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 RPLP1   
Synonyms LP1, P1, RPP1
Description ribosomal protein lateral stalk subunit P1
Transcript NM_001003   
Other Transcripts NM_213725   
Expression
Putative miRNA Targets on RPLP1
3'UTR of RPLP1
(miRNA target sites are highlighted)
>RPLP1|NM_001003|3'UTR
   1 ACCTCTTTTATAACATGTTCAATAAAAAGCTGAACTTT
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN28164786 4 COSMIC
COSN8590293 154 COSMIC
COSN6278962 212 COSMIC
COSN17590429 555 COSMIC
COSN15810711 611 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs765659388 3 dbSNP
rs1248806530 4 dbSNP
rs201427547 6 dbSNP
rs1406462480 9 dbSNP
rs1451544124 9 dbSNP
rs1339816580 11 dbSNP
rs202225518 12 dbSNP
rs1332051978 15 dbSNP
rs760411129 19 dbSNP
rs548004580 21 dbSNP
rs753479085 22 dbSNP
rs1382445777 23 dbSNP
rs1337943012 24 dbSNP
rs891749437 26 dbSNP
rs761416059 34 dbSNP
rs1297328209 37 dbSNP
rs200720703 39 dbSNP
rs1326047288 40 dbSNP
rs1424172314 44 dbSNP
rs752174225 46 dbSNP
rs201563838 47 dbSNP
rs1381151634 52 dbSNP
rs1448146397 56 dbSNP
rs768035130 57 dbSNP
rs1471819991 59 dbSNP
rs752982175 62 dbSNP
rs1477541695 64 dbSNP
rs974630507 67 dbSNP
rs1327414287 70 dbSNP
rs1361465680 81 dbSNP
rs1028850976 86 dbSNP
rs1425948656 88 dbSNP
rs1453828595 95 dbSNP
rs1261542510 114 dbSNP
rs1050913476 116 dbSNP
rs1216338593 117 dbSNP
rs1488445891 121 dbSNP
rs1336409651 123 dbSNP
rs564613487 124 dbSNP
rs967890130 125 dbSNP
rs1354988982 128 dbSNP
rs1284727953 131 dbSNP
rs1246959634 136 dbSNP
rs1381055509 146 dbSNP
rs1230819825 154 dbSNP
rs139070897 155 dbSNP
rs547455572 159 dbSNP
rs923709615 160 dbSNP
rs1300203730 161 dbSNP
rs1403709572 170 dbSNP
rs1390045727 176 dbSNP
rs1163889494 178 dbSNP
rs1018048078 180 dbSNP
rs1280648523 181 dbSNP
rs570755023 189 dbSNP
rs1422091810 191 dbSNP
rs539130213 191 dbSNP
rs867697105 200 dbSNP
rs995197145 201 dbSNP
rs1025901530 202 dbSNP
rs951698043 204 dbSNP
rs1466112874 206 dbSNP
rs1188771591 228 dbSNP
rs1419493333 229 dbSNP
rs142400150 231 dbSNP
rs1257284307 232 dbSNP
rs1219020219 233 dbSNP
rs769295132 234 dbSNP
rs549904170 246 dbSNP
rs1474132857 250 dbSNP
rs1173887403 258 dbSNP
rs918052935 259 dbSNP
rs927481703 267 dbSNP
rs969979577 270 dbSNP
rs1470556152 271 dbSNP
rs1176360279 276 dbSNP
rs1404309163 278 dbSNP
rs1170541814 286 dbSNP
rs930819056 288 dbSNP
rs1437773090 309 dbSNP
rs1166765284 315 dbSNP
rs1171150073 317 dbSNP
rs1477532929 320 dbSNP
rs1200393512 325 dbSNP
rs772786408 326 dbSNP
rs1326142170 331 dbSNP
rs886527772 337 dbSNP
rs1428896933 341 dbSNP
rs925401468 345 dbSNP
rs1319884381 347 dbSNP
rs1276293294 359 dbSNP
rs1276635417 361 dbSNP
rs1324402257 370 dbSNP
rs1275591141 372 dbSNP
rs751112039 374 dbSNP
rs72758420 375 dbSNP
rs1330733068 376 dbSNP
rs1052419085 377 dbSNP
rs1448214955 380 dbSNP
rs913897189 387 dbSNP
rs560508781 389 dbSNP
rs945943191 390 dbSNP
rs1051471850 396 dbSNP
rs890932662 400 dbSNP
rs1209188901 402 dbSNP
rs1260605163 403 dbSNP
rs1444853726 415 dbSNP
rs1437304027 421 dbSNP
rs1200565376 425 dbSNP
rs996119955 427 dbSNP
rs1006756337 429 dbSNP
rs1235607551 431 dbSNP
rs529645880 431 dbSNP
rs1442746493 434 dbSNP
rs757950325 435 dbSNP
rs1039454801 436 dbSNP
rs1351740523 442 dbSNP
rs1308699465 443 dbSNP
rs1427872112 455 dbSNP
rs1240953286 468 dbSNP
rs1463912 490 dbSNP
rs554743133 507 dbSNP
rs185533009 508 dbSNP
rs1360062792 515 dbSNP
rs1336535413 516 dbSNP
rs1399131972 525 dbSNP
rs951124951 525 dbSNP
rs991845101 540 dbSNP
rs1325815624 543 dbSNP
rs1346197908 546 dbSNP
rs1404465815 548 dbSNP
rs1281286126 551 dbSNP
rs1352331585 552 dbSNP
rs1181161918 553 dbSNP
rs115934157 554 dbSNP
rs1217444193 555 dbSNP
rs1239024268 555 dbSNP
rs1285511587 555 dbSNP
rs1294306855 555 dbSNP
rs35544190 555 dbSNP
rs78250796 555 dbSNP
rs796442422 555 dbSNP
rs377136654 556 dbSNP
rs1025663594 557 dbSNP
rs969012516 562 dbSNP
rs1348305118 564 dbSNP
rs1211220285 566 dbSNP
rs767971809 574 dbSNP
rs969572428 578 dbSNP
rs1290191855 580 dbSNP
rs754792202 582 dbSNP
rs980354788 592 dbSNP
rs927565339 595 dbSNP
rs752955410 596 dbSNP
rs1298384556 601 dbSNP
rs190255732 602 dbSNP
rs925361319 603 dbSNP
rs1253353560 604 dbSNP
rs1473826529 605 dbSNP
rs1183198443 608 dbSNP
rs1363547875 613 dbSNP
rs930851384 613 dbSNP
rs1468963137 614 dbSNP
rs1415854960 616 dbSNP
rs577082958 619 dbSNP
rs1477336324 620 dbSNP
rs181510849 633 dbSNP
rs555768445 638 dbSNP
rs35605364 646 dbSNP
rs1424095067 650 dbSNP
rs988185097 652 dbSNP
rs913879598 655 dbSNP
rs1220925767 669 dbSNP
rs756389818 672 dbSNP
rs1372501191 675 dbSNP
rs764154932 677 dbSNP
rs1217216957 678 dbSNP
rs933329871 688 dbSNP
rs1391847037 690 dbSNP
rs986722200 694 dbSNP
rs753963296 699 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 GSM1084064. RNA binding protein: AGO2. Condition:CLIP_noemetine_AbnovaAb HITS-CLIP data was present in GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb HITS-CLIP data was present in GSM1084066. RNA binding protein: AGO2. Condition:CLIP_noemetine_SantaCruzAb HITS-CLIP data was present in GSM1084067. RNA binding protein: AGO2. Condition:CLIP_emetine_SantaCruzAb HITS-CLIP data was present in GSM1084068. RNA binding protein: AGO2. Condition:CLIP_noemetine_SigmaAb HITS-CLIP data was present in GSM1084069. RNA binding protein: AGO2. Condition:CLIP_emetine_SigmaAb HITS-CLIP data was present in GSM1084078. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep2_AbnovaAb HITS-CLIP data was present in GSM1084079. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep2_AbnovaAb HITS-CLIP data was present in GSM1084080. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep2_SantaCruzAb ...

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

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 GSM1084064
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_AbnovaAb
Location of target site ENST00000260379.6 | 3UTR | AGUGGAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1084065
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_AbnovaAb
Location of target site ENST00000260379.6 | 3UTR | AAGUGGAAAAAAAAAAAGAU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1084066
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_SantaCruzAb
Location of target site ENST00000260379.6 | 3UTR | AAGUGGAAAAAAAAAAAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM1084067
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_SantaCruzAb
Location of target site ENST00000260379.6 | 3UTR | AGUGGAAAAAAAAAAAGAU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM1084068
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_SigmaAb
Location of target site ENST00000260379.6 | 3UTR | AAGUGGAAAAAAAAAAAGA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM1084069
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_SigmaAb
Location of target site ENST00000260379.6 | 3UTR | CAAAGUGGAAAAAAAAAAAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM1084078
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep2_AbnovaAb
Location of target site ENST00000260379.6 | 3UTR | AAGUGGAAAAAAAAAAAGAUUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 8 for dataset GSM1084079
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep2_AbnovaAb
Location of target site ENST00000260379.6 | 3UTR | AAGUGGAAAAAAAAAAAGAUU
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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