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 SMN1   
Synonyms BCD541, GEMIN1, SMA, SMA1, SMA2, SMA3, SMA4, SMA@, SMN, SMNT, T-BCD541, TDRD16A
Description survival of motor neuron 1, telomeric
Transcript NM_000344   
Other Transcripts NM_022874   
Expression
Putative miRNA Targets on SMN1
3'UTR of SMN1
(miRNA target sites are highlighted)
>SMN1|NM_000344|3'UTR
   1 GGAGAAATGCTGGCATAGAGCAGCACTAAATGACACCACTAAAGAAACGATCAGACAGATCTGGAATGTGAAGCGTTATA
  81 GAAGATAACTGGCCTCATTTCTTCAAAATATCAAGTGTTGGGAAAGAAAAAAGGAAGTGGAATGGGTAACTCTTCTTGAT
 161 TAAAAGTTATGTAATAACCAAATGCAATGTGAAATATTTTACTGGACTCTATTTTGAAAAACCATCTGTAAAAGACTGGG
 241 GTGGGGGTGGGAGGCCAGCACGGTGGTGAGGCAGTTGAGAAAATTTGAATGTGGATTAGATTTTGAATGATATTGGATAA
 321 TTATTGGTAATTTTATGAGCTGTGAGAAGGGTGTTGTAGTTTATAAAAGACTGTCTTAATTTGCATACTTAAGCATTTAG
 401 GAATGAAGTGTTAGAGTGTCTTAAAATGTTTCAAATGGTTTAACAAAATGTATGTGAGGCGTATGTGGCAAAATGTTACA
 481 GAATCTAACTGGTGGACATGGCTGTTCATTGTACTGTTTTTTTCTATCTTCTATATGTTTAAAAGTATATAATAAAAATA
 561 TTTAATTTTTTTTTAAAAAAAAAAAAAAAAAAA
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
632988 2 ClinVar
633423 3 ClinVar
634946 5 ClinVar
928626 5 ClinVar
929483 7 ClinVar
928624 449 ClinVar
984518 451 ClinVar
984519 455 ClinVar
COSN30485382 11 COSMIC
COSN30691299 32 COSMIC
COSN19707130 69 COSMIC
COSN31558297 640 COSMIC
COSN14515171 687 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs763144752 2 dbSNP
rs1286965446 3 dbSNP
rs1290417835 5 dbSNP
rs1204340462 10 dbSNP
rs767342186 12 dbSNP
rs750182922 14 dbSNP
rs766378848 17 dbSNP
rs1262447270 18 dbSNP
rs577891293 24 dbSNP
rs1230256976 35 dbSNP
rs544954304 36 dbSNP
rs1280672957 38 dbSNP
rs778340649 42 dbSNP
rs747829983 44 dbSNP
rs1250936445 45 dbSNP
rs757920139 48 dbSNP
rs767628721 49 dbSNP
rs1403395243 52 dbSNP
rs1324543254 55 dbSNP
rs1333185294 55 dbSNP
rs1400503327 73 dbSNP
rs1339881499 77 dbSNP
rs143838139 84 dbSNP
rs1457290823 86 dbSNP
rs1428064151 91 dbSNP
rs1317376161 100 dbSNP
rs1032028272 103 dbSNP
rs212214 104 dbSNP
rs1192146626 106 dbSNP
rs530720159 117 dbSNP
rs200563560 120 dbSNP
rs542796385 127 dbSNP
rs560975018 128 dbSNP
rs528159367 129 dbSNP
rs1329915779 161 dbSNP
rs1262658414 165 dbSNP
rs1221767506 166 dbSNP
rs1347321223 179 dbSNP
rs1275686567 182 dbSNP
rs1441281938 200 dbSNP
rs546594138 203 dbSNP
rs1430408342 207 dbSNP
rs1325100475 208 dbSNP
rs1323122711 212 dbSNP
rs957796373 214 dbSNP
rs571132285 215 dbSNP
rs1187859258 217 dbSNP
rs1244569826 219 dbSNP
rs1448105561 221 dbSNP
rs1188314664 230 dbSNP
rs987923276 237 dbSNP
rs1474289128 242 dbSNP
rs147714462 243 dbSNP
rs1171280445 245 dbSNP
rs1460764422 257 dbSNP
rs1401613100 269 dbSNP
rs1208051170 282 dbSNP
rs1444230228 284 dbSNP
rs1279574411 288 dbSNP
rs199757161 291 dbSNP
rs1340479230 295 dbSNP
rs1229623735 299 dbSNP
rs1300192778 299 dbSNP
rs949327045 304 dbSNP
rs1335362253 310 dbSNP
rs1449547121 312 dbSNP
rs1359282242 340 dbSNP
rs550983818 345 dbSNP
rs577919667 348 dbSNP
rs1296600837 367 dbSNP
rs1326742009 373 dbSNP
rs1391632339 393 dbSNP
rs1229542835 395 dbSNP
rs1422809597 407 dbSNP
rs1443800522 407 dbSNP
rs1183568126 408 dbSNP
rs1432454004 415 dbSNP
rs777497726 416 dbSNP
rs1395959268 418 dbSNP
rs569157372 419 dbSNP
rs1365777150 423 dbSNP
rs1482164675 424 dbSNP
rs536454213 433 dbSNP
rs926533972 436 dbSNP
rs1354403358 452 dbSNP
rs1218856575 457 dbSNP
rs1443566217 463 dbSNP
rs1300489646 467 dbSNP
rs1307883951 468 dbSNP
rs554705316 475 dbSNP
rs1365910984 480 dbSNP
rs1234082399 481 dbSNP
rs1303651427 482 dbSNP
rs775678509 484 dbSNP
rs1311176164 486 dbSNP
rs1230584560 491 dbSNP
rs1379254663 492 dbSNP
rs1278370245 493 dbSNP
rs937332761 494 dbSNP
rs777092342 503 dbSNP
rs1423729044 505 dbSNP
rs1271699266 513 dbSNP
rs1166826948 514 dbSNP
rs1313812861 518 dbSNP
rs566640154 520 dbSNP
rs1176646142 530 dbSNP
rs1471670824 556 dbSNP
rs1254213481 560 dbSNP
rs1183233524 565 dbSNP
rs1490283815 567 dbSNP
rs1264119768 572 dbSNP
rs1224240356 573 dbSNP
rs1322783936 580 dbSNP
rs1284206754 583 dbSNP
rs1225995520 586 dbSNP
rs1377537077 589 dbSNP
rs1478429507 590 dbSNP
rs1178670674 594 dbSNP
rs1386453601 596 dbSNP
rs1295014804 602 dbSNP
rs1458242640 603 dbSNP
rs1456925602 605 dbSNP
rs1055815112 615 dbSNP
rs1160169470 618 dbSNP
rs1480192788 624 dbSNP
rs931408551 626 dbSNP
rs1383679265 630 dbSNP
rs1489028318 633 dbSNP
rs1242013050 639 dbSNP
rs1207444085 641 dbSNP
rs1330598304 647 dbSNP
rs1268133594 654 dbSNP
rs1310028323 654 dbSNP
rs200800214 654 dbSNP
rs1302999190 656 dbSNP
rs1361078560 661 dbSNP
rs1318450250 667 dbSNP
rs1330439808 668 dbSNP
rs1047258324 669 dbSNP
rs1159924681 674 dbSNP
rs1376091239 681 dbSNP
rs1465624686 681 dbSNP
rs1178553021 682 dbSNP
rs1223668490 685 dbSNP
rs1284651441 687 dbSNP
rs1466593713 689 dbSNP
rs1249213892 690 dbSNP
rs1326390901 691 dbSNP
rs1227425847 693 dbSNP
rs1257375806 698 dbSNP
rs887316179 699 dbSNP
rs1306697631 705 dbSNP
rs1295038855 706 dbSNP
rs1008821716 707 dbSNP
rs1487082581 708 dbSNP
rs1208416968 715 dbSNP
rs1267347133 724 dbSNP
rs1395493820 725 dbSNP
rs1400220203 730 dbSNP
rs1304795793 741 dbSNP
rs1452695745 756 dbSNP
rs1202149552 757 dbSNP
rs1370199776 758 dbSNP
rs1409873568 760 dbSNP
rs1472280201 764 dbSNP
rs1160239494 766 dbSNP
rs1365738701 767 dbSNP
rs1019826219 768 dbSNP
rs900102749 769 dbSNP
rs1257745751 772 dbSNP
rs1480071513 779 dbSNP
rs1272067035 780 dbSNP
rs1455209126 790 dbSNP
rs1342657331 791 dbSNP
rs1242589368 796 dbSNP
rs1291569503 796 dbSNP
rs1338770720 798 dbSNP
rs1314870896 808 dbSNP
rs1389666045 811 dbSNP
rs1370145742 816 dbSNP
rs1306450326 818 dbSNP
rs1431995507 827 dbSNP
rs1371627008 830 dbSNP
rs1405498533 836 dbSNP
rs1456784594 837 dbSNP
rs996439790 845 dbSNP
rs1187575338 857 dbSNP
rs1471994840 882 dbSNP
rs1032000102 902 dbSNP
rs1348121799 904 dbSNP
rs1408663744 905 dbSNP
rs1483252506 906 dbSNP
rs957766968 913 dbSNP
rs1307335359 920 dbSNP
rs1318345638 923 dbSNP
rs1207854365 929 dbSNP
rs987892077 943 dbSNP
rs1245575213 945 dbSNP
rs1242074814 951 dbSNP
rs1350006569 955 dbSNP
rs1021200425 956 dbSNP
rs1411985934 958 dbSNP
rs1360552358 959 dbSNP
rs970546124 961 dbSNP
rs1385472126 971 dbSNP
rs1393460210 973 dbSNP
rs1164379714 976 dbSNP
rs1456226433 980 dbSNP
rs1409201751 990 dbSNP
rs982370362 993 dbSNP
rs1196433148 995 dbSNP
rs1250203459 1006 dbSNP
rs1267947905 1009 dbSNP
rs1208096625 1010 dbSNP
rs1328575906 1010 dbSNP
rs1446418745 1010 dbSNP
rs1482800288 1019 dbSNP
rs1330029413 1021 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 ENST00000506163.1 | 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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