miRTarBase - #MIRT258346


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pre-miRNA Information
pre-miRNA hsa-mir-4270   
Genomic Coordinates chr3: 15496239 - 15496308
Description Homo sapiens miR-4270 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4270
Sequence 11| UCAGGGAGUCAGGGGAGGGC |30
Evidence Experimental
Experiments SOLiD
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs991570490 2 dbSNP
rs1417709982 10 dbSNP
rs960511282 12 dbSNP
rs928808979 14 dbSNP
rs1372156971 15 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol HOXA11   
Synonyms HOX1, HOX1I, RUSAT1
Description homeobox A11
Transcript NM_005523   
Expression
Putative miRNA Targets on HOXA11
3'UTR of HOXA11
(miRNA target sites are highlighted)		 
>HOXA11|NM_005523|3'UTR
   1 GACTCCAGCGGCTGGAATTGGGTGGGGGGCTTCATACACATGAGATAATATGCAGATTTTGCCCTTGACAAAGTCAAGCC
  81 ACATGGTGACTTTTGAAAAGAGGTGTGCAAGAGAGGGATGCATGGAGATAGCCCCACAGGAGGTGGTCTGGGACTCTCTT
 161 GATTAAGATCTCAGTGGTTAAGATTCCTAATAATCATTGGATTCTGAGAGCTGTGCATCAGCTAGAATGACAGGTTTGGG
 241 ACCCCTGGTGGTTCACTCTTGGAGCCTGCAGAGCTGCGGGCTGGGTGTGGTCTCCACTGGGGATTGGGCCCCTGCCAGAC
 321 CCCCTGGAGACTAACCCCACCACACCCTCCCTCTACTGGGAGCCTACCCACCCCCAGGACCCCTGAGTAAAAAAGCTGTG
 401 TGCTCTCCAAGCCCAGTTCAGCTTGGGGACAGGGGCAGGAGGAAGGGGTAGGATTACTAGGTGCCCAGAATGAGGCTGCT
 481 TTCCAAAGCCAATGTGAACAGCGGCTGGACTTGGAGGTAGCTTTGAGGTGGAAGAGGGCTGCAAATCCTTGTGGGAAAAG
 561 AAATCTATGATTCCAGGTGGCATCAGTGTCTTTCCACTCCTCCTAGCCACCCACCACACTGATCCAGCCCTGAGTTCCTA
 641 GCCACCGCCTCCTACAGCCCACCTGGCTTTTCTTTCTACCAAATGAGGGTCTTGGTTCCAGCCTGCCACTCAGGCCCAAA
 721 GCCTCGACACAGAGTGGACTGTTCCCTGAGGTGGGAGATGTGGAAAAGCCAAGAGGCTGCAGCCAGGCCACTGGCCCCTG
 801 AGATCTCTGCAGGAAATGGCTGTGGAGTGTGGCAGTTTGGCAAACTCTCCACCACACGTAATGAAACTTGGATTTGCTCA
 881 GTGTCTGGCTGCAGAGCAGTGGGCCTGGCCAGCAGGTCCCCAGCTTTGGCTATGAGGGCCTTGAGTCCCCCAAAACACCG
 961 GGTTCCAGCACCACACTCAGCCCTCATTGGCTCTTGAACTGAGCTTGGAAGCTTCTGGTGACCTTCCAAGAGCCTGAGAG
1041 TGAGGTGGAATTATTTTAAAAGATAAATATTATATTATATATATATATATTTCCCTGAAGGAACCAAAGCGAATTTTAAA
1121 AGATGCAATGTAGAGGGGAAAAGAGATGATGAAAATATTTAAAGGCCCTATCTGTTTACAGTGTTCCGTGGTTAAACTCG
1201 CTCACTGCTAAGAATATTTGAATGTATGCTTCATACAGGGATGGTGTTCAAAAAACTTGTAAATAAAGGAACCATAATCA
1281 ATTTTCTTTTCTTTCTTTCTCTTTTTCTTTTTTCTTTTGCCATTAGTTGATTTCCTTTAGGGTGTTGGAGGGGGTGGAAA
1361 AGGTATTGAGAATGGTCTTTTTAATCTCTTGCAACATTTGGAAAGAGTTAGGGAAATGCTCAGAGGCAGTCGGCCTGGCC
1441 GGCCTGGGGATCTCATCTGGGAAAGCCAGGCACCCTCCCATTGAATCTCCTTTGCCTCCCTGTGTTAAGAAATGTCTGTT
1521 GGCTCCATTTGTACTGGGAGTGTTGGCCTGTCCTCAATTCTGGTTCTTACCCACCGTGTGTGTTGCAGCACTTATACAGG
1601 CAACTGGGCACAAGGAAAATAAAGACGGTGGAAATTTGA
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' cgGGAGGGGACUGAGGGACu 5'
            :||||::|| ||||||| 
Target 5' aaTCTCCTTTGCCTCCCTGt 3'
 1484 - 1503 170.00 -27.10
2 
miRNA  3' cgggagggGACUGAGGGACu 5'
                  ||| :|||||| 
Target 5' agagtggaCTG-TTCCCTGa 3'
 731 - 749 131.00 -15.40
3 
miRNA  3' cgGGAGGGGACUGAGGGAcu 5'
            || || |   ||||||  
Target 5' ccCCACCACACCCTCCCTct 3'
 335 - 354 130.00 -16.50
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30140907 20 COSMIC
COSN30181751 24 COSMIC
COSN30486110 42 COSMIC
COSN14282714 44 COSMIC
COSN30193675 49 COSMIC
COSN31505437 87 COSMIC
COSN30150748 125 COSMIC
COSN30168487 132 COSMIC
COSN28889767 216 COSMIC
COSN7976356 405 COSMIC
COSN31546092 464 COSMIC
COSN30173960 468 COSMIC
COSN21770689 496 COSMIC
COSN31609765 560 COSMIC
COSN29778705 1076 COSMIC
COSN30165104 1084 COSMIC
COSN31571653 1111 COSMIC
COSN17038024 1215 COSMIC
rs17501090 961 GWAS
rs6461992 1584 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs755805936 3 dbSNP
rs184605433 5 dbSNP
rs17427861 6 dbSNP
rs751075694 8 dbSNP
rs201081293 9 dbSNP
rs1025013154 10 dbSNP
rs1203984450 11 dbSNP
rs1325039343 12 dbSNP
rs752576612 14 dbSNP
rs1010447674 15 dbSNP
rs778514371 18 dbSNP
rs765082062 21 dbSNP
rs1309802100 25 dbSNP
rs1239273706 26 dbSNP
rs868538518 27 dbSNP
rs754825702 30 dbSNP
rs759857446 31 dbSNP
rs1331343541 33 dbSNP
rs1454827995 38 dbSNP
rs776938360 39 dbSNP
rs766487741 40 dbSNP
rs1286093871 41 dbSNP
rs1454381787 42 dbSNP
rs760737881 44 dbSNP
rs377744532 49 dbSNP
rs1417079950 50 dbSNP
rs906971936 52 dbSNP
rs1319797396 63 dbSNP
rs1280305459 67 dbSNP
rs536684764 68 dbSNP
rs1045410394 78 dbSNP
rs1418790523 80 dbSNP
rs1032649522 84 dbSNP
rs566789760 86 dbSNP
rs770470576 109 dbSNP
rs1038754200 110 dbSNP
rs1457810580 116 dbSNP
rs918830277 117 dbSNP
rs1459848397 119 dbSNP
rs1008718199 123 dbSNP
rs1294492922 124 dbSNP
rs1396215804 126 dbSNP
rs748995496 131 dbSNP
rs546991718 138 dbSNP
rs533371181 143 dbSNP
rs941614614 146 dbSNP
rs564523002 155 dbSNP
rs1020943566 160 dbSNP
rs1048110938 161 dbSNP
rs1397924418 165 dbSNP
rs1404519096 166 dbSNP
rs755798686 168 dbSNP
rs985610829 169 dbSNP
rs1466440717 172 dbSNP
rs1292079846 173 dbSNP
rs1319867323 176 dbSNP
rs1460224090 180 dbSNP
rs551089087 183 dbSNP
rs929217038 193 dbSNP
rs955429186 197 dbSNP
rs531002821 204 dbSNP
rs562126285 205 dbSNP
rs1480175118 218 dbSNP
rs1203330920 220 dbSNP
rs1254288023 228 dbSNP
rs1029731093 230 dbSNP
rs1187331159 233 dbSNP
rs1411636721 239 dbSNP
rs1426142048 242 dbSNP
rs1237703231 248 dbSNP
rs1428181570 250 dbSNP
rs978479882 251 dbSNP
rs542437019 253 dbSNP
rs1409994124 258 dbSNP
rs1038404251 260 dbSNP
rs941324627 273 dbSNP
rs1020614648 277 dbSNP
rs1011459673 278 dbSNP
rs1313305908 285 dbSNP
rs927400750 287 dbSNP
rs3210747 293 dbSNP
rs528751640 296 dbSNP
rs113615033 297 dbSNP
rs1483508943 301 dbSNP
rs1034163214 302 dbSNP
rs539802863 310 dbSNP
rs1484262569 311 dbSNP
rs906931113 321 dbSNP
rs1419463467 325 dbSNP
rs1448149614 325 dbSNP
rs1045544324 331 dbSNP
rs1430076897 332 dbSNP
rs1174890418 337 dbSNP
rs148122528 339 dbSNP
rs1356973365 344 dbSNP
rs1302872795 345 dbSNP
rs1364395612 346 dbSNP
rs1432730330 349 dbSNP
rs577227574 351 dbSNP
rs994228907 352 dbSNP
rs557371112 359 dbSNP
rs1218909225 361 dbSNP
rs1213773943 363 dbSNP
rs543899928 371 dbSNP
rs917400440 372 dbSNP
rs575323346 373 dbSNP
rs956345080 378 dbSNP
rs1191049378 385 dbSNP
rs555254052 390 dbSNP
rs1454084960 395 dbSNP
rs1171144949 396 dbSNP
rs1422654069 399 dbSNP
rs1415768810 404 dbSNP
rs978434901 412 dbSNP
rs1455627945 417 dbSNP
rs1322434428 423 dbSNP
rs1365706543 424 dbSNP
rs1247055848 429 dbSNP
rs1380724766 433 dbSNP
rs964336522 435 dbSNP
rs1017314624 436 dbSNP
rs1272808386 447 dbSNP
rs1370015322 448 dbSNP
rs34878915 449 dbSNP
rs1008561165 452 dbSNP
rs890306552 453 dbSNP
rs769354206 457 dbSNP
rs1026121255 459 dbSNP
rs993725790 472 dbSNP
rs922686927 488 dbSNP
rs17501104 492 dbSNP
rs566606347 502 dbSNP
rs1197223340 507 dbSNP
rs989908736 508 dbSNP
rs1478845831 510 dbSNP
rs957248581 511 dbSNP
rs1034289067 512 dbSNP
rs777358748 516 dbSNP
rs755360261 521 dbSNP
rs553316274 528 dbSNP
rs971252297 534 dbSNP
rs1024151835 536 dbSNP
rs1321344738 541 dbSNP
rs1442209941 543 dbSNP
rs1437527525 552 dbSNP
rs1287932556 560 dbSNP
rs1348817541 565 dbSNP
rs1230330572 568 dbSNP
rs1038020615 573 dbSNP
rs146596714 576 dbSNP
rs1356273137 578 dbSNP
rs896915337 580 dbSNP
rs905829308 583 dbSNP
rs1038011619 585 dbSNP
rs570858753 598 dbSNP
rs1005659052 603 dbSNP
rs780525961 604 dbSNP
rs1250650472 605 dbSNP
rs890019068 611 dbSNP
rs1471375642 614 dbSNP
rs142408967 615 dbSNP
rs1472464006 623 dbSNP
rs934154370 628 dbSNP
rs1203537708 630 dbSNP
rs1415745742 630 dbSNP
rs950083952 639 dbSNP
rs1307128172 642 dbSNP
rs1290820548 646 dbSNP
rs917308171 647 dbSNP
rs551337477 652 dbSNP
rs1339935412 654 dbSNP
rs934820221 656 dbSNP
rs1286433870 658 dbSNP
rs568557724 660 dbSNP
rs548466425 661 dbSNP
rs945459928 662 dbSNP
rs915327546 665 dbSNP
rs1379760116 669 dbSNP
rs989476015 671 dbSNP
rs1278356690 677 dbSNP
rs766837551 680 dbSNP
rs978947908 682 dbSNP
rs927184768 685 dbSNP
rs979980519 688 dbSNP
rs964348008 691 dbSNP
rs1167731812 694 dbSNP
rs79451821 697 dbSNP
rs191849713 700 dbSNP
rs559578016 702 dbSNP
rs1325987880 704 dbSNP
rs1431926769 706 dbSNP
rs1168691457 708 dbSNP
rs1401632510 709 dbSNP
rs987197062 716 dbSNP
rs546078057 721 dbSNP
rs188099452 723 dbSNP
rs563715583 725 dbSNP
rs375777673 726 dbSNP
rs1024117976 727 dbSNP
rs1344739781 746 dbSNP
rs1230221959 752 dbSNP
rs1251565186 754 dbSNP
rs17501097 759 dbSNP
rs575213572 760 dbSNP
rs1017118158 766 dbSNP
rs1461768255 768 dbSNP
rs1005173569 770 dbSNP
rs1246019356 783 dbSNP
rs1016198531 785 dbSNP
rs1193580302 787 dbSNP
rs1405670227 789 dbSNP
rs1176590204 795 dbSNP
rs1464677867 805 dbSNP
rs1478332349 807 dbSNP
rs183830192 816 dbSNP
rs541622285 819 dbSNP
rs1248190939 835 dbSNP
rs1457231208 846 dbSNP
rs1319102436 850 dbSNP
rs1197029885 852 dbSNP
rs1489902208 857 dbSNP
rs372347060 858 dbSNP
rs757370146 880 dbSNP
rs889484616 883 dbSNP
rs1230605960 887 dbSNP
rs1044443911 891 dbSNP
rs142922642 892 dbSNP
rs998355777 896 dbSNP
rs1356011060 909 dbSNP
rs117834808 910 dbSNP
rs1042533981 928 dbSNP
rs1053602495 937 dbSNP
rs148548092 940 dbSNP
rs1266320881 941 dbSNP
rs893885190 944 dbSNP
rs1201264138 947 dbSNP
rs926072995 948 dbSNP
rs570795992 950 dbSNP
rs866921420 952 dbSNP
rs943596631 953 dbSNP
rs1156973794 956 dbSNP
rs1391489380 958 dbSNP
rs191585043 959 dbSNP
rs188759036 960 dbSNP
rs17501090 961 dbSNP
rs1342886685 963 dbSNP
rs1284774394 970 dbSNP
rs1345709265 971 dbSNP
rs1157761051 981 dbSNP
rs919048304 983 dbSNP
rs1285841706 984 dbSNP
rs1331133034 985 dbSNP
rs1414912150 986 dbSNP
rs574357418 987 dbSNP
rs972190920 996 dbSNP
rs1264699739 1012 dbSNP
rs1487370268 1025 dbSNP
rs949925099 1030 dbSNP
rs1173983013 1032 dbSNP
rs563805866 1043 dbSNP
rs1268422427 1065 dbSNP
rs1482819055 1067 dbSNP
rs1194708824 1070 dbSNP
rs543828909 1074 dbSNP
rs1016075395 1077 dbSNP
rs972579243 1077 dbSNP
rs1486991556 1081 dbSNP
rs17501084 1084 dbSNP
rs1215178362 1085 dbSNP
rs1367130735 1090 dbSNP
rs374538002 1091 dbSNP
rs562071494 1091 dbSNP
rs969317987 1091 dbSNP
rs1027915868 1093 dbSNP
rs1224317317 1101 dbSNP
rs1024894112 1104 dbSNP
rs528617847 1108 dbSNP
rs367888889 1109 dbSNP
rs77444786 1110 dbSNP
rs756937328 1111 dbSNP
rs1254136792 1113 dbSNP
rs999320696 1114 dbSNP
rs1181318140 1118 dbSNP
rs1254718174 1119 dbSNP
rs1426011092 1122 dbSNP
rs1164608407 1123 dbSNP
rs1323321157 1124 dbSNP
rs1428768206 1133 dbSNP
rs377600618 1134 dbSNP
rs893928907 1143 dbSNP
rs904715234 1148 dbSNP
rs1442338838 1154 dbSNP
rs1266760541 1155 dbSNP
rs1301699626 1156 dbSNP
rs1401407030 1166 dbSNP
rs374041480 1168 dbSNP
rs1359444889 1170 dbSNP
rs938050448 1172 dbSNP
rs905297071 1173 dbSNP
rs1046414107 1177 dbSNP
rs552380318 1187 dbSNP
rs67971665 1188 dbSNP
rs867823157 1190 dbSNP
rs764279908 1192 dbSNP
rs762751004 1198 dbSNP
rs939955161 1199 dbSNP
rs933009674 1200 dbSNP
rs867620177 1201 dbSNP
rs775179953 1209 dbSNP
rs971858629 1211 dbSNP
rs1421233848 1212 dbSNP
rs1410118521 1220 dbSNP
rs963485546 1232 dbSNP
rs908943132 1264 dbSNP
rs1172588172 1271 dbSNP
rs372861799 1272 dbSNP
rs17472245 1278 dbSNP
rs550276083 1280 dbSNP
rs969201787 1286 dbSNP
rs1337279661 1290 dbSNP
rs1364323996 1292 dbSNP
rs1024902259 1296 dbSNP
rs1432666590 1298 dbSNP
rs1271660968 1299 dbSNP
rs953771620 1300 dbSNP
rs1028050300 1301 dbSNP
rs184159521 1305 dbSNP
rs1325727195 1306 dbSNP
rs1204904086 1307 dbSNP
rs1245473210 1311 dbSNP
rs1202283279 1314 dbSNP
rs1268084870 1322 dbSNP
rs960084936 1330 dbSNP
rs1461279531 1333 dbSNP
rs541323635 1334 dbSNP
rs58212052 1340 dbSNP
rs998855412 1348 dbSNP
rs1020623180 1349 dbSNP
rs75993563 1349 dbSNP
rs201009141 1350 dbSNP
rs3837134 1350 dbSNP
rs1481151799 1351 dbSNP
rs1491384317 1351 dbSNP
rs561572484 1353 dbSNP
rs1320115478 1355 dbSNP
rs904641381 1357 dbSNP
rs555512277 1359 dbSNP
rs573004664 1362 dbSNP
rs889249775 1363 dbSNP
rs1347571907 1367 dbSNP
rs1334161191 1368 dbSNP
rs1224227319 1373 dbSNP
rs1287740826 1377 dbSNP
rs79891240 1380 dbSNP
rs1046552326 1386 dbSNP
rs1013585435 1389 dbSNP
rs933545869 1407 dbSNP
rs1460323050 1420 dbSNP
rs1490722815 1423 dbSNP
rs192875544 1431 dbSNP
rs577182999 1432 dbSNP
rs1424644720 1434 dbSNP
rs1471600395 1435 dbSNP
rs1160200454 1440 dbSNP
rs557225444 1440 dbSNP
rs1404581311 1441 dbSNP
rs537004454 1443 dbSNP
rs1181839273 1446 dbSNP
rs1367697276 1446 dbSNP
rs1307561817 1448 dbSNP
rs941702761 1449 dbSNP
rs1048195331 1450 dbSNP
rs1280680142 1452 dbSNP
rs1356207012 1456 dbSNP
rs574765728 1457 dbSNP
rs908995756 1466 dbSNP
rs980480250 1467 dbSNP
rs1361245398 1468 dbSNP
rs1444489817 1469 dbSNP
rs1222747301 1475 dbSNP
rs1250488870 1478 dbSNP
rs370411558 1480 dbSNP
rs535094258 1486 dbSNP
rs965167320 1489 dbSNP
rs149842603 1491 dbSNP
rs17427847 1503 dbSNP
rs917730779 1504 dbSNP
rs992100721 1524 dbSNP
rs956866638 1527 dbSNP
rs1161449319 1530 dbSNP
rs542049338 1532 dbSNP
rs987844893 1533 dbSNP
rs1221797935 1536 dbSNP
rs958514475 1547 dbSNP
rs1312214452 1550 dbSNP
rs1030901364 1563 dbSNP
rs1377555157 1568 dbSNP
rs79389911 1570 dbSNP
rs552316727 1575 dbSNP
rs1340406547 1576 dbSNP
rs182434774 1577 dbSNP
rs776751737 1579 dbSNP
rs1007560478 1582 dbSNP
rs6461992 1584 dbSNP
rs1014052453 1585 dbSNP
rs1030889303 1585 dbSNP
rs1197048798 1594 dbSNP
rs997675363 1595 dbSNP
rs779105076 1603 dbSNP
rs10244326 1607 dbSNP
rs749408765 1609 dbSNP
rs1424161809 1613 dbSNP
rs1445052819 1614 dbSNP
rs1187645277 1619 dbSNP
rs530375207 1621 dbSNP
rs1011922051 1622 dbSNP
rs199820715 1624 dbSNP
rs941684279 1626 dbSNP
rs1048331151 1627 dbSNP
rs1339227355 1628 dbSNP
rs201060089 1628 dbSNP
rs386711531 1628 dbSNP
rs1407424998 1629 dbSNP
rs771623431 1629 dbSNP
rs887399768 1631 dbSNP
rs1295783380 1633 dbSNP
rs1044853105 1638 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection ...

- Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell.

Article - Hafner M; Landthaler M; Burger L; Khorshid et al.
- Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293
Disease 3207.0
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 GSM714642. RNA binding protein: AGO2. Condition:completeT1 "PAR-CLIP data was present in GSM714644. RNA binding protein: AGO2. Condition:completeT1 ...

- Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' cgggaggggacuGAGGGACu 5'
                      :|||||| 
Target 5' auauauauauauUUCCCUG- 3'
 		17 - 35
Article - Kishore S; Jaskiewicz L; Burger L; Hausser et al.
- Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
Experimental Support 3 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 3207.0
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... "PAR-CLIP data was present in GSM1065667. RNA binding protein: AGO1. Condition:4-thiouridine ...

- Memczak S; Jens M; Elefsinioti A; Torti F; et al., 2013, Nature.

Article - Memczak S; Jens M; Elefsinioti A; Torti F; et al.
- Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
CLIP-seq Support 1 for dataset GSM4903831
Method / RBP HITS-CLIP / AGO
Cell line / Condition Human neurons / 124TD_shELAVL3_a
Location of target site NM_005523 | 3UTR | CUCCUUUGCCUCCCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161238
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_005523 | 3UTR | UCCCUGAGGUGGGAGAUGUGGAAAAGCCAAGAGGCUGCAGCCAGGCCACUGGCCCCUGAGAUCUCUGCAGGAAAUGGCUGUGGAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903834
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_b
Location of target site NM_005523 | 3UTR | AAGCCUCGACACAGAGUGGACUGUUCCCUGAGGUGGGAGAUGUGGAAAAGCCAAGAGGCUGCAGCCAGGCCACUGGCCCCUGAGAUCUCUGCAGGAAAUGGCUGUGGAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4903835
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_c
Location of target site NM_005523 | 3UTR | GGACUGUUCCCUGAGGUGGGAGAUGUGGAAAAGCCAAGAGGCUGCAGCCAGGCCACUGGCCCCUGAGAUCUCUGCAGGAAAUGGCUGUGGAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM4903836
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_a
Location of target site NM_005523 | 3UTR | AAGCCUCGACACAGAGUGGACUGUUCCCUGAGGUGGGAGAUGUGGAAAAGCCAAGAGGCUGCAGCCAGGCCACUGGCCCCUGAGAUCUCUGCAGGAAAUGGCUGUGGAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM4903837
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_b
Location of target site NM_005523 | 3UTR | CACUCAGGCCCAAAGCCUCGACACAGAGUGGACUGUUCCCUGAGGUGGGAGAUGUGGAAAAGCCAAGAGGCUGCAGCCAGGCCACUGGCCCCUGAGAUCUCUGCAGGAAAUGGCUGUGGAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM714642
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000006015.3 | 3UTR | AUAAAUAUUAUAUUAUAUAUAUAUAUAUUUCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 8 for dataset GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000006015.3 | 3UTR | AUAAAUAUUAUAUUAUAUAUAUAUAUAUUUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 9 for dataset GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000006015.3 | 3UTR | AUAAAUAUUAUAUUAUAUAUAUAUAUAUUUCCCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 10 for dataset GSM1065667
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_6
Location of target site ENST00000006015.3 | 3UTR | AUAAAUAUUAUAUUAUAUAUAUAUAUAUUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
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
146 hsa-miR-4270 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT056076 PIP4K2A phosphatidylinositol-5-phosphate 4-kinase type 2 alpha 2 2
MIRT057833 SLC30A7 solute carrier family 30 member 7 2 2
MIRT109295 TXLNG taxilin gamma 2 2
MIRT117521 MIDN midnolin 2 2
MIRT183504 BTG2 BTG anti-proliferation factor 2 2 2
MIRT258346 HOXA11 homeobox A11 2 6
MIRT275743 TFDP1 transcription factor Dp-1 2 2
MIRT284426 CAPN15 calpain 15 2 2
MIRT386430 CCL22 C-C motif chemokine ligand 22 2 2
MIRT443374 PLXNA2 plexin A2 2 2
MIRT445251 SEMA5A semaphorin 5A 2 2
MIRT445767 CCND3 cyclin D3 2 2
MIRT447231 ABI2 abl interactor 2 2 2
MIRT451224 ZNF444 zinc finger protein 444 2 2
MIRT451433 TJP3 tight junction protein 3 2 4
MIRT451959 TMPRSS5 transmembrane protease, serine 5 2 2
MIRT452006 FKBP5 FK506 binding protein 5 2 2
MIRT452300 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 2
MIRT452717 DTHD1 death domain containing 1 2 2
MIRT453361 ZNF3 zinc finger protein 3 2 2
MIRT453458 GLG1 golgi glycoprotein 1 2 2
MIRT453832 SAA1 serum amyloid A1 2 2
MIRT453928 COMMD5 COMM domain containing 5 2 4
MIRT454312 ZNF134 zinc finger protein 134 2 2
MIRT454493 SLC29A1 solute carrier family 29 member 1 (Augustine blood group) 2 2
MIRT454836 POLR2J3 RNA polymerase II subunit J3 2 2
MIRT455142 TBC1D25 TBC1 domain family member 25 2 2
MIRT455922 RAPGEF1 Rap guanine nucleotide exchange factor 1 2 2
MIRT456163 TTF2 transcription termination factor 2 2 2
MIRT456395 KLHL12 kelch like family member 12 2 2
MIRT456786 MTHFSD methenyltetrahydrofolate synthetase domain containing 2 2
MIRT457164 MXRA7 matrix remodeling associated 7 2 2
MIRT457190 ERC1 ELKS/RAB6-interacting/CAST family member 1 2 2
MIRT457415 RPL36 ribosomal protein L36 2 2
MIRT457630 UPK3BL uroplakin 3B like 1 2 2
MIRT458720 VPS39 VPS39, HOPS complex subunit 2 2
MIRT458745 CES2 carboxylesterase 2 2 2
MIRT459269 ADRBK1 G protein-coupled receptor kinase 2 2 2
MIRT459490 CCL11 C-C motif chemokine ligand 11 2 2
MIRT460319 SH3RF1 SH3 domain containing ring finger 1 2 2
MIRT461005 SYT7 synaptotagmin 7 2 2
MIRT461579 SCO1 SCO1, cytochrome c oxidase assembly protein 2 4
MIRT461820 SNAP23 synaptosome associated protein 23 2 2
MIRT463332 ZFHX3 zinc finger homeobox 3 2 2
MIRT463449 ZC3HAV1L zinc finger CCCH-type containing, antiviral 1 like 2 2
MIRT464272 VCL vinculin 2 2
MIRT464895 UBALD1 UBA like domain containing 1 2 2
MIRT465556 TOB2 transducer of ERBB2, 2 2 2
MIRT466360 THBS1 thrombospondin 1 2 2
MIRT466956 STAT3 signal transducer and activator of transcription 3 2 2
MIRT467321 SPATA2 spermatogenesis associated 2 2 2
MIRT467440 SND1 staphylococcal nuclease and tudor domain containing 1 2 2
MIRT467823 SLC29A2 solute carrier family 29 member 2 2 2
MIRT471173 PHB2 prohibitin 2 2 2
MIRT471397 PDPR pyruvate dehydrogenase phosphatase regulatory subunit 2 2
MIRT471754 OGT O-linked N-acetylglucosamine (GlcNAc) transferase 2 2
MIRT471846 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 2
MIRT472020 NPTXR neuronal pentraxin receptor 2 2
MIRT472224 NGFR nerve growth factor receptor 2 2
MIRT472439 NBL1 neuroblastoma 1, DAN family BMP antagonist 2 2
MIRT472541 NACC1 nucleus accumbens associated 1 2 2
MIRT473195 MINOS1-NBL1 MINOS1-NBL1 readthrough 2 2
MIRT473211 MINK1 misshapen like kinase 1 2 2
MIRT473668 MARCKSL1 MARCKS like 1 2 2
MIRT474852 KHSRP KH-type splicing regulatory protein 2 2
MIRT474939 KCTD15 potassium channel tetramerization domain containing 15 2 2
MIRT477330 EPHA2 EPH receptor A2 2 2
MIRT477395 ENTPD7 ectonucleoside triphosphate diphosphohydrolase 7 2 2
MIRT477466 ELMSAN1 ELM2 and Myb/SANT domain containing 1 2 2
MIRT477974 DPM2 dolichyl-phosphate mannosyltransferase subunit 2, regulatory 2 2
MIRT478331 DDN dendrin 2 2
MIRT479481 CDK2 cyclin dependent kinase 2 2 2
MIRT481212 ATXN7L3B ataxin 7 like 3B 2 2
MIRT481263 ATXN7L3 ataxin 7 like 3 2 2
MIRT481409 ASXL1 additional sex combs like 1, transcriptional regulator 2 2
MIRT482051 AMD1 adenosylmethionine decarboxylase 1 2 2
MIRT482396 AEN apoptosis enhancing nuclease 2 2
MIRT483160 PCSK2 proprotein convertase subtilisin/kexin type 2 2 7
MIRT483370 CYP4A22 cytochrome P450 family 4 subfamily A member 22 2 2
MIRT483520 QRSL1 glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1 2 4
MIRT484059 CYP4A11 cytochrome P450 family 4 subfamily A member 11 2 2
MIRT487075 CLASP1 cytoplasmic linker associated protein 1 2 4
MIRT487421 CACNB1 calcium voltage-gated channel auxiliary subunit beta 1 2 2
MIRT488359 PAX2 paired box 2 2 2
MIRT488592 ST7L suppression of tumorigenicity 7 like 2 2
MIRT489556 SOX11 SRY-box 11 2 4
MIRT489804 KRT80 keratin 80 2 4
MIRT489865 ATP2A3 ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3 2 2
MIRT490014 KIFC2 kinesin family member C2 2 2
MIRT490036 PCSK4 proprotein convertase subtilisin/kexin type 4 2 2
MIRT491070 ACVR1B activin A receptor type 1B 2 2
MIRT494016 DUSP9 dual specificity phosphatase 9 2 2
MIRT494816 AKAP11 A-kinase anchoring protein 11 2 2
MIRT495991 LTBP2 latent transforming growth factor beta binding protein 2 2 2
MIRT496272 SLC2A13 solute carrier family 2 member 13 2 2
MIRT500454 ZFP36L1 ZFP36 ring finger protein like 1 2 2
MIRT507989 BCL2L13 BCL2 like 13 2 4
MIRT509713 ANKRD23 ankyrin repeat domain 23 2 2
MIRT527984 TSLP thymic stromal lymphopoietin 2 2
MIRT530448 SULT1B1 sulfotransferase family 1B member 1 2 2
MIRT531235 FANCC Fanconi anemia complementation group C 2 2
MIRT534590 RPL28 ribosomal protein L28 2 2
MIRT535990 MED28 mediator complex subunit 28 2 4
MIRT537280 GABRA5 gamma-aminobutyric acid type A receptor alpha5 subunit 2 2
MIRT539924 DUSP28 dual specificity phosphatase 28 2 2
MIRT554711 RNF146 ring finger protein 146 2 2
MIRT558962 CAMSAP2 calmodulin regulated spectrin associated protein family member 2 2 2
MIRT568497 ARHGDIA Rho GDP dissociation inhibitor alpha 2 2
MIRT568875 LY6H lymphocyte antigen 6 family member H 2 2
MIRT568987 CACNA1C calcium voltage-gated channel subunit alpha1 C 2 2
MIRT569990 TMEM184A transmembrane protein 184A 2 2
MIRT570485 THRA thyroid hormone receptor, alpha 2 2
MIRT572826 MYO1C myosin IC 2 2
MIRT608199 ERBB2 erb-b2 receptor tyrosine kinase 2 2 2
MIRT613220 CCDC85C coiled-coil domain containing 85C 2 4
MIRT629782 PTDSS2 phosphatidylserine synthase 2 2 2
MIRT635332 RASSF4 Ras association domain family member 4 2 2
MIRT653632 SLC30A3 solute carrier family 30 member 3 2 2
MIRT664572 GUF1 GUF1 homolog, GTPase 2 2
MIRT667855 IPCEF1 interaction protein for cytohesin exchange factors 1 2 2
MIRT668820 CYLD CYLD lysine 63 deubiquitinase 2 2
MIRT671274 ETFDH electron transfer flavoprotein dehydrogenase 2 2
MIRT681448 CIITA class II major histocompatibility complex transactivator 2 2
MIRT684817 BRIX1 BRX1, biogenesis of ribosomes 2 2
MIRT685861 ANGEL1 angel homolog 1 2 2
MIRT688812 CAPZB capping actin protein of muscle Z-line beta subunit 2 2
MIRT691198 NIF3L1 NGG1 interacting factor 3 like 1 2 2
MIRT696947 CERK ceramide kinase 2 2
MIRT699741 SERBP1 SERPINE1 mRNA binding protein 1 2 2
MIRT701259 NUP35 nucleoporin 35 2 2
MIRT701935 MLLT1 MLLT1, super elongation complex subunit 2 2
MIRT703332 GDPD5 glycerophosphodiester phosphodiesterase domain containing 5 2 2
MIRT705519 ARL6IP1 ADP ribosylation factor like GTPase 6 interacting protein 1 2 2
MIRT706065 PKD1 polycystin 1, transient receptor potential channel interacting 2 2
MIRT713238 SV2B synaptic vesicle glycoprotein 2B 2 2
MIRT714670 CHRNE cholinergic receptor nicotinic epsilon subunit 2 2
MIRT715001 TSPAN11 tetraspanin 11 2 2
MIRT715356 VCAM1 vascular cell adhesion molecule 1 2 2
MIRT715971 FADS3 fatty acid desaturase 3 2 2
MIRT719585 FNBP4 formin binding protein 4 2 2
MIRT719667 DMRT2 doublesex and mab-3 related transcription factor 2 2 2
MIRT723360 ASCL2 achaete-scute family bHLH transcription factor 2 2 2
MIRT734985 GADD45A growth arrest and DNA damage inducible alpha 2 0
MIRT735022 MMP19 matrix metallopeptidase 19 3 0
MIRT737359 SATB2 SATB homeobox 2 3 0
MIRT756223 MCM3 minichromosome maintenance complex component 3 3 1
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-4 Dexamethasone approved 5743 Microarray primary rat thymocytes 20847043 2010 up-regulated
miR-4270 Ginsenoside Rh2 NULL 119307 Microarray NSCLC cell line A549 23152132 2013 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4270 Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-miR-4270 Fulvestrant 17756771 NSC719276 approved sensitive High Breast Cancer cell line (MCF-7)
hsa-miR-4270 Cisplatin 5460033 NSC119875 approved resistant High Hypopharyngeal Cancer cell line (FaDu)
hsa-mir-4270 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-miR-4270 Cisplatin 5460033 NSC119875 approved resistant cell line (CAL-27) (cytosolic RNA)
hsa-miR-4270 Cisplatin 5460033 NSC119875 approved sensitive cell line (CAL-27) (total RNA)
hsa-miR-4270 Cisplatin 5460033 NSC119875 approved resistant cell line (CP20)
hsa-miR-4270 Cisplatin 5460033 NSC119875 approved resistant cell line (CIS)
hsa-miR-4270 Osimertinib 71496458 NSC779217 approved resistant cell line (H1975)
hsa-miR-4270 Gemcitabine 60750 NSC613327 approved resistant cell line (MDA-231)
hsa-miR-4270 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4270 Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM16)
hsa-miR-4270 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-4270 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (100 ng/ml)
hsa-miR-4270 Gemcitabine 60750 NSC613327 approved resistant cell line (Panc1-GR4)

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