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 SMN2   
Synonyms BCD541, C-BCD541, GEMIN1, SMNC, TDRD16B
Description survival of motor neuron 2, centromeric
Transcript NM_017411   
Other Transcripts NM_022875 , NM_022876 , NM_022877   
Expression
Putative miRNA Targets on SMN2
3'UTR of SMN2
(miRNA target sites are highlighted)
>SMN2|NM_017411|3'UTR
   1 GGAGAAATGCTGGCATAGAGCAGCACTAAATGACACCACTAAAGAAACGATCAGACAGATCTGGAATGTGAAGCGTTATA
  81 GAAGATAACTGGCCTCATTTCTTCAAAATATCAAGTGTTGGGAAAGAAAAAAGGAAGTGGAATGGGTAACTCTTCTTGAT
 161 TAAAAGTTATGTAATAACCAAATGCAATGTGAAATATTTTACTGGACTCTATTTTGAAAAACCATCTGTAAAAGACTGAG
 241 GTGGGGGTGGGAGGCCAGCACGGTGGTGAGGCAGTTGAGAAAATTTGAATGTGGATTAGATTTTGAATGATATTGGATAA
 321 TTATTGGTAATTTTATGAGCTGTGAGAAGGGTGTTGTAGTTTATAAAAGACTGTCTTAATTTGCATACTTAAGCATTTAG
 401 GAATGAAGTGTTAGAGTGTCTTAAAATGTTTCAAATGGTTTAACAAAATGTATGTGAGGCGTATGTGGCAAAATGTTACA
 481 GAATCTAACTGGTGGACATGGCTGTTCATTGTACTGTTTTTTTCTATCTTCTATATGTTTAAAAGTATATAATAAAAATA
 561 TTTAATTTTTTTTTAAATTAAAAAAA
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' uuuaauCCAUCA--CCGUCACCUu 5'
                |||:||  |||||| || 
Target 5' cagcacGGTGGTGAGGCAGTTGAg 3'
256 - 279 134.00 -16.70
2
miRNA  3' uuuaauccaucaccgUCACCUu 5'
                         |||||| 
Target 5' ggaaagaaaaaaggaAGTGGAa 3'
121 - 142 120.00 -11.60
3
miRNA  3' uuuaauccaucaccGUCACCUu 5'
                        ::||||| 
Target 5' ttacagaatctaacTGGTGGAc 3'
476 - 497 108.00 -5.60
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30155350 24 COSMIC
COSN30114158 26 COSMIC
COSN30132367 35 COSMIC
COSN31514250 97 COSMIC
COSN30121597 489 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1270114068 3 dbSNP
rs1342290988 14 dbSNP
rs553413974 16 dbSNP
rs372142764 19 dbSNP
rs1290080354 25 dbSNP
rs1358222212 29 dbSNP
rs1222782753 32 dbSNP
rs1384455045 33 dbSNP
rs770200953 33 dbSNP
rs773669015 36 dbSNP
rs578046537 41 dbSNP
rs763390976 41 dbSNP
rs766798732 43 dbSNP
rs545800399 49 dbSNP
rs1263665585 71 dbSNP
rs1431338680 72 dbSNP
rs1192983458 77 dbSNP
rs564381826 82 dbSNP
rs1436079212 83 dbSNP
rs531439953 84 dbSNP
rs1446519409 97 dbSNP
rs543593916 104 dbSNP
rs1181337366 105 dbSNP
rs912462160 108 dbSNP
rs1454047811 109 dbSNP
rs1248101136 113 dbSNP
rs1197505215 116 dbSNP
rs1290997763 120 dbSNP
rs561490407 142 dbSNP
rs1386687601 150 dbSNP
rs1219698824 155 dbSNP
rs1304845402 160 dbSNP
rs1373193369 179 dbSNP
rs1237833987 180 dbSNP
rs1334378840 183 dbSNP
rs1309536713 186 dbSNP
rs369745691 187 dbSNP
rs1285469324 189 dbSNP
rs1301822738 189 dbSNP
rs1317737753 200 dbSNP
rs1218259777 211 dbSNP
rs1262249653 215 dbSNP
rs145999618 216 dbSNP
rs212213 219 dbSNP
rs1472791518 239 dbSNP
rs1253552617 243 dbSNP
rs1268160521 246 dbSNP
rs1455151821 255 dbSNP
rs558936076 261 dbSNP
rs1176222456 291 dbSNP
rs1452870807 291 dbSNP
rs532921933 293 dbSNP
rs551824084 295 dbSNP
rs1289916277 296 dbSNP
rs1348023044 299 dbSNP
rs942673049 299 dbSNP
rs1262123396 302 dbSNP
rs1229459817 307 dbSNP
rs1345250317 308 dbSNP
rs1281976356 346 dbSNP
rs1039429804 363 dbSNP
rs1406698446 364 dbSNP
rs1317655174 366 dbSNP
rs1419274414 371 dbSNP
rs1387501199 390 dbSNP
rs1160159809 400 dbSNP
rs1242612808 401 dbSNP
rs1451302150 407 dbSNP
rs1181485630 409 dbSNP
rs775943972 415 dbSNP
rs1478937099 416 dbSNP
rs751859181 416 dbSNP
rs1246792673 418 dbSNP
rs1311396232 419 dbSNP
rs1444767103 420 dbSNP
rs1249561451 423 dbSNP
rs570323404 432 dbSNP
rs1208935172 433 dbSNP
rs1393233338 446 dbSNP
rs1399001434 447 dbSNP
rs1261603789 452 dbSNP
rs1317770757 465 dbSNP
rs1225898799 466 dbSNP
rs1327488099 470 dbSNP
rs1270124323 471 dbSNP
rs921958591 482 dbSNP
rs1437927696 486 dbSNP
rs936001833 492 dbSNP
rs1382496956 493 dbSNP
rs537296015 494 dbSNP
rs1285581931 495 dbSNP
rs549602808 503 dbSNP
rs1167239570 505 dbSNP
rs1310887109 520 dbSNP
rs1391440959 526 dbSNP
rs1188830047 538 dbSNP
rs1460555774 541 dbSNP
rs891886061 543 dbSNP
rs1010785738 556 dbSNP
rs1443339984 571 dbSNP
rs1212853735 577 dbSNP
rs1213288540 584 dbSNP
rs1344444914 601 dbSNP
rs567819267 603 dbSNP
rs1045930550 605 dbSNP
rs1380945904 608 dbSNP
rs1469763818 631 dbSNP
rs1450014510 632 dbSNP
rs1359494343 654 dbSNP
rs139591666 681 dbSNP
rs1323191655 684 dbSNP
rs1231797934 691 dbSNP
rs1408096174 693 dbSNP
rs907444125 701 dbSNP
rs1001817278 706 dbSNP
rs1443474940 719 dbSNP
rs576032516 730 dbSNP
rs1183211252 736 dbSNP
rs1411193783 744 dbSNP
rs1474707823 767 dbSNP
rs1203059190 771 dbSNP
rs1484285264 784 dbSNP
rs1275974934 790 dbSNP
rs1166096038 794 dbSNP
rs1221922559 796 dbSNP
rs78949991 797 dbSNP
rs1357348905 816 dbSNP
rs1420523941 816 dbSNP
rs1379652661 818 dbSNP
rs1464499164 818 dbSNP
rs1034417156 830 dbSNP
rs962324163 845 dbSNP
rs1328798399 849 dbSNP
rs1372401123 857 dbSNP
rs995150741 863 dbSNP
rs1355148122 872 dbSNP
rs1025314465 879 dbSNP
rs1166507292 880 dbSNP
rs1405538185 893 dbSNP
rs951169882 913 dbSNP
rs987035756 914 dbSNP
rs1175918305 924 dbSNP
rs1473771161 929 dbSNP
rs1253234999 930 dbSNP
rs1199290656 945 dbSNP
rs1489889524 955 dbSNP
rs1444467363 959 dbSNP
rs1301257588 961 dbSNP
rs1316487735 969 dbSNP
rs1282417441 973 dbSNP
rs1355048295 976 dbSNP
rs1352073380 978 dbSNP
rs1234205993 982 dbSNP
rs1288951080 990 dbSNP
rs1293650354 996 dbSNP
rs1364901662 998 dbSNP
rs1336739169 1006 dbSNP
rs1344302134 1008 dbSNP
rs1436569916 1008 dbSNP
rs1212688337 1010 dbSNP
rs1413110922 1010 dbSNP
rs1459196587 1010 dbSNP
rs912422058 1019 dbSNP
rs1437842764 1021 dbSNP
rs1205987364 1022 dbSNP
rs1235307379 1024 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293S
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 GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb ...

- Karginov FV; Hannon GJ, 2013, Genes & development.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' uuuaauccaucaccgUCACCUu 5'
                         |||||| 
Target 5' --------aaaaggaAGUGGAa 3'
1 - 14
Article - Karginov FV; Hannon GJ
- Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
CLIP-seq Support 1 for dataset GSM1084065
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_AbnovaAb
Location of target site ENST00000380743.4 | 3UTR | AAAAGGAAGUGGAAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
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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