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 ATF5   
Synonyms ATFX, HMFN0395
Description activating transcription factor 5
Transcript NM_012068   
Expression
Putative miRNA Targets on ATF5
3'UTR of ATF5
(miRNA target sites are highlighted)
>ATF5|NM_012068|3'UTR
   1 AAGGGCAGGGGTGTGGCTTCTGGGGGCTGGTCTTCAGCTCTGGCGCCTTCATCCCCCTGCCTCTACCTTCATTCCAAACC
  81 CCTCTCGGCCGGGTGCAGTGGCTTATGCTTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGAGGATCGTTTGAGGCCAG
 161 GAGGTCAATACCAGCCTGGGCAACATAGTAAGACCCTGTCTCTATTAAAAAAAAAAAATCAACCCTTCTTCCCCACCAAA
 241 CCACCCAACTCCTCTCTACTCTTATCCTTTTATCCTCTGTCTCTGCTTATCACCTCTCTTGCGTATTTCTGGATCTCCTT
 321 CCCTCCTTTCTCGTCCAAATCATGAAATGTTTGGCCTTAGTCAATGTCTATGCCCGTCACATAACAGCCGAGGCACCGAG
 401 GCCCACAGGGAAGCAGCTGGGAGCTTGGAAACCTGGTCTCTTGAATTTCAAACCTGGTTTCTTACAGGTGGTTGTCTGGG
 481 GTGGGTGGAGTGGCGACAGGATAGAGCTGAAGGACTATGCAAATGAGGAAGTAAGTCAGGGCGGGCTTTGAGAAGGGGAC
 561 CCATATCCTACAGGCAAAAAGCAGGCTAGGTGACCTTGGGACACTACGCTAAGGGAGGGAGGCTAAAGGCGGCCAGGTTT
 641 GCAGTGCGGGAAGATGAGCAGGCCAGTGGGAGGAGGGGCAGGGCAGGGCTGTAGTTGGTGACTGGGTGTTCATTTTAGCT
 721 CTAAGAAAAAAAATCAGTGTTTCGTGAAGGTGTTGGAGAGGGGCTGTGTCTGGGTGAGGGATGGCGGGGTACTGATTTTT
 801 TTGGGAGGTTATGAGCAAAAATAAAACGAAACATTTCCTCTGGCAAAAAAAAAAAAAAAAAA
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' gaCACCCCCGUCCUCCCCGc 5'
            |||||   ||||||||| 
Target 5' caGTGGG---AGGAGGGGCa 3'
664 - 680 163.00 -26.00
2
miRNA  3' gaCAC--CCCCGUC--CUCCCCGc 5'
            |||  || |: |  ||||||| 
Target 5' tcGTGAAGGTGTTGGAGAGGGGCt 3'
742 - 765 150.00 -17.00
3
miRNA  3' gacACCC--CCGUCCUCCCCGc 5'
             ||||  ||  |||| ||| 
Target 5' gtcTGGGGTGGGTGGAGTGGCg 3'
474 - 495 127.00 -27.00
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSM7356791 1 COSMIC
COSN30526866 11 COSMIC
COSN18742251 23 COSMIC
COSN30696972 32 COSMIC
COSN30644434 46 COSMIC
COSN30526654 146 COSMIC
COSN27892208 242 COSMIC
COSN26406040 521 COSMIC
COSN31612104 585 COSMIC
COSN19660861 632 COSMIC
COSN31588134 639 COSMIC
COSN29462357 747 COSMIC
COSN26678211 763 COSMIC
COSN26635190 764 COSMIC
COSN1217538 786 COSMIC
COSN8754080 787 COSMIC
COSN31529037 829 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1342521568 3 dbSNP
rs1219443328 5 dbSNP
rs1365782687 6 dbSNP
rs1213552021 10 dbSNP
rs779755053 11 dbSNP
rs371198290 12 dbSNP
rs948910883 13 dbSNP
rs778348707 17 dbSNP
rs8667 23 dbSNP
rs1485623599 27 dbSNP
rs1029854759 32 dbSNP
rs771658237 33 dbSNP
rs1209437528 38 dbSNP
rs1264670675 39 dbSNP
rs1488361040 41 dbSNP
rs928610536 44 dbSNP
rs775152136 45 dbSNP
rs377206874 46 dbSNP
rs756425258 51 dbSNP
rs1172959369 53 dbSNP
rs1296228104 54 dbSNP
rs1045130715 56 dbSNP
rs763435749 57 dbSNP
rs1432776586 58 dbSNP
rs766469352 62 dbSNP
rs1362513340 69 dbSNP
rs867766398 71 dbSNP
rs774334873 72 dbSNP
rs759694028 78 dbSNP
rs767801404 80 dbSNP
rs752983524 81 dbSNP
rs1443823300 82 dbSNP
rs755908199 84 dbSNP
rs753805118 85 dbSNP
rs757195194 87 dbSNP
rs778451301 88 dbSNP
rs551763240 90 dbSNP
rs757945452 91 dbSNP
rs779621645 92 dbSNP
rs1452959179 94 dbSNP
rs1208792201 95 dbSNP
rs1210630695 98 dbSNP
rs1003736231 102 dbSNP
rs1353796031 103 dbSNP
rs1294695041 104 dbSNP
rs1233558479 115 dbSNP
rs1057295062 119 dbSNP
rs889616944 122 dbSNP
rs1339525752 133 dbSNP
rs745453376 133 dbSNP
rs1276089680 135 dbSNP
rs1432798160 136 dbSNP
rs1436140707 146 dbSNP
rs891987702 149 dbSNP
rs1019531337 159 dbSNP
rs764940328 165 dbSNP
rs1404886279 177 dbSNP
rs966387248 182 dbSNP
rs1021802363 185 dbSNP
rs570059776 187 dbSNP
rs796296195 189 dbSNP
rs1423287682 191 dbSNP
rs1185202141 199 dbSNP
rs1476671207 203 dbSNP
rs537468124 205 dbSNP
rs1274511816 207 dbSNP
rs1382593209 207 dbSNP
rs368432247 207 dbSNP
rs540026942 207 dbSNP
rs968959784 208 dbSNP
rs1482744575 212 dbSNP
rs1316987694 214 dbSNP
rs990588394 217 dbSNP
rs1216153992 219 dbSNP
rs916048080 225 dbSNP
rs1006860156 226 dbSNP
rs1434248365 227 dbSNP
rs1368787376 228 dbSNP
rs1328020314 229 dbSNP
rs970247140 234 dbSNP
rs1168736848 257 dbSNP
rs1411955411 260 dbSNP
rs555879669 262 dbSNP
rs1420711085 263 dbSNP
rs780235018 264 dbSNP
rs750081999 265 dbSNP
rs1018726520 272 dbSNP
rs574093153 275 dbSNP
rs1193797649 278 dbSNP
rs1457018352 282 dbSNP
rs757988785 284 dbSNP
rs1206207063 292 dbSNP
rs1386813390 295 dbSNP
rs1037409327 299 dbSNP
rs1217343939 302 dbSNP
rs1319805811 303 dbSNP
rs965488871 304 dbSNP
rs977266120 306 dbSNP
rs1305713902 314 dbSNP
rs1180107671 318 dbSNP
rs368125399 319 dbSNP
rs779564256 322 dbSNP
rs111938191 323 dbSNP
rs931348722 333 dbSNP
rs951167134 334 dbSNP
rs201635494 339 dbSNP
rs1175866924 342 dbSNP
rs1433401964 343 dbSNP
rs909759331 347 dbSNP
rs1173694213 348 dbSNP
rs1438488068 350 dbSNP
rs889616579 354 dbSNP
rs1178503888 360 dbSNP
rs3170545 367 dbSNP
rs1044725643 369 dbSNP
rs1040929619 371 dbSNP
rs1342614417 372 dbSNP
rs927656313 376 dbSNP
rs572205606 377 dbSNP
rs1337623813 378 dbSNP
rs1316346654 380 dbSNP
rs117069489 389 dbSNP
rs1374421146 390 dbSNP
rs957736017 391 dbSNP
rs1052642938 393 dbSNP
rs375794902 398 dbSNP
rs1023427611 399 dbSNP
rs1258743013 403 dbSNP
rs1010335641 409 dbSNP
rs1044297 410 dbSNP
rs904777412 424 dbSNP
rs1160727544 432 dbSNP
rs1007593603 439 dbSNP
rs1018257191 443 dbSNP
rs1244792870 444 dbSNP
rs748041221 455 dbSNP
rs1185499941 464 dbSNP
rs1476036344 464 dbSNP
rs998212427 466 dbSNP
rs928830174 467 dbSNP
rs1370989104 469 dbSNP
rs1484886561 476 dbSNP
rs575611275 483 dbSNP
rs961903490 491 dbSNP
rs1025713360 495 dbSNP
rs1231723994 502 dbSNP
rs1357679979 524 dbSNP
rs1294301681 525 dbSNP
rs543050230 534 dbSNP
rs1383516751 536 dbSNP
rs1290084018 538 dbSNP
rs951446945 543 dbSNP
rs983919872 544 dbSNP
rs985492998 559 dbSNP
rs561412869 564 dbSNP
rs969327360 565 dbSNP
rs1396981293 567 dbSNP
rs944141806 581 dbSNP
rs1486214327 582 dbSNP
rs1040832666 586 dbSNP
rs1211992385 587 dbSNP
rs1337292560 590 dbSNP
rs981117508 594 dbSNP
rs529007673 604 dbSNP
rs780677708 608 dbSNP
rs368326999 609 dbSNP
rs893459307 610 dbSNP
rs1383298799 622 dbSNP
rs1369538962 624 dbSNP
rs1323380154 626 dbSNP
rs1442643294 628 dbSNP
rs987785152 631 dbSNP
rs8647 632 dbSNP
rs1283809486 635 dbSNP
rs1023375475 637 dbSNP
rs1374617942 638 dbSNP
rs1170983996 644 dbSNP
rs1432534921 647 dbSNP
rs1252432914 648 dbSNP
rs749541753 649 dbSNP
rs1322882668 651 dbSNP
rs1201752060 656 dbSNP
rs1257681724 670 dbSNP
rs1043205121 676 dbSNP
rs559908455 678 dbSNP
rs771235742 680 dbSNP
rs1195463994 681 dbSNP
rs533404143 692 dbSNP
rs942953442 703 dbSNP
rs76748318 712 dbSNP
rs1429961457 716 dbSNP
rs1193906255 722 dbSNP
rs570394746 723 dbSNP
rs1347876693 724 dbSNP
rs1428060330 726 dbSNP
rs1300588648 734 dbSNP
rs961574031 744 dbSNP
rs866079832 745 dbSNP
rs1389329685 756 dbSNP
rs1398287086 764 dbSNP
rs1298591465 768 dbSNP
rs1434017401 769 dbSNP
rs774498511 774 dbSNP
rs761883284 780 dbSNP
rs952704063 786 dbSNP
rs368527347 787 dbSNP
rs962727540 791 dbSNP
rs1181274089 793 dbSNP
rs998556753 794 dbSNP
rs1177886306 795 dbSNP
rs1379896924 796 dbSNP
rs1025656422 806 dbSNP
rs985401117 813 dbSNP
rs1485618741 817 dbSNP
rs759514673 822 dbSNP
rs1237191833 823 dbSNP
rs1344700115 826 dbSNP
rs181581046 828 dbSNP
rs1278461267 830 dbSNP
rs1236412339 833 dbSNP
rs1337229755 834 dbSNP
rs1206100638 837 dbSNP
rs549418578 839 dbSNP
rs1016756835 842 dbSNP
rs375346357 844 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' gacaCCCCCGUC-CUCCCCGc 5'
              || | ::| ||||||| 
Target 5' ---aGGUGUUGGAGAGGGGCu 3'
1 - 18
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]
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 ENST00000423777.2 | 3UTR | AGGUGUUGGAGAGGGGCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
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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