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 CHD4   
Synonyms CHD-4, Mi-2b, Mi2-BETA, SIHIWES
Description chromodomain helicase DNA binding protein 4
Transcript NM_001273   
Expression
Putative miRNA Targets on CHD4
3'UTR of CHD4
(miRNA target sites are highlighted)
>CHD4|NM_001273|3'UTR
   1 AGATGCAGACTGATACCACCTCCACCGCTGAGCAGTGACCTTCCTCACTTTCTCTTGTCCCAGCTTCTCCCCTGGGGGCC
  81 TGAGAGACCCTCACCTTCCTTCTGCCCATCTTCCATGTTGTAAAGGAACAGCCCCAGTGCACTGGGGGAGGGGAGGGAGT
 161 GAGGGGCAGTGGTGCCCTTCCTGCAGAAGAGACATGCAGCAGTAGCGCTGGCGCCATCTGCAGGAGCTGGCGGGCTGGCC
 241 TTCTGGACCCTGGCTTCTCCCCACTGTAACGCCTGTTACACACAAACTGTTGTGGGTTCCTGCCAGGCTTGAAGAAAATG
 321 ATCTGAATTTTTTCCTCCTTTTGGTTTTATTTTGTTGGTTTATTTTGTGTTTTCTTTTCTCCTTTTTGGGGGGTATTCAG
 401 AGTGGGCTGGGCCCCTGGGCGAGACACAGCTACCTCTGTTGGCATCTTTTTAATACCAGGAACCCAGCGGCTCTAGCCAC
 481 TGAGCGGCTAAATGAAATAAAGTGGAAAAAAAAAAAAAGGAAAAAACCAAAAGCATAAAAAACCACAGCAAATTTCTTGA
 561 TGAAAATTGAAAATAAAAGTTTCCTTGTATTTTAAAAAAAAAAAAAAA
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' gaCACCCCCGUC-CUCCCCGc 5'
            | || || || ||||||| 
Target 5' gaGGGGAGGGAGTGAGGGGCa 3'
148 - 168 158.00 -25.60
2
miRNA  3' gacaCCCCCGU---CCUC-CCCGc 5'
              |||||:|    ||| |||| 
Target 5' tttgGGGGGTATTCAGAGTGGGCt 3'
385 - 408 124.00 -21.70
3
miRNA  3' gacacccCCGU-CCUCCCCGc 5'
                 | ||  ||| ||| 
Target 5' ggctctaGCCACTGAGCGGCt 3'
469 - 489 109.00 -7.80
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31510581 57 COSMIC
COSN30146431 82 COSMIC
COSN30146512 86 COSMIC
COSN5186746 87 COSMIC
COSN30460002 96 COSMIC
COSN5264377 99 COSMIC
COSN30543141 106 COSMIC
COSN30466023 107 COSMIC
COSN30107216 147 COSMIC
COSN30138190 163 COSMIC
COSN31526256 249 COSMIC
COSN26552882 254 COSMIC
COSN20092481 265 COSMIC
COSN20159021 300 COSMIC
COSN31514180 329 COSMIC
COSN31565941 374 COSMIC
COSN26563523 420 COSMIC
COSN31546047 421 COSMIC
COSN20109111 505 COSMIC
COSN20109112 506 COSMIC
COSN24304322 506 COSMIC
COSN31481080 583 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs779691620 1 dbSNP
rs867781306 8 dbSNP
rs750214515 11 dbSNP
rs112636750 16 dbSNP
rs1273637417 16 dbSNP
rs761705137 23 dbSNP
rs1157649676 24 dbSNP
rs753811207 27 dbSNP
rs1204902675 29 dbSNP
rs375386448 30 dbSNP
rs760852905 39 dbSNP
rs371501457 43 dbSNP
rs772457322 46 dbSNP
rs878925203 47 dbSNP
rs767355615 49 dbSNP
rs1317314787 51 dbSNP
rs1026021792 54 dbSNP
rs368227033 56 dbSNP
rs898161450 57 dbSNP
rs906891732 64 dbSNP
rs1425134528 69 dbSNP
rs1045444455 72 dbSNP
rs1409991756 74 dbSNP
rs1023353657 79 dbSNP
rs1174865663 86 dbSNP
rs570774016 88 dbSNP
rs949588155 94 dbSNP
rs2267968 99 dbSNP
rs533871420 102 dbSNP
rs1470481248 104 dbSNP
rs1336439164 106 dbSNP
rs1419734968 117 dbSNP
rs1343592635 129 dbSNP
rs577551370 144 dbSNP
rs1430126065 145 dbSNP
rs896262857 151 dbSNP
rs1057310026 157 dbSNP
rs938868035 169 dbSNP
rs1460714638 175 dbSNP
rs1243473404 177 dbSNP
rs1052995369 183 dbSNP
rs903432569 190 dbSNP
rs936895933 191 dbSNP
rs773139218 201 dbSNP
rs1446125427 205 dbSNP
rs1216061990 206 dbSNP
rs1264754189 208 dbSNP
rs1479158467 213 dbSNP
rs1259755508 222 dbSNP
rs975545195 229 dbSNP
rs964113156 231 dbSNP
rs912531996 232 dbSNP
rs975462047 238 dbSNP
rs750504212 243 dbSNP
rs1400381177 248 dbSNP
rs1299003110 250 dbSNP
rs951259791 254 dbSNP
rs1244360282 257 dbSNP
rs1403136217 259 dbSNP
rs1382544674 260 dbSNP
rs1025551283 261 dbSNP
rs543601543 265 dbSNP
rs962597553 270 dbSNP
rs1025524050 271 dbSNP
rs537546275 279 dbSNP
rs1288508376 280 dbSNP
rs1224042570 281 dbSNP
rs568613560 287 dbSNP
rs1454380601 291 dbSNP
rs1365548815 295 dbSNP
rs1001262309 306 dbSNP
rs1162623037 308 dbSNP
rs1443886449 313 dbSNP
rs1385748246 322 dbSNP
rs1185243377 323 dbSNP
rs1201600356 324 dbSNP
rs906968692 327 dbSNP
rs1362467724 331 dbSNP
rs1045384516 340 dbSNP
rs753633533 350 dbSNP
rs1009913036 351 dbSNP
rs1422834837 354 dbSNP
rs549124129 372 dbSNP
rs15150 374 dbSNP
rs1391539970 378 dbSNP
rs1260683825 381 dbSNP
rs1334974455 381 dbSNP
rs73045994 382 dbSNP
rs1311010071 383 dbSNP
rs1356755849 389 dbSNP
rs1244778659 390 dbSNP
rs1011949659 392 dbSNP
rs1357820993 413 dbSNP
rs1212172072 415 dbSNP
rs896231811 421 dbSNP
rs1034809657 422 dbSNP
rs1240400230 437 dbSNP
rs1443081176 438 dbSNP
rs1244565740 442 dbSNP
rs1369176629 446 dbSNP
rs1003003276 449 dbSNP
rs192895387 456 dbSNP
rs1316335574 461 dbSNP
rs903359032 465 dbSNP
rs547247769 468 dbSNP
rs1451520213 477 dbSNP
rs533487633 479 dbSNP
rs1312923662 484 dbSNP
rs1012261922 485 dbSNP
rs1324984555 486 dbSNP
rs1295142846 494 dbSNP
rs1382941424 495 dbSNP
rs1002749830 498 dbSNP
rs1339371591 498 dbSNP
rs893416063 499 dbSNP
rs779392929 502 dbSNP
rs1301417409 503 dbSNP
rs77870850 504 dbSNP
rs1297228802 505 dbSNP
rs1039670385 506 dbSNP
rs754174255 506 dbSNP
rs758479656 506 dbSNP
rs564494202 513 dbSNP
rs1478147644 517 dbSNP
rs1165387894 518 dbSNP
rs1159682210 519 dbSNP
rs1403657308 519 dbSNP
rs201057993 519 dbSNP
rs762151199 519 dbSNP
rs780818304 519 dbSNP
rs1294315230 520 dbSNP
rs1340563175 520 dbSNP
rs912607102 525 dbSNP
rs1321895564 527 dbSNP
rs928601410 527 dbSNP
rs1209776028 529 dbSNP
rs1447437393 533 dbSNP
rs892712894 533 dbSNP
rs1372242027 543 dbSNP
rs1203614271 546 dbSNP
rs1193495550 553 dbSNP
rs1488627935 574 dbSNP
rs1195793174 575 dbSNP
rs1427031448 575 dbSNP
rs918433356 579 dbSNP
rs929782468 579 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' -aGGGGAGGGAGUGAGGG--- 3'
1 - 17
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 GSM4903825
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / PID14_NS
Location of target site NM_001273 | 3UTR | ACCUCCACCGCUGAGCAGUGACCUUCCUCACUUUCUCUUGUCCCAGCUUCUCCCCUGGGGGCCUGAGAGACCCUCACCUUCCUUCUGCCCAUCUUCCAUGUUGUAAAGGAACAGCCCCAGUGCACUGGGGGAGGGGAGGGAGUGA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161237
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903826
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / PID21_NS
Location of target site NM_001273 | 3UTR | ACUGGGGGAGGGGAGGGAGUGA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161237
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903828
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / PID21_9124
Location of target site NM_001273 | 3UTR | GCACUGGGGGAGGGGAGGGAGUGA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161237
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_001273 | 3UTR | CCUCACUUUCUCUUGUCCCAGCUUCUCCCCUGGGGGCCUGAGAGACCCUCACCUUCCUUCUGCCCAUCUUCCAUGUUGUAAAGGAACAGCCCCAGUGCACUGGGGGAGGGGAGGGAGUGA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM4903834
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_b
Location of target site NM_001273 | 3UTR | CUGGGGGCCUGAGAGACCCUCACCUUCCUUCUGCCCAUCUUCCAUGUUGUAAAGGAACAGCCCCAGUGCACUGGGGGAGGGGAGGGAGUGA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM4903835
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_c
Location of target site NM_001273 | 3UTR | UCCCAGCUUCUCCCCUGGGGGCCUGAGAGACCCUCACCUUCCUUCUGCCCAUCUUCCAUGUUGUAAAGGAACAGCCCCAGUGCACUGGGGGAGGGGAGGGAGUGA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM4903836
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_a
Location of target site NM_001273 | 3UTR | GAGAGACCCUCACCUUCCUUCUGCCCAUCUUCCAUGUUGUAAAGGAACAGCCCCAGUGCACUGGGGGAGGGGAGGGAGUGA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 8 for dataset GSM4903837
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_b
Location of target site NM_001273 | 3UTR | UAAAGGAACAGCCCCAGUGCACUGGGGGAGGGGAGGGAGUGA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 9 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_001273 | 3UTR | CAGCUUCUCCCCUGGGGGCCUGAGAGACCCUCACCUUCCUUCUGCCCAUCUUCCAUGUUGUAAAGGAACAGCCCCAGUGCACUGGGGGAGGGGAGGGAGUGA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 10 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 ENST00000544484.1 | 3UTR | AGGGGAGGGAGUGAGGG
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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