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 CHST4   
Synonyms GST3, GlcNAc6ST2, HECGLCNAC6ST, LSST
Description carbohydrate sulfotransferase 4
Transcript NM_001166395   
Other Transcripts NM_005769   
Expression
Putative miRNA Targets on CHST4
3'UTR of CHST4
(miRNA target sites are highlighted)
>CHST4|NM_001166395|3'UTR
   1 GAGGGTTGAGAAGGCTTTGCTGCCACCTGGTGTCAGCCTCAGTCACTTTCTCTGAATGCTTCTGAGCCTTGCCTACATCT
  81 CTGAGCCTTAACTACATGTCTGTGGGTATCACACTGAGTGTGAGTTGTGTCCACACGTGCTCAAGCAGAAGGACTTTTGT
 161 GTCCATGCTTGTGTCTAGAAAACAGACTGGGGAACCTTATGTGAGCAGCACATCCCACCAGTGAAACAGGGTATTGCTCT
 241 TCTTCTTTTCTTGATCTTCCTGTCTGGGCAGACTTCAGAGACTTTGTGGCCTGGAGGCCTATTAAGCACGACACAGTATC
 321 AGTGGAATTGATCCATAAACCTCCCTGTCCACATCTTGCCCAATGGGGAATGGATCTTTCACCAAAGAGCTCACCAGCAT
 401 TTTCCACAGAGATGCAAATTCTGAGCCCTTGGAGTTCCCAGTGGATTCAAGGAAGGAAGTGGGAACAAGGTTGGATGCCT
 481 ACTTATGAGCTTGACCATCACAGCTATCGGTAATCAGAAATATGAAACAAAATCTCTGCACAAAAGAGCAAGCTCTTAAG
 561 TTCACAGGGTGCCTGGGCTGCATTTGAATATCACTTCCCCTCTGCATTTTCCCATCACATAGAAGACTTTGACCTGTGAA
 641 GCTGCCATCTGTTAATACTAAAATTCCCAAATAAGGTTCTGTTTAGAATGTCCCTTTTTATGCTTCTTAATTATTAGCAG
 721 TAAATGTTCATTTTTATGGGATCCTAAGCTAAAAAAAAAAAAAAAAAAAAAAA
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' gcacgacacAGTATCAGTGGAa 3'
306 - 327 149.00 -13.00
2
miRNA  3' uuuAAUCCAUC-ACCGUCACCUu 5'
             ||:|  || |  ||||||| 
Target 5' cccTTGG--AGTTCCCAGTGGAt 3'
426 - 446 147.00 -12.50
3
miRNA  3' uuuAAUCCAU-CACCGUCACCUu 5'
             |||  ||  || | ||||: 
Target 5' gccTTAACTACATGTCTGTGGGt 3'
85 - 107 107.00 -7.10
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN19692818 4 COSMIC
COSN30178567 5 COSMIC
COSN30524916 11 COSMIC
COSN30474036 28 COSMIC
COSN30104424 38 COSMIC
COSN30451004 68 COSMIC
COSN30108396 84 COSMIC
COSN31536826 109 COSMIC
COSN15623659 295 COSMIC
COSN21704102 331 COSMIC
COSN31528895 357 COSMIC
COSN2502123 398 COSMIC
COSN31513419 419 COSMIC
COSN31596404 518 COSMIC
COSN26958028 525 COSMIC
COSN30113978 535 COSMIC
COSN15623660 552 COSMIC
COSN31486631 612 COSMIC
COSN22018393 727 COSMIC
COSN26604372 762 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1445393439 4 dbSNP
rs771662092 5 dbSNP
rs760401567 6 dbSNP
rs766097253 9 dbSNP
rs543439024 20 dbSNP
rs759421392 24 dbSNP
rs561504798 27 dbSNP
rs757356463 32 dbSNP
rs897638234 33 dbSNP
rs1311307613 43 dbSNP
rs767694226 44 dbSNP
rs1395309564 49 dbSNP
rs1042852633 57 dbSNP
rs924073592 63 dbSNP
rs528866075 73 dbSNP
rs1054225283 98 dbSNP
rs1307825866 103 dbSNP
rs893017377 116 dbSNP
rs890129637 119 dbSNP
rs1439515368 120 dbSNP
rs1007676548 121 dbSNP
rs1395148365 122 dbSNP
rs1276215655 137 dbSNP
rs779439820 138 dbSNP
rs1359189089 147 dbSNP
rs1345169285 149 dbSNP
rs1218113064 161 dbSNP
rs547530558 165 dbSNP
rs1278189499 168 dbSNP
rs1017262143 172 dbSNP
rs1425406113 175 dbSNP
rs565739831 177 dbSNP
rs533166439 178 dbSNP
rs1205624907 186 dbSNP
rs1250736562 188 dbSNP
rs1435835761 191 dbSNP
rs551284258 193 dbSNP
rs373418096 196 dbSNP
rs181628654 201 dbSNP
rs906851637 203 dbSNP
rs1011092943 204 dbSNP
rs1248660577 206 dbSNP
rs1002569708 209 dbSNP
rs1193018345 215 dbSNP
rs768111793 222 dbSNP
rs966819735 228 dbSNP
rs145349950 231 dbSNP
rs1360953764 232 dbSNP
rs780683070 234 dbSNP
rs1243592830 235 dbSNP
rs959479552 237 dbSNP
rs1006356956 238 dbSNP
rs1396273653 238 dbSNP
rs1016442691 241 dbSNP
rs1339026885 244 dbSNP
rs550179004 253 dbSNP
rs991259787 264 dbSNP
rs1425893139 266 dbSNP
rs964912929 267 dbSNP
rs1161596491 276 dbSNP
rs1457544912 280 dbSNP
rs568126901 287 dbSNP
rs199747801 293 dbSNP
rs1373864175 295 dbSNP
rs909866632 306 dbSNP
rs1476733343 310 dbSNP
rs941945135 311 dbSNP
rs1490835572 317 dbSNP
rs535414716 326 dbSNP
rs79003257 330 dbSNP
rs929083398 331 dbSNP
rs954855749 332 dbSNP
rs185459619 334 dbSNP
rs1007297153 337 dbSNP
rs1406084993 338 dbSNP
rs572202057 345 dbSNP
rs1273800205 347 dbSNP
rs540064191 350 dbSNP
rs558052606 351 dbSNP
rs576701339 352 dbSNP
rs1300079195 359 dbSNP
rs1039131604 361 dbSNP
rs893447488 364 dbSNP
rs923987527 383 dbSNP
rs543780262 384 dbSNP
rs150034652 386 dbSNP
rs1252110500 396 dbSNP
rs200992894 398 dbSNP
rs1452345983 410 dbSNP
rs1193115518 414 dbSNP
rs1193704532 416 dbSNP
rs1457094421 418 dbSNP
rs902772195 429 dbSNP
rs1251178933 438 dbSNP
rs573688919 446 dbSNP
rs914399628 451 dbSNP
rs1035183316 460 dbSNP
rs959746791 467 dbSNP
rs990895959 471 dbSNP
rs1189828388 472 dbSNP
rs1399859443 476 dbSNP
rs1337096677 478 dbSNP
rs1016959478 479 dbSNP
rs1399850576 480 dbSNP
rs1171906438 482 dbSNP
rs1372991380 485 dbSNP
rs550243965 487 dbSNP
rs1044273701 491 dbSNP
rs907138378 492 dbSNP
rs973320278 498 dbSNP
rs1165296118 504 dbSNP
rs919213398 507 dbSNP
rs1002926052 509 dbSNP
rs929199338 510 dbSNP
rs1047396811 517 dbSNP
rs188707245 518 dbSNP
rs1005970714 539 dbSNP
rs1016054056 540 dbSNP
rs1281300577 542 dbSNP
rs1352044317 542 dbSNP
rs1435172585 556 dbSNP
rs559538208 569 dbSNP
rs1296875514 577 dbSNP
rs996368368 582 dbSNP
rs1376390377 584 dbSNP
rs1315960599 587 dbSNP
rs943128043 589 dbSNP
rs1476242144 595 dbSNP
rs1030976343 599 dbSNP
rs1168454667 614 dbSNP
rs532879743 616 dbSNP
rs954992922 621 dbSNP
rs1333342099 627 dbSNP
rs1324548827 628 dbSNP
rs1387063812 631 dbSNP
rs551588372 645 dbSNP
rs563320145 652 dbSNP
rs1418594438 653 dbSNP
rs147675299 657 dbSNP
rs140801632 661 dbSNP
rs1185024676 664 dbSNP
rs1357365302 665 dbSNP
rs1471637658 666 dbSNP
rs1031000160 668 dbSNP
rs1236079097 670 dbSNP
rs946426033 672 dbSNP
rs1448037203 676 dbSNP
rs1288826284 678 dbSNP
rs1215139627 680 dbSNP
rs762881010 691 dbSNP
rs1353050916 692 dbSNP
rs1292670237 696 dbSNP
rs1230236573 703 dbSNP
rs1042030545 710 dbSNP
rs1431230428 726 dbSNP
rs1328086568 727 dbSNP
rs1213343245 738 dbSNP
rs1296231615 742 dbSNP
rs1271480051 751 dbSNP
rs369871645 751 dbSNP
rs902804801 757 dbSNP
rs866108924 759 dbSNP
rs958066577 760 dbSNP
rs1003782912 770 dbSNP
rs1445718843 773 dbSNP
rs1403188231 775 dbSNP
rs989511523 777 dbSNP
rs1190074394 784 dbSNP
rs1163001017 790 dbSNP
rs770827182 792 dbSNP
rs916689187 793 dbSNP
rs567173299 796 dbSNP
rs895287664 799 dbSNP
rs1475072885 803 dbSNP
rs774485688 806 dbSNP
rs535502311 814 dbSNP
rs1269614507 819 dbSNP
rs1223881563 820 dbSNP
rs948535018 821 dbSNP
rs759512075 828 dbSNP
rs547375178 835 dbSNP
rs112350648 845 dbSNP
rs767500197 855 dbSNP
rs1457317095 864 dbSNP
rs938611876 865 dbSNP
rs752766001 869 dbSNP
rs1276130151 871 dbSNP
rs539525454 873 dbSNP
rs1217927272 880 dbSNP
rs558204408 883 dbSNP
rs1287724449 889 dbSNP
rs1348837315 894 dbSNP
rs1329096610 898 dbSNP
rs1411365197 911 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_124A_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell miR-124 + A 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.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' uuuaauCCAUCACCGUCACCuu 5'
                || : |  ||||||  
Target 5' -----uGGAGUUCCCAGUGG-- 3'
1 - 15
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_124A_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell miR-124 + A
Location of target site ENST00000338482.5 | 3UTR | UGGAGUUCCCAGUGG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
CLIP-seq Viewer Link
CLIP-seq Support 2 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 ENST00000338482.5 | 3UTR | UGGAGUUCCCAGUGG
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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