miRTarBase - #MIRT036277


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pre-miRNA Information
pre-miRNA hsa-mir-1229   
Genomic Coordinates chr5: 179798278 - 179798346
Synonyms MIRN1229, hsa-mir-1229, MIR1229
Description Homo sapiens miR-1229 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-1229-3p
Sequence 47| CUCUCACCACUGCCCUCCCACAG |69
Evidence Experimental
Experiments Cloned
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN20086841 1 COSMIC
COSN16303113 8 COSMIC
COSM6273761 14 COSMIC
COSM1066702 23 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs754734738 1 dbSNP
rs1479021409 8 dbSNP
rs200647784 9 dbSNP
rs1429872559 12 dbSNP
rs1373546432 13 dbSNP
rs766644214 15 dbSNP
rs758465824 18 dbSNP
rs1396376879 22 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol PTPRF   
Synonyms BNAH2, LAR
Description protein tyrosine phosphatase, receptor type F
Transcript NM_002840   
Other Transcripts NM_130440   
Expression
Putative miRNA Targets on PTPRF
3'UTR of PTPRF
(miRNA target sites are highlighted)		 
>PTPRF|NM_002840|3'UTR
   1 CTACCGCTCCCCTCTCCTCCGCCACCCCCGCCGTGGGGCTCCGGAGGGGACCCAGCTCCTCTGAGCCATACCGACCATCG
  81 TCCAGCCCTCCTACGCAGATGCTGTCACTGGCAGAGCACAGCCCACGGGGATCACAGCGTTTCAGGAACGTTGCCACACC
 161 AATCAGAGAGCCTAGAACATCCCTGGGCAAGTGGATGGCCCAGCAGGCAGGCACTGTGGCCCTTCTGTCCACCAGACCCA
 241 CCTGGAGCCCGCTTCAAGCTCTCTGTTGCGCTCCCGCATTTCTCATGCTTCTTCTCATGGGGTGGGGTTGGGGCAAAGCC
 321 TCCTTTTTAATACATTAAGTGGGGTAGACTGAGGGATTTTAGCCTCTTCCCTCTGATTTTTCCTTTCGCGAATCCGTATC
 401 TGCAGAATGGGCCACTGTAGGGGTTGGGGTTTATTTTGTTTTGTTTTTTTTTTTCTTGAGTTCACTTTGGATCCTTATTT
 481 TGTATGACTTCTGCTGAAGGACAGAACATTGCCTTCCTCGTGCAGAGCTGGGGCTGCCAGCCTGAGCGGAGGCTCGGCCG
 561 TGGGCCGGGAGGCAGTGCTGATCCGGCTGCTCCTCCAGCCCTTCAGACGAGATCCTGTTTCAGCTAAATGCAGGGAAACT
 641 CAATGTTTTTTTAAGTTTTGTTTTCCCTTTAAAGCCTTTTTTTAGGCCACATTGACAGTGGTGGGCGGGGAGAAGATAGG
 721 GAACACTCATCCCTGGTCGTCTATCCCAGTGTGTGTTTAACATTCACAGCCCAGAACCACAGATGTGTCTGGGAGAGCCT
 801 GGCAAGGCATTCCTCATCACCATCGTGTTTGCAAAGGTTAAAACAAAAACAAAAAACCACAAAAATAAAAAACAAAAAAA
 881 ACAAAAAACCCAAGAAAAAAAAAAAGAGTCAGCCCTTGGCTTCTGCTTCAAACCCTCAAGAGGGGAAGCAACTCCGTGTG
 961 CCTGGGGTTCCCGAGGGAGCTGCTGGCTGACCTGGGCCCACAGAGCCTGGCTTTGGTCCCCAGCATTGCAGTATGGTGTG
1041 GTGTTTGTAGGCTGTGGGGTCTGGCTGTGTGGCCAAGGTGAATAGCACAGGTTAGGGTGTGTGCCACACCCCATGCACCT
1121 CAGGGCCAAGCGGGGGCGTGGCTGGCCTTTCAGGTCCAGGCCAGTGGGCCTGGTAGCACATGTCTGTCCTCAGAGCAGGG
1201 GCCAGATGATTTTCCTCCCTGGTTTGCAGCTGTTTTCAAAGCCCCCGATAATCGCTCTTTTCCACTCCAAGATGCCCTCA
1281 TAAACCAATGTGGCAAGACTACTGGACTTCTATCAATGGTACTCTAATCAGTCCTTATTATCCCAGCTTGCTGAGGGGCA
1361 GGGAGAGCGCCTCTTCCTCTGGGCAGCGCTATCTAGATAGGTAAGTGGGGGCGGGGAAGGGTGCATAGCTGTTTTAGCTG
1441 AGGGACGTGGTGCCGACGTCCCCAAACCTAGCTAGGCTAAGTCAAGATCAACATTCCAGGGTTGGTAATGTTGGATGATG
1521 AAACATTCATTTTTACCTTGTGGATGCTAGTGCTGTAGAGTTCACTGTTGTACACAGTCTGTTTTCTATTTGTTAAGAAA
1601 AACTACAGCATCATTGCATAATTCTTGATGGTAATAAATTTGAATAATCAGATTTCTTACAAACCAGGAAAAAAAAAAAA
1681 AAAAAA
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' gacacccucCCGUCACCACUCuc 5'
                   | ||||||||:|  
Target 5' ggccacattGACAGTGGTGGGcg 3'
 685 - 707 126.00 -17.80
2 
miRNA  3' gacACCCUCCCGUCACCACUcuc 5'
             || | || ||  |||||   
Target 5' ggcTGTGTGGCCA-AGGTGAata 3'
 1063 - 1084 115.00 -14.12
3 
miRNA  3' gacACCCUCCCGUCACCACUCuc 5'
             || | |||||| || |||  
Target 5' tgcTGAG-GGGCAG-GGAGAGcg 3'
 1349 - 1369 114.00 -20.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30191026 4 COSMIC
COSN31493735 6 COSMIC
COSN31540972 6 COSMIC
COSN13546301 7 COSMIC
COSN30475936 17 COSMIC
COSN30104293 19 COSMIC
COSN30522118 20 COSMIC
COSN30100843 21 COSMIC
COSN30482587 28 COSMIC
COSN26991033 30 COSMIC
COSN31503622 33 COSMIC
COSN24297451 34 COSMIC
COSN31502564 37 COSMIC
COSN30193374 44 COSMIC
COSN16130872 45 COSMIC
COSN30150132 45 COSMIC
COSN13546303 59 COSMIC
COSN30502193 70 COSMIC
COSN30187324 73 COSMIC
COSN26635738 74 COSMIC
COSN30131488 80 COSMIC
COSN30495403 80 COSMIC
COSN31601381 95 COSMIC
COSN30161023 96 COSMIC
COSN26440585 162 COSMIC
COSN25575671 179 COSMIC
COSN4603780 307 COSMIC
COSN18777721 455 COSMIC
COSN25304224 498 COSMIC
COSN8470448 576 COSMIC
COSN26649852 687 COSMIC
COSN28808451 824 COSMIC
COSN19655896 851 COSMIC
COSN25554550 857 COSMIC
COSN8470449 871 COSMIC
COSN31487994 906 COSMIC
COSN16128175 1116 COSMIC
COSN16131707 1152 COSMIC
COSN31542479 1340 COSMIC
COSN31564540 1413 COSMIC
COSN31545846 1441 COSMIC
COSN26505494 1447 COSMIC
COSN16626360 1579 COSMIC
COSN31515421 1645 COSMIC
COSN16129668 1650 COSMIC
rs72673097 252 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1256293636 3 dbSNP
rs755004036 4 dbSNP
rs1380633934 5 dbSNP
rs369551279 6 dbSNP
rs769423424 7 dbSNP
rs777303787 11 dbSNP
rs1237972970 12 dbSNP
rs748783332 13 dbSNP
rs775283573 14 dbSNP
rs373276106 15 dbSNP
rs1203940214 16 dbSNP
rs770382639 19 dbSNP
rs773894461 20 dbSNP
rs375151591 21 dbSNP
rs369952718 22 dbSNP
rs762085668 23 dbSNP
rs1467751161 25 dbSNP
rs765438541 25 dbSNP
rs373367448 30 dbSNP
rs377036580 31 dbSNP
rs751737122 33 dbSNP
rs754963221 34 dbSNP
rs973446485 40 dbSNP
rs368899845 43 dbSNP
rs929393703 44 dbSNP
rs752479708 46 dbSNP
rs1016479224 48 dbSNP
rs570547207 69 dbSNP
rs539468719 72 dbSNP
rs570743034 74 dbSNP
rs890961261 80 dbSNP
rs993667231 81 dbSNP
rs1210637730 82 dbSNP
rs772512205 84 dbSNP
rs1312177140 86 dbSNP
rs573467565 95 dbSNP
rs1335296174 96 dbSNP
rs749660576 98 dbSNP
rs899751880 117 dbSNP
rs536099288 118 dbSNP
rs954871692 125 dbSNP
rs1011636694 127 dbSNP
rs377470816 128 dbSNP
rs1021305345 131 dbSNP
rs773672788 139 dbSNP
rs757603415 140 dbSNP
rs1245977908 144 dbSNP
rs539467425 150 dbSNP
rs555727386 151 dbSNP
rs575781647 160 dbSNP
rs765005753 161 dbSNP
rs1256443433 162 dbSNP
rs544355533 163 dbSNP
rs1488842439 165 dbSNP
rs1286759350 166 dbSNP
rs564146178 167 dbSNP
rs1350630765 169 dbSNP
rs1266482496 170 dbSNP
rs991618545 175 dbSNP
rs1247104935 182 dbSNP
rs989487407 183 dbSNP
rs1023148068 184 dbSNP
rs913858411 188 dbSNP
rs1342553172 192 dbSNP
rs1315996282 211 dbSNP
rs1399827831 215 dbSNP
rs115324559 216 dbSNP
rs1164912012 219 dbSNP
rs974091953 228 dbSNP
rs919246218 231 dbSNP
rs950815987 233 dbSNP
rs1478613119 234 dbSNP
rs1239967247 242 dbSNP
rs1191496047 243 dbSNP
rs981971925 244 dbSNP
rs1249418061 248 dbSNP
rs1216093340 250 dbSNP
rs72673097 252 dbSNP
rs1182924276 253 dbSNP
rs371811751 256 dbSNP
rs1272649990 260 dbSNP
rs1383102237 262 dbSNP
rs1406910077 264 dbSNP
rs1165269674 266 dbSNP
rs1268577519 269 dbSNP
rs1344807978 270 dbSNP
rs911988594 271 dbSNP
rs560151700 276 dbSNP
rs943813889 277 dbSNP
rs1393582579 279 dbSNP
rs1039577702 285 dbSNP
rs1331480689 288 dbSNP
rs1055286072 290 dbSNP
rs1452478322 291 dbSNP
rs1166949604 297 dbSNP
rs921153062 302 dbSNP
rs55647429 303 dbSNP
rs941058331 317 dbSNP
rs150847540 322 dbSNP
rs1252844297 328 dbSNP
rs898110070 334 dbSNP
rs902848024 339 dbSNP
rs1229222107 340 dbSNP
rs562583701 341 dbSNP
rs1051941337 342 dbSNP
rs1056766164 343 dbSNP
rs895586096 347 dbSNP
rs1305388993 350 dbSNP
rs1315960926 352 dbSNP
rs369506012 353 dbSNP
rs114773270 354 dbSNP
rs1023119714 364 dbSNP
rs1352256477 367 dbSNP
rs1380540984 374 dbSNP
rs963903484 375 dbSNP
rs1414705472 387 dbSNP
rs995097672 388 dbSNP
rs1027017015 389 dbSNP
rs368342124 390 dbSNP
rs1010933949 391 dbSNP
rs1471220861 394 dbSNP
rs987473205 396 dbSNP
rs1182223779 397 dbSNP
rs6696481 401 dbSNP
rs539505691 406 dbSNP
rs139903281 409 dbSNP
rs566855750 413 dbSNP
rs535810053 417 dbSNP
rs1389416053 425 dbSNP
rs959475561 427 dbSNP
rs1334847442 430 dbSNP
rs990661793 442 dbSNP
rs1274529553 444 dbSNP
rs867714450 444 dbSNP
rs909664647 444 dbSNP
rs1310681702 445 dbSNP
rs868206752 447 dbSNP
rs376571493 449 dbSNP
rs1159832202 455 dbSNP
rs1449490195 458 dbSNP
rs575774447 459 dbSNP
rs538461167 471 dbSNP
rs558351526 489 dbSNP
rs1473135376 491 dbSNP
rs1259947873 493 dbSNP
rs921091187 501 dbSNP
rs750301676 520 dbSNP
rs756279907 521 dbSNP
rs1042942752 531 dbSNP
rs924523393 538 dbSNP
rs1283399650 543 dbSNP
rs1051972866 548 dbSNP
rs577824810 549 dbSNP
rs1008180077 556 dbSNP
rs1039183611 561 dbSNP
rs1340690769 563 dbSNP
rs1444064891 567 dbSNP
rs367863653 568 dbSNP
rs1056737655 579 dbSNP
rs1159005392 581 dbSNP
rs1406093385 585 dbSNP
rs780268019 586 dbSNP
rs1481964541 589 dbSNP
rs1163112648 593 dbSNP
rs1184123749 598 dbSNP
rs1475016251 607 dbSNP
rs754015175 609 dbSNP
rs1480263813 610 dbSNP
rs1044577370 616 dbSNP
rs1174358210 633 dbSNP
rs1427359827 636 dbSNP
rs1222174072 637 dbSNP
rs1336366121 641 dbSNP
rs1415485908 643 dbSNP
rs899323522 644 dbSNP
rs1353077744 650 dbSNP
rs995422537 655 dbSNP
rs1412033333 668 dbSNP
rs1026528622 677 dbSNP
rs1232112373 683 dbSNP
rs1350718047 688 dbSNP
rs755073476 690 dbSNP
rs1222596396 691 dbSNP
rs1318169310 692 dbSNP
rs1297206359 693 dbSNP
rs555395725 702 dbSNP
rs1003514222 706 dbSNP
rs190180934 707 dbSNP
rs748639663 708 dbSNP
rs1340026101 710 dbSNP
rs1460932811 715 dbSNP
rs1207014090 717 dbSNP
rs1373911207 718 dbSNP
rs959318449 721 dbSNP
rs1426558671 734 dbSNP
rs1418498407 736 dbSNP
rs1191499841 737 dbSNP
rs1252348915 738 dbSNP
rs1469788881 739 dbSNP
rs1250992405 740 dbSNP
rs974823813 744 dbSNP
rs1022837964 748 dbSNP
rs181616057 752 dbSNP
rs573572526 754 dbSNP
rs1306174417 767 dbSNP
rs747017196 770 dbSNP
rs968539485 772 dbSNP
rs979019140 773 dbSNP
rs1167450468 782 dbSNP
rs924521913 802 dbSNP
rs1235430791 821 dbSNP
rs1373844184 823 dbSNP
rs1301861648 825 dbSNP
rs934564551 826 dbSNP
rs1397261085 828 dbSNP
rs1300163680 838 dbSNP
rs1174039924 840 dbSNP
rs1388834214 840 dbSNP
rs1460675433 840 dbSNP
rs1192931591 845 dbSNP
rs1455378479 845 dbSNP
rs909729201 845 dbSNP
rs1432234372 846 dbSNP
rs1439816265 851 dbSNP
rs1252023288 858 dbSNP
rs962493628 861 dbSNP
rs1256163184 863 dbSNP
rs1130522 867 dbSNP
rs972457269 867 dbSNP
rs918299520 869 dbSNP
rs1234169272 870 dbSNP
rs1365350132 870 dbSNP
rs1336818223 871 dbSNP
rs1403895166 873 dbSNP
rs1313705349 874 dbSNP
rs1389675341 874 dbSNP
rs1436429730 874 dbSNP
rs933691590 874 dbSNP
rs1172989176 883 dbSNP
rs1373364410 883 dbSNP
rs1454269068 883 dbSNP
rs1365427413 887 dbSNP
rs1179053923 889 dbSNP
rs772742914 889 dbSNP
rs916911584 890 dbSNP
rs1486885342 894 dbSNP
rs201298308 894 dbSNP
rs1130523 895 dbSNP
rs879143289 895 dbSNP
rs879224963 895 dbSNP
rs912154098 895 dbSNP
rs145370622 896 dbSNP
rs1269134832 897 dbSNP
rs552049495 900 dbSNP
rs574957781 901 dbSNP
rs1294181157 903 dbSNP
rs1339963179 904 dbSNP
rs1039666862 905 dbSNP
rs1491332008 906 dbSNP
rs1230521070 907 dbSNP
rs756801665 907 dbSNP
rs1275011619 909 dbSNP
rs1358492931 910 dbSNP
rs946828468 921 dbSNP
rs1292251878 922 dbSNP
rs1042503740 924 dbSNP
rs1166402876 926 dbSNP
rs902595446 928 dbSNP
rs1256282727 932 dbSNP
rs1187296379 945 dbSNP
rs147659161 953 dbSNP
rs1452460366 956 dbSNP
rs1044118385 957 dbSNP
rs531475270 965 dbSNP
rs1235171432 971 dbSNP
rs1332969411 973 dbSNP
rs1035011584 974 dbSNP
rs1227969954 982 dbSNP
rs184834399 987 dbSNP
rs1048375566 989 dbSNP
rs1316193230 999 dbSNP
rs886637517 1008 dbSNP
rs570439684 1011 dbSNP
rs1384951802 1014 dbSNP
rs1416795452 1016 dbSNP
rs1168134296 1023 dbSNP
rs1475971446 1024 dbSNP
rs1019248904 1025 dbSNP
rs533296997 1026 dbSNP
rs1449426354 1034 dbSNP
rs1254104492 1037 dbSNP
rs996580855 1047 dbSNP
rs1022352595 1048 dbSNP
rs955106357 1060 dbSNP
rs1196580972 1064 dbSNP
rs1341676734 1066 dbSNP
rs986900163 1078 dbSNP
rs968549500 1088 dbSNP
rs978228889 1096 dbSNP
rs1371655689 1105 dbSNP
rs1305518758 1106 dbSNP
rs910901437 1107 dbSNP
rs942339134 1112 dbSNP
rs1329190750 1114 dbSNP
rs1411327865 1122 dbSNP
rs1319219646 1130 dbSNP
rs1166522124 1132 dbSNP
rs747462734 1132 dbSNP
rs540396539 1133 dbSNP
rs1031446213 1138 dbSNP
rs975026107 1139 dbSNP
rs915462374 1141 dbSNP
rs1182569447 1148 dbSNP
rs1437127404 1150 dbSNP
rs946903908 1156 dbSNP
rs1204246700 1158 dbSNP
rs1348322147 1164 dbSNP
rs1042578276 1165 dbSNP
rs1231969124 1168 dbSNP
rs1242312596 1169 dbSNP
rs1366764248 1174 dbSNP
rs1241264465 1179 dbSNP
rs955911907 1184 dbSNP
rs768586733 1206 dbSNP
rs1443657997 1213 dbSNP
rs1285797824 1214 dbSNP
rs902624796 1237 dbSNP
rs939405213 1242 dbSNP
rs1429556379 1243 dbSNP
rs1376418788 1247 dbSNP
rs537432031 1248 dbSNP
rs560451224 1251 dbSNP
rs1424997038 1252 dbSNP
rs1159228937 1254 dbSNP
rs775140763 1255 dbSNP
rs189730110 1257 dbSNP
rs1243041034 1269 dbSNP
rs566784404 1273 dbSNP
rs1422640136 1280 dbSNP
rs980195011 1281 dbSNP
rs1190042531 1287 dbSNP
rs535816870 1289 dbSNP
rs1284796799 1296 dbSNP
rs920329185 1302 dbSNP
rs549077723 1307 dbSNP
rs898415843 1309 dbSNP
rs993984319 1311 dbSNP
rs1415040960 1313 dbSNP
rs930376870 1317 dbSNP
rs1025418488 1319 dbSNP
rs1047499592 1326 dbSNP
rs1472887427 1329 dbSNP
rs955178920 1332 dbSNP
rs762617225 1334 dbSNP
rs944892808 1344 dbSNP
rs1473096018 1355 dbSNP
rs1405860425 1357 dbSNP
rs139767865 1358 dbSNP
rs986587237 1363 dbSNP
rs1320700084 1369 dbSNP
rs556138842 1370 dbSNP
rs900771133 1380 dbSNP
rs1394288697 1383 dbSNP
rs996161637 1386 dbSNP
rs1022703553 1388 dbSNP
rs903875751 1389 dbSNP
rs1266974682 1391 dbSNP
rs1238544108 1400 dbSNP
rs1291038850 1401 dbSNP
rs1227027159 1407 dbSNP
rs1000014440 1408 dbSNP
rs1378857763 1413 dbSNP
rs990214964 1413 dbSNP
rs1031079112 1414 dbSNP
rs1331544199 1420 dbSNP
rs538501568 1422 dbSNP
rs1461978532 1426 dbSNP
rs1229065870 1429 dbSNP
rs1163049890 1443 dbSNP
rs1423070787 1445 dbSNP
rs1262658604 1446 dbSNP
rs768132802 1447 dbSNP
rs773892267 1448 dbSNP
rs946936308 1455 dbSNP
rs558388767 1456 dbSNP
rs376077434 1458 dbSNP
rs1296785569 1459 dbSNP
rs571869696 1461 dbSNP
rs181200218 1462 dbSNP
rs1363660842 1468 dbSNP
rs1056558035 1472 dbSNP
rs1373250888 1476 dbSNP
rs553815311 1492 dbSNP
rs779452917 1498 dbSNP
rs1038314962 1499 dbSNP
rs1355266125 1520 dbSNP
rs573584395 1522 dbSNP
rs951786139 1526 dbSNP
rs1389548617 1527 dbSNP
rs983193555 1529 dbSNP
rs1455230320 1538 dbSNP
rs1250627130 1540 dbSNP
rs767502837 1541 dbSNP
rs1480759293 1551 dbSNP
rs994057787 1561 dbSNP
rs3189536 1565 dbSNP
rs1207134950 1581 dbSNP
rs1159256011 1590 dbSNP
rs1340478007 1595 dbSNP
rs542631623 1598 dbSNP
rs1235639855 1604 dbSNP
rs944829843 1607 dbSNP
rs145294623 1614 dbSNP
rs74511822 1616 dbSNP
rs1299287705 1619 dbSNP
rs922120744 1620 dbSNP
rs185205908 1625 dbSNP
rs1374406668 1630 dbSNP
rs1407804234 1632 dbSNP
rs1369689331 1633 dbSNP
rs1173976360 1639 dbSNP
rs932213811 1640 dbSNP
rs1375798842 1642 dbSNP
rs1304540801 1650 dbSNP
rs1419140651 1654 dbSNP
rs1252313381 1659 dbSNP
rs754039090 1661 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Flp-In T-REx 293-hAGO1 cells
Location of target site CDS
Original Description (Extracted from the article) ... Validation of interactions identified by CLASH suppports their reliability. ...

- Helwak A; Kudla G; Dudnakova T; Tollervey D, 2013, Cell.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' gacACC---CUCCCGUCACCACUCUc 5'
             |||   ||| |::| |||| || 
Target 5' caaTGGGCAGAGTGTGGAGGTG-GAc 3'
 		1 - 25
Article - Helwak A; Kudla G; Dudnakova T; Tollervey D
- Cell, 2013
MicroRNAs (miRNAs) play key roles in gene regulation, but reliable bioinformatic or experimental identification of their targets remains difficult. To provide an unbiased view of human miRNA targets, we developed a technique for ligation and sequencing of miRNA-target RNA duplexes associated with human AGO1. Here, we report data sets of more than 18,000 high-confidence miRNA-mRNA interactions. The binding of most miRNAs includes the 5' seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. Moreover, seed interactions are generally accompanied by specific, nonseed base pairing. 18% of miRNA-mRNA interactions involve the miRNA 3' end, with little evidence for 5' contacts, and some of these were functionally validated. Analyses of miRNA:mRNA base pairing showed that miRNA species systematically differ in their target RNA interactions, and strongly overrepresented motifs were found in the interaction sites of several miRNAs. We speculate that these affect the response of RISC to miRNA-target binding.
LinkOut: [PMID: 23622248]
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
GSE42095 Differentiated embryonic stem cells 0.621 7.8e-4 0.697 1.1e-4 23 Click to see details
GSE38974 Chronic obstructive pulmonary disease 0.353 4.2e-2 0.333 5.2e-2 25 Click to see details
GSE19783 ER+ ER+ breast cancer -0.299 1.0e-1 -0.128 3.0e-1 20 Click to see details
GSE19536 Breast cancer -0.122 1.1e-1 -0.119 1.2e-1 100 Click to see details
GSE21032 Prostate cancer 0.133 1.2e-1 0.144 9.7e-2 83 Click to see details
GSE19350 CNS germ cell tumors 0.311 1.6e-1 0.281 1.9e-1 12 Click to see details
GSE28544 Breast cancer -0.202 1.7e-1 -0.032 4.4e-1 24 Click to see details
GSE21687 Ependynoma primary tumors -0.115 1.8e-1 -0.157 1.1e-1 64 Click to see details
GSE28260 Renal cortex and medulla 0.257 2.0e-1 0.242 2.1e-1 13 Click to see details
GSE32688 Pancreatic cancer 0.115 2.7e-1 -0.068 3.6e-1 32 Click to see details
GSE35602 Colorectal cancer stromal tissue -0.127 2.7e-1 -0.136 2.6e-1 25 Click to see details
GSE38226 Liver fibrosis -0.137 2.8e-1 -0.369 5.0e-2 21 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis -0.134 2.9e-1 -0.056 4.1e-1 20 Click to see details
GSE14794 Lymphoblastoid cells -0.054 3.1e-1 -0.021 4.2e-1 90 Click to see details
GSE26953 Aortic valvular endothelial cells 0.055 4.0e-1 0.081 3.5e-1 24 Click to see details
GSE17498 Multiple myeloma 0.037 4.1e-1 0.063 3.5e-1 40 Click to see details
GSE15076 Monocyte-derived dendritic cells 0.041 4.6e-1 0.200 3.0e-1 9 Click to see details
GSE19783 ER- ER- breast cancer -0.002 4.9e-1 -0.015 4.5e-1 79 Click to see details
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
STAD 0.556 0.01 0.644 0 16 Click to see details
PRAD 0.896 0.02 0.900 0.02 5 Click to see details
PAAD -0.846 0.08 -0.800 0.1 4 Click to see details
COAD -0.731 0.13 -0.800 0.1 4 Click to see details
CHOL -0.65 0.18 -0.400 0.3 4 Click to see details
THCA -0.13 0.23 -0.106 0.28 34 Click to see details
KICH -0.17 0.29 -0.247 0.21 13 Click to see details
UCEC -0.176 0.33 -0.083 0.42 9 Click to see details
KIRP 0.093 0.33 0.059 0.39 24 Click to see details
KIRC -0.057 0.35 -0.123 0.19 51 Click to see details
LIHC 0.07 0.36 0.121 0.26 30 Click to see details
BRCA -0.047 0.38 0.000 0.5 42 Click to see details
HNSC -0.103 0.39 -0.018 0.48 10 Click to see details
LUAD 0.212 0.39 0.400 0.3 4 Click to see details
BLCA -0.085 0.44 0.200 0.35 6 Click to see details
LUSC -0.029 0.45 -0.035 0.44 21 Click to see details
LUSC -0.029 0.45 -0.035 0.44 21 Click to see details
LUSC -0.029 0.45 -0.035 0.44 21 Click to see details
LUSC -0.029 0.45 -0.035 0.44 21 Click to see details
LUSC -0.029 0.45 -0.035 0.44 21 Click to see details
LUSC -0.029 0.45 -0.035 0.44 21 Click to see details
196 hsa-miR-1229-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT036258 VWA8 von Willebrand factor A domain containing 8 1 1
MIRT036259 SORBS3 sorbin and SH3 domain containing 3 1 1
MIRT036260 HIST1H3A histone cluster 1 H3 family member a 1 1
MIRT036261 TIA1 TIA1 cytotoxic granule associated RNA binding protein 1 1
MIRT036262 COIL coilin 1 1
MIRT036263 PBRM1 polybromo 1 1 1
MIRT036264 KRT28 keratin 28 1 1
MIRT036265 RPL7A ribosomal protein L7a 1 1
MIRT036266 EEF2 eukaryotic translation elongation factor 2 1 1
MIRT036267 CEP152 centrosomal protein 152 1 1
MIRT036268 CPT1B carnitine palmitoyltransferase 1B 1 1
MIRT036269 CEP55 centrosomal protein 55 1 1
MIRT036270 ZMYM2 zinc finger MYM-type containing 2 1 1
MIRT036271 CRISP3 cysteine rich secretory protein 3 1 1
MIRT036272 CDKN1A cyclin dependent kinase inhibitor 1A 1 1
MIRT036273 ADPRHL2 ADP-ribosylhydrolase like 2 1 1
MIRT036274 PHRF1 PHD and ring finger domains 1 1 1
MIRT036275 RPL3 ribosomal protein L3 1 1
MIRT036276 CSDE1 cold shock domain containing E1 1 1
MIRT036277 PTPRF protein tyrosine phosphatase, receptor type F 1 1
MIRT036278 ZNF264 zinc finger protein 264 1 1
MIRT036279 AHCYL1 adenosylhomocysteinase like 1 1 1
MIRT036280 GAPDH glyceraldehyde-3-phosphate dehydrogenase 1 1
MIRT036281 INTS10 integrator complex subunit 10 1 1
MIRT036282 TARDBP TAR DNA binding protein 1 1
MIRT036283 CTNND1 catenin delta 1 1 1
MIRT036284 KCTD15 potassium channel tetramerization domain containing 15 1 1
MIRT036285 CEP350 centrosomal protein 350 1 1
MIRT036286 C19orf10 myeloid derived growth factor 1 1
MIRT036287 TNRC6B trinucleotide repeat containing 6B 1 1
MIRT036288 CHCHD2 coiled-coil-helix-coiled-coil-helix domain containing 2 1 1
MIRT036289 POLR2D RNA polymerase II subunit D 1 1
MIRT036290 PHC1 polyhomeotic homolog 1 1 1
MIRT036291 HNRNPD heterogeneous nuclear ribonucleoprotein D 1 1
MIRT036292 OPA3 OPA3, outer mitochondrial membrane lipid metabolism regulator 1 1
MIRT036293 AIF1L allograft inflammatory factor 1 like 1 1
MIRT036294 NEU3 neuraminidase 3 1 1
MIRT036295 DCTD dCMP deaminase 1 1
MIRT036296 TUBA1B tubulin alpha 1b 1 1
MIRT036297 HADHB hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit 1 1
MIRT036298 ACOT7 acyl-CoA thioesterase 7 1 1
MIRT036299 MDK midkine 1 1
MIRT036300 INO80D INO80 complex subunit D 1 1
MIRT036301 LDOC1L retrotransposon Gag like 6 1 1
MIRT036302 C2orf44 WD repeat and coiled coil containing 1 1
MIRT036303 SRCAP Snf2 related CREBBP activator protein 1 1
MIRT036304 EPB41L2 erythrocyte membrane protein band 4.1 like 2 1 1
MIRT036305 REXO2 RNA exonuclease 2 1 1
MIRT036306 CTNNBL1 catenin beta like 1 1 1
MIRT036307 SAFB scaffold attachment factor B 1 1
MIRT036308 PPP6R1 protein phosphatase 6 regulatory subunit 1 1 1
MIRT036309 FEN1 flap structure-specific endonuclease 1 1 1
MIRT036310 LRBA LPS responsive beige-like anchor protein 1 1
MIRT036311 SCAMP5 secretory carrier membrane protein 5 1 1
MIRT036312 DAG1 dystroglycan 1 1 1
MIRT036313 HYPK huntingtin interacting protein K 1 1
MIRT036314 HIST1H4C histone cluster 1 H4 family member c 1 1
MIRT036315 CDC42EP4 CDC42 effector protein 4 1 1
MIRT036316 ERC1 ELKS/RAB6-interacting/CAST family member 1 1 1
MIRT036317 GTF2I general transcription factor IIi 1 1
MIRT036318 RPGRIP1L RPGRIP1 like 1 1
MIRT036319 ATP5A1 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle 1 1
MIRT036320 TRRAP transformation/transcription domain associated protein 1 1
MIRT036321 PHF8 PHD finger protein 8 1 1
MIRT036322 TSC22D3 TSC22 domain family member 3 1 1
MIRT036323 MPP2 membrane palmitoylated protein 2 1 1
MIRT036324 NAA50 N(alpha)-acetyltransferase 50, NatE catalytic subunit 1 1
MIRT036325 ALS2 ALS2, alsin Rho guanine nucleotide exchange factor 1 1
MIRT036326 KMT2D lysine methyltransferase 2D 1 1
MIRT036327 ITGA5 integrin subunit alpha 5 1 1
MIRT036328 ABCC5 ATP binding cassette subfamily C member 5 1 1
MIRT036329 KIF24 kinesin family member 24 1 1
MIRT036330 PPP4C protein phosphatase 4 catalytic subunit 1 1
MIRT036331 FMNL2 formin like 2 1 1
MIRT036332 NF2 neurofibromin 2 1 1
MIRT036333 NUP210 nucleoporin 210 1 1
MIRT036334 CTDNEP1 CTD nuclear envelope phosphatase 1 1 1
MIRT036335 EIF4G2 eukaryotic translation initiation factor 4 gamma 2 1 1
MIRT036336 CTCF CCCTC-binding factor 1 1
MIRT036337 LRIT1 leucine rich repeat, Ig-like and transmembrane domains 1 1 1
MIRT036338 SFPQ splicing factor proline and glutamine rich 1 1
MIRT036339 CDIPT CDP-diacylglycerol--inositol 3-phosphatidyltransferase 1 1
MIRT036340 NAPEPLD N-acyl phosphatidylethanolamine phospholipase D 1 1
MIRT036341 SLC39A7 solute carrier family 39 member 7 1 1
MIRT036342 KDM5C lysine demethylase 5C 1 1
MIRT036343 ACLY ATP citrate lyase 1 1
MIRT036344 MED19 mediator complex subunit 19 1 1
MIRT036345 SRP72 signal recognition particle 72 1 1
MIRT036346 RUVBL2 RuvB like AAA ATPase 2 1 1
MIRT036347 CLSTN3 calsyntenin 3 1 1
MIRT036348 SAE1 SUMO1 activating enzyme subunit 1 1 1
MIRT036349 TUBG1 tubulin gamma 1 1 1
MIRT036350 FOXP1 forkhead box P1 1 1
MIRT036351 ZNF687 zinc finger protein 687 1 1
MIRT036352 HNRNPUL1 heterogeneous nuclear ribonucleoprotein U like 1 1 1
MIRT036353 HNRNPA3 heterogeneous nuclear ribonucleoprotein A3 1 1
MIRT036354 RNF40 ring finger protein 40 1 1
MIRT036355 KPNB1 karyopherin subunit beta 1 1 1
MIRT036356 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 1 1
MIRT036357 DDX23 DEAD-box helicase 23 1 1
MIRT036358 BET1L Bet1 golgi vesicular membrane trafficking protein like 1 1
MIRT036359 BRD2 bromodomain containing 2 1 1
MIRT036360 EML1 echinoderm microtubule associated protein like 1 1 1
MIRT036361 BAP1 BRCA1 associated protein 1 1 1
MIRT036362 STAT5B signal transducer and activator of transcription 5B 1 1
MIRT036363 SUPT5H SPT5 homolog, DSIF elongation factor subunit 1 1
MIRT036364 GPI glucose-6-phosphate isomerase 1 1
MIRT036365 PTBP3 polypyrimidine tract binding protein 3 1 1
MIRT036366 RPS15 ribosomal protein S15 1 1
MIRT036367 ZDHHC7 zinc finger DHHC-type containing 7 1 1
MIRT036368 ARL6IP1 ADP ribosylation factor like GTPase 6 interacting protein 1 1 1
MIRT036369 SNX12 sorting nexin 12 1 1
MIRT036370 OTUD7B OTU deubiquitinase 7B 1 1
MIRT036371 AP2M1 adaptor related protein complex 2 mu 1 subunit 1 1
MIRT036372 C9orf114 SPOUT domain containing methyltransferase 1 1 1
MIRT036373 MAPKAPK2 mitogen-activated protein kinase-activated protein kinase 2 1 1
MIRT036374 FOXK1 forkhead box K1 1 1
MIRT036375 SIK2 salt inducible kinase 2 1 1
MIRT036376 SCD stearoyl-CoA desaturase 1 1
MIRT036377 PHGDH phosphoglycerate dehydrogenase 1 1
MIRT036378 PITPNB phosphatidylinositol transfer protein beta 1 1
MIRT036379 MAD2L2 mitotic arrest deficient 2 like 2 1 1
MIRT036380 TUSC3 tumor suppressor candidate 3 1 1
MIRT036381 PRKRIP1 PRKR interacting protein 1 1 1
MIRT036382 DCAF7 DDB1 and CUL4 associated factor 7 1 1
MIRT036383 NME2 NME/NM23 nucleoside diphosphate kinase 2 1 1
MIRT036384 YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta 1 1
MIRT036385 SLC16A13 solute carrier family 16 member 13 1 1
MIRT036386 PRDX4 peroxiredoxin 4 1 1
MIRT036387 NXPE3 neurexophilin and PC-esterase domain family member 3 1 1
MIRT036388 IGF2BP1 insulin like growth factor 2 mRNA binding protein 1 1 1
MIRT036389 CPNE1 copine 1 1 1
MIRT036390 PSMC5 proteasome 26S subunit, ATPase 5 1 1
MIRT036391 PAK4 p21 (RAC1) activated kinase 4 1 1
MIRT059262 CELF1 CUGBP Elav-like family member 1 2 2
MIRT061283 IPO7 importin 7 2 2
MIRT080097 IER3IP1 immediate early response 3 interacting protein 1 2 2
MIRT345981 BIRC5 baculoviral IAP repeat containing 5 2 8
MIRT366471 KLHL15 kelch like family member 15 2 2
MIRT379534 HNRNPK heterogeneous nuclear ribonucleoprotein K 2 2
MIRT443697 HUNK hormonally up-regulated Neu-associated kinase 2 4
MIRT472347 NETO2 neuropilin and tolloid like 2 2 2
MIRT497842 GATA6 GATA binding protein 6 2 4
MIRT510408 ZNF268 zinc finger protein 268 2 4
MIRT519621 ZNF781 zinc finger protein 781 2 2
MIRT519830 ZFP69B ZFP69 zinc finger protein B 2 4
MIRT530712 ORMDL3 ORMDL sphingolipid biosynthesis regulator 3 2 2
MIRT530802 GPR182 G protein-coupled receptor 182 2 2
MIRT534374 SETD7 SET domain containing lysine methyltransferase 7 2 2
MIRT535541 P2RY2 purinergic receptor P2Y2 2 2
MIRT536016 MCUR1 mitochondrial calcium uniporter regulator 1 2 2
MIRT556019 MYBL1 MYB proto-oncogene like 1 2 2
MIRT560009 ZNF525 zinc finger protein 525 2 2
MIRT560072 ZNF195 zinc finger protein 195 2 2
MIRT565948 RRAGD Ras related GTP binding D 2 2
MIRT570131 IL1RL2 interleukin 1 receptor like 2 2 2
MIRT570887 ZNF780A zinc finger protein 780A 2 4
MIRT609775 VWC2L von Willebrand factor C domain containing protein 2 like 2 4
MIRT611445 NRIP3 nuclear receptor interacting protein 3 2 2
MIRT611975 ZNF175 zinc finger protein 175 2 2
MIRT612871 IGFBP5 insulin like growth factor binding protein 5 2 4
MIRT613012 GABPB1 GA binding protein transcription factor beta subunit 1 2 4
MIRT617515 PTDSS1 phosphatidylserine synthase 1 2 2
MIRT636095 ZDHHC22 zinc finger DHHC-type containing 22 2 2
MIRT637442 ZNF324B zinc finger protein 324B 2 2
MIRT638303 SCO1 SCO1, cytochrome c oxidase assembly protein 2 2
MIRT638920 CALCOCO2 calcium binding and coiled-coil domain 2 2 2
MIRT640590 TM9SF4 transmembrane 9 superfamily member 4 2 2
MIRT646760 WDR3 WD repeat domain 3 2 2
MIRT652591 TIMM8A translocase of inner mitochondrial membrane 8A 2 2
MIRT654866 PPL periplakin 2 2
MIRT654952 PMEPA1 prostate transmembrane protein, androgen induced 1 2 2
MIRT656021 MYO5B myosin VB 2 2
MIRT657078 JMY junction mediating and regulatory protein, p53 cofactor 2 2
MIRT657880 GFPT1 glutamine--fructose-6-phosphate transaminase 1 2 2
MIRT659231 CXCR5 C-X-C motif chemokine receptor 5 2 2
MIRT662904 MED18 mediator complex subunit 18 2 2
MIRT685610 C12orf49 chromosome 12 open reading frame 49 2 2
MIRT687424 NRIP1 nuclear receptor interacting protein 1 2 2
MIRT692293 CNNM3 cyclin and CBS domain divalent metal cation transport mediator 3 2 2
MIRT693749 ZNF383 zinc finger protein 383 2 2
MIRT695121 PRY2 PTPN13-like, Y-linked 2 2 2
MIRT695138 PRY PTPN13-like, Y-linked 2 2
MIRT709581 LETMD1 LETM1 domain containing 1 2 2
MIRT709737 TRIM27 tripartite motif containing 27 2 2
MIRT711058 UGT2B4 UDP glucuronosyltransferase family 2 member B4 2 2
MIRT714189 TRAF7 TNF receptor associated factor 7 2 2
MIRT715924 CHD4 chromodomain helicase DNA binding protein 4 2 2
MIRT719463 SRF serum response factor 2 2
MIRT720172 PANK2 pantothenate kinase 2 2 2
MIRT720456 RAB31 RAB31, member RAS oncogene family 2 2
MIRT721642 ZNF207 zinc finger protein 207 2 2
MIRT721996 CLLU1OS chronic lymphocytic leukemia up-regulated 1 opposite strand 2 2
MIRT722187 DNAJC9 DnaJ heat shock protein family (Hsp40) member C9 2 2
MIRT725196 PTRF caveolae associated protein 1 2 2
MIRT725518 FAM229B family with sequence similarity 229 member B 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-1229 Progesterone approved 5994 Microarray Breast cancer 22330642 2012 down-regulated
miR-1229 5-Fluorouracil approved 3385 Microarray CNE cells 22614822 2012 up-regulated
miR-1229 Goserelin approved 47725 Microarray prostate 22674191 2012 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-1229 Fluorouracil 3385 NSC19893 approved sensitive cell line (KYSE)
hsa-miR-1229-3p Cisplatin 5460033 NSC119875 approved sensitive High Gastric Cancer cell line (SGC7901)
hsa-miR-1229-3p Doxorubicin 31703 NSC123127 approved sensitive High Gastric Cancer cell line (SGC7901)
hsa-miR-1229-3p Fluorouracil 3385 NSC19893 approved sensitive High Gastric Cancer cell line (SGC7901)
hsa-miR-1229-3p Vincristine 5978 approved sensitive High Gastric Cancer cell line (SGC7901)
hsa-miR-1229-3p Oxaliplatin 6857599 NSC266046 approved sensitive High Colorectal Cancer cell line (HCT-116)
hsa-miR-1229-3p Oxaliplatin 6857599 NSC266046 approved resistant High Colorectal Cancer cell line (HT-29)
hsa-miR-1229-3p Sorafenib 216239 NSC747971 approved sensitive High Hepatocellular Carcinoma cell line (Huh-7, PLC)
hsa-miR-1229-3p Trametinib 11707110 NSC758246 approved resistant High Melanoma cell line (WM266) (1uM)
hsa-miR-1229-3p Vemurafenib 42611257 NSC761431 approved resistant High Melanoma cell line (WM266) (1uM)
hsa-miR-1229-3p Fluorouracil 3385 NSC19893 approved resistant Low Gastric Cancer cell line (HGC-27, GFP-MKN45)
hsa-miR-1229-3p Sorafenib 216239 NSC747971 approved sensitive High Hepatocellular Carcinoma cell line (Huh-7, PLC)
hsa-miR-1229-3p Temozolomide 5394 NSC362856 approved resistant cell line (U251)
hsa-miR-1229-3p Osimertinib 71496458 NSC779217 approved resistant cell line (HCC827)
hsa-miR-1229-3p Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-1229-3p Vemurafenib 42611257 NSC761431 approved resistant cell line (451Lu)
hsa-miR-1229-3p Cisplatin 5460033 NSC119875 approved resistant cell line (A549)
hsa-miR-1229-3p Tamoxifen 2733525 NSC180973 approved sensitive cell line (LCC2)
hsa-miR-1229-3p Gemcitabine 60750 NSC613327 approved resistant cell line (MDA-231)
hsa-miR-1229-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-1229-3p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)

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