AKT serine/threonine kinase 3 2 2
MIRT563810 TUBA1B tubulin alpha 1b 2 2
MIRT564607 ZNF711 zinc finger protein 711 2 2
MIRT564881 YWHAE tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon 2 2
MIRT566724 MSL2 MSL complex subunit 2 2 2
MIRT566900 CSRP3 cysteine and glycine rich protein 3 2 2
MIRT570002 COL1A2 collagen type I alpha 2 chain 2 2
MIRT612300 ZFP14 ZFP14 zinc finger protein 2 2
MIRT618334 ZNF813 zinc finger protein 813 2 2
MIRT627658 RSBN1 round spermatid basic protein 1 2 2
MIRT630660 PLAG1 PLAG1 zinc finger 2 2
MIRT640802 MYCL1 MYCL proto-oncogene, bHLH transcription factor 1 1
MIRT651370 ZBTB21 zinc finger and BTB domain containing 21 2 2
MIRT709227 GPSM2 G protein signaling modulator 2 2 2
MIRT712058 ZBTB34 zinc finger and BTB domain containing 34 2 2
MIRT725006 ZPBP zona pellucida binding protein 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-569 Doxorubicin 31703 NSC123127 approved resistant High Breast Cancer cell line (MCF-7)
hsa-miR-569 Verapamil 2520 NSC272366 approved resistant High Breast Cancer cell line (MCF-7)
hsa-miR-569 Trametinib 11707110 NSC758246 approved sensitive High Melanoma cell line (M14) (50nM)
hsa-miR-569 Vemurafenib 42611257 NSC761431 approved sensitive High Melanoma cell line (M14) (50nM)
hsa-mir-569 Fluorouracil 3385 NSC19893 approved sensitive cell line (OE19)
hsa-mir-569 Cisplatin 5460033 NSC119875 approved sensitive cell line (BxPC3)
hsa-miR-569 Tamoxifen 2733525 NSC180973 approved resistant cell line (LCC2)
hsa-miR-569 Fluorouracil 3385 NSC19893 approved resistant cell line (KM12C) (72 h)
hsa-miR-569 Sunitinib 5329102 NSC750690 approved resistant tissue (CardB)
hsa-miR-569 Paclitaxel 36314 NSC125973 approved sensitive cell line (SKOV3)
hsa-miR-569 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-569 Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-miR-569 Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide/Methotrexate/Gemcitabine resistant cell line (Bats-72)

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