miRTarBase - #MIRT674244


—
pre-miRNA Information
pre-miRNA hsa-mir-4707   
Genomic Coordinates chr14: 22956950 - 22957029
Description Homo sapiens miR-4707 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4707-3p
Sequence 52| AGCCCGCCCCAGCCGAGGUUCU |73
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1180125593 2 dbSNP
rs1390998288 5 dbSNP
rs2273626 6 dbSNP
rs765507627 7 dbSNP
rs1299611135 9 dbSNP
rs1158707105 11 dbSNP
rs535691977 15 dbSNP
rs952013388 17 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol NUP62   
Synonyms IBSN, SNDI, p62
Description nucleoporin 62
Transcript NM_012346   
Other Transcripts NM_016553 , NM_153718 , NM_153719   
Expression
Putative miRNA Targets on NUP62
3'UTR of NUP62
(miRNA target sites are highlighted)		 
>NUP62|NM_012346|3'UTR
   1 GCGACAGCAGCCCTGGGGCCCGCAGGTCCCTAGGGAGTTCATGAGGGGAATGCGCCCTGTTGTCTGTAGTTTGGGGTTGT
  81 GGCAAGATACTTGTTTGTTTGTTTCTTTCTTTCACATGACTGCCCTTGACATGATCGCTGTGTGCTTTGCGTTTTTCCAT
 161 TTAGGAGGGTATTCTGGGCCTTCTGCCCAGGCAGCAGCCTCATGGGTGTGGCTTCTGTGGCTTTCATTTGAGTATCTTTG
 241 GCCCCTTTTCACCTACTGCGACCACCCACCTCATCCTGGCTCAGCCTGGTGATGGAGAAGTGCTGATGGTCTTGGTCCCA
 321 GCCAGGGTCGTGGGGGCAGCCACTCTCTCCAAAGCATAGTCATAGGTGTCATGAAAAAATACCAAATGTAAGAGAACCTC
 401 CAAGTCAGGGCGCAGTGGCTCACCCCTGTAATCTCAGCACTTTGGGTGGCCAAGGCGGGCAGATGACTTGAGGTCAGGAG
 481 TTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGTCAGGTGTGGTGGACGCCTG
 561 TGATCTCAATCTCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCAGGAGGTGTTGCAGTGAACCAAGATCA
 641 CACCACTGCACTCCAGCCTAGGCAACAGAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAGAAACTCCCAGGAGACAGC
 721 AGCCTAGTTTTCGAGTGTGAGCTTGTGCTTGTGAAAGCTAACCATGCTAACCACCAAGGCAAAGCAGCACAGTGTGAATA
 801 GAACAGAGCGGGATCAAGAATTTCACAGAAGACAGGTCAGCTGAGGGGCCTGCACACACAGGGTGTTGAGGAACCACAGA
 881 TGGGCGCCGAGAGGCCTGCCTTTTGCCTGGCCCAGGCTCACCCCCACCTTGGGCCTCACCTCCTCCAGGAAGCCTTCCCA
 961 GCTACCCGAAGCTCAGGTGGCCTTCTTGCAGGTCCCCGTAGCACCCTGAGCCTGTACCTTGGGTGGCACTTGTTATGCTA
1041 TCCTGTGCTAGCCGTTTGTGCCTCGTCTCGCTGTTAGATTGTGAGTTCCCATGGGCAGAGACCCACTGTCGTTCCCCGTG
1121 TGTCCCCAGCCCGGTCCCTGTCACATTTGTTAAATGAAAGAACAATGAAGCCCAGTGTAACGTCAGTCCACAGAAATAGC
1201 CACAGCTTCCAGTGGTGGCCGTAGACTTGGCTCGGAACTTAGTGGCACCAGAGTAACTCTAGTCAGTTACAGTAAAATCC
1281 ACTGTGTGTGGAAGGCAGAAGCTAGCGGTTGTATCCCAAGCATCTTTTGTATTTGTCTTTATACTTTGCTGAATTCTCTG
1361 AAATACCTATTACTGTATGTTGCTTTTCTAAATAAATGTATTGTGAAACCAAAAAAAAAAAAAAAAAA
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' ucuUGGAGCCGACC----CCGCCCGa 5'
             ||:|:|| |||    ||||||| 
Target 5' agcACTTTGGGTGGCCAAGGCGGGCa 3'
 436 - 461 165.00 -27.80
2 
miRNA  3' ucUUG--GAG----CCGACCCCGCCCga 5'
            |:|  |||    ||||| ||| ||  
Target 5' tcAGCTACTCGGGAGGCTGAGGCAGGag 3'
 572 - 599 112.00 -17.80
3 
miRNA  3' ucUUGG--AGCCGACCCCGCCCGa 5'
            ||::  || | || ||:|| | 
Target 5' aaAATTAGTCAGGTGTGGTGGACg 3'
 533 - 556 110.00 -11.10
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31495067 25 COSMIC
COSN30134016 33 COSMIC
COSN31519230 40 COSMIC
COSN31583733 41 COSMIC
COSN30538132 82 COSMIC
COSN24107439 134 COSMIC
COSN8261543 453 COSMIC
COSN4778509 839 COSMIC
COSN7447919 849 COSMIC
COSN21570364 889 COSMIC
COSN21621382 1302 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs372281472 2 dbSNP
rs375449846 3 dbSNP
rs765043638 10 dbSNP
rs761632740 15 dbSNP
rs1308346592 19 dbSNP
rs764355720 21 dbSNP
rs760945372 22 dbSNP
rs775435783 23 dbSNP
rs1401400885 30 dbSNP
rs1218592190 33 dbSNP
rs1423869890 39 dbSNP
rs1416667336 40 dbSNP
rs1180647216 41 dbSNP
rs1482975166 46 dbSNP
rs772132592 48 dbSNP
rs906846027 53 dbSNP
rs45540835 54 dbSNP
rs1472067116 56 dbSNP
rs1277439580 65 dbSNP
rs948649371 71 dbSNP
rs532206411 78 dbSNP
rs186001015 79 dbSNP
rs1355200327 83 dbSNP
rs1457811940 90 dbSNP
rs775828349 93 dbSNP
rs955675213 95 dbSNP
rs1486986271 97 dbSNP
rs11547267 101 dbSNP
rs919347451 105 dbSNP
rs975633969 105 dbSNP
rs1017075889 106 dbSNP
rs1006014943 110 dbSNP
rs1160611393 116 dbSNP
rs951878189 129 dbSNP
rs1290271799 130 dbSNP
rs972098514 131 dbSNP
rs1419116523 132 dbSNP
rs145144537 137 dbSNP
rs1402783247 147 dbSNP
rs993551209 148 dbSNP
rs1331938417 149 dbSNP
rs896127652 150 dbSNP
rs745899876 151 dbSNP
rs1350893825 154 dbSNP
rs1379130346 171 dbSNP
rs774427219 179 dbSNP
rs1347750433 181 dbSNP
rs1199183948 189 dbSNP
rs953798627 189 dbSNP
rs1255906795 191 dbSNP
rs1458464204 192 dbSNP
rs1002040433 200 dbSNP
rs560839227 202 dbSNP
rs1465260543 203 dbSNP
rs905035903 208 dbSNP
rs1439201796 210 dbSNP
rs1174334003 213 dbSNP
rs1022507279 215 dbSNP
rs771070946 216 dbSNP
rs1350709603 218 dbSNP
rs1467537130 224 dbSNP
rs1011501113 234 dbSNP
rs892608821 240 dbSNP
rs1401275943 242 dbSNP
rs1031445287 252 dbSNP
rs1333011361 256 dbSNP
rs1403951873 260 dbSNP
rs946852094 263 dbSNP
rs998631479 265 dbSNP
rs1413597495 269 dbSNP
rs1159722278 271 dbSNP
rs141228323 273 dbSNP
rs1319093132 280 dbSNP
rs1200872716 281 dbSNP
rs1045460612 291 dbSNP
rs1176266781 301 dbSNP
rs1480055932 305 dbSNP
rs1191934781 308 dbSNP
rs948372084 308 dbSNP
rs1431474317 313 dbSNP
rs933998689 329 dbSNP
rs181506876 330 dbSNP
rs1403296621 336 dbSNP
rs563111900 337 dbSNP
rs1044276 338 dbSNP
rs11547266 341 dbSNP
rs975666499 343 dbSNP
rs1293711355 344 dbSNP
rs942928991 354 dbSNP
rs910084066 356 dbSNP
rs930489890 358 dbSNP
rs919114656 359 dbSNP
rs1319683430 362 dbSNP
rs9523 364 dbSNP
rs1276709662 381 dbSNP
rs1317609742 383 dbSNP
rs1222631840 397 dbSNP
rs546501513 402 dbSNP
rs1026501227 409 dbSNP
rs374146319 410 dbSNP
rs371234041 411 dbSNP
rs911974511 412 dbSNP
rs986097884 414 dbSNP
rs1195669366 416 dbSNP
rs1034607016 421 dbSNP
rs145149204 424 dbSNP
rs1002113969 425 dbSNP
rs1351224845 427 dbSNP
rs191069827 430 dbSNP
rs989727552 434 dbSNP
rs1360539827 438 dbSNP
rs1349594121 444 dbSNP
rs957162107 445 dbSNP
rs1299229010 447 dbSNP
rs1422009046 452 dbSNP
rs1378984346 456 dbSNP
rs1158620706 457 dbSNP
rs1031206650 459 dbSNP
rs1425327921 460 dbSNP
rs1192508127 461 dbSNP
rs1011177294 463 dbSNP
rs1267867534 465 dbSNP
rs1217089545 468 dbSNP
rs1489176766 470 dbSNP
rs1182223902 473 dbSNP
rs1003708886 480 dbSNP
rs1421698702 482 dbSNP
rs1162457656 483 dbSNP
rs1127729 484 dbSNP
rs1420935947 484 dbSNP
rs1024026271 491 dbSNP
rs1345088320 497 dbSNP
rs1013009560 511 dbSNP
rs894117649 514 dbSNP
rs1049185956 515 dbSNP
rs994793331 533 dbSNP
rs1377357505 534 dbSNP
rs3859440 538 dbSNP
rs1310197473 541 dbSNP
rs1238015450 545 dbSNP
rs1367201268 545 dbSNP
rs901215427 547 dbSNP
rs569495944 548 dbSNP
rs1039719557 551 dbSNP
rs1036192912 552 dbSNP
rs942961208 555 dbSNP
rs910116497 556 dbSNP
rs1182624743 565 dbSNP
rs944503832 567 dbSNP
rs551138336 569 dbSNP
rs538382570 573 dbSNP
rs571314916 574 dbSNP
rs911985770 581 dbSNP
rs1050506535 582 dbSNP
rs972225355 586 dbSNP
rs931996327 587 dbSNP
rs1207677220 603 dbSNP
rs1487644631 604 dbSNP
rs1265050568 608 dbSNP
rs1245675079 611 dbSNP
rs1299786015 612 dbSNP
rs1323569160 613 dbSNP
rs915271551 616 dbSNP
rs759982814 619 dbSNP
rs1314847400 620 dbSNP
rs546317922 622 dbSNP
rs1349744526 623 dbSNP
rs1368308401 624 dbSNP
rs1428201684 624 dbSNP
rs1288786675 631 dbSNP
rs528083527 637 dbSNP
rs1388198139 638 dbSNP
rs1292571966 640 dbSNP
rs1299151247 641 dbSNP
rs1421862671 642 dbSNP
rs1310273591 646 dbSNP
rs771534605 647 dbSNP
rs1351125486 648 dbSNP
rs1156241753 649 dbSNP
rs1472561857 656 dbSNP
rs1413287091 657 dbSNP
rs1458806042 662 dbSNP
rs1176337019 664 dbSNP
rs1231820608 668 dbSNP
rs1184834118 670 dbSNP
rs1374048891 672 dbSNP
rs749721095 673 dbSNP
rs767699595 673 dbSNP
rs778271976 674 dbSNP
rs1175903179 676 dbSNP
rs1415548086 678 dbSNP
rs1267008676 679 dbSNP
rs1210656635 680 dbSNP
rs1489549529 681 dbSNP
rs762042884 681 dbSNP
rs1034678771 682 dbSNP
rs1491035750 682 dbSNP
rs1402830302 686 dbSNP
rs1266342309 688 dbSNP
rs1208144260 691 dbSNP
rs1328444941 692 dbSNP
rs1268667965 693 dbSNP
rs751769989 694 dbSNP
rs989876245 694 dbSNP
rs768263073 695 dbSNP
rs1438679166 696 dbSNP
rs746610162 696 dbSNP
rs61338594 697 dbSNP
rs982282641 698 dbSNP
rs1280097884 699 dbSNP
rs1212332225 701 dbSNP
rs1491369382 701 dbSNP
rs1005012763 702 dbSNP
rs1196407122 702 dbSNP
rs1223121211 702 dbSNP
rs1245540241 702 dbSNP
rs1271823353 702 dbSNP
rs1319653832 702 dbSNP
rs1364976874 702 dbSNP
rs1480402045 702 dbSNP
rs4009637 702 dbSNP
rs5828417 702 dbSNP
rs759363509 702 dbSNP
rs762766968 702 dbSNP
rs764413393 702 dbSNP
rs775167721 702 dbSNP
rs869180975 702 dbSNP
rs1298692166 703 dbSNP
rs373706111 703 dbSNP
rs373724192 704 dbSNP
rs746535490 705 dbSNP
rs1229620226 706 dbSNP
rs1288964838 706 dbSNP
rs1356591956 706 dbSNP
rs749617319 706 dbSNP
rs969005914 706 dbSNP
rs779447445 707 dbSNP
rs1218013768 711 dbSNP
rs1353879572 711 dbSNP
rs1022183549 718 dbSNP
rs1024078223 722 dbSNP
rs1012690905 726 dbSNP
rs370422917 732 dbSNP
rs548884388 733 dbSNP
rs1027356302 739 dbSNP
rs1473907975 740 dbSNP
rs1161616276 742 dbSNP
rs1384723578 746 dbSNP
rs956748879 747 dbSNP
rs994909142 752 dbSNP
rs1030832604 755 dbSNP
rs897750351 764 dbSNP
rs1036204360 765 dbSNP
rs1380367979 766 dbSNP
rs1334792593 768 dbSNP
rs1180117278 769 dbSNP
rs1449815889 773 dbSNP
rs1312396650 777 dbSNP
rs998712024 782 dbSNP
rs1008698909 792 dbSNP
rs1240206709 800 dbSNP
rs1258806142 802 dbSNP
rs890264676 806 dbSNP
rs1050670197 809 dbSNP
rs754991983 810 dbSNP
rs893876691 814 dbSNP
rs751060095 816 dbSNP
rs1251057362 822 dbSNP
rs1053792063 831 dbSNP
rs548980353 839 dbSNP
rs1342676722 840 dbSNP
rs1039748960 842 dbSNP
rs758048701 844 dbSNP
rs1452566180 847 dbSNP
rs1381318322 848 dbSNP
rs1242738105 856 dbSNP
rs982336521 857 dbSNP
rs750088770 858 dbSNP
rs75368221 861 dbSNP
rs151270836 862 dbSNP
rs577315096 868 dbSNP
rs991387540 879 dbSNP
rs1402669534 884 dbSNP
rs1167009635 885 dbSNP
rs1057291496 886 dbSNP
rs565372770 888 dbSNP
rs186984993 889 dbSNP
rs1239001367 893 dbSNP
rs927737722 893 dbSNP
rs973101013 897 dbSNP
rs1202162604 898 dbSNP
rs545044451 911 dbSNP
rs1262815879 917 dbSNP
rs56779488 919 dbSNP
rs1238822844 923 dbSNP
rs142182842 926 dbSNP
rs1008795110 930 dbSNP
rs890361510 935 dbSNP
rs1418528013 941 dbSNP
rs760040332 941 dbSNP
rs1378100606 942 dbSNP
rs1478926584 943 dbSNP
rs1173973810 945 dbSNP
rs8429 946 dbSNP
rs1332911449 947 dbSNP
rs1465822522 947 dbSNP
rs1393723985 949 dbSNP
rs1390293582 950 dbSNP
rs893896823 953 dbSNP
rs1054250123 957 dbSNP
rs1031282729 966 dbSNP
rs1222154279 967 dbSNP
rs538005990 968 dbSNP
rs1444579555 978 dbSNP
rs1358892775 981 dbSNP
rs1264054787 988 dbSNP
rs902537952 997 dbSNP
rs180934958 998 dbSNP
rs1480370757 1002 dbSNP
rs1210508051 1005 dbSNP
rs949649806 1012 dbSNP
rs1018383945 1013 dbSNP
rs539212905 1028 dbSNP
rs916814913 1036 dbSNP
rs888449531 1040 dbSNP
rs571708629 1041 dbSNP
rs1172439243 1042 dbSNP
rs1370956326 1043 dbSNP
rs1461093477 1048 dbSNP
rs931440112 1053 dbSNP
rs994860166 1054 dbSNP
rs897388579 1064 dbSNP
rs140472122 1065 dbSNP
rs938868779 1067 dbSNP
rs147222334 1069 dbSNP
rs1044795143 1070 dbSNP
rs1245723559 1071 dbSNP
rs1267309495 1078 dbSNP
rs45577034 1080 dbSNP
rs1160423407 1082 dbSNP
rs1220198530 1083 dbSNP
rs914926445 1085 dbSNP
rs989149284 1091 dbSNP
rs1014554932 1093 dbSNP
rs1259328938 1102 dbSNP
rs555667842 1104 dbSNP
rs548552246 1108 dbSNP
rs1422190887 1110 dbSNP
rs537044484 1110 dbSNP
rs111373388 1111 dbSNP
rs976636738 1116 dbSNP
rs996055389 1117 dbSNP
rs563598151 1118 dbSNP
rs1032153443 1119 dbSNP
rs1315053797 1121 dbSNP
rs1357441010 1126 dbSNP
rs1222189901 1132 dbSNP
rs11083988 1133 dbSNP
rs1217772263 1139 dbSNP
rs1258770121 1140 dbSNP
rs1485391779 1142 dbSNP
rs533162053 1145 dbSNP
rs1288781059 1148 dbSNP
rs1442312846 1160 dbSNP
rs1027427053 1163 dbSNP
rs902567575 1164 dbSNP
rs143688089 1165 dbSNP
rs1278445974 1166 dbSNP
rs1157508582 1172 dbSNP
rs1344996354 1174 dbSNP
rs897121324 1175 dbSNP
rs1013589990 1176 dbSNP
rs1338994615 1181 dbSNP
rs1035955779 1182 dbSNP
rs895432901 1189 dbSNP
rs1055771034 1195 dbSNP
rs931521699 1197 dbSNP
rs1281033571 1201 dbSNP
rs1310082777 1211 dbSNP
rs1379153639 1218 dbSNP
rs770088909 1220 dbSNP
rs1282034546 1221 dbSNP
rs62126289 1223 dbSNP
rs1210551617 1225 dbSNP
rs1361003417 1233 dbSNP
rs1459712612 1239 dbSNP
rs114164962 1245 dbSNP
rs189025201 1254 dbSNP
rs1238290259 1260 dbSNP
rs1398895092 1261 dbSNP
rs907589509 1265 dbSNP
rs1176039673 1266 dbSNP
rs1384297005 1282 dbSNP
rs534293886 1283 dbSNP
rs1434187099 1284 dbSNP
rs954516048 1298 dbSNP
rs575889617 1306 dbSNP
rs115030648 1307 dbSNP
rs1332233739 1308 dbSNP
rs1356400501 1315 dbSNP
rs975086152 1319 dbSNP
rs1478347369 1322 dbSNP
rs1265816174 1324 dbSNP
rs11547265 1331 dbSNP
rs1215007595 1333 dbSNP
rs545327924 1335 dbSNP
rs1446959669 1337 dbSNP
rs28586965 1342 dbSNP
rs1219676327 1344 dbSNP
rs1200507530 1347 dbSNP
rs1032186441 1348 dbSNP
rs754900634 1356 dbSNP
rs184961731 1366 dbSNP
rs893539738 1369 dbSNP
rs1439090849 1371 dbSNP
rs1201824932 1377 dbSNP
rs1232871398 1379 dbSNP
rs1346554958 1380 dbSNP
rs535947677 1385 dbSNP
rs1194846295 1387 dbSNP
rs566897667 1395 dbSNP
rs1260859348 1399 dbSNP
rs74961846 1410 dbSNP
rs1202170459 1411 dbSNP
rs1427664551 1415 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_124B_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell miR-124 + B ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' ucuuggagccGAC-CCCGCCCga 5'
                    :|| || | ||  
Target 5' ---agaugacUUGAGGUCAGGa- 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 GSM1084044. RNA binding protein: AGO2. Condition:CLIP_noarsenite_rep3 ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' ucuuggagccGAC-CCCGCCCga 5'
                    :|| || | ||  
Target 5' ---agaugacUUGAGGUCAGGag 3'
 		1 - 20
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_124B_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell miR-124 + B
Location of target site ENST00000422090.2 | 3UTR | AGAUGACUUGAGGUCAGGA
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 GSM1084044
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noarsenite_rep3
Location of target site ENST00000422090.2 | 3UTR | AGAUGACUUGAGGUCAGGAGUUCGAGACCAGCCUGG
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
91 hsa-miR-4707-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT442514 SYT7 synaptotagmin 7 2 4
MIRT457799 NQO2 N-ribosyldihydronicotinamide:quinone reductase 2 2 2
MIRT466318 THRA thyroid hormone receptor, alpha 2 2
MIRT486129 TRAF3 TNF receptor associated factor 3 2 2
MIRT492341 SEPT8 septin 8 2 2
MIRT495690 KCNC3 potassium voltage-gated channel subfamily C member 3 2 2
MIRT496928 DPYSL5 dihydropyrimidinase like 5 2 2
MIRT499518 MAFK MAF bZIP transcription factor K 2 2
MIRT501367 REXO1 RNA exonuclease 1 homolog 2 4
MIRT501636 PIAS4 protein inhibitor of activated STAT 4 2 4
MIRT521071 SLC25A16 solute carrier family 25 member 16 2 2
MIRT525700 PCYT2 phosphate cytidylyltransferase 2, ethanolamine 2 2
MIRT532722 DDTL D-dopachrome tautomerase like 2 2
MIRT533137 WWC1 WW and C2 domain containing 1 2 4
MIRT537288 G3BP1 G3BP stress granule assembly factor 1 2 4
MIRT570555 PHF21B PHD finger protein 21B 2 2
MIRT573469 MTRNR2L9 MT-RNR2-like 9 2 2
MIRT576750 Tmem127 transmembrane protein 127 2 2
MIRT609342 DAAM2 dishevelled associated activator of morphogenesis 2 2 2
MIRT610638 PIGM phosphatidylinositol glycan anchor biosynthesis class M 2 2
MIRT612591 RANGAP1 Ran GTPase activating protein 1 2 2
MIRT614237 WDR53 WD repeat domain 53 2 4
MIRT622784 PGK1 phosphoglycerate kinase 1 2 2
MIRT628880 MED16 mediator complex subunit 16 2 2
MIRT629550 SPN sialophorin 2 2
MIRT634714 DDX19B DEAD-box helicase 19B 2 2
MIRT634932 GTF2H2C GTF2H2 family member C 2 4
MIRT635341 RBL1 RB transcriptional corepressor like 1 2 2
MIRT637838 CPT1A carnitine palmitoyltransferase 1A 2 2
MIRT644311 NFKBID NFKB inhibitor delta 2 2
MIRT649206 KIAA1715 lunapark, ER junction formation factor 2 2
MIRT657262 HSPA4L heat shock protein family A (Hsp70) member 4 like 2 2
MIRT658919 DPY19L4 dpy-19 like 4 2 2
MIRT663608 SEC23B Sec23 homolog B, coat complex II component 2 2
MIRT667425 MFAP2 microfibril associated protein 2 2 2
MIRT667667 KREMEN1 kringle containing transmembrane protein 1 2 2
MIRT668144 GDPD1 glycerophosphodiester phosphodiesterase domain containing 1 2 2
MIRT668540 ERGIC1 endoplasmic reticulum-golgi intermediate compartment 1 2 2
MIRT670039 NFRKB nuclear factor related to kappaB binding protein 2 2
MIRT670875 RAB10 RAB10, member RAS oncogene family 2 2
MIRT672694 ZNF677 zinc finger protein 677 2 2
MIRT673107 MFSD2A major facilitator superfamily domain containing 2A 2 2
MIRT673508 TNFAIP8L1 TNF alpha induced protein 8 like 1 2 4
MIRT674244 NUP62 nucleoporin 62 2 4
MIRT676541 IRGQ immunity related GTPase Q 2 2
MIRT676787 CXorf38 chromosome X open reading frame 38 2 4
MIRT677600 PRKX protein kinase, X-linked 2 2
MIRT678607 MRPL17 mitochondrial ribosomal protein L17 2 2
MIRT678940 MYADM myeloid associated differentiation marker 2 2
MIRT679104 CD99 CD99 molecule (Xg blood group) 2 2
MIRT679196 WNT2B Wnt family member 2B 2 2
MIRT679325 ZMYM4 zinc finger MYM-type containing 4 2 2
MIRT679634 BRMS1L breast cancer metastasis-suppressor 1 like 2 2
MIRT679819 TMEM106B transmembrane protein 106B 2 2
MIRT679898 FBXO48 F-box protein 48 2 2
MIRT680579 ZNF784 zinc finger protein 784 2 2
MIRT680600 SZT2 SZT2, KICSTOR complex subunit 2 2
MIRT682991 RNF40 ring finger protein 40 2 4
MIRT683483 ZNF7 zinc finger protein 7 2 2
MIRT683681 MICA MHC class I polypeptide-related sequence A 2 2
MIRT684122 CEP104 centrosomal protein 104 2 2
MIRT684774 MYO1F myosin IF 2 2
MIRT685698 BHMT2 betaine--homocysteine S-methyltransferase 2 2 2
MIRT686471 LINC00598 long intergenic non-protein coding RNA 598 2 2
MIRT687940 HMGB1 high mobility group box 1 2 2
MIRT688627 CRISPLD2 cysteine rich secretory protein LCCL domain containing 2 2 2
MIRT689110 ZBTB25 zinc finger and BTB domain containing 25 2 2
MIRT690063 MBD1 methyl-CpG binding domain protein 1 2 2
MIRT691067 NUGGC nuclear GTPase, germinal center associated 2 2
MIRT691317 KIAA1841 KIAA1841 2 2
MIRT692778 SYNPO2L synaptopodin 2 like 2 2
MIRT694087 KIAA0930 KIAA0930 2 2
MIRT696148 WDR59 WD repeat domain 59 2 2
MIRT696176 GNB5 G protein subunit beta 5 2 2
MIRT696434 SUGP1 SURP and G-patch domain containing 1 2 2
MIRT697974 TSPAN6 tetraspanin 6 2 2
MIRT698917 SPEM1 spermatid maturation 1 2 2
MIRT699312 SLC35F5 solute carrier family 35 member F5 2 4
MIRT700500 PTPN4 protein tyrosine phosphatase, non-receptor type 4 2 2
MIRT700557 PTBP1 polypyrimidine tract binding protein 1 2 2
MIRT701817 MRPL37 mitochondrial ribosomal protein L37 2 2
MIRT702045 METTL21A methyltransferase like 21A 2 2
MIRT702215 LPCAT1 lysophosphatidylcholine acyltransferase 1 2 2
MIRT702337 KLHL7 kelch like family member 7 2 2
MIRT704139 DNAL1 dynein axonemal light chain 1 2 2
MIRT704189 LDHD lactate dehydrogenase D 2 2
MIRT705344 ATP1B3 ATPase Na+/K+ transporting subunit beta 3 2 2
MIRT706097 ENTPD4 ectonucleoside triphosphate diphosphohydrolase 4 2 2
MIRT709068 FAHD1 fumarylacetoacetate hydrolase domain containing 1 2 2
MIRT717579 VTA1 vesicle trafficking 1 2 2
MIRT722440 ZBTB7B zinc finger and BTB domain containing 7B 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4707 Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-mir-4707 Fluorouracil 3385 NSC19893 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-mir-4707 Dabrafenib 44462760 NSC764134 approved resistant cell line (A375)
hsa-mir-4707 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-miR-4707-3p Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-4707-3p Tripterygium wilfordii Hook F sensitive tissue
hsa-miR-4707-3p Cisplatin 5460033 NSC119875 approved resistant cell line (A549)
hsa-miR-4707-3p Tamoxifen 2733525 NSC180973 approved resistant cell line (LCC2)
hsa-miR-4707-3p Neoadjuvant chemotherapy resistant tissue (breast cancer)
hsa-miR-4707-3p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)

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