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 TRAFD1   
Synonyms FLN29
Description TRAF-type zinc finger domain containing 1
Transcript NM_001143906   
Other Transcripts NM_006700   
Expression
Putative miRNA Targets on TRAFD1
3'UTR of TRAFD1
(miRNA target sites are highlighted)
>TRAFD1|NM_001143906|3'UTR
   1 TGGTGTCTCCAGAGACTTTACATCGGTTCCTGTCTTCTGTGCACAGCAGCACTTGCCGCTGTGCAGGCCCACCTCTTTGG
  81 CTCTTTGGGTGGGAGAGTTTTTCCAGATTTTAGATTTTTCTAGGTTATGGCCATTTTGTGTCTTTTGAGGTTGTGCTGTG
 161 GGGGTTTGGGTTTGAGGGAAGGGAGCAGGGTGGCGGTTGAGGAACGCTTCAGCCTTAGCTGCTACCTTTCGGCAGCAGTG
 241 AAATACAAGCTGCAGCCTCGGCTGCCAGGGCTCCCTTTTGACTTATTGTCGCCACTGCCCCTTGGTGCTGTGTGGTCCCA
 321 GTGGAAGGAGGGGAAGATTTTGGAAACCTGGTAGCCACCAGTAAGGTGATTCTCTGCCCTGTTGGGGCCTAAATTTGGGG
 401 GCTTTTGGGCAACCTCTCCGTGTACTGCGTCTGTCCACACTCGATTGGGCCCCAGGTGTGTATGAGGCGCTCTGGTAAGG
 481 TGCTCAGGCCAGTTGCAATGTCTGTCAGTAACGAGGCTTTTGATGTGTTGAGCTGGAGGTGAGTGGACCGGGGGCTGTGT
 561 TTTAAGCTGCTTCCTTGGCATTTGGCATCACTGCCTTCTGTTCCCGGGGGAGCATGGATCTTTTGTCCTCACTGCTTTCT
 641 AATGGGGAGGGCTGAGGGCTCCCTGTCCCCACAGCAGGTATGTTGGGCTCTGCCCCAGCCCCACACTTGCTCTGAAAACC
 721 AAGTGTCAGAGCCCCTTCCCCTTGTTTTTATTTTACTGTTATAATAATTATTAACTTCCTTGTAATAGAAATAAAGTTTG
 801 TACTTGGAGTTCAAAAAAAAAAAAAAAAAA
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' uuuaAUCCAUCACCGUCACCUu 5'
              |: ||:||  ||||||| 
Target 5' gtgcTGTGTGGTCCCAGTGGAa 3'
305 - 326 158.00 -16.10
2
miRNA  3' uuUAA-UCCAUCACC-GUCACCUu 5'
            :|| || |:| ||  |||||| 
Target 5' gtGTTGAGCTGGAGGTGAGTGGAc 3'
525 - 548 128.00 -12.50
3
miRNA  3' uuuAAUCCAUCACCGUCACCUu 5'
             || || |   |||||| | 
Target 5' cctTTCGGCA---GCAGTGAAa 3'
225 - 243 120.00 -7.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN1142294 14 COSMIC
COSN30119832 59 COSMIC
COSN30150502 78 COSMIC
COSN30491121 88 COSMIC
COSN30144974 90 COSMIC
COSN30128025 120 COSMIC
COSN30133693 195 COSMIC
COSN26601359 339 COSMIC
COSN31596786 436 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1229830365 4 dbSNP
rs1298662945 5 dbSNP
rs1346856045 6 dbSNP
rs974709742 22 dbSNP
rs1282382472 23 dbSNP
rs369157267 25 dbSNP
rs746657222 26 dbSNP
rs1259000324 33 dbSNP
rs1448265379 38 dbSNP
rs768363638 39 dbSNP
rs73207615 46 dbSNP
rs749665100 49 dbSNP
rs1398094063 58 dbSNP
rs917640571 59 dbSNP
rs1216058045 61 dbSNP
rs1382645147 62 dbSNP
rs1296745427 64 dbSNP
rs141081643 67 dbSNP
rs1299896223 74 dbSNP
rs1042202329 90 dbSNP
rs1343185360 94 dbSNP
rs1445920000 97 dbSNP
rs1358736933 98 dbSNP
rs73207616 114 dbSNP
rs1431970415 133 dbSNP
rs879069840 134 dbSNP
rs1388747659 137 dbSNP
rs181181425 139 dbSNP
rs577070714 153 dbSNP
rs1445843254 164 dbSNP
rs1258882975 165 dbSNP
rs879129930 191 dbSNP
rs538311762 195 dbSNP
rs1479541815 196 dbSNP
rs186817919 198 dbSNP
rs927495333 200 dbSNP
rs763451045 206 dbSNP
rs996763154 207 dbSNP
rs1049379040 218 dbSNP
rs552659381 219 dbSNP
rs886601152 226 dbSNP
rs1310498349 227 dbSNP
rs12305571 231 dbSNP
rs1378570059 232 dbSNP
rs891180490 233 dbSNP
rs1004720961 260 dbSNP
rs1411974868 265 dbSNP
rs1369094916 274 dbSNP
rs541833432 287 dbSNP
rs898645354 291 dbSNP
rs995721280 292 dbSNP
rs1034310574 297 dbSNP
rs959620645 298 dbSNP
rs1163330149 309 dbSNP
rs991797907 310 dbSNP
rs1028961321 311 dbSNP
rs903742084 322 dbSNP
rs563167806 343 dbSNP
rs1000736847 355 dbSNP
rs1031371280 356 dbSNP
rs1250620737 358 dbSNP
rs956554618 365 dbSNP
rs575481062 382 dbSNP
rs1169327088 383 dbSNP
rs1352341946 385 dbSNP
rs1467931807 388 dbSNP
rs1024667249 391 dbSNP
rs966389924 409 dbSNP
rs1307884219 413 dbSNP
rs546157855 415 dbSNP
rs978232748 420 dbSNP
rs992425126 421 dbSNP
rs925092465 426 dbSNP
rs1406062120 427 dbSNP
rs1451051807 428 dbSNP
rs1287993926 429 dbSNP
rs1322717389 429 dbSNP
rs12318805 430 dbSNP
rs1213997362 431 dbSNP
rs1393382077 431 dbSNP
rs974605564 434 dbSNP
rs1457896860 435 dbSNP
rs1345263656 436 dbSNP
rs921817274 440 dbSNP
rs1471329669 441 dbSNP
rs1410700201 443 dbSNP
rs919588693 444 dbSNP
rs930999940 446 dbSNP
rs1265061088 451 dbSNP
rs933252202 459 dbSNP
rs1209163314 460 dbSNP
rs1051021854 463 dbSNP
rs908143104 469 dbSNP
rs940843906 470 dbSNP
rs1460868738 471 dbSNP
rs1040953451 475 dbSNP
rs901895017 481 dbSNP
rs1201674354 498 dbSNP
rs187534030 513 dbSNP
rs1249752081 514 dbSNP
rs891106612 526 dbSNP
rs1386565465 537 dbSNP
rs1185394288 540 dbSNP
rs940063210 550 dbSNP
rs771810593 551 dbSNP
rs1052344537 552 dbSNP
rs1467310422 555 dbSNP
rs528296554 555 dbSNP
rs996046793 573 dbSNP
rs1375578417 574 dbSNP
rs1033861857 580 dbSNP
rs1197831524 585 dbSNP
rs1013392354 588 dbSNP
rs1177656991 590 dbSNP
rs1429019801 591 dbSNP
rs1249771258 596 dbSNP
rs1186643567 597 dbSNP
rs1025231010 603 dbSNP
rs547868482 604 dbSNP
rs1201245558 605 dbSNP
rs559813488 606 dbSNP
rs1468751011 607 dbSNP
rs1323151403 611 dbSNP
rs1343351605 620 dbSNP
rs1346236342 620 dbSNP
rs1013829299 633 dbSNP
rs1025259544 640 dbSNP
rs1430142147 643 dbSNP
rs1026763794 665 dbSNP
rs1287139717 668 dbSNP
rs530013793 673 dbSNP
rs1397285227 674 dbSNP
rs775812882 679 dbSNP
rs977825104 679 dbSNP
rs775295177 681 dbSNP
rs1043201 686 dbSNP
rs1391838239 687 dbSNP
rs957819808 701 dbSNP
rs1448862513 705 dbSNP
rs974952356 708 dbSNP
rs1043203 713 dbSNP
rs1283755552 714 dbSNP
rs1444218148 718 dbSNP
rs1254286997 721 dbSNP
rs548539270 748 dbSNP
rs933176733 759 dbSNP
rs1277286686 761 dbSNP
rs569993431 763 dbSNP
rs1226828950 765 dbSNP
rs1221391855 766 dbSNP
rs1285327255 768 dbSNP
rs1246304267 770 dbSNP
rs1338233181 775 dbSNP
rs987333603 776 dbSNP
rs1372175141 782 dbSNP
rs138888954 787 dbSNP
rs149284206 793 dbSNP
rs1385729977 804 dbSNP
rs570672244 807 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' ---------ggaaggAGGGGAa 3'
1 - 13
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 ENST00000257604.5 | 3UTR | GGAAGGAGGGGAAGAUUUUGGAAAC
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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