pre-miRNA Information
pre-miRNA hsa-mir-6509   
Genomic Coordinates chr7: 135206994 - 135207078
Description Homo sapiens miR-6509 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-6509-3p
Sequence 52| UUCCACUGCCACUACCUAAUUU |73
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs778601614 1 dbSNP
rs754554776 3 dbSNP
rs767798995 3 dbSNP
rs145322812 4 dbSNP
rs773941257 5 dbSNP
rs768273593 9 dbSNP
rs984565062 12 dbSNP
rs748872915 13 dbSNP
rs774861125 14 dbSNP
rs13241975 20 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol PPP1R3F   
Synonyms HB2E, LL0XNC01-7P3.1, R3F
Description protein phosphatase 1 regulatory subunit 3F
Transcript NM_001184745   
Other Transcripts NM_033215   
Expression
Putative miRNA Targets on PPP1R3F
3'UTR of PPP1R3F
(miRNA target sites are highlighted)
>PPP1R3F|NM_001184745|3'UTR
   1 GCTCTGCTTGTGGGATCAGCAGAGGCTTAAGATGGGATACATGGCCTGTGCAGTGAGGGGACCTGGGTCCTTTGCTTCTG
  81 AGAATGCTCAACTGAAAGAGAGGCCTTCTCATCCCCAAGCTCTCCAGTCAACACAGGGCTCCCTGTGGTGACACCAGTGG
 161 AGATGAGGGAACGGGTAGATGGTGTGAGTGAGGGGAACTTTTAGAGTGGAACTGGGCATGTCCTCCGCCTACCCCCCGAG
 241 CCTGTATTTATTTTTGTATAATTCTCTGGATGAGGGAGAGTGGTCGTGAGCTGGTCTTGGGGCACAATTACCCAGAGATA
 321 TATTTATTAACAGCCAACCTGTGCAACCTGCTGGAGCTTTATTTTTAATTTAATTTATATAGAGTACCTATTATTATATG
 401 CCACAATAGAGCTCTATGAGAAACAGTGTCTTGCGGTGTAGTGTTCTCCTGTTTGGGCATGAGTGTGCAGGGTGGTCACT
 481 TTCTGTGGGAGGATCACAGTGGGGAGTTGGGGGTGGGACGTGGTCGCCTGCTGCTGCTTCAACATGTCTTTCCTTGAAGA
 561 TGTGTGTCTCCTCGTCTCGTGGTCCTAATCCATATGGTTCTTTGTCTTTTCCACATTCTGCCTGTGGGACCCTACAGGTG
 641 TGTATTTGGATGGTGGTGGTGGGAGCCAGGGAGGAAGAGTGGCAGCCACATGAGGGTTTGGTGTCAGTCACATGGTTGCA
 721 GTGGTAGCTGTGGTCTCCTGTGGATGTGGGGACATCAGTTGTGAATCAGCCACAAGGTTTTGAGGTTACTGAAAAAACAG
 801 CCTTTGACACCAGCAGGGAGACCCCTTAGTCCCTGAGATAAGGAAGGCCTCAGAAAGGAAAGAGGAGTTAATGTACTGCA
 881 GTACTTGGTAGCACAGTTGCTGTCCACAGACATCACATTTCTACTAAAAACAGGAAGCCCAGAAGCTTTGAAAGAAAGAT
 961 ATATATTTATTGCATGCAAATAAAAAACTGCTCAACAAAATAAAAAAAAAAAAAAAAAAAA
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' uuuaaucCAUCAC---CGUCACCUu 5'
                 ||:|||    ||||||| 
Target 5' gctccctGTGGTGACACCAGTGGAg 3'
138 - 162 151.00 -16.90
2
miRNA  3' uuUAAUCCAUCACCGUCACCuu 5'
            :| |  |:|| |||||||  
Target 5' caGTCACATGGTTGCAGTGGta 3'
705 - 726 140.00 -14.40
3
miRNA  3' uuuaAUCCAUC-ACCGUCACCUu 5'
              |:|| :| |  ||||||: 
Target 5' tctgTGGGAGGATCACAGTGGGg 3'
482 - 504 134.00 -14.40
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs782254387 7 dbSNP
rs782493937 8 dbSNP
rs782578951 14 dbSNP
rs782174154 20 dbSNP
rs782429832 26 dbSNP
rs1218866057 28 dbSNP
rs782010230 31 dbSNP
rs782256657 41 dbSNP
rs782366082 42 dbSNP
rs1290956504 74 dbSNP
rs1198407488 80 dbSNP
rs964940221 81 dbSNP
rs996460083 85 dbSNP
rs1280613982 87 dbSNP
rs181513756 89 dbSNP
rs951731648 92 dbSNP
rs1273309740 96 dbSNP
rs146642259 103 dbSNP
rs907625922 105 dbSNP
rs781882097 109 dbSNP
rs1324027700 119 dbSNP
rs782514738 128 dbSNP
rs1464884420 135 dbSNP
rs1398079303 138 dbSNP
rs960543750 146 dbSNP
rs1172685619 161 dbSNP
rs1477876542 173 dbSNP
rs1423787899 174 dbSNP
rs1189106356 188 dbSNP
rs782663825 193 dbSNP
rs782299743 194 dbSNP
rs1246914726 203 dbSNP
rs1198469546 211 dbSNP
rs916441004 214 dbSNP
rs947962976 217 dbSNP
rs73634218 223 dbSNP
rs185349462 227 dbSNP
rs879970390 228 dbSNP
rs1311682296 231 dbSNP
rs936009337 235 dbSNP
rs1276668976 236 dbSNP
rs1221000725 238 dbSNP
rs1368630333 239 dbSNP
rs1308756803 246 dbSNP
rs1445821381 255 dbSNP
rs1374325151 260 dbSNP
rs1053179627 266 dbSNP
rs1333301212 280 dbSNP
rs1466019562 284 dbSNP
rs1358505895 286 dbSNP
rs891893496 287 dbSNP
rs1415662754 293 dbSNP
rs1425468984 302 dbSNP
rs1177567665 303 dbSNP
rs1438237095 308 dbSNP
rs1240340980 313 dbSNP
rs1179645730 315 dbSNP
rs1009005998 322 dbSNP
rs1483240780 331 dbSNP
rs1040929305 342 dbSNP
rs868906188 349 dbSNP
rs1212382506 364 dbSNP
rs1312810783 367 dbSNP
rs996429049 395 dbSNP
rs1027912252 397 dbSNP
rs781935488 423 dbSNP
rs1391749150 425 dbSNP
rs781847099 431 dbSNP
rs1378411894 433 dbSNP
rs1300979904 434 dbSNP
rs190098037 435 dbSNP
rs1359178499 443 dbSNP
rs1014654907 455 dbSNP
rs960720551 461 dbSNP
rs991953721 472 dbSNP
rs1159676527 480 dbSNP
rs916409996 494 dbSNP
rs782591500 505 dbSNP
rs1254719504 507 dbSNP
rs1184062430 510 dbSNP
rs1483630230 520 dbSNP
rs782172876 521 dbSNP
rs1214540507 525 dbSNP
rs1489427978 527 dbSNP
rs1286985434 528 dbSNP
rs1239553156 535 dbSNP
rs1320849682 545 dbSNP
rs1310503607 554 dbSNP
rs1229893281 556 dbSNP
rs1356004634 562 dbSNP
rs41513244 563 dbSNP
rs3788817 574 dbSNP
rs1362106062 575 dbSNP
rs1289042345 579 dbSNP
rs3838190 579 dbSNP
rs1367031299 580 dbSNP
rs1167537697 587 dbSNP
rs1424968769 593 dbSNP
rs1423523550 595 dbSNP
rs1191662176 596 dbSNP
rs782375885 597 dbSNP
rs868975600 612 dbSNP
rs1478826002 623 dbSNP
rs781972240 626 dbSNP
rs782221753 628 dbSNP
rs913260886 651 dbSNP
rs1488037602 660 dbSNP
rs1263524574 664 dbSNP
rs1223477551 666 dbSNP
rs1335441383 668 dbSNP
rs1277448686 684 dbSNP
rs1216285052 745 dbSNP
rs782326211 752 dbSNP
rs1341778815 774 dbSNP
rs1295871744 792 dbSNP
rs944779655 802 dbSNP
rs1388131378 805 dbSNP
rs1295717581 812 dbSNP
rs1462276333 822 dbSNP
rs1400267361 866 dbSNP
rs1169113684 867 dbSNP
rs1478857126 879 dbSNP
rs1424339716 907 dbSNP
rs1198239964 912 dbSNP
rs1431717199 914 dbSNP
rs1269706112 921 dbSNP
rs1192744022 949 dbSNP
rs1468716385 950 dbSNP
rs1257368138 962 dbSNP
rs1040520657 963 dbSNP
rs1319399400 982 dbSNP
rs1251454184 989 dbSNP
rs1231876892 994 dbSNP
rs1329045480 999 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HeLa
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in Chi_124B_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell miR-124 + B ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

Article - Chi SW; Zang JB; Mele A; Darnell RB
- Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
CLIP-seq Support 1 for dataset Chi_124B_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell miR-124 + B
Location of target site ENST00000055335.6 | 3UTR | AGGGGAACUUUUAGAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
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
82 hsa-miR-6509-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT055374 PDCD4 programmed cell death 4 2 4
MIRT378341 MARCKS myristoylated alanine rich protein kinase C substrate 2 2
MIRT444668 CDKL2 cyclin dependent kinase like 2 2 2
MIRT446953 CD248 CD248 molecule 2 2
MIRT460332 CAMK4 calcium/calmodulin dependent protein kinase IV 2 6
MIRT464078 VPS4A vacuolar protein sorting 4 homolog A 2 2
MIRT464586 UBN2 ubinuclein 2 2 2
MIRT468482 SESN3 sestrin 3 2 2
MIRT468962 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT475455 HSPA8 heat shock protein family A (Hsp70) member 8 2 2
MIRT482403 ADRB1 adrenoceptor beta 1 2 10
MIRT486992 ZFAND2B zinc finger AN1-type containing 2B 2 2
MIRT489397 TUBB2A tubulin beta 2A class IIa 2 2
MIRT526319 UGT2A1 UDP glucuronosyltransferase family 2 member A1 complex locus 2 2
MIRT526560 UGT2A2 UDP glucuronosyltransferase family 2 member A2 2 2
MIRT526732 ZNF138 zinc finger protein 138 2 8
MIRT531581 STXBP5L syntaxin binding protein 5 like 2 2
MIRT532011 NOX5 NADPH oxidase 5 2 2
MIRT533407 TXLNG taxilin gamma 2 2
MIRT533436 TRPC5 transient receptor potential cation channel subfamily C member 5 2 2
MIRT533866 TBL1XR1 transducin beta like 1 X-linked receptor 1 2 2
MIRT539254 ANKRD50 ankyrin repeat domain 50 2 2
MIRT541451 C15orf48 chromosome 15 open reading frame 48 2 2
MIRT566794 MIER3 MIER family member 3 2 2
MIRT569294 SURF6 surfeit 6 2 2
MIRT571336 RABGEF1 RAB guanine nucleotide exchange factor 1 2 2
MIRT572802 PPP3CB protein phosphatase 3 catalytic subunit beta 2 2
MIRT572813 MYO1C myosin IC 2 2
MIRT574219 DMRT2 doublesex and mab-3 related transcription factor 2 2 2
MIRT607259 GRAMD1B GRAM domain containing 1B 2 4
MIRT609307 CHD4 chromodomain helicase DNA binding protein 4 2 2
MIRT615459 REPS1 RALBP1 associated Eps domain containing 1 2 2
MIRT616861 RPLP1 ribosomal protein lateral stalk subunit P1 2 2
MIRT619415 NOS1AP nitric oxide synthase 1 adaptor protein 2 2
MIRT619652 COX19 COX19, cytochrome c oxidase assembly factor 2 2
MIRT625325 TNFRSF13B TNF receptor superfamily member 13B 2 2
MIRT638980 ARFIP2 ADP ribosylation factor interacting protein 2 2 2
MIRT639458 ZNF429 zinc finger protein 429 2 2
MIRT640550 SMCR8 Smith-Magenis syndrome chromosome region, candidate 8 2 2
MIRT641473 B4GALNT3 beta-1,4-N-acetyl-galactosaminyltransferase 3 2 2
MIRT642720 ATXN3 ataxin 3 2 2
MIRT643048 SMN1 survival of motor neuron 1, telomeric 2 2
MIRT644921 SMN2 survival of motor neuron 2, centromeric 2 2
MIRT645875 ZNF275 zinc finger protein 275 2 2
MIRT649824 LIPG lipase G, endothelial type 2 2
MIRT649851 GYS2 glycogen synthase 2 2 2
MIRT649972 TRAFD1 TRAF-type zinc finger domain containing 1 2 2
MIRT650675 ZNF259 ZPR1 zinc finger 1 1
MIRT651319 ZCCHC2 zinc finger CCHC-type containing 2 2 2
MIRT652876 TAB1 TGF-beta activated kinase 1 (MAP3K7) binding protein 1 2 2
MIRT652881 SYVN1 synoviolin 1 2 2
MIRT654144 RPAP2 RNA polymerase II associated protein 2 2 2
MIRT657080 JMY junction mediating and regulatory protein, p53 cofactor 2 2
MIRT657181 INO80C INO80 complex subunit C 2 2
MIRT657830 GJD3 gap junction protein delta 3 2 2
MIRT657897 GDF7 growth differentiation factor 7 2 2
MIRT659631 CDKN2AIP CDKN2A interacting protein 2 2
MIRT663115 SPTA1 spectrin alpha, erythrocytic 1 2 2
MIRT664739 METTL16 methyltransferase like 16 2 2
MIRT667551 LRAT lecithin retinol acyltransferase 2 2
MIRT668552 ERCC1 ERCC excision repair 1, endonuclease non-catalytic subunit 2 2
MIRT682893 XIAP X-linked inhibitor of apoptosis 2 2
MIRT683092 PRRG4 proline rich and Gla domain 4 2 2
MIRT683102 TIMM10B translocase of inner mitochondrial membrane 10B 2 2
MIRT697648 WNK1 WNK lysine deficient protein kinase 1 2 2
MIRT709158 ZNF419 zinc finger protein 419 2 2
MIRT713220 RCAN2 regulator of calcineurin 2 2 2
MIRT713277 LAIR1 leukocyte associated immunoglobulin like receptor 1 2 2
MIRT715008 CYP1B1 cytochrome P450 family 1 subfamily B member 1 2 2
MIRT715051 SYNJ2BP synaptojanin 2 binding protein 2 2
MIRT715696 PNMAL2 paraneoplastic Ma antigen family member 8B 2 2
MIRT717250 TMEM246 transmembrane protein 246 2 2
MIRT717322 PGK1 phosphoglycerate kinase 1 2 2
MIRT717587 MTHFD1L methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like 2 2
MIRT718122 CHST4 carbohydrate sulfotransferase 4 2 2
MIRT718418 CALN1 calneuron 1 2 2
MIRT718750 ZNF490 zinc finger protein 490 2 2
MIRT720048 PPP1R3F protein phosphatase 1 regulatory subunit 3F 2 2
MIRT721497 THRB thyroid hormone receptor beta 2 2
MIRT722531 EPRS glutamyl-prolyl-tRNA synthetase 2 2
MIRT723279 KRTAP21-2 keratin associated protein 21-2 2 2
MIRT724813 MSX2 msh homeobox 2 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-6509-3p Temozolomide 5394 NSC362856 approved sensitive cell line (U251)
hsa-miR-6509-3p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-6509-3p Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-6509-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-6509-3p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)

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