pre-miRNA Information
pre-miRNA hsa-mir-6839   
Genomic Coordinates chr7: 64679064 - 64679176
Description Homo sapiens miR-6839 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-6839-3p
Sequence 92| UUGGGUUUUCUCUUCAAUCCAG |113
Evidence Experimental
Experiments Meta-analysis
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN15661209 19 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1426245091 3 dbSNP
rs533324498 6 dbSNP
rs1169594864 16 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol SYNGAP1   
Synonyms MRD5, RASA1, RASA5, SYNGAP
Description synaptic Ras GTPase activating protein 1
Transcript NM_006772   
Expression
Putative miRNA Targets on SYNGAP1
3'UTR of SYNGAP1
(miRNA target sites are highlighted)
>SYNGAP1|NM_006772|3'UTR
   1 CCCACCCAGCATCAGAGACCTTCTCTTCCTTTCCTGTGCACCCCACCCTGTAACAGCACCAACCACCAGGATTGGACATC
  81 ACCGAGGAACAGCGGGATTGCCTCCCCGAATGCCTCCCTGGGAGGCACACTGATTGCCCACCCCCACCACTGCACCATTT
 161 CCAGGAGGGAGAGTGGGGACCCTCAGCCGCCCCCTTTTCCTTCCCATTGGGGTGCTGCCCTCTCTTTGACCCCCAGGGAC
 241 CCTTGCCCCAGGACACCGCCTACCCCGTACAGACCCCTTCACTCCGGGGTGCTATCCCCATCCTCTGCCTCATCGTTCCC
 321 CTGAGCACTGGGGGACAGACCCTCACCCCCACCCTGGGGGTGTGGCACCTCCAAACTTTCAACTTCAGGGTGATTTTTTT
 401 AGCAGTAACCAGAGCTGACAATCTAACTCCCCTCCACCGCCCCATTTTGGCCTCCCCTGCCCCCCTTGTTATGGGGAGGG
 481 GACCCCGGGTGAGGGGGCCCTATTACCCCTTGATTTCTCAGGAGCGTCTGGGGGGGCTCAGCACGCACAAACTCCTTCTC
 561 CTTCTACCACTCTTAAATTTACTCCCTCCCCACCCAGAACCCAGATGGGGTGGAGGGGGCCACCGGGGCAGGGAGGGGGC
 641 GGCAAGGGGGGAATGGGAGTTGTCTCCCCTTCTCCCCACACCTGATCTGCTCTCGGCTGGTCCCAGAGCGGGGTGAGGGG
 721 GCTTATGCCCCCCCCTCCCCCAGTGTGTTGGGTGGGGTGGAATTGAGGTTAGGGTGAGGGGTCAGGGTTTAGGAGGGTGT
 801 GTATGTTGGGAGGACAGGCTAGTTGATCTGTCCTACTCTGACACACAGTCCCCTCTGCCCCTTCCTTCTCTCTTCTTGGT
 881 CTCTACTCCCAGGGGGAGGGGGGAACTTACTCTAGGAAAAGCCATGTCTCTCTCCCCCAGGGTGGGGGGACCTGTGTTGG
 961 AGGAGGGGTGTTGGGGGGCCCCCTTCCATGACTCTGTCCCCTGGGGGAGGTAGGACAGGGCTGGGCTTCCCTCTCATCCT
1041 CCCCCTCCCAATCTCCTTCCACCTCCCTCCCTCCCGCCAGCTCCACGATTTTTCGGTGTTTCTCTGTACATAGTTTTCTG
1121 GCGGGATAGGGGAGGTAGGATGGATGGGGTTTGGGGTGGGTAGGCCATGGGAGGGGAGAAGCCCCTCCTTGGCACCCCCT
1201 CTTCCCTGACTGCTGTCCCCTACCCAGCCTTGCCCCCTTCATCCTTTTGCGTTTGGTATTGAGACTCTCCTAGACTCTAC
1281 TCCTCTTTCTTTTGTATGGACAGTTCCCCTTCAGTCCCATCCCCCTACACATACACCCAGCCGGGGCCAAATTTATACTT
1361 ATATAAAAGTTGTAAATATGTGAAATTTTATCCCTGTGCCCTTTCCCCACCTCAGGCCCTACCCCTGGACCCTCCCCAAC
1441 CTTCCTTCTCTCTTCTTTGGCTGTTGTAATTATCTGGGGTTTGTACTGTACATATCCGGGGTGTGTGTGTGTGGGCTGGG
1521 GGCAACCCTTCTGTACAGAGCTTCCTGGCCCCCTCCCCCCCCGCCCCTCTGCTTCCCTCCCCACCCACCACCTCAAGGGT
1601 AGGGAGTTGCTCTTCCTACCTGTTTTATTTTGTTTTCTCGTTCTCCCTCCCCACCCCACTCCCAGCCTTATCTATCCCCC
1681 CTCACTGTCCCCTTTTCTCCACTCCCAGCCCCATTTCCTTTTTTTCTGGAGTGTGTGGTGAAACAGAAAAAAACATGTTT
1761 AATAAACGGAGATTGTTCTTTTAA
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' gaccuaacuucucUUUUGGGUu 5'
                       |:|||||| 
Target 5' tccctccccacccAGAACCCAg 3'
583 - 604 129.00 -9.50
2
miRNA  3' gaccUAACUUCUC--UUUUGGGuu 5'
              || |:||:|  :||:|||  
Target 5' ggccATGGGAGGGGAGAAGCCCct 3'
1163 - 1186 124.00 -18.40
3
miRNA  3' gaccUAACUUCUCUUUUGGGUu 5'
              | |  || ||||| ||| 
Target 5' acttACTCTAG-GAAAAGCCAt 3'
905 - 925 121.00 -7.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
1206643 5 ClinVar
COSN30476609 16 COSMIC
COSN31567232 18 COSMIC
COSN31565638 108 COSMIC
COSN31549931 118 COSMIC
COSN31595529 121 COSMIC
COSN31662894 189 COSMIC
COSN31523519 408 COSMIC
COSN31962614 1219 COSMIC
COSN31531313 1333 COSMIC
COSN29751187 1451 COSMIC
COSN29540415 1619 COSMIC
COSN14665042 1659 COSMIC
COSN25102158 1740 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs777143637 2 dbSNP
rs781535944 5 dbSNP
rs1205362715 7 dbSNP
rs1234634606 8 dbSNP
rs768005445 10 dbSNP
rs1181730681 20 dbSNP
rs1446978596 21 dbSNP
rs1353539543 22 dbSNP
rs1314594747 23 dbSNP
rs1419038160 24 dbSNP
rs1476430927 28 dbSNP
rs1168966599 29 dbSNP
rs1397732817 30 dbSNP
rs367907637 36 dbSNP
rs1408977868 38 dbSNP
rs764693973 41 dbSNP
rs775042442 42 dbSNP
rs1167900966 43 dbSNP
rs906692971 44 dbSNP
rs762571531 45 dbSNP
rs763835038 46 dbSNP
rs371821639 57 dbSNP
rs1024663834 63 dbSNP
rs570246788 65 dbSNP
rs1052624511 73 dbSNP
rs891486331 78 dbSNP
rs1484979082 81 dbSNP
rs1011209316 85 dbSNP
rs537296679 89 dbSNP
rs1231308246 91 dbSNP
rs558681767 94 dbSNP
rs1043080263 95 dbSNP
rs576935882 97 dbSNP
rs534765005 109 dbSNP
rs958155532 113 dbSNP
rs553168613 121 dbSNP
rs1019476941 126 dbSNP
rs1295062534 130 dbSNP
rs1397494162 133 dbSNP
rs1349786701 141 dbSNP
rs186837972 142 dbSNP
rs1295982795 146 dbSNP
rs889286005 148 dbSNP
rs1322417506 154 dbSNP
rs1460209018 169 dbSNP
rs994107512 170 dbSNP
rs138935161 189 dbSNP
rs1472588848 190 dbSNP
rs561282481 199 dbSNP
rs954555811 208 dbSNP
rs149438267 213 dbSNP
rs1436794162 219 dbSNP
rs1290297709 237 dbSNP
rs1211989916 239 dbSNP
rs1362001468 241 dbSNP
rs1466982793 242 dbSNP
rs1218186336 243 dbSNP
rs1301147539 244 dbSNP
rs1274882143 247 dbSNP
rs1214094363 248 dbSNP
rs56250036 255 dbSNP
rs916531688 258 dbSNP
rs912622179 267 dbSNP
rs969540446 268 dbSNP
rs1284980888 271 dbSNP
rs1445097364 275 dbSNP
rs940009822 285 dbSNP
rs982597727 286 dbSNP
rs1036994825 290 dbSNP
rs1242961346 310 dbSNP
rs565037252 315 dbSNP
rs1488189747 316 dbSNP
rs1191900993 317 dbSNP
rs755882643 318 dbSNP
rs868289308 319 dbSNP
rs1055366145 321 dbSNP
rs1191816901 326 dbSNP
rs928184550 329 dbSNP
rs935484069 337 dbSNP
rs1194049200 341 dbSNP
rs1455042161 342 dbSNP
rs1052529262 353 dbSNP
rs1406190677 355 dbSNP
rs902239289 361 dbSNP
rs1231396710 362 dbSNP
rs915501778 363 dbSNP
rs1402848822 370 dbSNP
rs532268722 374 dbSNP
rs1434867872 375 dbSNP
rs777084233 380 dbSNP
rs1345481944 381 dbSNP
rs1042767993 384 dbSNP
rs1454819992 394 dbSNP
rs766858278 394 dbSNP
rs1171897787 407 dbSNP
rs1436604815 410 dbSNP
rs889441210 411 dbSNP
rs1188087242 416 dbSNP
rs1006668757 421 dbSNP
rs1427716125 429 dbSNP
rs547544960 439 dbSNP
rs1372558256 440 dbSNP
rs900897129 443 dbSNP
rs1441493391 458 dbSNP
rs1486175959 459 dbSNP
rs954540241 460 dbSNP
rs987267329 460 dbSNP
rs374819728 461 dbSNP
rs1280605490 464 dbSNP
rs1025451611 473 dbSNP
rs961492202 476 dbSNP
rs1298277318 478 dbSNP
rs1383098733 482 dbSNP
rs1348243132 484 dbSNP
rs1355404847 485 dbSNP
rs1311547870 487 dbSNP
rs1225306778 488 dbSNP
rs1416700566 493 dbSNP
rs773577131 501 dbSNP
rs972803976 503 dbSNP
rs1168022755 510 dbSNP
rs1460718506 514 dbSNP
rs1374969693 527 dbSNP
rs1428845806 530 dbSNP
rs919948104 530 dbSNP
rs749685999 531 dbSNP
rs1257678959 532 dbSNP
rs1479478806 533 dbSNP
rs931310439 535 dbSNP
rs1005881419 536 dbSNP
rs1235735093 537 dbSNP
rs529736056 538 dbSNP
rs1023672467 545 dbSNP
rs949564068 546 dbSNP
rs969781711 552 dbSNP
rs1389721174 554 dbSNP
rs1212068850 555 dbSNP
rs375628259 558 dbSNP
rs902688610 558 dbSNP
rs1416826340 561 dbSNP
rs1162516710 566 dbSNP
rs928071301 569 dbSNP
rs1476186218 571 dbSNP
rs935117339 578 dbSNP
rs1180537400 583 dbSNP
rs1416746726 586 dbSNP
rs956754100 598 dbSNP
rs1053528720 602 dbSNP
rs13214818 605 dbSNP
rs1195958852 607 dbSNP
rs1467740449 615 dbSNP
rs1271737540 622 dbSNP
rs1215906820 623 dbSNP
rs893487143 626 dbSNP
rs1275076863 641 dbSNP
rs1468990586 646 dbSNP
rs1178535768 648 dbSNP
rs1231723208 650 dbSNP
rs995827559 651 dbSNP
rs1471355699 652 dbSNP
rs988269804 667 dbSNP
rs1178210379 670 dbSNP
rs1323695953 672 dbSNP
rs1413533675 673 dbSNP
rs915407064 676 dbSNP
rs529574637 683 dbSNP
rs1029333571 685 dbSNP
rs1391395581 688 dbSNP
rs947003778 695 dbSNP
rs1051102136 710 dbSNP
rs890337378 722 dbSNP
rs1008815772 728 dbSNP
rs1365091841 729 dbSNP
rs910911460 732 dbSNP
rs1453460799 733 dbSNP
rs1250728411 734 dbSNP
rs1461549643 741 dbSNP
rs1328081911 745 dbSNP
rs1333974434 748 dbSNP
rs1195918114 751 dbSNP
rs942377041 758 dbSNP
rs867701116 764 dbSNP
rs1469155040 766 dbSNP
rs570333334 775 dbSNP
rs1353457236 781 dbSNP
rs900933028 785 dbSNP
rs929674355 787 dbSNP
rs1369121209 790 dbSNP
rs1305845167 791 dbSNP
rs1442832758 797 dbSNP
rs1027045930 814 dbSNP
rs1279857911 831 dbSNP
rs1317354773 834 dbSNP
rs1380521091 838 dbSNP
rs952838964 841 dbSNP
rs769492440 845 dbSNP
rs1158775066 848 dbSNP
rs1378198384 853 dbSNP
rs1392912171 859 dbSNP
rs990804306 860 dbSNP
rs916834937 861 dbSNP
rs1275328778 862 dbSNP
rs1241960233 868 dbSNP
rs1191483959 869 dbSNP
rs1449276878 870 dbSNP
rs531071795 871 dbSNP
rs982322790 874 dbSNP
rs924141498 877 dbSNP
rs1046973681 879 dbSNP
rs888274193 882 dbSNP
rs935484035 889 dbSNP
rs1198154943 894 dbSNP
rs1005496868 897 dbSNP
rs893521918 897 dbSNP
rs1439999208 899 dbSNP
rs552373980 900 dbSNP
rs1328149769 901 dbSNP
rs1023955433 914 dbSNP
rs905086387 918 dbSNP
rs1237217765 925 dbSNP
rs1003967024 927 dbSNP
rs1034944447 928 dbSNP
rs1314164394 935 dbSNP
rs1466788486 950 dbSNP
rs113985177 960 dbSNP
rs956825967 962 dbSNP
rs1166569633 963 dbSNP
rs1476568695 964 dbSNP
rs1050137685 965 dbSNP
rs988176758 972 dbSNP
rs1259777854 973 dbSNP
rs1377512632 973 dbSNP
rs1484967049 973 dbSNP
rs1474452541 978 dbSNP
rs1437511580 979 dbSNP
rs890116230 990 dbSNP
rs1212620040 992 dbSNP
rs1008846659 993 dbSNP
rs1278780126 994 dbSNP
rs1232662214 999 dbSNP
rs1353483127 1004 dbSNP
rs570736611 1005 dbSNP
rs1014828826 1015 dbSNP
rs1022446646 1025 dbSNP
rs1166737790 1030 dbSNP
rs1326403382 1032 dbSNP
rs994653057 1040 dbSNP
rs764336572 1045 dbSNP
rs968602468 1051 dbSNP
rs986291207 1052 dbSNP
rs952789902 1060 dbSNP
rs1008988223 1062 dbSNP
rs910805944 1063 dbSNP
rs1420619046 1068 dbSNP
rs1182541454 1070 dbSNP
rs1231399641 1076 dbSNP
rs991311960 1077 dbSNP
rs115953368 1082 dbSNP
rs1212808235 1087 dbSNP
rs1374595266 1095 dbSNP
rs1412755912 1110 dbSNP
rs976419855 1111 dbSNP
rs970690715 1126 dbSNP
rs553470039 1138 dbSNP
rs1295336624 1141 dbSNP
rs1332652641 1142 dbSNP
rs1295002974 1145 dbSNP
rs1228432832 1166 dbSNP
rs1356419197 1171 dbSNP
rs922262939 1172 dbSNP
rs929747660 1183 dbSNP
rs1444007363 1186 dbSNP
rs982353393 1188 dbSNP
rs1046836044 1200 dbSNP
rs957099099 1209 dbSNP
rs146399784 1220 dbSNP
rs888305060 1226 dbSNP
rs770643108 1234 dbSNP
rs989623171 1245 dbSNP
rs915393014 1246 dbSNP
rs754045871 1252 dbSNP
rs568459139 1257 dbSNP
rs931783568 1259 dbSNP
rs905111964 1267 dbSNP
rs1405958565 1276 dbSNP
rs1003459359 1278 dbSNP
rs1050583629 1280 dbSNP
rs1341592339 1280 dbSNP
rs1215633110 1302 dbSNP
rs139658874 1307 dbSNP
rs1169943955 1322 dbSNP
rs116313386 1327 dbSNP
rs1192800469 1331 dbSNP
rs1009629184 1335 dbSNP
rs774216981 1344 dbSNP
rs759107672 1346 dbSNP
rs1281570195 1347 dbSNP
rs1036291606 1363 dbSNP
rs1353996871 1364 dbSNP
rs1485761601 1377 dbSNP
rs1302185592 1386 dbSNP
rs986709465 1395 dbSNP
rs1373569946 1399 dbSNP
rs1294475282 1408 dbSNP
rs1430728421 1410 dbSNP
rs1343917767 1434 dbSNP
rs1017734940 1436 dbSNP
rs1048928111 1440 dbSNP
rs894293132 1441 dbSNP
rs1476131800 1443 dbSNP
rs1171941814 1446 dbSNP
rs1452360497 1448 dbSNP
rs1269277864 1456 dbSNP
rs1191521068 1497 dbSNP
rs1168404853 1498 dbSNP
rs1240232240 1501 dbSNP
rs1485529622 1501 dbSNP
rs1394467235 1507 dbSNP
rs1353713114 1513 dbSNP
rs966735901 1518 dbSNP
rs976326260 1519 dbSNP
rs1231697224 1524 dbSNP
rs879906871 1527 dbSNP
rs1302460686 1531 dbSNP
rs1214329548 1533 dbSNP
rs1360520497 1541 dbSNP
rs576419988 1547 dbSNP
rs1400699955 1550 dbSNP
rs1374871635 1552 dbSNP
rs1381818716 1554 dbSNP
rs1165990606 1555 dbSNP
rs542057070 1555 dbSNP
rs543714158 1555 dbSNP
rs1316544501 1558 dbSNP
rs982421446 1561 dbSNP
rs1003464069 1563 dbSNP
rs1328249794 1563 dbSNP
rs967510911 1564 dbSNP
rs1031214704 1568 dbSNP
rs1438758177 1568 dbSNP
rs998557660 1569 dbSNP
rs957017003 1570 dbSNP
rs1346256354 1571 dbSNP
rs1488568323 1572 dbSNP
rs1237158942 1573 dbSNP
rs1281430853 1574 dbSNP
rs1353475848 1575 dbSNP
rs1325334889 1579 dbSNP
rs1256273889 1580 dbSNP
rs1208060524 1582 dbSNP
rs1204156171 1584 dbSNP
rs1484058861 1585 dbSNP
rs1256175911 1586 dbSNP
rs909636866 1587 dbSNP
rs1259292471 1588 dbSNP
rs558871238 1589 dbSNP
rs1448211230 1591 dbSNP
rs1193363979 1594 dbSNP
rs941086471 1597 dbSNP
rs1280670359 1603 dbSNP
rs1045341842 1611 dbSNP
rs926469230 1612 dbSNP
rs1355343709 1613 dbSNP
rs1291563149 1616 dbSNP
rs953651074 1621 dbSNP
rs1403215247 1623 dbSNP
rs1326897528 1626 dbSNP
rs939293134 1628 dbSNP
rs549739623 1644 dbSNP
rs1352604309 1646 dbSNP
rs1452439360 1648 dbSNP
rs911613332 1650 dbSNP
rs892358447 1655 dbSNP
rs1009534508 1658 dbSNP
rs1425002968 1659 dbSNP
rs1043671709 1660 dbSNP
rs903936025 1666 dbSNP
rs1194821130 1669 dbSNP
rs1479448525 1674 dbSNP
rs1395418550 1675 dbSNP
rs1260434038 1677 dbSNP
rs1452847638 1682 dbSNP
rs944364248 1690 dbSNP
rs1271751522 1691 dbSNP
rs1247126452 1694 dbSNP
rs1007642691 1695 dbSNP
rs1341093353 1702 dbSNP
rs1306358825 1704 dbSNP
rs1035991454 1706 dbSNP
rs1379391447 1708 dbSNP
rs548063400 1710 dbSNP
rs930612982 1712 dbSNP
rs1393647212 1714 dbSNP
rs1162649822 1731 dbSNP
rs1459011964 1741 dbSNP
rs1049438588 1747 dbSNP
rs894332257 1773 dbSNP
rs1382993163 1784 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HeLa
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 Chi_124A_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell miR-124 + A ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' gaccuaacUUCUCUUUUGGguu 5'
                  || | ||||||   
Target 5' augagaaaAAAAAAAAACC--- 3'
1 - 19
Article - Chi SW; Zang JB; Mele A; Darnell RB
- Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
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 GSM1084064. RNA binding protein: AGO2. Condition:CLIP_noemetine_AbnovaAb HITS-CLIP data was present in GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb HITS-CLIP data was present in GSM1084069. RNA binding protein: AGO2. Condition:CLIP_emetine_SigmaAb HITS-CLIP data was present in GSM1084083. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep2_SigmaAb ...

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

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 Chi_124A_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell miR-124 + A
Location of target site ENST00000456692.2 | 3UTR | AUGAGAAAAAAAAAAAACC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1084064
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_AbnovaAb
Location of target site ENST00000456692.2 | 3UTR | GAAUGAGAAAAAAAAAAAAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1084065
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_AbnovaAb
Location of target site ENST00000456692.2 | 3UTR | AUGAGAAAAAAAAAAAACC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM1084069
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_SigmaAb
Location of target site ENST00000456692.2 | 3UTR | AAUGAGAAAAAAAAAAAACC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM1084083
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep2_SigmaAb
Location of target site ENST00000456692.2 | 3UTR | AUGAGAAAAAAAAAAAAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
62 hsa-miR-6839-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT059162 TXNIP thioredoxin interacting protein 2 2
MIRT064872 ZBTB18 zinc finger and BTB domain containing 18 2 2
MIRT065802 HOXC8 homeobox C8 2 4
MIRT106005 SDCBP syndecan binding protein 2 2
MIRT275773 TFDP1 transcription factor Dp-1 2 2
MIRT314032 PAPD7 poly(A) RNA polymerase D7, non-canonical 2 2
MIRT360277 HIST1H2BE histone cluster 1 H2B family member e 2 8
MIRT360301 HIST1H2BH histone cluster 1 H2B family member h 2 2
MIRT450086 OR2A4 olfactory receptor family 2 subfamily A member 4 2 2
MIRT468815 RSRC2 arginine and serine rich coiled-coil 2 2 6
MIRT475093 IRF2BP2 interferon regulatory factor 2 binding protein 2 2 4
MIRT477575 EIF1AD eukaryotic translation initiation factor 1A domain containing 2 2
MIRT483926 LCORL ligand dependent nuclear receptor corepressor like 2 6
MIRT504381 HIST1H1C histone cluster 1 H1 family member c 2 4
MIRT506970 HNRNPUL1 heterogeneous nuclear ribonucleoprotein U like 1 2 6
MIRT507028 HIST1H3B histone cluster 1 H3 family member b 2 6
MIRT511561 HIST3H2BB histone cluster 3 H2B family member b 2 4
MIRT511650 HIST1H3D histone cluster 1 H3 family member d 2 6
MIRT511696 HIST1H2BL histone cluster 1 H2B family member l 2 4
MIRT511737 HIST1H2BB histone cluster 1 H2B family member b 2 6
MIRT511746 HIST1H2BA histone cluster 1 H2B family member a 2 8
MIRT515260 CSNK1E casein kinase 1 epsilon 2 2
MIRT516220 RAB3B RAB3B, member RAS oncogene family 2 4
MIRT523281 HIST1H1E histone cluster 1 H1 family member e 2 2
MIRT524121 DMXL1 Dmx like 1 2 2
MIRT530744 GPR82 G protein-coupled receptor 82 2 2
MIRT532214 CCDC117 coiled-coil domain containing 117 2 2
MIRT546182 TPRG1L tumor protein p63 regulated 1 like 2 2
MIRT558638 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT559562 ARF1 ADP ribosylation factor 1 2 4
MIRT560680 HIST1H1T histone cluster 1 H1 family member t 2 2
MIRT570746 AAK1 AP2 associated kinase 1 2 2
MIRT609518 RAB3IP RAB3A interacting protein 2 2
MIRT612583 SYNGAP1 synaptic Ras GTPase activating protein 1 2 4
MIRT615733 RIOK3 RIO kinase 3 2 2
MIRT616068 SIX1 SIX homeobox 1 2 2
MIRT617903 SGCD sarcoglycan delta 2 2
MIRT620851 SERPING1 serpin family G member 1 2 2
MIRT625107 SLC1A5 solute carrier family 1 member 5 2 2
MIRT625120 NUP93 nucleoporin 93 2 2
MIRT625893 LINC00632 long intergenic non-protein coding RNA 632 2 2
MIRT626569 MED7 mediator complex subunit 7 2 2
MIRT626694 ZFP14 ZFP14 zinc finger protein 2 4
MIRT626808 PRR11 proline rich 11 2 2
MIRT628131 HM13 histocompatibility minor 13 2 2
MIRT636596 DCAF5 DDB1 and CUL4 associated factor 5 2 2
MIRT649866 SLFN12L schlafen family member 12 like 2 2
MIRT652133 TRPM7 transient receptor potential cation channel subfamily M member 7 2 2
MIRT652663 TIMELESS timeless circadian clock 2 2
MIRT658335 FAM83D family with sequence similarity 83 member D 2 2
MIRT660615 ANKS4B ankyrin repeat and sterile alpha motif domain containing 4B 2 2
MIRT666304 SLC22A3 solute carrier family 22 member 3 2 2
MIRT668528 ERGIC2 ERGIC and golgi 2 2 2
MIRT692510 PARD3 par-3 family cell polarity regulator 2 2
MIRT694784 DHFRL1 dihydrofolate reductase 2 2 2
MIRT700510 PTPN14 protein tyrosine phosphatase, non-receptor type 14 2 2
MIRT701438 NFYA nuclear transcription factor Y subunit alpha 2 2
MIRT710155 MTRF1L mitochondrial translational release factor 1 like 2 2
MIRT711436 DLC1 DLC1 Rho GTPase activating protein 2 2
MIRT716979 GPR155 G protein-coupled receptor 155 2 2
MIRT720155 POU2F2 POU class 2 homeobox 2 2 2
MIRT722512 DSTYK dual serine/threonine and tyrosine protein kinase 2 2

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