miRTarBase - #MIRT469515


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pre-miRNA Information
pre-miRNA hsa-mir-628   
Genomic Coordinates chr15: 55372940 - 55373034
Synonyms MIRN628, hsa-mir-628, MIR628
Description Homo sapiens miR-628 stem-loop
Comment The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies .
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-628-3p
Sequence 61| UCUAGUAAGAGUGGCAGUCGA |81
Evidence Experimental
Experiments Microarray
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 7 15 - 55372968 29233923 MiREDiBase
A-to-I 8 15 - 55372967 29233923 MiREDiBase
C-to-U 19 15 - 55372956 20591823 MiREDiBase
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN26969715 1 COSMIC
COSN30123186 10 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1410255602 2 dbSNP
rs1401315366 3 dbSNP
rs1322836365 4 dbSNP
rs1158103480 8 dbSNP
rs1216611749 11 dbSNP
rs749619551 13 dbSNP
rs778157225 18 dbSNP
rs756600789 19 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol RBFOX2   
Synonyms FOX2, Fox-2, HNRBP2, HRNBP2, RBM9, RTA, dJ106I20.3, fxh
Description RNA binding protein, fox-1 homolog 2
Transcript NM_001031695   
Other Transcripts NM_001082576 , NM_001082577 , NM_001082578 , NM_001082579 , NM_014309   
Expression
Putative miRNA Targets on RBFOX2
3'UTR of RBFOX2
(miRNA target sites are highlighted)		 
>RBFOX2|NM_001031695|3'UTR
   1 AGTGACGTGAGACCCCTGCAAATGGGACAGCCCCCCAGTTCATGAGGCCTGGCTATTGCAATATTTACTAGTAGAGGAAC
  81 TCTATAGCAAGATGAAGAGGAAAAACAAACAAACAAACAAAAAAAAACACAAAAAAAGAAAGAATACTTTTTTATACCTC
 161 ACTATGTTCTTTGAATATGTATTTTTCCTTTAAATTTCTGCCTTTAATTCTTTTGTTCCAAAGATTGTGCATTTTTTTCT
 241 TTTTTTTTTTAAACTGTGGTAAAAAAAAAAAAAATAATGCATTTCCATGTCTGTATGTCCGTGCTTAGCTTATTCTATCA
 321 ATCACGGAAGAGGCAGTCAAGGAGGAAGGAGAGACATTAGGAGCCGATAAATGCATCTGATCAGAAATCAGCAGACAGAA
 401 TTACCAAAGTGTATCTGGTGCTGAATGACTGGGGGACAAGCAGAAGTGGAAGAGATCTTTCTGCAACAGGATATTCTTCT
 481 AGTCTTCTGAGTTTCTGGTCTTTGACAGGCAATTCTGGTTGGCTGTGGCTGGAATCCACATGCTGATAGATAGGAATTTG
 561 TGCTTACAAAGCAGGAGAATTAAAAAGACGCTTTCCTCTCCTCTTCCCTCCTGTCTTCTCCGTTCTTTTTACAATCATCT
 641 TACACGCACAGCCTGAGACAGCTGGCATAGTTTTTGGAATTATAGTATTGATATTTCCAAACGTGCTCTCAGACAGTGGA
 721 TAATAAACACCTCATTAGGAAACCGATCTCAGAATGAACTCTGGAGTATGAAAAAGATCATTTCTTTTTGTTCCTGTAAC
 801 CTAGCATTCCTTCTAGGCTTCTTCTCCTTTAATTGAACCACAGCTTAGCTCATGTATTCTTTTATTAACACCCTGCTCTC
 881 ATGTCCATAAGATTCAGGAATTTAGGACCCAGGGACAGAAAAGTGAATAAGCCAGTGACCAGATTTCCCCCAGATGTCTT
 961 GAGGATTAGAAGTACAAATTGTTGACAGCCATTAAAGAGGGTGAGGAAGGGAAAAGGAATATTAGAAGATCTGGTATTTC
1041 TTACTTTTTTCTTGCCTCAGAAAGTACAAAGTTTAAAAAATAGAATAAAGAATCTGCTGGGGAAAGATAGAGTACCAGGT
1121 CCTAGGTCAGTAGTCCCTGGAAGTTTTGGTGATGAGGACATGGAAGGGCAGGCAGAGGCACTTTGTACTTGCTCCAAAGC
1201 CATAGGAATTTTCATCTTCCAGAGCCTTTATGAGTCACTTCTCTATCCACAGTCTTGAGCCTGTGGCTATCCCGCTGAGC
1281 TTCTCACTGTCCTCCAAAAACACCCCGCTGAGCACCCGGACCACTTTGTACACATTAACACTACAGGACATAAAATGCAG
1361 AGGCCCTGAGATTGCTGCCCTCCCATATTGGAAGGAGGGTCTGCGATGGCAAGGGTCTTCTATATCACCAGAAAGAGTCG
1441 CGCAGTGAGTCACTGCCGTTGCCATCTGGCTGTAATTTTCTATGTTATCAAGGTAGGAGGGAGTGTTTCTCTTCTAGCTG
1521 TTAGATAGAACTGATAAAAGCAAGTGTCCTACAGCATTTCCCAAATGAAGGCATTAGGAAATAGAAAAGCACGGTCTTTT
1601 TGGCTCCCTGGTCTAGTCACATTGGTACTAGGGTGACCTTTCACCCAAGGGACAGCTGCTAAAGGGAGTAATTCAGAGAC
1681 ATGGAGCTTCTGGTTATGGGTTTGTTTTGGGTTTGTTTTTAACTCCTGCCTCCACACATGTTCTTGACTGATAACTGACT
1761 CATGTCCCTGAATTAAAATGACTGACCTATGACAGCATCAAGCATTCTTTGTAAGCAGAGTGATATATCTGAGAGGGCGT
1841 TGACCTGTTGTGTAGAATACATATCCTTTCCCCCTTCAGAATCCTGTCTCGCCTCGTAACTGGGAGAGAGGCTGTGCCTG
1921 AAACTAGGGGCGATGTCAAGGAAGCTAGAGGCCTCGATGCAATTATTACTGACTCTGGGGAGGAAGACAGAGAATAAGGG
2001 GACACCAACTGCCCAGTCCACTGGCCATTTTTAAGGGTCCCCCCACCCCAAGCCAAAGTTTGGTTTGTTGCTGTTAAGAC
2081 AATTTTTGTTGTATGTATATAAATATTTTAGTTAGAGGAGCGGGGAATGGGATGCGGGCTTTCACAGTTCTAGGGAATGG
2161 GGGCAGGGAGGATTTTGCTTTTGCTTTTGCTTTGAGGGAGAACTTTAGCTGACTAAAAAAACAGAAGTTTGGGGTCATGA
2241 TCACAAAGGGGCCATTCCCAAAAGATGGCAAGCCACGTATTCAGTGGAGACTAGGCCAAATTCTAAATGGTTTTATCCAT
2321 AGCAGGGGAGAATAGGAGAATGAGTTTAAGAGTTTTTCTCTTCTTTTTTCCTAGAAAGAGGTAAGGATAATGGGAAAGGT
2401 AGAGAAGGCGGCTCCCACAGACCTTTTAAGAGAGGCAGAATCTTGAGCTTGAGGCACCTTGAGTGCATCTCAGTTCAGCT
2481 GGTTCTGGCTGAGGCCTCCAAAGGCAAGCTCTGTGCTTTCCAGTGGTTTCTGCTGCATTTCCAGGGATGGTGTTTAACAC
2561 CGCTTCCTCCAGCTCCCTTTTCTAAGAAAGAATAAATGGAGTTCTGCTTTTTATGAAAGGGTCTTTGGTTTTCAGTGTCA
2641 ACACTGAGAATTGGGGCTCTTGCAAGCATCTGGATTTCACAGTATCAACCTCCCCGTCACCTTTTGAACTTTGAGACTCC
2721 GTACGGTCAACTTCACCAGAGGCAGGTTGCTCGAAGCAGCACTGCTTGTCTGTTCCTGACTCTGGTTCTCACTGTATTAA
2801 AAAAGAGAGTCAGAGGAGTCTGGCATTTCGTGAGTTTGTTAGAGGATGCTGGCTGATAATTCCAGAAAACTTACTGATGC
2881 TAAATCACAGTACATGCATGATTCTTTTTCAGCTTTACTATAGTTCATGACCTGGACTTTCTGTACTCTTGGAAGCTGGG
2961 CTCCTTAAAGGAGGCCTCTAGTGAACACCTTTATCTCCATGTCCCTCTTAGAGCCCAGAGAGCTGCCCATAGGCATTTTC
3041 CAGAATTCCTCATGTCACCTAGTTCAATTTCCATTAACTCAGATCAGCCATTGTGATTCACCATTTGTCAGGCTCTCAGG
3121 TTTAACAAAACCTACTATCACCATCATCCTTCAACAGCCACAGTCTGAATTGAGCCAACATTTTTTTTTCTTTGAGAAAG
3201 AAGTGGACTGGGGCACAACTTTTAGTCTGAGGGGAGCTAGTGGAAATCTAGACAATAGAAGTCATCGATAGCAGCTTTTC
3281 CTCAAATGTGTGACTCCTCAGGGGCTAAACTGCTCTTAGCTTAGAATTATGCTTTACTAGAGATCTAGCAGATAAGTGGG
3361 TTAATCACTACCATCCTGTAACTAGTTATATAGCTTCCAGACATGAGGGAGACATCAAACAGGGATGGAAGCAACCCCAA
3441 GGATATGCAAGAAGGGCATGATGAACCCCCTTCCCTCTGGCAGGAGAACAAGGCCAACCAAGGGACAGACTGGAAAGCAC
3521 TTAGATGTTTAAGGAGGAGAAAGGGGAAGCTTTGACCAGTCCTTGCCTTTTGCCAAGTTCAGCCAGTTCTCCGCTGCTTG
3601 CAACCTCTAGCGCAGTAACATTTGCAGAATTGCAGATTTTCCCCCAGATACTAGGAGGAAAGGGACTTTGGGGGGTGGGG
3681 AAGGGGTCGTGGTGTTTTAAAAGCATAAGTTACCTGTTTGCACTGTTTTAAGATAGGAAAAAAAAATAGTGGGCAAGGTG
3761 AACATCAGACGTAAATTTGTGTGTTTTTATTTTGTCATGCTCTTGAAAATGTTTGACCATTTGTAGTATACACAGTGAAA
3841 CTTGATTCTCTGTTGCATAAAACACTATATTTTTTTGGAAATGTTACTGTCCAAAAGCCTCTTCCCTCCCTTTCCTTTTC
3921 CTATGTACTTCCTTCATACTTGCTTTACTGATCAGCCAGGCAATAGCCATCCAAGAGCTAGAGCATGAAACAGGGCCCTT
4001 TCCAAGTAGGCTCTGGGTGTCCTAAGCCAGCGTGTGCCCTCTGGTTTAGTGAGTGTAATAGAGTCCCTGGCACCTTTCTT
4081 TGCAAATGAGGCTAACAGACCAGACTGCAGCAAGTTATCAGATTCCTCAATCAGATGCACTAGGAGTGAGGAGCCCAGGG
4161 ATGGAGGGGGTTCCTGAAGTATTGCAGTTGGCTGTAGTAGCTGAGTTCTTTTCCATGTTACCGAAACTGTAGCCAGTTAC
4241 AGTTTACTCAGGAAAACGGTAGATCAATTCAGCCATGGTAGTGCTGGTTGGCAGGGATTGGTAACGGAGAGAACTGCTCA
4321 TCAGCCAAAACTCAAGCCTTGCCTTTTAGGAGGCCACCAGCAGAGGGACTTGGTCCTCCTTGTCTGGTACTTGTGTACAT
4401 GCCGGTGACCTGAGGACTCCACTCACACTGGCGAGCAAAAAGGGAGCAGTGATTCTCTTTTCTCTCCCCACCCCCTGCCC
4481 TTTGTTACCAACACCAGTTTCCCAGGGGGTACATGAGTTTCTGAATTTTTAAAAAATGTTTTTGGTTTGGTTTTTCTGGG
4561 GACTGATAAGTGCTTTAAGCAATGTCCATACCCCGTCAAGACTCCCAGCTTAGTCATTTTCTTGTATTTTTCTGTTCACA
4641 GTATTTGTGTGTGTGCTTGTTTTGGCAGCTCATTTTGGCTGTATTATATATTGAGTGATGAATTGATCCTCTTTTTTCCC
4721 TAAGGGATATGAATTGTTTTTCTTGTGTTATATTCTGCTTGTGAATAGCTGGAGCAAACCTGGGGCTGACACGCGTAAGC
4801 TAGGGCTGCAAAGCGAGAAGAGAGCCGGTGGAGTGTACTTGTCCCTGACAGGCTGACCTACCTGAGTCTCTGAGCTTTTC
4881 AGTCCAAATCTTTGCAAGGCTCAAAATGCCACAGAACCTCTCCTCTTCTCCCCACTCCCCATGGCAGGGACCGGACCATC
4961 CCTACATGCAACATGCTGTTCCTCCAGCCCCTCCCATTGCCATGGCAAAACAGGTACCTTTGGGGCATGGGGGCATTACA
5041 TGGGATGCTTGTGTAATCGACCACCTAGCCTTCTCTCTCCCCTCCCGTCCTCCCCCAGAATCACTTCCTAGGACACCCGA
5121 GCTGCTTGCCCAGGGTCCTGTTTCCCTGCTAACTCCAGAGAAGCATCCCAGGGCTTTGTGACAGTCTCTAATTCCCTTCC
5201 CTTCTCGTTAAGAATCATATTGTATAGTAGCTTTCAGACCATACAGTATTCATTGGGTTACTCCTATTATTATCAAGTAG
5281 CTGGAATTGTGAAGGTCGGAGTAGTTAGATCTTTAGCTTTTATTCCTTATTTTTTTGTATTACTCTCCATGTGTATAAAT
5361 TATTGATCATGTTGCTGGCTTTTATAAACTCTAAGCGAAGGAGGAGCACTGCCTCAGCCTTTGCACATGGTAATGAAGCA
5441 CTGTTTTTAAATAAAAGAGAGAAACACCATTAAAAAA
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' agcUGACGGUGAGAAUGAUCu 5'
             |:||| |: :||||||| 
Target 5' gctATTGCAATATTTACTAGt 3'
 52 - 72 162.00 -12.80
2 
miRNA  3' agCUGACGGUGAGAAUGAUCu 5'
            || |  ::|| ||||||| 
Target 5' taGAATTATGCT-TTACTAGa 3'
 3322 - 3341 150.00 -9.60
3 
miRNA  3' agcUGACGGU--GAGAAUGAUCu 5'
             ||| |||  || | ||||| 
Target 5' atcACTACCATCCTGTAACTAGt 3'
 3364 - 3386 132.00 -12.50
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSM186131 6 COSMIC
COSM8179501 7 COSMIC
COSM4004922 9 COSMIC
COSM270007 10 COSMIC
COSM8360080 10 COSMIC
COSN30475271 24 COSMIC
COSN30478131 25 COSMIC
COSN20073061 31 COSMIC
COSN30481548 33 COSMIC
COSN30451049 36 COSMIC
COSN31531207 88 COSMIC
COSN30154126 97 COSMIC
COSN31534378 109 COSMIC
COSN20117415 119 COSMIC
COSN8010334 122 COSMIC
COSN27501926 239 COSMIC
COSN23973507 254 COSMIC
COSN31535801 260 COSMIC
COSN20117414 261 COSMIC
COSN8017992 272 COSMIC
COSN29461439 275 COSMIC
COSN1261374 281 COSMIC
COSN31611228 284 COSMIC
COSN26565918 300 COSMIC
COSN26573545 326 COSMIC
COSN31588264 340 COSMIC
COSN31479988 349 COSMIC
COSN8017991 439 COSMIC
COSN31523897 1198 COSMIC
COSN16886387 1272 COSMIC
COSN20993431 1518 COSMIC
COSN31526747 1593 COSMIC
COSN31551569 1710 COSMIC
COSN31595724 1737 COSMIC
COSN31529462 1890 COSMIC
COSN30045394 1908 COSMIC
COSN9165262 1932 COSMIC
COSN8017990 2159 COSMIC
COSN9165261 2226 COSMIC
COSN31548570 2580 COSMIC
COSN31553268 2720 COSMIC
COSN1898392 3108 COSMIC
COSN5455649 3633 COSMIC
COSN8612639 3635 COSMIC
COSN31521367 3737 COSMIC
COSN5991956 4046 COSMIC
COSN31531223 4188 COSMIC
COSN31564975 4284 COSMIC
COSN28201664 4367 COSMIC
COSN5455648 4372 COSMIC
COSN20812989 4759 COSMIC
COSN10030144 4792 COSMIC
COSN10030143 4953 COSMIC
COSN28798551 5025 COSMIC
COSN25696641 5031 COSMIC
COSN1898391 5056 COSMIC
COSN31568395 5058 COSMIC
COSN30116438 5086 COSMIC
COSN31568118 5216 COSMIC
COSN30166583 5299 COSMIC
COSN27542704 5329 COSMIC
COSN31570133 5330 COSMIC
COSN23572885 5467 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1352427170 2 dbSNP
rs776577786 6 dbSNP
rs371844393 7 dbSNP
rs368537797 9 dbSNP
rs1302146011 14 dbSNP
rs768311951 17 dbSNP
rs1377018531 22 dbSNP
rs1389985358 23 dbSNP
rs758671765 24 dbSNP
rs748563938 27 dbSNP
rs991566214 27 dbSNP
rs1379859724 29 dbSNP
rs779417558 30 dbSNP
rs374999950 32 dbSNP
rs1312989799 33 dbSNP
rs1358895300 35 dbSNP
rs754303742 36 dbSNP
rs749176289 37 dbSNP
rs779721558 37 dbSNP
rs766867880 42 dbSNP
rs756739583 44 dbSNP
rs751057219 47 dbSNP
rs1211228868 52 dbSNP
rs545279111 54 dbSNP
rs1258512462 55 dbSNP
rs761124564 58 dbSNP
rs1316965416 60 dbSNP
rs376707088 65 dbSNP
rs926502197 67 dbSNP
rs1242461373 68 dbSNP
rs1449486692 85 dbSNP
rs1194727940 87 dbSNP
rs982374917 99 dbSNP
rs1461210191 102 dbSNP
rs934120265 109 dbSNP
rs1323442823 114 dbSNP
rs1167675250 115 dbSNP
rs576305834 118 dbSNP
rs374794528 119 dbSNP
rs117617596 122 dbSNP
rs1297855332 122 dbSNP
rs1335230331 122 dbSNP
rs970560630 122 dbSNP
rs146996497 125 dbSNP
rs1032004040 128 dbSNP
rs1201552380 128 dbSNP
rs555384019 128 dbSNP
rs957730839 128 dbSNP
rs988017628 128 dbSNP
rs1206356083 132 dbSNP
rs1259119632 138 dbSNP
rs1007345541 145 dbSNP
rs542490804 146 dbSNP
rs1430975995 151 dbSNP
rs1398889190 154 dbSNP
rs888880116 164 dbSNP
rs1405942652 166 dbSNP
rs1454799057 173 dbSNP
rs1290696235 181 dbSNP
rs1030052169 187 dbSNP
rs964522500 187 dbSNP
rs998100367 188 dbSNP
rs1174089222 203 dbSNP
rs897954182 209 dbSNP
rs1221424519 213 dbSNP
rs1317426107 215 dbSNP
rs1217933183 225 dbSNP
rs1037058350 229 dbSNP
rs1222598494 230 dbSNP
rs942277839 231 dbSNP
rs887806418 235 dbSNP
rs1055702551 239 dbSNP
rs1161829437 239 dbSNP
rs1362585263 239 dbSNP
rs1420201652 239 dbSNP
rs573895033 240 dbSNP
rs937320638 242 dbSNP
rs1303872913 245 dbSNP
rs1367652412 246 dbSNP
rs928725937 250 dbSNP
rs1225259087 251 dbSNP
rs1373868384 251 dbSNP
rs35925116 251 dbSNP
rs1242807358 254 dbSNP
rs1215074153 256 dbSNP
rs1246019913 259 dbSNP
rs1316291894 259 dbSNP
rs1293368013 260 dbSNP
rs1356795324 261 dbSNP
rs981517567 261 dbSNP
rs949244866 271 dbSNP
rs187725493 272 dbSNP
rs988091374 273 dbSNP
rs1039926848 275 dbSNP
rs1248989271 275 dbSNP
rs71658610 275 dbSNP
rs76084830 275 dbSNP
rs879230730 275 dbSNP
rs1347583634 276 dbSNP
rs1355348563 288 dbSNP
rs1296269824 293 dbSNP
rs534289647 300 dbSNP
rs1301644709 301 dbSNP
rs985805932 302 dbSNP
rs953040622 312 dbSNP
rs1008026423 315 dbSNP
rs910355306 317 dbSNP
rs1362143919 321 dbSNP
rs979335682 326 dbSNP
rs1250029310 327 dbSNP
rs1428027397 342 dbSNP
rs967918866 345 dbSNP
rs1020644554 349 dbSNP
rs1245512838 357 dbSNP
rs1433918049 359 dbSNP
rs1181374140 363 dbSNP
rs1009637681 365 dbSNP
rs1411904348 366 dbSNP
rs1170205612 374 dbSNP
rs1430525551 376 dbSNP
rs751791437 378 dbSNP
rs960527743 379 dbSNP
rs1035187682 395 dbSNP
rs796467520 413 dbSNP
rs28562663 415 dbSNP
rs1001921628 424 dbSNP
rs1474451167 429 dbSNP
rs774563214 432 dbSNP
rs767663315 440 dbSNP
rs1260291732 446 dbSNP
rs1270312383 447 dbSNP
rs1212254893 450 dbSNP
rs571625183 463 dbSNP
rs138820911 466 dbSNP
rs1293881112 471 dbSNP
rs538525364 475 dbSNP
rs1317599958 477 dbSNP
rs569486569 479 dbSNP
rs777893842 480 dbSNP
rs751665732 485 dbSNP
rs1460394085 488 dbSNP
rs1209466650 497 dbSNP
rs1005831333 506 dbSNP
rs1476505677 515 dbSNP
rs1055945854 520 dbSNP
rs1001950787 521 dbSNP
rs1480612955 522 dbSNP
rs1178365491 524 dbSNP
rs887344348 525 dbSNP
rs1403777892 537 dbSNP
rs549668936 539 dbSNP
rs1046273342 540 dbSNP
rs529439556 546 dbSNP
rs566728897 550 dbSNP
rs1428048808 554 dbSNP
rs1287862420 556 dbSNP
rs1345773508 558 dbSNP
rs1212329958 566 dbSNP
rs1224458702 568 dbSNP
rs1356787859 571 dbSNP
rs933987277 573 dbSNP
rs922594733 574 dbSNP
rs936459534 579 dbSNP
rs1040204589 582 dbSNP
rs925198078 589 dbSNP
rs1293309965 595 dbSNP
rs1262697080 602 dbSNP
rs1490586985 604 dbSNP
rs551520981 619 dbSNP
rs371513393 621 dbSNP
rs184549066 622 dbSNP
rs1486974215 625 dbSNP
rs1299679754 634 dbSNP
rs1410080916 640 dbSNP
rs1398399147 645 dbSNP
rs566156006 646 dbSNP
rs1365775962 659 dbSNP
rs564536871 667 dbSNP
rs913803723 669 dbSNP
rs1329779453 677 dbSNP
rs552989953 683 dbSNP
rs988038115 685 dbSNP
rs1426912991 691 dbSNP
rs1014602309 703 dbSNP
rs1285463643 706 dbSNP
rs1360424017 708 dbSNP
rs960662644 719 dbSNP
rs1034664522 721 dbSNP
rs1001974137 728 dbSNP
rs5755938 731 dbSNP
rs1450768360 733 dbSNP
rs1182280916 734 dbSNP
rs1420153546 744 dbSNP
rs1468570871 759 dbSNP
rs1157503651 761 dbSNP
rs1385377922 766 dbSNP
rs1426158491 770 dbSNP
rs952182036 776 dbSNP
rs1389595874 779 dbSNP
rs1405097204 784 dbSNP
rs1330017928 800 dbSNP
rs1338028914 801 dbSNP
rs1445293428 802 dbSNP
rs1034569792 806 dbSNP
rs1001791231 814 dbSNP
rs907232603 815 dbSNP
rs1263849597 820 dbSNP
rs1045719860 822 dbSNP
rs1196124706 824 dbSNP
rs1010761387 826 dbSNP
rs1435993409 828 dbSNP
rs891897437 831 dbSNP
rs1243679442 833 dbSNP
rs1054508886 841 dbSNP
rs969109870 850 dbSNP
rs1445860142 851 dbSNP
rs1017144851 852 dbSNP
rs1181251218 854 dbSNP
rs1367500808 856 dbSNP
rs1179391280 859 dbSNP
rs535966088 864 dbSNP
rs1168841642 868 dbSNP
rs1399170815 869 dbSNP
rs1464400691 870 dbSNP
rs867472854 871 dbSNP
rs1331201059 874 dbSNP
rs1407506690 876 dbSNP
rs755930359 878 dbSNP
rs1310713425 880 dbSNP
rs7511547 893 dbSNP
rs1250458499 895 dbSNP
rs1202028870 898 dbSNP
rs1271709747 903 dbSNP
rs925104878 906 dbSNP
rs1197793418 916 dbSNP
rs1263638447 919 dbSNP
rs1462629048 923 dbSNP
rs887407257 924 dbSNP
rs1336436639 928 dbSNP
rs1273273636 931 dbSNP
rs1428744645 934 dbSNP
rs1232089267 937 dbSNP
rs1026323495 940 dbSNP
rs1309050613 950 dbSNP
rs931902819 968 dbSNP
rs77463193 973 dbSNP
rs200514647 975 dbSNP
rs922952164 981 dbSNP
rs998420026 985 dbSNP
rs1391809504 991 dbSNP
rs901186953 1000 dbSNP
rs1301151626 1006 dbSNP
rs1039660739 1016 dbSNP
rs961986619 1018 dbSNP
rs1320468036 1028 dbSNP
rs1338741178 1029 dbSNP
rs907639802 1031 dbSNP
rs1283743515 1034 dbSNP
rs1325571817 1045 dbSNP
rs1464267945 1049 dbSNP
rs1396895393 1051 dbSNP
rs764166498 1054 dbSNP
rs1231062480 1056 dbSNP
rs1165827609 1058 dbSNP
rs1255342825 1059 dbSNP
rs984468345 1061 dbSNP
rs1206396975 1066 dbSNP
rs942815355 1068 dbSNP
rs544707017 1081 dbSNP
rs762978754 1087 dbSNP
rs1430505772 1099 dbSNP
rs1481704361 1108 dbSNP
rs1250290852 1110 dbSNP
rs1043578125 1112 dbSNP
rs1469545270 1119 dbSNP
rs567399351 1121 dbSNP
rs1034473074 1122 dbSNP
rs780931642 1124 dbSNP
rs775485249 1126 dbSNP
rs1358835117 1137 dbSNP
rs1332006825 1138 dbSNP
rs1002223720 1155 dbSNP
rs1261922986 1156 dbSNP
rs971655674 1169 dbSNP
rs1239720194 1170 dbSNP
rs913704303 1185 dbSNP
rs754929054 1187 dbSNP
rs988478247 1192 dbSNP
rs1024956045 1194 dbSNP
rs1317475653 1212 dbSNP
rs1304620892 1219 dbSNP
rs878874233 1220 dbSNP
rs531617408 1221 dbSNP
rs562605949 1223 dbSNP
rs1010245115 1224 dbSNP
rs542928453 1225 dbSNP
rs1283327975 1226 dbSNP
rs550584328 1234 dbSNP
rs751517601 1237 dbSNP
rs1373553559 1245 dbSNP
rs1222858523 1247 dbSNP
rs939260943 1250 dbSNP
rs891761815 1264 dbSNP
rs573832868 1269 dbSNP
rs1440320936 1271 dbSNP
rs927644652 1272 dbSNP
rs1033134323 1275 dbSNP
rs554017776 1282 dbSNP
rs1000273399 1283 dbSNP
rs1454763087 1285 dbSNP
rs1363668649 1286 dbSNP
rs1378616339 1293 dbSNP
rs1157289812 1306 dbSNP
rs980421396 1307 dbSNP
rs969160845 1313 dbSNP
rs1456158382 1315 dbSNP
rs1292763823 1317 dbSNP
rs1016691363 1318 dbSNP
rs1050250495 1331 dbSNP
rs983837944 1334 dbSNP
rs931782283 1335 dbSNP
rs1246097211 1339 dbSNP
rs951644392 1343 dbSNP
rs1293435189 1350 dbSNP
rs1319586047 1358 dbSNP
rs1219784928 1359 dbSNP
rs1192643988 1362 dbSNP
rs901770805 1363 dbSNP
rs1449477994 1369 dbSNP
rs1200998003 1377 dbSNP
rs1263226122 1379 dbSNP
rs1439107709 1381 dbSNP
rs1025786073 1385 dbSNP
rs1485538186 1388 dbSNP
rs765845419 1389 dbSNP
rs1163794352 1398 dbSNP
rs1463338358 1399 dbSNP
rs1329155149 1404 dbSNP
rs940365911 1405 dbSNP
rs901410535 1413 dbSNP
rs757953831 1422 dbSNP
rs367633849 1426 dbSNP
rs540718437 1440 dbSNP
rs578176250 1441 dbSNP
rs927490899 1442 dbSNP
rs764901887 1446 dbSNP
rs946125947 1451 dbSNP
rs1308388740 1453 dbSNP
rs1329490120 1453 dbSNP
rs892313794 1457 dbSNP
rs1052259180 1458 dbSNP
rs538229290 1469 dbSNP
rs939294718 1472 dbSNP
rs927859464 1475 dbSNP
rs558108414 1482 dbSNP
rs537820198 1483 dbSNP
rs1482399140 1484 dbSNP
rs909518833 1488 dbSNP
rs1032996542 1489 dbSNP
rs1420514498 1500 dbSNP
rs1478653922 1502 dbSNP
rs1384955006 1505 dbSNP
rs983890289 1512 dbSNP
rs951143595 1526 dbSNP
rs1437074812 1530 dbSNP
rs575619812 1533 dbSNP
rs1173333152 1534 dbSNP
rs1335616507 1534 dbSNP
rs1476845290 1535 dbSNP
rs530552288 1543 dbSNP
rs535756550 1565 dbSNP
rs1289034299 1570 dbSNP
rs1363673235 1571 dbSNP
rs976937432 1578 dbSNP
rs193055847 1592 dbSNP
rs546837643 1593 dbSNP
rs533620877 1594 dbSNP
rs569452170 1599 dbSNP
rs1040331265 1601 dbSNP
rs1209534062 1602 dbSNP
rs36085732 1602 dbSNP
rs940604661 1604 dbSNP
rs868634307 1606 dbSNP
rs374995625 1613 dbSNP
rs1007064443 1615 dbSNP
rs1262288582 1617 dbSNP
rs1480643166 1647 dbSNP
rs1174189887 1649 dbSNP
rs968706278 1653 dbSNP
rs1423001568 1664 dbSNP
rs1413364118 1677 dbSNP
rs1159242848 1680 dbSNP
rs1021559540 1681 dbSNP
rs1048694560 1682 dbSNP
rs1010762920 1708 dbSNP
rs1208381901 1708 dbSNP
rs891866631 1709 dbSNP
rs144941938 1710 dbSNP
rs1340220562 1720 dbSNP
rs1405950516 1721 dbSNP
rs927078979 1724 dbSNP
rs1228292716 1728 dbSNP
rs1003376220 1730 dbSNP
rs1285106891 1732 dbSNP
rs1356107797 1736 dbSNP
rs1214641388 1737 dbSNP
rs775940029 1738 dbSNP
rs1490437803 1740 dbSNP
rs950283837 1742 dbSNP
rs917395295 1752 dbSNP
rs906327235 1767 dbSNP
rs1177257048 1778 dbSNP
rs1417167836 1779 dbSNP
rs1381700617 1785 dbSNP
rs1417330773 1786 dbSNP
rs1157618144 1787 dbSNP
rs767831871 1789 dbSNP
rs551468737 1790 dbSNP
rs1406281575 1796 dbSNP
rs141298442 1797 dbSNP
rs1329834110 1809 dbSNP
rs1048045529 1826 dbSNP
rs562507072 1838 dbSNP
rs749407345 1839 dbSNP
rs1238083800 1844 dbSNP
rs976867428 1850 dbSNP
rs548963787 1854 dbSNP
rs1028411988 1855 dbSNP
rs998674742 1856 dbSNP
rs529243633 1861 dbSNP
rs1019183732 1872 dbSNP
rs1437227798 1886 dbSNP
rs1177505392 1890 dbSNP
rs1385439544 1891 dbSNP
rs560382702 1893 dbSNP
rs540458253 1895 dbSNP
rs1389110981 1896 dbSNP
rs1405154095 1902 dbSNP
rs577931110 1905 dbSNP
rs1332574159 1912 dbSNP
rs886378319 1917 dbSNP
rs1475500308 1918 dbSNP
rs1048939327 1924 dbSNP
rs985695885 1929 dbSNP
rs1341275607 1930 dbSNP
rs1247338825 1931 dbSNP
rs1282652315 1931 dbSNP
rs905522281 1932 dbSNP
rs1439305629 1942 dbSNP
rs1044184867 1948 dbSNP
rs949823625 1949 dbSNP
rs1456419683 1954 dbSNP
rs968927006 1955 dbSNP
rs770066555 1956 dbSNP
rs1300002231 1973 dbSNP
rs934786981 1975 dbSNP
rs1184884235 1983 dbSNP
rs1256251152 1989 dbSNP
rs1472650216 1990 dbSNP
rs1235200578 1992 dbSNP
rs765751573 1994 dbSNP
rs1464571016 2006 dbSNP
rs1293184928 2008 dbSNP
rs1402915534 2012 dbSNP
rs117149350 2013 dbSNP
rs956357906 2014 dbSNP
rs1332384544 2017 dbSNP
rs1337927567 2025 dbSNP
rs1329913007 2031 dbSNP
rs549611613 2034 dbSNP
rs921256384 2037 dbSNP
rs1397600252 2042 dbSNP
rs1315977708 2045 dbSNP
rs1166541011 2046 dbSNP
rs781036448 2049 dbSNP
rs1461503548 2055 dbSNP
rs1003336128 2061 dbSNP
rs1161367022 2063 dbSNP
rs965828694 2073 dbSNP
rs1015657449 2077 dbSNP
rs1471091730 2080 dbSNP
rs1194825929 2091 dbSNP
rs754771325 2094 dbSNP
rs1004687364 2097 dbSNP
rs950521472 2098 dbSNP
rs1027566246 2099 dbSNP
rs1467615484 2111 dbSNP
rs1170936615 2116 dbSNP
rs1044901045 2121 dbSNP
rs544697438 2122 dbSNP
rs779990179 2128 dbSNP
rs1044432317 2131 dbSNP
rs1013898611 2132 dbSNP
rs888356311 2135 dbSNP
rs1048572656 2136 dbSNP
rs934818049 2147 dbSNP
rs926108833 2149 dbSNP
rs1043363949 2150 dbSNP
rs929658626 2161 dbSNP
rs575510717 2163 dbSNP
rs1040810800 2169 dbSNP
rs1335528287 2178 dbSNP
rs1487486148 2180 dbSNP
rs371530983 2186 dbSNP
rs943768273 2188 dbSNP
rs757865943 2191 dbSNP
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rs1196829210 2202 dbSNP
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rs1418831778 2211 dbSNP
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rs749942759 2219 dbSNP
rs555773659 2220 dbSNP
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rs1292817941 2310 dbSNP
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rs775363208 2581 dbSNP
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rs188061884 2599 dbSNP
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rs1298436314 2620 dbSNP
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rs1317534343 2645 dbSNP
rs564316384 2651 dbSNP
rs1361914490 2655 dbSNP
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rs969883641 2678 dbSNP
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rs1424704511 2695 dbSNP
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rs182183370 2724 dbSNP
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rs768448693 2726 dbSNP
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rs766741087 2810 dbSNP
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rs1354031386 3212 dbSNP
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rs1056984333 3280 dbSNP
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rs977299799 3315 dbSNP
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rs1340390276 4010 dbSNP
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rs963170082 4027 dbSNP
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rs894611093 4032 dbSNP
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rs1028330697 4037 dbSNP
rs1436937172 4044 dbSNP
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rs1349669319 4100 dbSNP
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rs1007205909 4179 dbSNP
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rs760406605 4306 dbSNP
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rs770431976 4594 dbSNP
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rs1413150618 4669 dbSNP
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rs184776138 4695 dbSNP
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rs954944127 4815 dbSNP
rs943350013 4817 dbSNP
rs1167264661 4824 dbSNP
rs572725699 4826 dbSNP
rs996130110 4827 dbSNP
rs958241122 4830 dbSNP
rs1197415435 4834 dbSNP
rs1032436633 4835 dbSNP
rs1043123 4843 dbSNP
rs903034576 4849 dbSNP
rs193074709 4860 dbSNP
rs1281853900 4861 dbSNP
rs955244061 4864 dbSNP
rs1216331217 4875 dbSNP
rs552777231 4881 dbSNP
rs1355055129 4886 dbSNP
rs1029439923 4887 dbSNP
rs1214745540 4887 dbSNP
rs1439889396 4893 dbSNP
rs1351141550 4895 dbSNP
rs1203514969 4897 dbSNP
rs1280261109 4901 dbSNP
rs576785958 4903 dbSNP
rs1251713260 4907 dbSNP
rs771787876 4911 dbSNP
rs1219357257 4917 dbSNP
rs895729656 4920 dbSNP
rs1055679089 4923 dbSNP
rs1272506047 4925 dbSNP
rs1401779930 4926 dbSNP
rs937028915 4929 dbSNP
rs1341036460 4935 dbSNP
rs1297422001 4939 dbSNP
rs1417594790 4949 dbSNP
rs370281818 4952 dbSNP
rs567230055 4953 dbSNP
rs1427563765 4954 dbSNP
rs1016815525 4955 dbSNP
rs940416376 4957 dbSNP
rs1415220965 4958 dbSNP
rs1416481259 4960 dbSNP
rs1332141194 4963 dbSNP
rs908079646 4964 dbSNP
rs866171707 4965 dbSNP
rs1424561453 4972 dbSNP
rs1271550668 4973 dbSNP
rs557172563 4976 dbSNP
rs1226646974 4979 dbSNP
rs933612806 4985 dbSNP
rs1479123247 5000 dbSNP
rs922191582 5002 dbSNP
rs1213591050 5004 dbSNP
rs1254730595 5005 dbSNP
rs1441891562 5006 dbSNP
rs1194064549 5007 dbSNP
rs536955728 5012 dbSNP
rs1168211993 5013 dbSNP
rs1193447971 5023 dbSNP
rs1487500134 5024 dbSNP
rs1436390434 5026 dbSNP
rs761424513 5026 dbSNP
rs1210391383 5032 dbSNP
rs1170709370 5040 dbSNP
rs11542071 5041 dbSNP
rs1275961755 5042 dbSNP
rs1319799867 5046 dbSNP
rs548027879 5058 dbSNP
rs1433832615 5059 dbSNP
rs1303726569 5060 dbSNP
rs1372136573 5063 dbSNP
rs1235946377 5065 dbSNP
rs1318565227 5067 dbSNP
rs1345004975 5071 dbSNP
rs1206242644 5072 dbSNP
rs1277457836 5075 dbSNP
rs1270029827 5077 dbSNP
rs906722613 5079 dbSNP
rs1463654760 5080 dbSNP
rs1398012640 5082 dbSNP
rs1042597759 5084 dbSNP
rs945498462 5085 dbSNP
rs775733191 5086 dbSNP
rs61744622 5087 dbSNP
rs1449052469 5092 dbSNP
rs767281867 5093 dbSNP
rs537012179 5100 dbSNP
rs748696827 5107 dbSNP
rs565869048 5108 dbSNP
rs1467222044 5109 dbSNP
rs144766970 5118 dbSNP
rs369816045 5119 dbSNP
rs771500171 5122 dbSNP
rs1477089382 5136 dbSNP
rs1416427851 5137 dbSNP
rs972555857 5139 dbSNP
rs961195184 5140 dbSNP
rs1240450608 5143 dbSNP
rs1327203953 5145 dbSNP
rs1208131621 5146 dbSNP
rs1274053039 5148 dbSNP
rs895615335 5149 dbSNP
rs1182789927 5154 dbSNP
rs1034279170 5156 dbSNP
rs1266478305 5159 dbSNP
rs1001832784 5164 dbSNP
rs898852041 5174 dbSNP
rs774274454 5182 dbSNP
rs1183947406 5185 dbSNP
rs138989282 5195 dbSNP
rs1471988298 5197 dbSNP
rs1200034494 5199 dbSNP
rs866460474 5204 dbSNP
rs959326282 5206 dbSNP
rs1033326549 5207 dbSNP
rs1456122020 5216 dbSNP
rs1292561105 5220 dbSNP
rs1256820853 5221 dbSNP
rs1390518696 5224 dbSNP
rs1216732585 5225 dbSNP
rs1323375150 5228 dbSNP
rs886185387 5229 dbSNP
rs1227864550 5235 dbSNP
rs550441559 5242 dbSNP
rs551656971 5243 dbSNP
rs1227530053 5245 dbSNP
rs970477792 5251 dbSNP
rs1242941369 5252 dbSNP
rs34310596 5258 dbSNP
rs1020682836 5261 dbSNP
rs1480851796 5265 dbSNP
rs933499390 5266 dbSNP
rs1378774183 5274 dbSNP
rs1249540309 5278 dbSNP
rs1009741083 5283 dbSNP
rs749302912 5291 dbSNP
rs1054480843 5295 dbSNP
rs1401165116 5297 dbSNP
rs1163675367 5298 dbSNP
rs561447464 5299 dbSNP
rs373838355 5309 dbSNP
rs1170800559 5310 dbSNP
rs9610345 5327 dbSNP
rs1369089808 5329 dbSNP
rs1330692513 5336 dbSNP
rs889140807 5337 dbSNP
rs572694041 5339 dbSNP
rs370502120 5341 dbSNP
rs1352116780 5344 dbSNP
rs936901877 5345 dbSNP
rs1165974378 5346 dbSNP
rs1312301833 5349 dbSNP
rs925339095 5355 dbSNP
rs1308234409 5358 dbSNP
rs1230883282 5365 dbSNP
rs1423573368 5368 dbSNP
rs978492719 5369 dbSNP
rs1051735145 5370 dbSNP
rs1272286484 5384 dbSNP
rs1341170600 5393 dbSNP
rs1412007313 5393 dbSNP
rs772591081 5396 dbSNP
rs1439859157 5397 dbSNP
rs919343151 5402 dbSNP
rs1196198126 5405 dbSNP
rs1489463455 5407 dbSNP
rs769467467 5408 dbSNP
rs1451015413 5409 dbSNP
rs1036399648 5412 dbSNP
rs1388755879 5413 dbSNP
rs992214246 5414 dbSNP
rs14870 5425 dbSNP
rs1319728701 5426 dbSNP
rs984467195 5427 dbSNP
rs747780337 5433 dbSNP
rs1437612213 5440 dbSNP
rs1295640783 5443 dbSNP
rs188780133 5457 dbSNP
rs1311131815 5459 dbSNP
rs1242603789 5461 dbSNP
rs1364232772 5462 dbSNP
rs1234690936 5463 dbSNP
rs1280666370 5463 dbSNP
rs1310297536 5465 dbSNP
rs1377910657 5465 dbSNP
rs3177046 5466 dbSNP
rs1209329741 5467 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 GSM545217. RNA binding protein: AGO2. Condition:miR-7 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 23543.0
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 GSM714645. RNA binding protein: AGO2. Condition:completeT1 "PAR-CLIP data was present in GSM714646. RNA binding protein: AGO2. Condition:mildMNase "PAR-CLIP data was present in GSM714647. RNA binding protein: AGO2. Condition:mildMNase ...

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

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 23543.0
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 GSM1065668. RNA binding protein: AGO1. Condition:4-thiouridine "PAR-CLIP data was present in GSM1065669. RNA binding protein: AGO1. Condition:4-thiouridine "PAR-CLIP data was present in GSM1065670. RNA binding protein: AGO2. 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]
Experimental Support 4 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
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 GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

- Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio.

Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
CLIP-seq Support 1 for dataset GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_001082577 | 3UTR | UGACUCCUCAGGGGCUAAACUGCUCUUAGCUUAGAAUUAUGCUUUACUAGAGAUCUAGCAGAUAAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903834
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_b
Location of target site NM_014309 | 3UTR | AGAAGUCAUCGAUAGCAGCUUUUCCUCAAAUGUGUGACUCCUCAGGGGCUAAACUGCUCUUAGCUUAGAAUUAUGCUUUACUAGAGAUCUAGCAGAUAAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903835
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_c
Location of target site NM_014309 | 3UTR | AGUCUGAGGGGAGCUAGUGGAAAUCUAGACAAUAGAAGUCAUCGAUAGCAGCUUUUCCUCAAAUGUGUGACUCCUCAGGGGCUAAACUGCUCUUAGCUUAGAAUUAUGCUUUACUAGAGAUCUAGCAGAUAAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4903836
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_a
Location of target site NM_001082577 | 3UTR | GCAGCUUUUCCUCAAAUGUGUGACUCCUCAGGGGCUAAACUGCUCUUAGCUUAGAAUUAUGCUUUACUAGAGAUCUAGCAGAUAAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM4903837
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_b
Location of target site NM_001082577 | 3UTR | AUAGCAGCUUUUCCUCAAAUGUGUGACUCCUCAGGGGCUAAACUGCUCUUAGCUUAGAAUUAUGCUUUACUAGAGAUCUAGCAGAUAAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_014309 | 3UTR | CUCUUAGCUUAGAAUUAUGCUUUACUAGAGAUCUAGCAGAUAAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM545217
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-7 transfection
Location of target site ENST00000449924.2 | 3UTR | AGGCCUGGCUAUUGCAAUAUUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 8 for dataset GSM714645
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repB
Location of target site ENST00000449924.2 | 3UTR | AGGCCUGGCUAUUGCAAUAUUUACUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 9 for dataset GSM714646
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / mildMNase, repA
Location of target site ENST00000449924.2 | 3UTR | AGUUCAUGAGGCCUGGCUAUUGCAAUAUUUACUAGUAGAG
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 GSM714647
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / mildMNase, repB
Location of target site ENST00000449924.2 | 3UTR | UCAUGAGGCCUGGCUAUUGCAAUAUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 11 for dataset GSM1065668
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_7
Location of target site ENST00000449924.2 | 3UTR | AGGCCUGGCUAUUGCAAUAUUUACUA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 12 for dataset GSM1065669
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_8
Location of target site ENST00000449924.2 | 3UTR | AGGCCUGGCUAUUGCAAUAUUUACUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 13 for dataset GSM1065670
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / 4-thiouridine, 3_ML_LG
Location of target site ENST00000449924.2 | 3UTR | UUCAUGAGGCCUGGCUAUUGCAAUAUUUACUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 14 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000449924.2 | 3UTR | UUCAUGAGGCCUGGCUAUUGCAAUAUUUACUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
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
GSE28544 Breast cancer -0.503 6.1e-3 -0.452 1.3e-2 24 Click to see details
GSE32688 Pancreatic cancer -0.334 3.1e-2 -0.302 4.6e-2 32 Click to see details
GSE28260 Renal cortex and medulla 0.513 3.7e-2 0.527 3.2e-2 13 Click to see details
GSE19536 Breast cancer 0.17 4.5e-2 0.220 1.4e-2 100 Click to see details
GSE38974 Chronic obstructive pulmonary disease -0.269 9.7e-2 -0.326 5.6e-2 25 Click to see details
GSE19783 ER- ER- breast cancer 0.145 1.0e-1 0.168 6.9e-2 79 Click to see details
GSE27834 Pluripotent stem cells -0.306 1.2e-1 -0.194 2.4e-1 16 Click to see details
GSE19783 ER+ ER+ breast cancer 0.258 1.4e-1 0.254 1.4e-1 20 Click to see details
GSE19350 CNS germ cell tumors -0.267 2.0e-1 -0.168 3.0e-1 12 Click to see details
GSE38226 Liver fibrosis 0.161 2.4e-1 0.084 3.6e-1 21 Click to see details
GSE17306 Multiple myeloma -0.1 2.5e-1 -0.117 2.1e-1 49 Click to see details
GSE17498 Multiple myeloma 0.108 2.5e-1 0.018 4.6e-1 40 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis -0.148 2.7e-1 -0.140 2.8e-1 20 Click to see details
GSE14794 Lymphoblastoid cells -0.065 2.7e-1 -0.112 1.5e-1 90 Click to see details
GSE26953 Aortic valvular endothelial cells 0.089 3.4e-1 0.104 3.1e-1 24 Click to see details
GSE21849 B cell lymphoma 0.048 4.0e-1 0.443 8.0e-3 29 Click to see details
GSE42095 Differentiated embryonic stem cells 0.043 4.2e-1 0.054 4.0e-1 23 Click to see details
GSE21687 Ependynoma primary tumors 0.024 4.3e-1 -0.003 4.9e-1 64 Click to see details
GSE21687 Ependynoma primary tumors 0.024 4.3e-1 -0.003 4.9e-1 64 Click to see details
GSE21687 Ependynoma primary tumors 0.024 4.3e-1 -0.003 4.9e-1 64 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 -0.609 0 -0.553 0 28 Click to see details
ESCA -0.633 0.02 -0.536 0.04 11 Click to see details
KIRP -0.384 0.02 -0.357 0.03 29 Click to see details
KIRC -0.277 0.04 -0.252 0.06 40 Click to see details
THCA 0.205 0.06 0.245 0.03 58 Click to see details
PAAD -0.854 0.07 -1.000 0.5 4 Click to see details
PCPG 0.911 0.14 0.500 0.33 3 Click to see details
HNSC 0.172 0.16 0.118 0.25 35 Click to see details
BLCA -0.225 0.19 -0.289 0.13 17 Click to see details
LUAD -0.245 0.25 -0.321 0.18 10 Click to see details
LIHC -0.081 0.29 -0.138 0.17 49 Click to see details
BRCA 0.086 0.31 -0.038 0.42 34 Click to see details
LUSC -0.066 0.35 0.014 0.47 35 Click to see details
PRAD -0.062 0.36 -0.185 0.14 36 Click to see details
CHOL -0.164 0.36 -0.107 0.41 7 Click to see details
KICH 0.045 0.42 0.081 0.36 22 Click to see details
CESC -0.234 0.42 -0.500 0.33 3 Click to see details
UCEC 0.034 0.45 -0.051 0.42 18 Click to see details
UCEC 0.034 0.45 -0.051 0.42 18 Click to see details
27 hsa-miR-628-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT039584 CDC14A cell division cycle 14A 1 1
MIRT039585 AGO1 argonaute 1, RISC catalytic component 2 3
MIRT039586 TGFBRAP1 transforming growth factor beta receptor associated protein 1 1 1
MIRT039587 LRP6 LDL receptor related protein 6 1 1
MIRT071876 BTF3L4 basic transcription factor 3 like 4 2 2
MIRT097443 JMY junction mediating and regulatory protein, p53 cofactor 2 4
MIRT100100 ABT1 activator of basal transcription 1 2 8
MIRT147692 CBX4 chromobox 4 2 2
MIRT408248 PURA purine rich element binding protein A 2 2
MIRT442047 LRAT lecithin retinol acyltransferase 2 2
MIRT444412 RAB3IP RAB3A interacting protein 2 2
MIRT452599 REPIN1 replication initiator 1 2 2
MIRT469515 RBFOX2 RNA binding protein, fox-1 homolog 2 2 8
MIRT498192 AKR1B10 aldo-keto reductase family 1 member B10 2 2
MIRT500151 CREBBP CREB binding protein 2 2
MIRT507319 FAM60A SIN3-HDAC complex associated factor 2 6
MIRT508343 ZNF273 zinc finger protein 273 2 6
MIRT520480 TRIM13 tripartite motif containing 13 2 2
MIRT522461 MMP16 matrix metallopeptidase 16 2 4
MIRT547116 PHLPP2 PH domain and leucine rich repeat protein phosphatase 2 2 2
MIRT548675 CRNKL1 crooked neck pre-mRNA splicing factor 1 2 2
MIRT553756 TARBP2 TARBP2, RISC loading complex RNA binding subunit 2 4
MIRT559437 ARSJ arylsulfatase family member J 2 2
MIRT610490 GPC4 glypican 4 2 2
MIRT644682 TMCO1 transmembrane and coiled-coil domains 1 2 2
MIRT658214 FBXO21 F-box protein 21 2 2
MIRT756083 TP53 tumor protein p53 4 1
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-628 Cisplatin 5460033 NSC119875 approved sensitive cell line (BxPC3)
hsa-miR-628-3p Cisplatin 5460033 NSC119875 approved resistant High Tongue Squamous Cell Carcinoma cell line (Tca8113)
hsa-miR-628-3p Tamoxifen 2733525 NSC180973 approved resistant High Breast Cancer cell line (MCF-7, LY2)
hsa-miR-628-3p Erlotinib 176870 NSC718781 approved sensitive High Epithelial Cancer cell line (A549, UKY-29, H460, H1975, H1650, H3255, PC-9, H358)
hsa-miR-628-3p Siop Treatment Protocol sensitive High Nephroblastoma tissue
hsa-miR-628-3p Sunitinib 5329102 NSC750690 approved resistant High Metastatic Renal Cell Carcinoma tissue and cell line (Caki-2)
hsa-miR-628-3p Chemotherapy sensitive High Epithelial Ovarian Cancer tissue
hsa-miR-628-3p Platinum-based doublet chemotherapy resistant Low Lung Adenocarcinoma tissue
hsa-miR-628-3p Doxorubicin 31703 NSC123127 approved sensitive High Gastric Cancer cell line (SGC7901)
hsa-miR-628-3p Tamoxifen 2733525 NSC180973 approved resistant High Breast Cancer cell line (TAMR8)
hsa-miR-628-3p Aromatase Inhibitor sensitive Low Breast Cancer cell line (MCF-7)
hsa-miR-628-3p Dabrafenib 44462760 NSC764134 approved resistant High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-628-3p Vemurafenib 42611257 NSC761431 approved resistant High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-628-3p Ceritinib 57379345 NSC776422 approved sensitive High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-miR-628-3p Platinum 23939 sensitive High High-Grade Serous Ovarian Cancer tissue
hsa-miR-628-3p Cisplatin 5460033 NSC119875 approved sensitive High Bladder Cancer cell line (CDDP-R-BOY, CDDP-R-T24)
hsa-miR-628-3p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-628-3p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-628-3p Fluorouracil 3385 NSC19893 approved resistant cell line (KM12C) (72 h)
hsa-miR-628-3p Sunitinib 5329102 NSC750690 approved resistant tissue (CardB)
hsa-miR-628-3p Tamoxifen 2733525 NSC180973 approved resistant cell line (TamR8)
hsa-miR-628-3p Oxaliplatin 6857599 NSC266046 approved sensitive cell line (IGROV-1)
hsa-miR-628-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-628-3p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-628-3p Docetaxel+Cisplatin+5-Fluorouracil sensitive tissue (hypopharyngeal squamous cell carcinoma)

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