miRTarBase - #MIRT525601


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pre-miRNA Information
pre-miRNA hsa-mir-3120   
Genomic Coordinates chr1: 172138808 - 172138888
Description Homo sapiens miR-3120 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3120-5p
Sequence 13| CCUGUCUGUGCCUGCUGUACA |33
Evidence Experimental
Experiments Illumina
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 19 1 + 172138838 26449202, 27587585 MiREDiBase
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN26637643 8 COSMIC
COSN31603497 11 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs750386761 8 dbSNP
rs760725207 9 dbSNP
rs766486759 10 dbSNP
rs754055278 12 dbSNP
rs755288536 19 dbSNP
rs754726014 21 dbSNP
Putative Targets

Gene Information
Gene Symbol OLR1   
Synonyms CLEC8A, LOX1, LOXIN, SCARE1, SLOX1
Description oxidized low density lipoprotein receptor 1
Transcript NM_001172632   
Other Transcripts NM_001172633 , NM_002543   
Expression
Putative miRNA Targets on OLR1
3'UTR of OLR1
(miRNA target sites are highlighted)		 
>OLR1|NM_001172632|3'UTR
   1 AGTCCGAGGCGCTGTCTCCCAGACATACCCTTCAGGTACCTGTGCATATATACAACGAGGAGCTGTTTATGCGGAAAACT
  81 GCATTTTAGCTGCCTTCAGTATATGTCAGAAGAAGGCAAACCTAAGAGCACAGTGAATTTGAAGGCTCTGGAAGAAAAGA
 161 AAAAAGTCTTTGAGTTTTATTCTGGAATTTAAGCTATTCTTTGTCACTTGGGTGCCAAACATGAGAGCCCAGAAAACTGT
 241 CATTTAGCTGGCTGCAGAACTCCTTTGCAGAAACTGGGGTTCCAGGTGCCTGGCACCTTTATGTCAACATTTTTGATTCT
 321 AGCTACCTGTATTATTTCACCTAGCTTGTCCCAAGCTTCCCTGCCAGCCTGAAGTCCATTTTCCCCTTTTTATTTTAAAA
 401 TTTGACTCCTCTTCAAGCTTGAAAACCCTCTGAACTCAGTCTTCTTTACCTCATTATCACCTTCCCCTCACACTCCTAAA
 481 ATTGCATGAAAGACAGAACATGGAGAACTTGCTCAAGTGCAGGCAGAGAGCAAAAAGGGGAAATATGTCTGGGAAAAAGT
 561 GCACGTGAAGAAACAAAGAAGGACAGAGGCCATTCCGAAATCAAGAAACTCATGTTCTTAACTTTAAAAAAGGTATCAAT
 641 CCTTGGTTTTTAAACTGTGGTCCATCTCCAGACTCTACCACTTACGGACAGACAGACAGACAGACACACACACACACACA
 721 CACACACATTTTGGGACAAGTGGGGAGCCCAAGAAAGTAATTAGTAAGTGAGTGGTCTTTTCTGTAAGCTAATCCACAAC
 801 CTGTTACCACTTCCTGAATCAGTTATTATTTCTTCATTTTTTTTTCTACCAGAGGACAGATTAATAGATTTAACCCTTCA
 881 CAACAGTTCTTGTTAGAATCATGGGATGTGTGGCCCAGAGGTAAGAATAGAATTTCTTTCCCTAAAGAACATACCTTTTG
 961 TAGATGAACTCTTCTCAACTCTGTTTTGCTATGCTATAATTCCGAAACATACAAGACAAAAAAAATGAAGACACTCAATC
1041 TAGAACAAACTAAGCCAGGTATGCAAATATCGCTGAATAGAAACAGATGGAATTAGAAATATATCTTCTATTTTTAGGCT
1121 TCTATTTCCTTTCCACCCACTCTTCACAGGCTATTCTACTTTAAAGGAAGCCTTTTTATTTTGCTGCACACAATCTAGCA
1201 GGAATCTTTTTTTTTTTTTAAGAGCTGTGTCATCCTTATGTAGGCAAGAGATGTTTGCTTTTGTTAAAAGCTTTATTGAG
1281 ATATAATTAACATAAAATAAACTGAACATATTTAAAGTGTACTATTTGATAAGTTTTCACACCTTGTGGAGAACATGCAT
1361 ACTACAATTAAGAGAGTGAACATATCCATCATCCCTCAAAGTGTCACAATGCTCCTCCTGATGACTCCTCCCCAGAAAAC
1441 CACCAATCGGCTTTCATTTTGCATTTTGTAGTTTTATGTGAATGGAATCATATAGTATGTCTTTTTTTTTTGTCTGGCTT
1521 CTTTCACTTTGCATAATTATTTTGAGATTCATATGTCTCCATCTTGATGCTCGTATGAATTCATTCTTTTAAATGTTGAA
1601 TATTCCCTTGTATGGATATACCACAATTCATTTACCCATTTACTTGTTGATGACATTTGGGTTGTTTTAGTTTTGGGATA
1681 TTACAAATAAAGCTGCTGTGAACATTTGTGTACAAGAAAAAAAAAAAAAAAAA
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' acAUGUC-GUCCG--UGUCUGUCc 5'
            |||:| ||| |  |||||||| 
Target 5' ctTACGGACAGACAGACAGACAGa 3'
 681 - 704 165.00 -17.30
2 
miRNA  3' acaugucGUCCGUGUCUGUCc 5'
                 || |::|||:||| 
Target 5' acttgctCAAGTGCAGGCAGa 3'
 507 - 527 138.00 -11.40
3 
miRNA  3' acaUGUCGUCCGUGUCUGUCc 5'
             |: ||| | | |||||| 
Target 5' aaaATTGCATG-AAAGACAGa 3'
 478 - 497 125.00 -9.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
6995 324 ClinVar
COSM2063892 6 COSMIC
COSM5764029 10 COSMIC
COSM5535967 18 COSMIC
COSM3455191 20 COSMIC
COSM3870565 29 COSMIC
COSM9868864 35 COSMIC
COSM6577067 50 COSMIC
COSM8414884 55 COSMIC
COSM3383975 56 COSMIC
COSM6071191 60 COSMIC
COSM6874527 65 COSMIC
COSM7828832 68 COSMIC
COSM8572872 72 COSMIC
COSM6733321 73 COSMIC
COSM9466257 74 COSMIC
COSM5778955 89 COSMIC
COSM6071192 89 COSMIC
COSM4038082 91 COSMIC
COSM6733322 101 COSMIC
COSM8806900 105 COSMIC
COSM7319227 106 COSMIC
COSM6000205 107 COSMIC
COSM4749843 117 COSMIC
COSM5725976 126 COSMIC
COSM163081 127 COSMIC
COSN31542501 146 COSMIC
COSN30459011 148 COSMIC
COSN19699868 159 COSMIC
COSN31538871 159 COSMIC
COSN31573474 177 COSMIC
COSN30488879 185 COSMIC
COSN31580688 189 COSMIC
COSN31522199 190 COSMIC
COSN16580558 192 COSMIC
COSN31495270 195 COSMIC
COSN31601982 199 COSMIC
COSN7307657 222 COSMIC
COSN30112595 263 COSMIC
COSN31610403 294 COSMIC
COSN28707705 326 COSMIC
COSN31578787 377 COSMIC
COSN31527854 381 COSMIC
COSN31539884 382 COSMIC
COSN8585174 386 COSMIC
COSN8585173 391 COSMIC
COSN23880975 408 COSMIC
COSN5314378 413 COSMIC
COSN31541513 428 COSMIC
COSN31523266 568 COSMIC
COSN31596789 621 COSMIC
COSN24294675 626 COSMIC
COSN19337509 684 COSMIC
COSN23706840 699 COSMIC
COSN20109210 702 COSMIC
COSN24731251 703 COSMIC
COSN27221039 703 COSMIC
COSN22258462 885 COSMIC
COSN20758540 1086 COSMIC
COSN8692020 1193 COSMIC
COSN20109207 1206 COSMIC
COSN29767199 1501 COSMIC
COSN10096335 1669 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1056125322 2 dbSNP
rs199989233 5 dbSNP
rs986422401 6 dbSNP
rs1255753047 7 dbSNP
rs140400766 10 dbSNP
rs535180296 11 dbSNP
rs778185706 14 dbSNP
rs763828543 17 dbSNP
rs1434673386 18 dbSNP
rs1327080047 19 dbSNP
rs1320415681 22 dbSNP
rs146768121 28 dbSNP
rs765325570 31 dbSNP
rs1401481108 44 dbSNP
rs1174203633 46 dbSNP
rs1045169061 48 dbSNP
rs374394285 56 dbSNP
rs1388126264 64 dbSNP
rs897928133 65 dbSNP
rs753886560 70 dbSNP
rs374494106 72 dbSNP
rs370707474 73 dbSNP
rs1189764015 77 dbSNP
rs1184848638 79 dbSNP
rs1441345415 81 dbSNP
rs771828476 93 dbSNP
rs577739742 99 dbSNP
rs1477039270 101 dbSNP
rs1350439609 103 dbSNP
rs1272993571 106 dbSNP
rs1421643708 109 dbSNP
rs1410024324 112 dbSNP
rs143492178 113 dbSNP
rs1227908282 118 dbSNP
rs368924076 120 dbSNP
rs1340404592 124 dbSNP
rs557756840 126 dbSNP
rs1436152952 129 dbSNP
rs759534798 129 dbSNP
rs1339953580 130 dbSNP
rs1313134582 131 dbSNP
rs1313373404 132 dbSNP
rs1416569692 133 dbSNP
rs1340184018 136 dbSNP
rs775134477 139 dbSNP
rs1307252179 141 dbSNP
rs747491547 145 dbSNP
rs778031576 157 dbSNP
rs1161095451 159 dbSNP
rs758714127 160 dbSNP
rs1035542814 165 dbSNP
rs773946372 166 dbSNP
rs748491543 167 dbSNP
rs770787725 167 dbSNP
rs779149604 171 dbSNP
rs1227734693 172 dbSNP
rs574510080 175 dbSNP
rs753926543 179 dbSNP
rs1250060613 183 dbSNP
rs374709504 184 dbSNP
rs1438768383 187 dbSNP
rs1279899571 194 dbSNP
rs1441624839 196 dbSNP
rs1185211259 212 dbSNP
rs1243750059 222 dbSNP
rs1475721516 225 dbSNP
rs1449230326 232 dbSNP
rs905240653 248 dbSNP
rs575452645 260 dbSNP
rs1387732168 261 dbSNP
rs946641968 266 dbSNP
rs772122949 268 dbSNP
rs1260342489 275 dbSNP
rs893694356 278 dbSNP
rs1436056800 280 dbSNP
rs1173800270 282 dbSNP
rs4237962 287 dbSNP
rs935182876 296 dbSNP
rs1320748735 297 dbSNP
rs1346275719 308 dbSNP
rs1486244882 315 dbSNP
rs12316150 324 dbSNP
rs1220579826 325 dbSNP
rs1050283 326 dbSNP
rs1235123603 329 dbSNP
rs1028408951 335 dbSNP
rs942425571 340 dbSNP
rs1198479159 341 dbSNP
rs1286038381 351 dbSNP
rs1447385613 357 dbSNP
rs1207968205 364 dbSNP
rs753992352 367 dbSNP
rs910894520 371 dbSNP
rs962752685 376 dbSNP
rs1193785349 382 dbSNP
rs553080240 385 dbSNP
rs1476860510 392 dbSNP
rs1159974758 394 dbSNP
rs1293352545 395 dbSNP
rs749954561 397 dbSNP
rs1319054866 404 dbSNP
rs952287098 408 dbSNP
rs181195036 412 dbSNP
rs867663831 415 dbSNP
rs1323013548 418 dbSNP
rs1329444334 426 dbSNP
rs1241390733 439 dbSNP
rs962556349 443 dbSNP
rs1329519369 448 dbSNP
rs1301944369 453 dbSNP
rs1227629359 458 dbSNP
rs1035191354 465 dbSNP
rs887266038 467 dbSNP
rs190216641 472 dbSNP
rs1209882661 482 dbSNP
rs1367116272 498 dbSNP
rs1449405340 516 dbSNP
rs550520331 518 dbSNP
rs1163825184 525 dbSNP
rs1461801437 532 dbSNP
rs1364027568 538 dbSNP
rs1371641594 543 dbSNP
rs969409368 546 dbSNP
rs904902879 548 dbSNP
rs1328566318 551 dbSNP
rs531114395 562 dbSNP
rs1163210025 564 dbSNP
rs1023603158 565 dbSNP
rs1393217885 580 dbSNP
rs1197427842 582 dbSNP
rs1490856392 586 dbSNP
rs1350167170 588 dbSNP
rs1010836297 596 dbSNP
rs1336717209 597 dbSNP
rs1245370487 607 dbSNP
rs1044828971 609 dbSNP
rs1353568657 611 dbSNP
rs1292858329 625 dbSNP
rs1197107972 626 dbSNP
rs1204614835 632 dbSNP
rs946347111 634 dbSNP
rs893787694 636 dbSNP
rs1179602543 642 dbSNP
rs10505755 653 dbSNP
rs1475746746 654 dbSNP
rs1187375429 656 dbSNP
rs935268849 670 dbSNP
rs1168619940 673 dbSNP
rs999443857 674 dbSNP
rs1420758461 675 dbSNP
rs911724498 678 dbSNP
rs901042970 680 dbSNP
rs1282546718 681 dbSNP
rs548589878 685 dbSNP
rs17808009 686 dbSNP
rs781251301 688 dbSNP
rs931840641 689 dbSNP
rs151080645 690 dbSNP
rs1303394904 694 dbSNP
rs1390416623 695 dbSNP
rs1394825573 698 dbSNP
rs76039690 699 dbSNP
rs1462798533 701 dbSNP
rs1801809 703 dbSNP
rs59626458 703 dbSNP
rs58628154 704 dbSNP
rs1189811025 705 dbSNP
rs1491226407 705 dbSNP
rs61523668 705 dbSNP
rs754931154 705 dbSNP
rs113230765 707 dbSNP
rs1447750936 707 dbSNP
rs921316777 707 dbSNP
rs1399833687 709 dbSNP
rs1481460915 709 dbSNP
rs1269621841 717 dbSNP
rs1298255489 721 dbSNP
rs143220784 721 dbSNP
rs1181386315 725 dbSNP
rs35568748 726 dbSNP
rs371184661 727 dbSNP
rs377471306 728 dbSNP
rs1225632096 729 dbSNP
rs34435182 729 dbSNP
rs753989762 729 dbSNP
rs779614686 729 dbSNP
rs1387890384 749 dbSNP
rs1432235106 757 dbSNP
rs1327381390 758 dbSNP
rs1048109964 762 dbSNP
rs975540263 770 dbSNP
rs1197385782 772 dbSNP
rs1298761697 776 dbSNP
rs963016890 777 dbSNP
rs930990112 780 dbSNP
rs982989387 801 dbSNP
rs533021686 811 dbSNP
rs1035238383 821 dbSNP
rs1380944468 827 dbSNP
rs1221551585 838 dbSNP
rs1003634337 846 dbSNP
rs1473442619 846 dbSNP
rs972764606 866 dbSNP
rs1159692274 881 dbSNP
rs962280756 885 dbSNP
rs969597132 888 dbSNP
rs1023781996 901 dbSNP
rs185807023 903 dbSNP
rs1166860151 908 dbSNP
rs1349897100 912 dbSNP
rs1435137135 913 dbSNP
rs1010684674 914 dbSNP
rs893454575 921 dbSNP
rs377485340 930 dbSNP
rs999193802 944 dbSNP
rs147287871 949 dbSNP
rs890342284 951 dbSNP
rs1235616621 953 dbSNP
rs544245192 954 dbSNP
rs921813417 969 dbSNP
rs1237668504 970 dbSNP
rs1333675652 977 dbSNP
rs1483526888 984 dbSNP
rs1181768770 987 dbSNP
rs143980830 996 dbSNP
rs1183458665 1001 dbSNP
rs1392398940 1002 dbSNP
rs181429704 1003 dbSNP
rs34938789 1004 dbSNP
rs1371991555 1008 dbSNP
rs1335330189 1010 dbSNP
rs1471213984 1012 dbSNP
rs1430108466 1015 dbSNP
rs1307039101 1016 dbSNP
rs1158109973 1017 dbSNP
rs1348940847 1026 dbSNP
rs958068096 1037 dbSNP
rs1285287773 1040 dbSNP
rs1031000466 1043 dbSNP
rs1379142581 1048 dbSNP
rs1050286 1052 dbSNP
rs901057240 1059 dbSNP
rs1182717512 1061 dbSNP
rs1204632457 1062 dbSNP
rs552716540 1071 dbSNP
rs36051049 1072 dbSNP
rs1242254459 1076 dbSNP
rs1237966525 1083 dbSNP
rs1180080554 1088 dbSNP
rs1201731329 1088 dbSNP
rs1462630464 1089 dbSNP
rs75688283 1098 dbSNP
rs1449544816 1105 dbSNP
rs557031762 1109 dbSNP
rs1368376746 1122 dbSNP
rs1023839474 1123 dbSNP
rs957734255 1124 dbSNP
rs766688088 1130 dbSNP
rs1300464325 1137 dbSNP
rs931047379 1144 dbSNP
rs918248595 1147 dbSNP
rs1295664096 1150 dbSNP
rs35738181 1161 dbSNP
rs568346386 1170 dbSNP
rs940950941 1171 dbSNP
rs1313321210 1183 dbSNP
rs900328681 1186 dbSNP
rs1207844559 1192 dbSNP
rs1249891594 1193 dbSNP
rs1464944360 1201 dbSNP
rs1407533462 1204 dbSNP
rs1387901899 1205 dbSNP
rs201636631 1206 dbSNP
rs1399031033 1207 dbSNP
rs1037580454 1216 dbSNP
rs1172821628 1220 dbSNP
rs1449821884 1220 dbSNP
rs35678209 1220 dbSNP
rs373801260 1220 dbSNP
rs1387159690 1225 dbSNP
rs1332943348 1231 dbSNP
rs928212585 1232 dbSNP
rs1159390688 1244 dbSNP
rs1274486574 1265 dbSNP
rs1344022264 1270 dbSNP
rs1221519310 1274 dbSNP
rs757567609 1276 dbSNP
rs1269917294 1280 dbSNP
rs1329818069 1288 dbSNP
rs1444195875 1290 dbSNP
rs1245614758 1293 dbSNP
rs941862859 1302 dbSNP
rs1245839683 1303 dbSNP
rs948250438 1308 dbSNP
rs149011911 1317 dbSNP
rs528749641 1322 dbSNP
rs566290994 1324 dbSNP
rs138695853 1328 dbSNP
rs1446219204 1329 dbSNP
rs1392884858 1342 dbSNP
rs1238052024 1356 dbSNP
rs1323124261 1364 dbSNP
rs929955921 1365 dbSNP
rs1402837773 1367 dbSNP
rs1289937714 1371 dbSNP
rs1350907023 1374 dbSNP
rs927992878 1376 dbSNP
rs1258898464 1381 dbSNP
rs982763910 1383 dbSNP
rs1209978841 1391 dbSNP
rs1288675334 1392 dbSNP
rs1489745341 1393 dbSNP
rs969706948 1396 dbSNP
rs1031430070 1401 dbSNP
rs978089788 1409 dbSNP
rs1472478398 1411 dbSNP
rs1180639023 1414 dbSNP
rs1458452464 1417 dbSNP
rs1162778153 1426 dbSNP
rs916819721 1427 dbSNP
rs144993624 1430 dbSNP
rs958204361 1432 dbSNP
rs1019566399 1433 dbSNP
rs1006799142 1446 dbSNP
rs1285685937 1448 dbSNP
rs1050289 1449 dbSNP
rs1244846243 1451 dbSNP
rs1026780218 1462 dbSNP
rs1356677729 1466 dbSNP
rs1289110960 1467 dbSNP
rs1248700005 1468 dbSNP
rs1030034360 1472 dbSNP
rs1194486074 1483 dbSNP
rs372674682 1484 dbSNP
rs1380265633 1488 dbSNP
rs995262617 1490 dbSNP
rs1187487019 1491 dbSNP
rs35555206 1493 dbSNP
rs1429180943 1494 dbSNP
rs1037120761 1496 dbSNP
rs1370252355 1497 dbSNP
rs938383353 1503 dbSNP
rs1246301188 1506 dbSNP
rs534039079 1508 dbSNP
rs886291715 1511 dbSNP
rs1379861826 1512 dbSNP
rs201512084 1512 dbSNP
rs930095062 1512 dbSNP
rs530557200 1514 dbSNP
rs1424076409 1516 dbSNP
rs1364015165 1517 dbSNP
rs1165701950 1518 dbSNP
rs1426318055 1521 dbSNP
rs1046661827 1533 dbSNP
rs759152806 1534 dbSNP
rs948306010 1541 dbSNP
rs1224823171 1551 dbSNP
rs1258082537 1559 dbSNP
rs774385114 1568 dbSNP
rs916753005 1572 dbSNP
rs771043948 1573 dbSNP
rs990155780 1576 dbSNP
rs1185878383 1583 dbSNP
rs936802846 1585 dbSNP
rs1426924642 1593 dbSNP
rs866667095 1598 dbSNP
rs1178537787 1602 dbSNP
rs1379099006 1605 dbSNP
rs1466368930 1615 dbSNP
rs1171909929 1618 dbSNP
rs1403875545 1621 dbSNP
rs924133706 1626 dbSNP
rs1474361112 1627 dbSNP
rs1465330611 1629 dbSNP
rs1302959887 1635 dbSNP
rs977830938 1658 dbSNP
rs561499464 1661 dbSNP
rs954485031 1664 dbSNP
rs1261793011 1668 dbSNP
rs1331895279 1671 dbSNP
rs989574892 1674 dbSNP
rs1193813843 1683 dbSNP
rs1484943683 1684 dbSNP
rs1193070257 1701 dbSNP
rs974403688 1706 dbSNP
rs1490039822 1709 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions hESCs (WA-09)
Disease 4973.0
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 SRR359787. RNA binding protein: AGO2. Condition:4-thiouridine ...

- Lipchina I; Elkabetz Y; Hafner M; Sheridan et al., 2011, Genes & development.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' acaUGUCGUCCGUGUCUGUcc 5'
             ||| ||  |||| |||  
Target 5' --gACA-CACACACACACAca 3'
 		1 - 18
Article - Lipchina I; Elkabetz Y; Hafner M; Sheridan et al.
- Genes & development, 2011
MicroRNAs are important regulators in many cellular processes, including stem cell self-renewal. Recent studies demonstrated their function as pluripotency factors with the capacity for somatic cell reprogramming. However, their role in human embryonic stem (ES) cells (hESCs) remains poorly understood, partially due to the lack of genome-wide strategies to identify their targets. Here, we performed comprehensive microRNA profiling in hESCs and in purified neural and mesenchymal derivatives. Using a combination of AGO cross-linking and microRNA perturbation experiments, together with computational prediction, we identified the targets of the miR-302/367 cluster, the most abundant microRNAs in hESCs. Functional studies identified novel roles of miR-302/367 in maintaining pluripotency and regulating hESC differentiation. We show that in addition to its role in TGF-beta signaling, miR-302/367 promotes bone morphogenetic protein (BMP) signaling by targeting BMP inhibitors TOB2, DAZAP2, and SLAIN1. This study broadens our understanding of microRNA function in hESCs and is a valuable resource for future studies in this area.
LinkOut: [PMID: 22012620]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293S
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in GSM1084078. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep2_AbnovaAb ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' acaugucguccgUGUCUGUcc 5'
                      |||||||  
Target 5' -----------gACAGACAca 3'
 		1 - 10
Article - Karginov FV; Hannon GJ
- Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
CLIP-seq Support 1 for dataset GSM1084078
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep2_AbnovaAb
Location of target site ENST00000543993.1 | 3UTR | GACAGACACACACACACACACACACACAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset SRR359787
Method / RBP PAR-CLIP / AGO2
Cell line / Condition hESCs (WA-09) / 4-thiouridine, RNase T1
Location of target site ENST00000543993.1 | 3UTR | GACACACACACACACACACACACACAUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22012620 / SRX103431
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
134 hsa-miR-3120-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT096972 BDP1 B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB 2 2
MIRT442624 LOX lysyl oxidase 2 2
MIRT473438 MDM4 MDM4, p53 regulator 2 2
MIRT490011 KIFC2 kinesin family member C2 2 2
MIRT496449 N6AMT1 N-6 adenine-specific DNA methyltransferase 1 2 2
MIRT496752 TGIF2 TGFB induced factor homeobox 2 2 2
MIRT497721 CYP1A1 cytochrome P450 family 1 subfamily A member 1 2 2
MIRT498287 PADI3 peptidyl arginine deiminase 3 2 2
MIRT503195 ACVR1B activin A receptor type 1B 2 4
MIRT504760 TEP1 telomerase associated protein 1 2 4
MIRT517810 UGDH UDP-glucose 6-dehydrogenase 2 6
MIRT519686 ZNF622 zinc finger protein 622 2 4
MIRT520263 URGCP upregulator of cell proliferation 2 2
MIRT523051 ICMT isoprenylcysteine carboxyl methyltransferase 2 2
MIRT525601 OLR1 oxidized low density lipoprotein receptor 1 2 4
MIRT526995 ARL8B ADP ribosylation factor like GTPase 8B 2 2
MIRT528699 TRAF3IP2 TRAF3 interacting protein 2 2 4
MIRT533142 WNT10A Wnt family member 10A 2 2
MIRT537618 ERI1 exoribonuclease 1 2 2
MIRT539707 EIF3H eukaryotic translation initiation factor 3 subunit H 2 2
MIRT539752 CNBP CCHC-type zinc finger nucleic acid binding protein 2 2
MIRT539808 GAPVD1 GTPase activating protein and VPS9 domains 1 2 2
MIRT539941 IFNAR2 interferon alpha and beta receptor subunit 2 2 2
MIRT540424 FAM83F family with sequence similarity 83 member F 2 2
MIRT540509 CXCL10 C-X-C motif chemokine ligand 10 2 2
MIRT540720 GUF1 GUF1 homolog, GTPase 2 2
MIRT541630 PARP2 poly(ADP-ribose) polymerase 2 2 2
MIRT542286 POLR3K RNA polymerase III subunit K 2 2
MIRT542456 AKR7A2 aldo-keto reductase family 7 member A2 2 2
MIRT542550 MRPS10 mitochondrial ribosomal protein S10 2 2
MIRT542771 PPAP2B phospholipid phosphatase 3 2 2
MIRT550085 TRAPPC2 trafficking protein particle complex 2 2 2
MIRT551458 CARKD NAD(P)HX dehydratase 2 2
MIRT555622 PHLPP2 PH domain and leucine rich repeat protein phosphatase 2 2 2
MIRT569136 KATNAL1 katanin catalytic subunit A1 like 1 2 2
MIRT572328 HSPB6 heat shock protein family B (small) member 6 2 2
MIRT574607 LZIC leucine zipper and CTNNBIP1 domain containing 2 2
MIRT575583 Mcm8 minichromosome maintenance 8 homologous recombination repair factor 2 4
MIRT576125 Hrk harakiri, BCL2 interacting protein (contains only BH3 domain) 2 5
MIRT576657 Fam216a family with sequence similarity 216, member A 2 2
MIRT607222 ACSM2A acyl-CoA synthetase medium chain family member 2A 2 4
MIRT607292 CD300E CD300e molecule 2 6
MIRT607746 ANGPT4 angiopoietin 4 2 2
MIRT607905 SPRYD4 SPRY domain containing 4 2 2
MIRT608159 HRK harakiri, BCL2 interacting protein 2 7
MIRT608657 ABCF3 ATP binding cassette subfamily F member 3 2 4
MIRT609115 ZNF703 zinc finger protein 703 2 6
MIRT610231 ACOT9 acyl-CoA thioesterase 9 2 2
MIRT610870 NUDCD3 NudC domain containing 3 2 2
MIRT611217 MC2R melanocortin 2 receptor 2 2
MIRT614858 PLEKHA6 pleckstrin homology domain containing A6 2 2
MIRT616966 LMX1A LIM homeobox transcription factor 1 alpha 2 2
MIRT617258 GLIPR1L2 GLI pathogenesis related 1 like 2 2 2
MIRT618009 SLC9A3R2 SLC9A3 regulator 2 2 2
MIRT619067 BSND barttin CLCNK type accessory beta subunit 2 4
MIRT619295 FAM26E calcium homeostasis modulator family member 5 2 2
MIRT619348 GINM1 glycoprotein integral membrane 1 2 2
MIRT619362 CFHR5 complement factor H related 5 2 2
MIRT619541 PIWIL2 piwi like RNA-mediated gene silencing 2 2 2
MIRT619782 NRIP2 nuclear receptor interacting protein 2 2 2
MIRT619994 NPAP1 nuclear pore associated protein 1 2 2
MIRT621030 CDC14B cell division cycle 14B 2 2
MIRT622033 STAT5A signal transducer and activator of transcription 5A 2 2
MIRT622728 PITPNM3 PITPNM family member 3 2 2
MIRT623144 NAV2 neuron navigator 2 2 2
MIRT623600 IPO9 importin 9 2 2
MIRT624608 B3GALT5 beta-1,3-galactosyltransferase 5 2 2
MIRT624905 CTCFL CCCTC-binding factor like 2 2
MIRT625030 SPC24 SPC24, NDC80 kinetochore complex component 2 2
MIRT625688 MCM8 minichromosome maintenance 8 homologous recombination repair factor 2 5
MIRT626531 EMCN endomucin 2 2
MIRT627204 ZDHHC20 zinc finger DHHC-type containing 20 2 2
MIRT628033 LSAMP limbic system-associated membrane protein 2 2
MIRT628203 FREM2 FRAS1 related extracellular matrix protein 2 2 2
MIRT631012 LINS lines homolog 1 2 2
MIRT633195 HSPE1-MOB4 HSPE1-MOB4 readthrough 2 2
MIRT633890 CACNG8 calcium voltage-gated channel auxiliary subunit gamma 8 2 2
MIRT634023 MOB4 MOB family member 4, phocein 2 2
MIRT634416 PLCXD3 phosphatidylinositol specific phospholipase C X domain containing 3 2 2
MIRT636866 ARSE arylsulfatase E (chondrodysplasia punctata 1) 2 2
MIRT642527 ANKRD9 ankyrin repeat domain 9 2 2
MIRT645408 FAM110A family with sequence similarity 110 member A 2 2
MIRT645635 SYTL4 synaptotagmin like 4 2 2
MIRT646013 TNFAIP8L2 TNF alpha induced protein 8 like 2 2 2
MIRT646686 ASGR2 asialoglycoprotein receptor 2 2 2
MIRT652838 TACO1 translational activator of cytochrome c oxidase I 2 2
MIRT655156 PHF21B PHD finger protein 21B 2 2
MIRT658491 EXOC7 exocyst complex component 7 2 2
MIRT659398 CORO2A coronin 2A 2 2
MIRT666825 PRCP prolylcarboxypeptidase 2 2
MIRT666866 POU2F2 POU class 2 homeobox 2 2 2
MIRT668224 GABRA1 gamma-aminobutyric acid type A receptor alpha1 subunit 2 2
MIRT673288 PDE3A phosphodiesterase 3A 2 2
MIRT673878 KLF2 Kruppel like factor 2 2 2
MIRT681721 KCNE4 potassium voltage-gated channel subfamily E regulatory subunit 4 2 2
MIRT682406 PARD6B par-6 family cell polarity regulator beta 2 2
MIRT684109 MCM10 minichromosome maintenance 10 replication initiation factor 2 2
MIRT684423 TUFT1 tuftelin 1 2 2
MIRT684684 OR7D2 olfactory receptor family 7 subfamily D member 2 2 2
MIRT686638 TMEM184C transmembrane protein 184C 2 2
MIRT689457 NXN nucleoredoxin 2 2
MIRT689627 NAA30 N(alpha)-acetyltransferase 30, NatC catalytic subunit 2 2
MIRT690773 PLA2G2C phospholipase A2 group IIC 2 2
MIRT690822 SGSM2 small G protein signaling modulator 2 2 2
MIRT693669 MXRA7 matrix remodeling associated 7 2 2
MIRT695553 CLPB ClpB homolog, mitochondrial AAA ATPase chaperonin 2 2
MIRT695872 C19orf52 translocase of inner mitochondrial membrane 29 2 2
MIRT698160 TNFRSF13C TNF receptor superfamily member 13C 2 2
MIRT699933 RUFY2 RUN and FYVE domain containing 2 2 2
MIRT708639 UBE2W ubiquitin conjugating enzyme E2 W 2 2
MIRT710816 RAB11FIP4 RAB11 family interacting protein 4 2 2
MIRT711242 TRAT1 T-cell receptor associated transmembrane adaptor 1 2 2
MIRT711542 MSH3 mutS homolog 3 2 2
MIRT711749 DTX1 deltex E3 ubiquitin ligase 1 2 2
MIRT712303 PGM2L1 phosphoglucomutase 2 like 1 2 2
MIRT712922 RPF2 ribosome production factor 2 homolog 2 2
MIRT714027 SYDE2 synapse defective Rho GTPase homolog 2 2 2
MIRT714768 TERF1 telomeric repeat binding factor 1 2 2
MIRT714844 ADAMTS17 ADAM metallopeptidase with thrombospondin type 1 motif 17 2 2
MIRT715223 NPVF neuropeptide VF precursor 2 2
MIRT716110 GMPS guanine monophosphate synthase 2 2
MIRT716174 FAM71F2 family with sequence similarity 71 member F2 2 2
MIRT716383 C6orf223 chromosome 6 open reading frame 223 2 2
MIRT716527 KSR2 kinase suppressor of ras 2 2 2
MIRT716962 P2RY6 pyrimidinergic receptor P2Y6 2 2
MIRT717605 DSTYK dual serine/threonine and tyrosine protein kinase 2 2
MIRT717696 PTGS1 prostaglandin-endoperoxide synthase 1 2 2
MIRT721360 ENTHD1 ENTH domain containing 1 2 2
MIRT721381 MACC1 MACC1, MET transcriptional regulator 2 2
MIRT721935 RASSF2 Ras association domain family member 2 2 2
MIRT722094 SUSD1 sushi domain containing 1 2 2
MIRT722837 C17orf102 chromosome 17 open reading frame 102 2 2
MIRT722990 TOR1A torsin family 1 member A 2 2
MIRT724174 ABCF2 ATP binding cassette subfamily F member 2 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3120-5p Cisplatin 5460033 NSC119875 approved sensitive cell line
hsa-miR-3120-5p Prednisone/Azathioprine/Methotrexate/Cyclophosphamide/Mycophenolate mofetil sensitive tissue (myasthenia gravis)
hsa-miR-3120-5p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)

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