pre-miRNA Information
pre-miRNA hsa-mir-4749   
Genomic Coordinates chr19: 49854591 - 49854651
Description Homo sapiens miR-4749 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4749-3p
Sequence 42| CGCCCCUCCUGCCCCCACAG |61
Evidence Experimental
Experiments Illumina
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN19730808 2 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs147943327 1 dbSNP
rs148982635 2 dbSNP
rs372882504 3 dbSNP
rs200056596 4 dbSNP
rs570340094 5 dbSNP
rs778438436 11 dbSNP
rs748573000 13 dbSNP
rs770230641 14 dbSNP
rs201103722 16 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol USP49   
Synonyms -
Description ubiquitin specific peptidase 49
Transcript NM_018561   
Expression
Putative miRNA Targets on USP49
3'UTR of USP49
(miRNA target sites are highlighted)
>USP49|NM_018561|3'UTR
   1 TTTGTCCACATTTTATTGTTTTCCTTTTATTTCCATCCCATGGATTACCTAGAGGGAAATTACATACATCAAAAATCCAG
  81 TGGAAAGAATTGTGAAAATTGGGTTGGGCGCCGTGGCTCACACCTGTAATCCTAGCGCTTTGGGAGGCCGCGGTGGGTGG
 161 ATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTTAAACCCCGTCTCTACTAAAATAGTACAAAAATTAG
 241 CCGGGCGTGGTGGTGGGCACTGGTAATCCCAGGTACTCAAGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGCAGA
 321 GGTTGCAGTGAGCCAAGATTATGCCACTGCACTTCAGCCTGGGTGACAGAGCAAGACTCTTATCTCAAAAAAAATAAAAA
 401 GAATTATGAAAGTTGGATTCAAATTTTGGGTATATTACTAAGTAACAACATATGGTTGTTCTAAGAATTAAAAGGAACTG
 481 ACATGTAAAAGTGCTTAGAACAGGACCTAGGCCCTGTGCAATGGCTCACACCTGTAATTCCAACACTTTGGGAGGCAGAG
 561 GCGGGAGGATTGCTTGAGGCCGAGGGTTCAAGACTAGCCTGGGCAACATAGCGAGACTGCATCTCTACAAAAAATTTAAA
 641 AATTATCCAGGTGTAATGGTGTGCACCTGTGATCCTAGCTACTTGGGAGGCTGAGGTGGGAGAATTGCTCAAGCCCAGGA
 721 GTTTGAAGTTGCAATGAGCTATGATTTCACCACTGCATTCTAGCCTGGGCAACAGAGTGAGATCCTGACTCAAATAAATA
 801 AATAAGAAGAGCAGTTGCCTACCACATAGTACTTATTCAGTCAGTGTTAGAGGATATTGTAGTATTATCAAAAGTATTGG
 881 TTATTGATAATATTACTGTTTTGTGGTAATGCTACTTCTGCACACCCCAGTTTCCTTCTTGGTTATGCAGAAACAGTAGA
 961 ACCTGTGTAACCTCAAGGAGATATTGTATGAATCTCACTAGCCGCAGCTTATAATAAAGCCGAGAACATTTAAAAAAAAA
1041 AAAAAAAAA
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' gacACCC-CCGUCCUCCCCgc 5'
             |||| |||| |||| |  
Target 5' cttTGGGAGGCA-GAGGCGgg 3'
546 - 565 112.00 -22.10
2
miRNA  3' gacACCCCCGUCCUCCCcgc 5'
             || || |  |||||   
Target 5' gctTGAGGCC--GAGGGttc 3'
572 - 589 109.00 -11.20
3
miRNA  3' gacaCCCCCGUC-CUCCCCGc 5'
              ||| |::| |: |||| 
Target 5' agccGGGCGTGGTGGTGGGCa 3'
239 - 259 108.00 -16.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN18731430 5 COSMIC
COSN30490599 7 COSMIC
COSN31602046 13 COSMIC
COSN32054021 14 COSMIC
COSN19707510 23 COSMIC
COSN30490553 24 COSMIC
COSN30463017 34 COSMIC
COSN30517658 37 COSMIC
COSN30455550 49 COSMIC
COSN30450438 55 COSMIC
COSN30472556 82 COSMIC
COSN1333122 102 COSMIC
COSN27004427 109 COSMIC
COSN31606064 110 COSMIC
COSN14227938 113 COSMIC
COSN28764870 124 COSMIC
COSN30133326 137 COSMIC
COSN30110805 152 COSMIC
COSN30167674 181 COSMIC
COSN4927802 386 COSMIC
COSN9783303 465 COSMIC
COSN20989356 802 COSMIC
COSN31519324 874 COSMIC
COSN26638106 962 COSMIC
COSN24322655 968 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1407246729 1 dbSNP
rs751773617 4 dbSNP
rs537758423 5 dbSNP
rs1329968761 7 dbSNP
rs1489726594 10 dbSNP
rs1024410131 11 dbSNP
rs751154209 14 dbSNP
rs764375388 18 dbSNP
rs777455286 21 dbSNP
rs762718423 29 dbSNP
rs758359513 33 dbSNP
rs1290518602 42 dbSNP
rs752693112 44 dbSNP
rs1472877683 48 dbSNP
rs765055310 49 dbSNP
rs896217963 52 dbSNP
rs1397554851 55 dbSNP
rs1030718128 61 dbSNP
rs999602371 64 dbSNP
rs903497483 67 dbSNP
rs568722297 76 dbSNP
rs1189368594 78 dbSNP
rs1298377467 80 dbSNP
rs927116075 87 dbSNP
rs1388214267 99 dbSNP
rs777878574 100 dbSNP
rs1382410646 101 dbSNP
rs981222287 102 dbSNP
rs1158446537 103 dbSNP
rs567488444 109 dbSNP
rs528685016 110 dbSNP
rs988188819 112 dbSNP
rs1050912673 113 dbSNP
rs1029911550 115 dbSNP
rs1308433650 116 dbSNP
rs934123745 119 dbSNP
rs1374234837 125 dbSNP
rs918674457 127 dbSNP
rs972803290 134 dbSNP
rs569261235 136 dbSNP
rs1269812053 138 dbSNP
rs1480881955 139 dbSNP
rs546300353 146 dbSNP
rs143673611 149 dbSNP
rs563758713 150 dbSNP
rs543769344 151 dbSNP
rs530744623 152 dbSNP
rs1386318520 158 dbSNP
rs561991364 170 dbSNP
rs1319317773 181 dbSNP
rs9394832 182 dbSNP
rs572984623 185 dbSNP
rs1445669890 190 dbSNP
rs1336967270 196 dbSNP
rs1328976519 197 dbSNP
rs1226406994 199 dbSNP
rs1311700209 200 dbSNP
rs1031189494 208 dbSNP
rs1325161829 209 dbSNP
rs1387663315 210 dbSNP
rs9471661 212 dbSNP
rs1329834579 213 dbSNP
rs1456493630 221 dbSNP
rs903547688 222 dbSNP
rs1057035768 235 dbSNP
rs191815065 238 dbSNP
rs780165842 241 dbSNP
rs577377983 242 dbSNP
rs557426484 243 dbSNP
rs1050964661 246 dbSNP
rs1477111952 247 dbSNP
rs1042906839 249 dbSNP
rs933820633 255 dbSNP
rs896962519 260 dbSNP
rs537421052 276 dbSNP
rs1160832234 285 dbSNP
rs1445297869 287 dbSNP
rs568707219 300 dbSNP
rs1401836738 301 dbSNP
rs941435154 309 dbSNP
rs1459023596 319 dbSNP
rs1273686182 328 dbSNP
rs1052386052 330 dbSNP
rs935371129 338 dbSNP
rs1342298753 340 dbSNP
rs922613581 349 dbSNP
rs909925370 351 dbSNP
rs1276198939 352 dbSNP
rs1044368719 359 dbSNP
rs948689582 360 dbSNP
rs1233533181 362 dbSNP
rs976933325 365 dbSNP
rs917503888 369 dbSNP
rs1261663482 373 dbSNP
rs964282394 377 dbSNP
rs993074001 379 dbSNP
rs1329719390 395 dbSNP
rs187341435 397 dbSNP
rs528615647 398 dbSNP
rs1174905925 399 dbSNP
rs1345625865 400 dbSNP
rs1421300663 406 dbSNP
rs1296041295 407 dbSNP
rs1339793606 423 dbSNP
rs952566359 429 dbSNP
rs1275564695 432 dbSNP
rs868013728 440 dbSNP
rs978267031 442 dbSNP
rs1334134334 446 dbSNP
rs1317674517 450 dbSNP
rs1219289563 453 dbSNP
rs146830233 457 dbSNP
rs1404471501 463 dbSNP
rs1022003038 475 dbSNP
rs1200748618 478 dbSNP
rs1173319932 479 dbSNP
rs1439325215 482 dbSNP
rs552338609 484 dbSNP
rs959653069 487 dbSNP
rs953653860 491 dbSNP
rs1035372746 492 dbSNP
rs1359636105 495 dbSNP
rs1425266992 503 dbSNP
rs1030011049 504 dbSNP
rs1325440447 513 dbSNP
rs1347990869 519 dbSNP
rs1434407302 521 dbSNP
rs1274293463 527 dbSNP
rs1001422906 544 dbSNP
rs1242557181 562 dbSNP
rs998084612 563 dbSNP
rs905807891 568 dbSNP
rs566267907 569 dbSNP
rs1043265651 570 dbSNP
rs1450320222 579 dbSNP
rs1011449649 581 dbSNP
rs1209358012 582 dbSNP
rs897003744 584 dbSNP
rs971427924 587 dbSNP
rs1036864558 596 dbSNP
rs1176362703 603 dbSNP
rs1006084500 604 dbSNP
rs935421755 612 dbSNP
rs552322910 613 dbSNP
rs1041038625 616 dbSNP
rs143695492 618 dbSNP
rs1242735718 619 dbSNP
rs948743338 621 dbSNP
rs911517282 635 dbSNP
rs1329549844 636 dbSNP
rs1376356961 656 dbSNP
rs917222451 664 dbSNP
rs1057512537 666 dbSNP
rs1286277026 667 dbSNP
rs1354887246 673 dbSNP
rs952876435 681 dbSNP
rs1258186551 683 dbSNP
rs1458709795 694 dbSNP
rs1196435465 698 dbSNP
rs934907912 698 dbSNP
rs1374552327 700 dbSNP
rs182075759 705 dbSNP
rs978942831 715 dbSNP
rs972451175 718 dbSNP
rs1342276044 724 dbSNP
rs1168425674 725 dbSNP
rs1334920743 733 dbSNP
rs563599361 734 dbSNP
rs1358820752 736 dbSNP
rs1168536893 754 dbSNP
rs1399875809 762 dbSNP
rs1396771392 764 dbSNP
rs959788082 782 dbSNP
rs558945860 784 dbSNP
rs914995626 788 dbSNP
rs985183047 792 dbSNP
rs541516709 806 dbSNP
rs530523216 809 dbSNP
rs953705879 811 dbSNP
rs979789438 811 dbSNP
rs1320539589 812 dbSNP
rs1216291367 819 dbSNP
rs1256817430 823 dbSNP
rs1345343481 826 dbSNP
rs140056867 828 dbSNP
rs1021578278 840 dbSNP
rs77616180 844 dbSNP
rs528327734 847 dbSNP
rs1031485283 849 dbSNP
rs999537983 857 dbSNP
rs1191620956 862 dbSNP
rs1422979459 864 dbSNP
rs1466779038 865 dbSNP
rs1239194355 868 dbSNP
rs901295448 870 dbSNP
rs1041021043 871 dbSNP
rs1015893208 873 dbSNP
rs559604282 877 dbSNP
rs1299144137 885 dbSNP
rs1487700774 892 dbSNP
rs1342961565 896 dbSNP
rs1398671290 902 dbSNP
rs370368214 914 dbSNP
rs1331177468 920 dbSNP
rs1235037328 926 dbSNP
rs1253899505 930 dbSNP
rs1005345359 934 dbSNP
rs1343760010 941 dbSNP
rs1217103237 948 dbSNP
rs1287829105 959 dbSNP
rs1487294606 961 dbSNP
rs865924123 972 dbSNP
rs1261209080 974 dbSNP
rs1433830171 975 dbSNP
rs1218370827 976 dbSNP
rs1376166195 978 dbSNP
rs546005708 981 dbSNP
rs377212482 984 dbSNP
rs1159680057 985 dbSNP
rs1362814395 986 dbSNP
rs918727795 989 dbSNP
rs1422494392 992 dbSNP
rs1023020443 995 dbSNP
rs16895020 996 dbSNP
rs369696948 1003 dbSNP
rs980170401 1004 dbSNP
rs969718746 1016 dbSNP
rs543494629 1018 dbSNP
rs752207550 1021 dbSNP
rs1351224824 1022 dbSNP
rs1338549178 1025 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 GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' gacaCCCCCGUCCUCCCCGc 5'
              || ||||| |||||| 
Target 5' ---aGGAGGCAGAAGGGGCa 3'
1 - 17
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 GSM1084065
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_AbnovaAb
Location of target site ENST00000394253.3 | 3UTR | AGGAGGCAGAAGGGGCAGUGAGCCGAGAU
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
63 hsa-miR-4749-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT082256 MED29 mediator complex subunit 29 2 4
MIRT112161 OTUD3 OTU deubiquitinase 3 2 2
MIRT150036 MIDN midnolin 2 2
MIRT246308 HIST2H2AA3 histone cluster 2 H2A family member a3 2 4
MIRT246320 HIST2H2AA4 histone cluster 2 H2A family member a4 2 4
MIRT248254 SP1 Sp1 transcription factor 2 2
MIRT257944 GIGYF1 GRB10 interacting GYF protein 1 2 2
MIRT466973 STARD7 StAR related lipid transfer domain containing 7 2 4
MIRT492322 SETD1B SET domain containing 1B 2 2
MIRT496204 EFCAB1 EF-hand calcium binding domain 1 2 2
MIRT497568 CCR6 C-C motif chemokine receptor 6 2 2
MIRT502990 CCDC71L coiled-coil domain containing 71 like 2 8
MIRT508300 SIX5 SIX homeobox 5 2 4
MIRT522472 ZAK mitogen-activated protein kinase kinase kinase 20 2 2
MIRT525825 VIMP selenoprotein S 2 4
MIRT528154 BCL2L1 BCL2 like 1 2 2
MIRT532606 SPTLC2 serine palmitoyltransferase long chain base subunit 2 2 2
MIRT551302 RPRM reprimo, TP53 dependent G2 arrest mediator homolog 2 2
MIRT568777 FAM53C family with sequence similarity 53 member C 2 6
MIRT570896 METTL21A methyltransferase like 21A 2 2
MIRT570963 TMBIM4 transmembrane BAX inhibitor motif containing 4 2 2
MIRT571167 ZNF85 zinc finger protein 85 2 2
MIRT576751 Tmem127 transmembrane protein 127 2 2
MIRT609854 DAZAP2 DAZ associated protein 2 2 2
MIRT627101 PDRG1 p53 and DNA damage regulated 1 2 2
MIRT637060 PRKAG1 protein kinase AMP-activated non-catalytic subunit gamma 1 2 2
MIRT639423 PKP1 plakophilin 1 2 2
MIRT643208 TYW3 tRNA-yW synthesizing protein 3 homolog 2 4
MIRT646251 PRSS38 protease, serine 38 2 2
MIRT647145 CYP27C1 cytochrome P450 family 27 subfamily C member 1 2 2
MIRT647429 ZKSCAN2 zinc finger with KRAB and SCAN domains 2 2 2
MIRT650666 GAPDHP44 glyceraldehyde 3 phosphate dehydrogenase pseudogene 44 2 2
MIRT651816 USP49 ubiquitin specific peptidase 49 2 2
MIRT657376 HMGA1 high mobility group AT-hook 1 2 2
MIRT658105 FOXK1 forkhead box K1 2 2
MIRT658161 FCHSD1 FCH and double SH3 domains 1 2 2
MIRT662754 LRRC3C leucine rich repeat containing 3C 2 2
MIRT667209 NIPAL1 NIPA like domain containing 1 2 2
MIRT687003 RPL35 ribosomal protein L35 2 2
MIRT707057 NACC2 NACC family member 2 2 2
MIRT709048 MRO maestro 2 2
MIRT709054 MGAT5B mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B 2 2
MIRT709446 VWA2 von Willebrand factor A domain containing 2 2 2
MIRT709847 SNX12 sorting nexin 12 2 2
MIRT710790 IFNLR1 interferon lambda receptor 1 2 2
MIRT711696 GMPR guanosine monophosphate reductase 2 2
MIRT712462 KCNC3 potassium voltage-gated channel subfamily C member 3 2 2
MIRT713884 MOB3A MOB kinase activator 3A 2 2
MIRT715329 NTN1 netrin 1 2 2
MIRT715927 CHD4 chromodomain helicase DNA binding protein 4 2 2
MIRT716533 ATF5 activating transcription factor 5 2 2
MIRT716937 CACNB1 calcium voltage-gated channel auxiliary subunit beta 1 2 2
MIRT717007 MFSD6 major facilitator superfamily domain containing 6 2 2
MIRT719139 DPYSL5 dihydropyrimidinase like 5 2 2
MIRT720853 MEF2D myocyte enhancer factor 2D 2 2
MIRT721484 LTB4R2 leukotriene B4 receptor 2 2 2
MIRT721517 DKK3 dickkopf WNT signaling pathway inhibitor 3 2 2
MIRT722895 LRRC20 leucine rich repeat containing 20 2 2
MIRT723066 GGA1 golgi associated, gamma adaptin ear containing, ARF binding protein 1 2 2
MIRT723086 INSIG1 insulin induced gene 1 2 2
MIRT723353 ASCL2 achaete-scute family bHLH transcription factor 2 2 2
MIRT723483 MINOS1 mitochondrial inner membrane organizing system 1 2 2
MIRT724576 NOTCH2 notch 2 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4749 Fluorouracil 3385 NSC19893 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-mir-4749 Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-mir-4749 Paclitaxel 36314 NSC125973 approved resistant cell line (W1)
hsa-miR-4749-3p Cisplatin 5460033 NSC119875 approved resistant High Hypopharyngeal Cancer cell line (FaDu)
hsa-miR-4749-3p Tamoxifen+Fulvestrant sensitive cell line (LCC9)
hsa-miR-4749-3p Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-miR-4749-3p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)
hsa-miR-4749-3p Cisplatin 5460033 NSC119875 approved resistant cell line (OVSAHO)
hsa-miR-4749-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (TOV-112D)

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