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 SPTA1   
Synonyms EL2, HPP, HS3, SPH3, SPTA
Description spectrin alpha, erythrocytic 1
Transcript NM_003126   
Expression
Putative miRNA Targets on SPTA1
3'UTR of SPTA1
(miRNA target sites are highlighted)
>SPTA1|NM_003126|3'UTR
   1 TAAGCAGCTCCTCGTGGATCGTAGAAAATCTTAGTGTCGTGGGAAATTTACTGGGGGGCAAAGAGTACAGGCAAATGTGG
  81 AAGATAAAGATGGCCTCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCTTGTGTTTGTGTGCATATTACATTTAT
 161 TGTAGGATCTTAAAAAATCTCAAGGGTGGGAGATAGAAAGGTTAATAGAGTTGGAGGAGTGGAAGCTATTTTGTATGCAA
 241 CTAGTCACTGCTGAGGGGTGTCAAAGTTTCTATTTTTATTTGTTCTGTTTTGCACGTCTTTATCATTTTGCTTTATTCCG
 321 ATTATAGAATAAAGTAATTCTTTTTAAAAATATTTTTTGGGGCAAAGTTAAGTAAAATGTTGAGCTTCTATATTTCTGGG
 401 AACTGTACTCATATAAGAGTGGGCAGCTAATTTTACTGTAAAGAAGGGCCATGGTATAGTAGATAAATAAAATCCAAGGC
 481 AATTTTCAAACAATTTTTTTAAACTTTGGAATGTGTTTAAATTTAAATTTGAAAATAAAGATATTTGATTTTCTGGGG
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' uuUAAUC-CAUCACCGUCACCUu 5'
            | ||| || |  | |||||| 
Target 5' ttAATAGAGTTGGAGGAGTGGAa 3'
202 - 224 128.00 -14.40
2
miRNA  3' uuuaaUC-CAUCACCGU---CACCUu 5'
               || |||  ||||   ||||| 
Target 5' ggcaaAGAGTACAGGCAAATGTGGAa 3'
57 - 82 113.00 -12.60
3
miRNA  3' uuuaauccaucaccgUCACCUu 5'
                         |||||: 
Target 5' ctgtactcatataagAGTGGGc 3'
403 - 424 104.00 -6.30
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
292935 39 ClinVar
292934 68 ClinVar
292933 98 ClinVar
292925 133 ClinVar
292926 133 ClinVar
292927 133 ClinVar
292928 133 ClinVar
292929 133 ClinVar
292930 133 ClinVar
292931 133 ClinVar
292932 133 ClinVar
292924 134 ClinVar
292923 167 ClinVar
292922 276 ClinVar
292921 294 ClinVar
292920 295 ClinVar
292919 296 ClinVar
875791 319 ClinVar
292918 323 ClinVar
874858 341 ClinVar
874857 379 ClinVar
873913 387 ClinVar
873912 420 ClinVar
292917 501 ClinVar
873911 509 ClinVar
COSN30172743 9 COSMIC
COSN26996696 13 COSMIC
COSN31572501 14 COSMIC
COSN13479900 16 COSMIC
COSN24298063 19 COSMIC
COSN27789776 21 COSMIC
COSN31508305 34 COSMIC
COSN31576096 34 COSMIC
COSN30539687 38 COSMIC
COSN13479897 39 COSMIC
COSN30464432 43 COSMIC
COSN30542333 50 COSMIC
COSN28844109 53 COSMIC
COSN31494929 53 COSMIC
COSN31507331 57 COSMIC
COSN26996697 58 COSMIC
COSN28084245 63 COSMIC
COSN30468517 87 COSMIC
COSN30184221 88 COSMIC
COSN30480133 89 COSMIC
COSN31598816 93 COSMIC
COSN20095453 98 COSMIC
COSN20095457 98 COSMIC
COSN30528013 103 COSMIC
COSN18714052 134 COSMIC
COSN30493958 139 COSMIC
COSN6401430 140 COSMIC
COSN20073982 142 COSMIC
COSN26150674 165 COSMIC
COSN30608821 167 COSMIC
COSN31529899 175 COSMIC
COSN28832719 190 COSMIC
COSN28832966 237 COSMIC
COSN32056558 319 COSMIC
COSN29387038 323 COSMIC
COSN28397742 347 COSMIC
COSN17335934 368 COSMIC
COSN17797593 445 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs200530620 1 dbSNP
rs749091377 2 dbSNP
rs772956304 3 dbSNP
rs769800813 4 dbSNP
rs747560060 6 dbSNP
rs1348516433 7 dbSNP
rs780729873 10 dbSNP
rs374235146 14 dbSNP
rs779865952 19 dbSNP
rs534141025 20 dbSNP
rs369500677 21 dbSNP
rs1426049996 28 dbSNP
rs1190838841 34 dbSNP
rs998043428 37 dbSNP
rs757763322 38 dbSNP
rs202171095 39 dbSNP
rs764226297 41 dbSNP
rs1482674969 43 dbSNP
rs760799031 46 dbSNP
rs752854376 48 dbSNP
rs1039132711 53 dbSNP
rs1163743882 54 dbSNP
rs1389450582 57 dbSNP
rs943417368 58 dbSNP
rs1403084351 59 dbSNP
rs1404408644 63 dbSNP
rs1319953507 64 dbSNP
rs186892978 68 dbSNP
rs1401004485 75 dbSNP
rs1297919623 77 dbSNP
rs1339131720 85 dbSNP
rs1049569835 87 dbSNP
rs1285275530 88 dbSNP
rs1355800603 90 dbSNP
rs929301791 93 dbSNP
rs919531937 94 dbSNP
rs995337947 95 dbSNP
rs964342122 97 dbSNP
rs1488714505 98 dbSNP
rs55832242 98 dbSNP
rs568682203 98 dbSNP
rs867901344 99 dbSNP
rs939533467 100 dbSNP
rs1159872458 101 dbSNP
rs1164809042 103 dbSNP
rs1380550676 105 dbSNP
rs1418672485 110 dbSNP
rs890815140 112 dbSNP
rs1052022190 120 dbSNP
rs1475382660 121 dbSNP
rs1422888001 123 dbSNP
rs926748248 123 dbSNP
rs980549621 127 dbSNP
rs1487389517 129 dbSNP
rs550688663 131 dbSNP
rs1239762599 133 dbSNP
rs1284132402 133 dbSNP
rs1311508451 133 dbSNP
rs1340320362 133 dbSNP
rs1346945667 133 dbSNP
rs1354470870 133 dbSNP
rs1445946104 133 dbSNP
rs372359921 133 dbSNP
rs66981873 133 dbSNP
rs769691410 133 dbSNP
rs868674912 133 dbSNP
rs879208333 133 dbSNP
rs886045379 133 dbSNP
rs866529035 134 dbSNP
rs376905669 135 dbSNP
rs999259757 135 dbSNP
rs903594665 137 dbSNP
rs1176158517 138 dbSNP
rs1269032844 140 dbSNP
rs988239811 141 dbSNP
rs1433372462 149 dbSNP
rs1197689978 162 dbSNP
rs1377474261 163 dbSNP
rs775325981 165 dbSNP
rs3768535 167 dbSNP
rs1173537000 168 dbSNP
rs998074475 172 dbSNP
rs571654703 174 dbSNP
rs899675416 176 dbSNP
rs1056717743 178 dbSNP
rs1287944403 179 dbSNP
rs1018487768 185 dbSNP
rs1005383565 188 dbSNP
rs887895525 194 dbSNP
rs1049133463 200 dbSNP
rs1335885150 201 dbSNP
rs1278191594 204 dbSNP
rs939573997 205 dbSNP
rs1220228862 209 dbSNP
rs929326020 221 dbSNP
rs897799695 229 dbSNP
rs1217321516 233 dbSNP
rs1278763862 244 dbSNP
rs907886894 247 dbSNP
rs1196229478 257 dbSNP
rs1266742873 258 dbSNP
rs1056648963 260 dbSNP
rs1488510830 266 dbSNP
rs1364627327 271 dbSNP
rs12128275 276 dbSNP
rs1264822806 282 dbSNP
rs886045378 294 dbSNP
rs12601 295 dbSNP
rs886045377 296 dbSNP
rs757145948 304 dbSNP
rs1461802144 305 dbSNP
rs1168910943 313 dbSNP
rs1370322692 316 dbSNP
rs866250197 317 dbSNP
rs561434223 319 dbSNP
rs987865697 321 dbSNP
rs867404163 323 dbSNP
rs1298527428 325 dbSNP
rs1339565856 336 dbSNP
rs1478772586 340 dbSNP
rs867313542 341 dbSNP
rs1187218274 343 dbSNP
rs1477712467 351 dbSNP
rs1243350597 353 dbSNP
rs955279557 356 dbSNP
rs1030646704 359 dbSNP
rs1489039628 360 dbSNP
rs999142924 361 dbSNP
rs1488154047 363 dbSNP
rs746759449 370 dbSNP
rs976671141 379 dbSNP
rs964347208 381 dbSNP
rs549664412 387 dbSNP
rs1469234496 393 dbSNP
rs1022008305 394 dbSNP
rs1012368267 401 dbSNP
rs531152825 404 dbSNP
rs1421707669 409 dbSNP
rs1005827752 413 dbSNP
rs1159455782 414 dbSNP
rs1057004471 415 dbSNP
rs1428384855 419 dbSNP
rs1197068796 420 dbSNP
rs1304519700 424 dbSNP
rs879849461 424 dbSNP
rs1394971608 428 dbSNP
rs1312233005 437 dbSNP
rs939646759 440 dbSNP
rs886689972 446 dbSNP
rs1028165412 449 dbSNP
rs1218178981 452 dbSNP
rs1353521999 491 dbSNP
rs1214004478 493 dbSNP
rs1364834103 494 dbSNP
rs1258296077 497 dbSNP
rs993506500 500 dbSNP
rs1241416789 501 dbSNP
rs34122435 501 dbSNP
rs897830675 504 dbSNP
rs1441609692 505 dbSNP
rs1441169747 508 dbSNP
rs1379850044 512 dbSNP
rs1398754101 516 dbSNP
rs1056429827 522 dbSNP
rs183671800 531 dbSNP
rs1359706196 533 dbSNP
rs1465519820 536 dbSNP
rs1329056310 547 dbSNP
rs1378546887 561 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 ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' uuUAAUC-CAUCACCGUCACCUu 5'
            | ||| || |  | |||||| 
Target 5' --AAUAGAGUUGGAGGAGUGGAa 3'
1 - 21
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 ENST00000368147.4 | 3UTR | AAUAGAGUUGGAGGAGUGGAAGCU
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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