pre-miRNA Information
pre-miRNA hsa-mir-2909   
Genomic Coordinates chr17: 37033745 - 37033813
Description Homo sapiens miR-2909 stem-loop
Comment This miRNA was referred to as hmiR-che-1 in .
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-2909
Sequence 4| GUUAGGGCCAACAUCUCUUGG |24
Evidence Experimental
Experiments QPCR
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs187707102 7 dbSNP
rs1375183104 8 dbSNP
rs1174848003 11 dbSNP
rs576577155 21 dbSNP
Putative Targets

Gene Information
Gene Symbol TXNDC16   
Synonyms ERp90, KIAA1344
Description thioredoxin domain containing 16
Transcript NM_001160047   
Other Transcripts NM_020784   
Expression
Putative miRNA Targets on TXNDC16
3'UTR of TXNDC16
(miRNA target sites are highlighted)
>TXNDC16|NM_001160047|3'UTR
   1 TTTTATAGGGCTGTGGTTTCCAAAATTTTTTTGGCATGATAGACTTAATTTATTTCCTTAAAGAATAATATTAAATCATT
  81 TCAAGTTTGCAGACTAGTGCCATCCAATAGAATTATAATATAAGTCACATATTTTATTTAAAATTTTCTAGTAACTACAT
 161 TAAACAAAGTAAAAGTGAGCAGGGCAAAATAATTTTGATATTACTTTTCACCCAGTAGTATACCCAAAATAGCGAAATAT
 241 AGAAATTATTAATGAGATATTTTACATCCTTTTTTGTACCAAGTCTTCTAAATGCAGTACATATTTTATACTTACTGCAT
 321 TTCTTACTTCCGAGTAGCCATATTTCAAGTGTTCCTTGCCACATGTGGCCTGTGACTACTGTATTGGACAGTTCAGTACT
 401 AGACAAAAACTAGCATAATTAACTTAGTTCTAGCCATGATTTCTATTTGGATTAAAATTAAACTCTAATCACAGTTAACT
 481 CCACAGTGCATTCATGCAGCTGACAGTTATATTTGTTTTATTGGAGTCATGATATTAAAATCAGCGTTTGTCAACCTCAG
 561 GGGATATTTAGCAATTGTCGGGAGACATTTTTGATGTCATGACTAGGGCAGTTATTGACATTTAGTGAGTAGAGGCCAGG
 641 GATCCTGCTAAATAACCTGCATTGGACAGCGCCCCACAACAAAGAATTATCCTGCCCGAAATGGTAGTCGTGCCAAGGCT
 721 GAGTAACCTTGTGTTAAAAGTAACCTGTGGCAGACTAGGTTTCCAGAATTTCCTGGTTCTGCTCACGTATCATGTTTGAA
 801 AAAATTTTGGCTATTAAAGATATGTATTAGATGGTCTTATCCTGATTATTACCTGGATACAACTTGATCTTTTCTAATAT
 881 TTTCAGAAAGTGATGGGATAACCCTAGAAGAGGACTCAGAATGATATTTATATTTTAAGTGAGTCTTAAAACCTCCTCTT
 961 ATTTCTACAAGTTATATGGCTAAATTTCAGATTGAACAGGGATTCAGCATTCTGCCATCTCCTCATGGAAAGAGAGGCTC
1041 CCTCATCTGAAGCGTCTCTGAAATCTACCCTTGCAAGCTTCAGACAAATCAGTTGATCTCCCTGAGCCACACGGCCTCAT
1121 TCTGTGAGGGAGGGAAAGATTAGCCAAAGAGTTAATTTTCATTCCAAATCACTTAGCTGTTAGACTGATCTGTTTGTAGC
1201 AGTTGTTTGTCTCATTTTTGCTCTGTGCATTTTTTGAGACATTTGTTGAGAATATTCTATTTGGTGCTCTACTGTATTTT
1281 TCTTTTTAATATCTACTTGATATCTTGTTCTTTAAATTTTCTTCACATATGGTTTGCCTGATACAACTGATTTTTATAAC
1361 TGAAATTTAAGGAATCTAACAGCTAAAACTCAGTAAGTGCATATATTTCCTTATAACATAGACCCGTTGCTACTCTCAGC
1441 ACCCTCTCCTCAATTTTTTTTCCTGTAGCATGTGATGCCTGATTAAACTCATTTTCATTTGCTTTTATTTCTAATATGGG
1521 AACAATGAGAGTGAACTCTAAATATAGGTTGTAGTAATAAAACATCATTAGCCTAATTATTAGAAAATGCTAATTAAGTA
1601 CCAGCACATAGAAACATGAAATTGCTTAGTCATTGTACCTTTGTCAGCAATTTTGACAGTCATTAATGTTTGTCATAATT
1681 TTAAATAAAGTGTCTGGGTTTCAGAATACCTTCAAAAAAAAAAA
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' ggUUCUCUACA------ACCGGGAUug 5'
            |||| ||||      |||:|:||  
Target 5' taAAGATATGTATTAGATGGTCTTAtc 3'
815 - 841 117.00 -11.70
2
miRNA  3' ggUUCUCUACAA--CCGGGAUUg 5'
            |||| ||  |   |||| || 
Target 5' caAAGA-ATTATCCTGCCCGAAa 3'
680 - 701 116.00 -6.20
3
miRNA  3' gguucucUACAACCGGGAUUg 5'
                 | ||  |:|:||| 
Target 5' atattttAAGTGAGTCTTAAa 3'
930 - 950 114.00 -6.40
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31542172 3 COSMIC
COSN27000740 8 COSMIC
COSN31507193 9 COSMIC
COSN30459242 10 COSMIC
COSN30183020 13 COSMIC
COSN27000741 17 COSMIC
COSN5854176 26 COSMIC
COSN30116860 38 COSMIC
COSN30143928 54 COSMIC
COSN22996894 68 COSMIC
COSN30157323 82 COSMIC
COSN8588722 84 COSMIC
COSN30534199 129 COSMIC
COSN31583456 145 COSMIC
COSN15807476 853 COSMIC
COSN21952262 1371 COSMIC
COSN6253495 1425 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1443216530 5 dbSNP
rs771087254 13 dbSNP
rs1212675186 22 dbSNP
rs749461597 23 dbSNP
rs778126336 25 dbSNP
rs1444539530 27 dbSNP
rs540316568 28 dbSNP
rs770647972 33 dbSNP
rs1382733523 37 dbSNP
rs1437224288 38 dbSNP
rs940748030 39 dbSNP
rs1308143898 48 dbSNP
rs1402467146 57 dbSNP
rs979512636 63 dbSNP
rs917364491 68 dbSNP
rs1331927054 79 dbSNP
rs1358406857 81 dbSNP
rs1447292092 86 dbSNP
rs1311308664 88 dbSNP
rs966449611 92 dbSNP
rs1237961380 96 dbSNP
rs1021134787 100 dbSNP
rs1010378827 119 dbSNP
rs1276908027 124 dbSNP
rs927288332 124 dbSNP
rs937396601 124 dbSNP
rs1213704912 134 dbSNP
rs146815854 136 dbSNP
rs530166586 140 dbSNP
rs1240506946 146 dbSNP
rs1456875649 159 dbSNP
rs968954953 164 dbSNP
rs1377747141 165 dbSNP
rs1304759819 175 dbSNP
rs760832435 176 dbSNP
rs1170407365 177 dbSNP
rs1369169008 178 dbSNP
rs1035848076 179 dbSNP
rs561333163 182 dbSNP
rs1465896006 190 dbSNP
rs1001734171 194 dbSNP
rs988959362 197 dbSNP
rs906164702 200 dbSNP
rs1037674120 209 dbSNP
rs1446017317 210 dbSNP
rs776155748 223 dbSNP
rs77380289 226 dbSNP
rs141812431 229 dbSNP
rs953699832 232 dbSNP
rs933451233 233 dbSNP
rs923093462 234 dbSNP
rs1219631782 247 dbSNP
rs1455535788 248 dbSNP
rs1393265167 252 dbSNP
rs1197890899 254 dbSNP
rs377566102 257 dbSNP
rs974616026 259 dbSNP
rs1268707384 267 dbSNP
rs1452790845 270 dbSNP
rs897093032 276 dbSNP
rs1267655269 281 dbSNP
rs1477980545 296 dbSNP
rs1172534986 303 dbSNP
rs1421268212 308 dbSNP
rs1015417992 315 dbSNP
rs943229829 318 dbSNP
rs187233217 331 dbSNP
rs545590947 332 dbSNP
rs1321674261 333 dbSNP
rs1057177857 338 dbSNP
rs937429623 346 dbSNP
rs2767540 355 dbSNP
rs113867563 357 dbSNP
rs111386743 358 dbSNP
rs749002417 362 dbSNP
rs148028233 367 dbSNP
rs143569645 368 dbSNP
rs1228571052 376 dbSNP
rs554538258 380 dbSNP
rs913512348 385 dbSNP
rs1195446151 392 dbSNP
rs1260629256 399 dbSNP
rs1001660542 422 dbSNP
rs777401749 427 dbSNP
rs1016946676 438 dbSNP
rs1188013094 441 dbSNP
rs537450728 445 dbSNP
rs1370050485 465 dbSNP
rs568761925 466 dbSNP
rs1456383762 468 dbSNP
rs1006498950 482 dbSNP
rs1365080557 485 dbSNP
rs1312952318 494 dbSNP
rs1420419328 495 dbSNP
rs1436107051 497 dbSNP
rs1300224932 505 dbSNP
rs562654046 510 dbSNP
rs989376571 514 dbSNP
rs1313972983 521 dbSNP
rs1342765835 527 dbSNP
rs1171969080 529 dbSNP
rs769294275 530 dbSNP
rs866958450 542 dbSNP
rs552072135 545 dbSNP
rs549177747 546 dbSNP
rs1218190771 551 dbSNP
rs985194456 553 dbSNP
rs1200815694 555 dbSNP
rs997600495 559 dbSNP
rs771096785 561 dbSNP
rs901933768 562 dbSNP
rs1421956312 563 dbSNP
rs538585195 579 dbSNP
rs943195197 580 dbSNP
rs1160541573 581 dbSNP
rs1343652283 586 dbSNP
rs1453394895 591 dbSNP
rs973757976 593 dbSNP
rs1404847986 594 dbSNP
rs1450948223 599 dbSNP
rs961271616 605 dbSNP
rs566311178 613 dbSNP
rs184069300 614 dbSNP
rs1256018059 615 dbSNP
rs1196905127 621 dbSNP
rs754622142 632 dbSNP
rs11623681 639 dbSNP
rs72684222 641 dbSNP
rs1233573584 644 dbSNP
rs913550039 647 dbSNP
rs1316906675 658 dbSNP
rs991878503 659 dbSNP
rs376121226 662 dbSNP
rs148841547 668 dbSNP
rs369631096 669 dbSNP
rs368048072 670 dbSNP
rs905978073 671 dbSNP
rs960405600 674 dbSNP
rs926388950 678 dbSNP
rs1177005886 681 dbSNP
rs1379606851 683 dbSNP
rs980216067 686 dbSNP
rs1391911862 688 dbSNP
rs1176166487 691 dbSNP
rs1398283230 695 dbSNP
rs530832594 697 dbSNP
rs1295916282 702 dbSNP
rs970182568 703 dbSNP
rs1016462083 705 dbSNP
rs1006878697 710 dbSNP
rs1320982175 716 dbSNP
rs1167407742 731 dbSNP
rs1222672075 733 dbSNP
rs1474237256 737 dbSNP
rs1319890263 740 dbSNP
rs1196711548 742 dbSNP
rs951038189 749 dbSNP
rs1232260577 751 dbSNP
rs1367978399 758 dbSNP
rs1191858555 763 dbSNP
rs1183080141 768 dbSNP
rs1440054739 772 dbSNP
rs1249108199 776 dbSNP
rs1198386142 786 dbSNP
rs1424838341 787 dbSNP
rs1026697413 794 dbSNP
rs1469222547 804 dbSNP
rs997528350 807 dbSNP
rs1467540696 816 dbSNP
rs944297050 818 dbSNP
rs912704703 820 dbSNP
rs901897689 826 dbSNP
rs1457912923 830 dbSNP
rs192281871 831 dbSNP
rs932372010 834 dbSNP
rs1404009603 840 dbSNP
rs1007669496 841 dbSNP
rs1212609145 844 dbSNP
rs545699645 848 dbSNP
rs1322259435 852 dbSNP
rs1222392683 853 dbSNP
rs1283096579 876 dbSNP
rs573607123 877 dbSNP
rs1489914448 896 dbSNP
rs903669570 906 dbSNP
rs1239228417 922 dbSNP
rs973726958 925 dbSNP
rs1478975226 928 dbSNP
rs10148968 930 dbSNP
rs908212057 931 dbSNP
rs992059840 932 dbSNP
rs945282189 934 dbSNP
rs1445713134 938 dbSNP
rs913822133 943 dbSNP
rs960925927 945 dbSNP
rs1565970 946 dbSNP
rs7154210 947 dbSNP
rs1298371275 953 dbSNP
rs939039211 955 dbSNP
rs1362074725 956 dbSNP
rs1428299798 959 dbSNP
rs138747036 962 dbSNP
rs980477229 967 dbSNP
rs1312874844 969 dbSNP
rs1471227455 971 dbSNP
rs1221862153 974 dbSNP
rs1362536254 980 dbSNP
rs962469682 992 dbSNP
rs909370366 1015 dbSNP
rs145718693 1017 dbSNP
rs951001509 1022 dbSNP
rs1026582666 1026 dbSNP
rs1011617783 1027 dbSNP
rs1215106702 1031 dbSNP
rs1449513326 1042 dbSNP
rs764354461 1044 dbSNP
rs1053545023 1046 dbSNP
rs1205169749 1053 dbSNP
rs537817222 1054 dbSNP
rs1341133029 1062 dbSNP
rs1359566544 1063 dbSNP
rs1449982865 1069 dbSNP
rs1334542572 1077 dbSNP
rs574880730 1083 dbSNP
rs558160700 1086 dbSNP
rs891397222 1088 dbSNP
rs1245333775 1091 dbSNP
rs1310156259 1092 dbSNP
rs1353090137 1093 dbSNP
rs1306923805 1098 dbSNP
rs760859363 1112 dbSNP
rs1294946690 1124 dbSNP
rs1007639898 1128 dbSNP
rs374901819 1129 dbSNP
rs1239351706 1134 dbSNP
rs1380396012 1138 dbSNP
rs373161097 1140 dbSNP
rs1205977844 1141 dbSNP
rs1049908920 1149 dbSNP
rs1461315067 1154 dbSNP
rs903975533 1163 dbSNP
rs186071901 1166 dbSNP
rs932839964 1171 dbSNP
rs1022507905 1185 dbSNP
rs1468255299 1190 dbSNP
rs1157583404 1191 dbSNP
rs1305350706 1195 dbSNP
rs141971847 1196 dbSNP
rs1330718188 1199 dbSNP
rs1405250663 1203 dbSNP
rs1447492145 1214 dbSNP
rs1332093174 1220 dbSNP
rs1319276037 1222 dbSNP
rs1402483499 1223 dbSNP
rs565126803 1228 dbSNP
rs752787109 1238 dbSNP
rs1358728992 1239 dbSNP
rs1345979304 1240 dbSNP
rs1158513705 1245 dbSNP
rs1225727519 1249 dbSNP
rs1261721898 1252 dbSNP
rs1323422697 1255 dbSNP
rs892354501 1261 dbSNP
rs1253323841 1268 dbSNP
rs1397509900 1273 dbSNP
rs15755 1282 dbSNP
rs566472082 1291 dbSNP
rs1056293183 1293 dbSNP
rs1246923612 1300 dbSNP
rs1481247756 1302 dbSNP
rs1196992318 1303 dbSNP
rs939300983 1307 dbSNP
rs1428391459 1327 dbSNP
rs1192135039 1334 dbSNP
rs1465977871 1345 dbSNP
rs904861209 1356 dbSNP
rs1394259817 1358 dbSNP
rs1044750508 1371 dbSNP
rs1038088553 1374 dbSNP
rs1331884487 1378 dbSNP
rs1407045035 1383 dbSNP
rs1281736470 1401 dbSNP
rs11039 1403 dbSNP
rs1253528956 1409 dbSNP
rs909642769 1410 dbSNP
rs985338552 1411 dbSNP
rs536061579 1418 dbSNP
rs75381963 1425 dbSNP
rs1283264864 1426 dbSNP
rs919447604 1430 dbSNP
rs1215342383 1440 dbSNP
rs550811911 1443 dbSNP
rs1195061610 1452 dbSNP
rs1371259485 1452 dbSNP
rs960641555 1453 dbSNP
rs926565072 1462 dbSNP
rs1366314311 1482 dbSNP
rs966315470 1495 dbSNP
rs1301472174 1501 dbSNP
rs1366683781 1516 dbSNP
rs1365195191 1517 dbSNP
rs1017614347 1528 dbSNP
rs531068379 1537 dbSNP
rs180963743 1549 dbSNP
rs1325178074 1550 dbSNP
rs1227397323 1557 dbSNP
rs1285338035 1561 dbSNP
rs1022093590 1566 dbSNP
rs762342351 1590 dbSNP
rs1433174193 1594 dbSNP
rs1338438715 1598 dbSNP
rs1022391627 1605 dbSNP
rs145661225 1606 dbSNP
rs796374103 1607 dbSNP
rs1488449197 1610 dbSNP
rs1206657106 1614 dbSNP
rs1259455265 1615 dbSNP
rs528783865 1616 dbSNP
rs892286712 1620 dbSNP
rs189732900 1621 dbSNP
rs1415539607 1623 dbSNP
rs1446451762 1624 dbSNP
rs1377778813 1626 dbSNP
rs1034851090 1633 dbSNP
rs1454548972 1635 dbSNP
rs901461268 1638 dbSNP
rs1174629036 1646 dbSNP
rs1383213139 1650 dbSNP
rs956145422 1657 dbSNP
rs1337904773 1662 dbSNP
rs1414210694 1666 dbSNP
rs151290779 1668 dbSNP
rs905122752 1673 dbSNP
rs1240790637 1685 dbSNP
rs1258616168 1691 dbSNP
rs1044679943 1697 dbSNP
Experimental Support 1 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 GSM1084072. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep1_AbnovaAb ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' gguuCUCUACAAC-CGGGauug 5'
              |||    || ||||    
Target 5' gcguGAGCCACUGCGCCCggcc 3'
3 - 24
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 GSM1084072
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep1_AbnovaAb
Location of target site ENST00000281741.4 | 3UTR | AGGCGUGAGCCACUGCGCCCGGCCC
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
33 hsa-miR-2909 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT254788 XRCC6 X-ray repair cross complementing 6 2 4
MIRT464426 UHMK1 U2AF homology motif kinase 1 2 2
MIRT478185 DDX6 DEAD-box helicase 6 2 6
MIRT481768 APEX1 apurinic/apyrimidinic endodeoxyribonuclease 1 2 2
MIRT489915 RTKN rhotekin 2 2
MIRT500566 VPS4A vacuolar protein sorting 4 homolog A 2 8
MIRT510700 SREK1IP1 SREK1 interacting protein 1 2 6
MIRT513331 CDK2 cyclin dependent kinase 2 2 4
MIRT524310 CTC1 CST telomere replication complex component 1 2 4
MIRT533571 TOMM40L translocase of outer mitochondrial membrane 40 like 2 2
MIRT537784 EIF4E3 eukaryotic translation initiation factor 4E family member 3 2 2
MIRT540489 ZMAT4 zinc finger matrin-type 4 2 8
MIRT547020 PPP1CB protein phosphatase 1 catalytic subunit beta 2 2
MIRT549561 C19orf12 chromosome 19 open reading frame 12 2 2
MIRT557346 HBP1 HMG-box transcription factor 1 2 4
MIRT564692 ZNF322P1 zinc finger protein 322 pseudogene 1 2 2
MIRT570167 LIPG lipase G, endothelial type 2 2
MIRT621677 UBE2QL1 ubiquitin conjugating enzyme E2 Q family like 1 2 2
MIRT629121 APPL1 adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 1 2 4
MIRT633745 MCM9 minichromosome maintenance 9 homologous recombination repair factor 2 2
MIRT634178 TXNDC16 thioredoxin domain containing 16 2 2
MIRT646387 SLC22A6 solute carrier family 22 member 6 2 2
MIRT651181 ZNF281 zinc finger protein 281 2 2
MIRT651892 UFD1L ubiquitin recognition factor in ER associated degradation 1 2 2
MIRT675180 KIF1C kinesin family member 1C 2 2
MIRT682670 CPM carboxypeptidase M 2 2
MIRT685990 NEK4 NIMA related kinase 4 2 2
MIRT698850 SRSF2 serine and arginine rich splicing factor 2 2 2
MIRT699396 SLC2A1 solute carrier family 2 member 1 2 2
MIRT723260 SREK1 splicing regulatory glutamic acid and lysine rich protein 1 2 2
MIRT725320 NFASC neurofascin 2 2
MIRT734596 CD276 CD276 molecule 2 0
MIRT734938 PTEN phosphatase and tensin homolog 2 0
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-2909 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-2909 Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide sensitive cell line (Bads-200)

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