pre-miRNA Information
pre-miRNA hsa-mir-4491   
Genomic Coordinates chr11: 111347757 - 111347824
Description Homo sapiens miR-4491 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4491
Sequence 46| AAUGUGGACUGGUGUGACCAAA |67
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1043555759 4 dbSNP
rs1182248607 6 dbSNP
rs527936256 7 dbSNP
rs755554417 14 dbSNP
rs779628583 16 dbSNP
rs1471408223 19 dbSNP
rs909066815 20 dbSNP
Putative Targets

Gene Information
Gene Symbol MYCN   
Synonyms MODED, N-myc, NMYC, ODED, bHLHe37
Description MYCN proto-oncogene, bHLH transcription factor
Transcript NM_005378   
Expression
Putative miRNA Targets on MYCN
3'UTR of MYCN
(miRNA target sites are highlighted)
>MYCN|NM_005378|3'UTR
   1 ACGCTTCTCAAAACTGGACAGTCACTGCCACTTTGCACATTTTGATTTTTTTTTTAAACAAACATTGTGTTGACATTAAG
  81 AATGTTGGTTTACTTTCAAATCGGTCCCCTGTCGAGTTCGGCTCTGGGTGGGCAGTAGGACCACCAGTGTGGGGTTCTGC
 161 TGGGACCTTGGAGAGCCTGCATCCCAGGATGCTGGGTGGCCCTGCAGCCTCCTCCACCTCACCTCCATGACAGCGCTAAA
 241 CGTTGGTGACGGTTGGGAGCCTCTGGGGCTGTTGAAGTCACCTTGTGTGTTCCAAGTTTCCAAACAACAGAAAGTCATTC
 321 CTTCTTTTTAAAATGGTGCTTAAGTTCCAGCAGATGCCACATAAGGGGTTTGCCATTTGATACCCCTGGGGAACATTTCT
 401 GTAAATACCATTGACACATCCGCCTTTTGTATACATCCTGGGTAATGAGAGGTGGCTTTTGCGGCCAGTATTAGACTGGA
 481 AGTTCATACCTAAGTACTGTAATAATACCTCAATGTTTGAGGAGCATGTTTTGTATACAAATATATTGTTAATCTCTGTT
 561 ATGTACTGTACTAATTCTTACACTGCCTGTATACTTTAGTATGACGCTGATACATAACTAAATTTGATACTTATATTTTC
 641 GTATGAAAATGAGTTGTGAAAGTTTTGAGTAGATATTACTTTATCACTTTTTGAACTAAGAAACTTTTGTAAAGAAATTT
 721 ACTATATATATATGCCTTTTTCCTAGCCTGTTTCTTCCTGTTAATGTATTTGTTCATGTTTGGTGCATAGAACTGGGTAA
 801 ATGCAAAGTTCTGTGTTTAATTTCTTCAAAATGTATATATTTAGTGCTGCATCTTATAGCACTTTGAAATACCTCATGTT
 881 TATGAAAATAAATAGCTTAAAATTAAATGAAAAAAAAA
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' aaacCAGUGUGGUC-A-GGUGUAa 5'
              ||: || ||| | |||||| 
Target 5' ttaaGTTCCAGCAGATGCCACATa 3'
340 - 363 130.00 -14.20
2
miRNA  3' aaacCAGUG-UGGU--CAGGUGUAa 5'
              ||||| :|||   | ||||| 
Target 5' gacaGTCACTGCCACTTTGCACATt 3'
17 - 41 128.00 -15.40
3
miRNA  3' aaaCCAGUGUG--GUC-----AGGUGUAa 5'
             ||| :| |  |||     ||||| | 
Target 5' ctgGGTGGCCCTGCAGCCTCCTCCACCTc 3'
192 - 220 117.00 -11.92
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30160871 9 COSMIC
COSN28834392 13 COSMIC
COSN30110591 19 COSMIC
COSN30643020 33 COSMIC
COSN13944546 56 COSMIC
COSN2534717 56 COSMIC
COSN30109403 95 COSMIC
COSN31538009 103 COSMIC
COSN31489830 104 COSMIC
COSN25579138 110 COSMIC
COSN22019905 122 COSMIC
COSN30530960 176 COSMIC
COSN28834391 226 COSMIC
COSN23425338 235 COSMIC
COSN28736733 251 COSMIC
COSN31489877 311 COSMIC
COSN28758249 317 COSMIC
COSN21790520 344 COSMIC
COSN29716185 423 COSMIC
COSN24299335 464 COSMIC
COSN26556122 559 COSMIC
COSN31524294 574 COSMIC
COSN31547754 578 COSMIC
COSN31488222 607 COSMIC
COSN32056460 612 COSMIC
COSN31519512 621 COSMIC
COSN15090505 627 COSMIC
COSN19579372 641 COSMIC
COSN24298963 683 COSMIC
COSN31520351 715 COSMIC
COSN31553588 747 COSMIC
rs922 251 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs141392135 3 dbSNP
rs1187132361 7 dbSNP
rs919150013 17 dbSNP
rs781551930 25 dbSNP
rs1379415785 32 dbSNP
rs1486169668 40 dbSNP
rs1188147846 44 dbSNP
rs1234994672 46 dbSNP
rs763183120 46 dbSNP
rs766472509 46 dbSNP
rs1259455331 47 dbSNP
rs192196240 55 dbSNP
rs748437145 56 dbSNP
rs903290907 56 dbSNP
rs558288322 57 dbSNP
rs144532405 58 dbSNP
rs62116683 59 dbSNP
rs1044109140 64 dbSNP
rs1054389587 70 dbSNP
rs148464851 89 dbSNP
rs371145074 94 dbSNP
rs1413848691 97 dbSNP
rs555597087 100 dbSNP
rs142866857 103 dbSNP
rs1437452995 111 dbSNP
rs936143704 114 dbSNP
rs778828407 115 dbSNP
rs541057129 121 dbSNP
rs540227340 122 dbSNP
rs1179431098 125 dbSNP
rs559222525 125 dbSNP
rs1457376504 141 dbSNP
rs577556715 143 dbSNP
rs1236393442 147 dbSNP
rs1223711066 149 dbSNP
rs1291268300 161 dbSNP
rs1026038743 163 dbSNP
rs998602682 170 dbSNP
rs745765302 172 dbSNP
rs951782155 192 dbSNP
rs984414161 198 dbSNP
rs1445529737 208 dbSNP
rs1033382306 209 dbSNP
rs958978914 212 dbSNP
rs560249723 216 dbSNP
rs1017017077 217 dbSNP
rs1238422244 221 dbSNP
rs1164677378 226 dbSNP
rs1403967389 227 dbSNP
rs1382485375 230 dbSNP
rs1309494188 233 dbSNP
rs917405371 234 dbSNP
rs748119936 235 dbSNP
rs374300561 236 dbSNP
rs1193035131 238 dbSNP
rs1488839332 243 dbSNP
rs1246065096 244 dbSNP
rs1026650331 245 dbSNP
rs376446365 245 dbSNP
rs994654504 245 dbSNP
rs1048 247 dbSNP
rs922 251 dbSNP
rs936127085 252 dbSNP
rs1054378251 261 dbSNP
rs1023999805 270 dbSNP
rs1219364831 273 dbSNP
rs1366221318 282 dbSNP
rs1293466773 303 dbSNP
rs1434896052 312 dbSNP
rs969684746 313 dbSNP
rs1214190208 321 dbSNP
rs773220376 337 dbSNP
rs925682391 340 dbSNP
rs936176363 346 dbSNP
rs1237348555 349 dbSNP
rs1456329363 351 dbSNP
rs1424495243 355 dbSNP
rs79703814 355 dbSNP
rs1478789148 362 dbSNP
rs1040673088 366 dbSNP
rs1215711046 367 dbSNP
rs901770772 381 dbSNP
rs934298889 384 dbSNP
rs1422849304 387 dbSNP
rs1210303211 392 dbSNP
rs141300189 395 dbSNP
rs1298500513 396 dbSNP
rs1219914055 407 dbSNP
rs1342983609 409 dbSNP
rs1047595173 410 dbSNP
rs889820375 411 dbSNP
rs1304838704 418 dbSNP
rs1466699734 422 dbSNP
rs942646204 423 dbSNP
rs1174095110 425 dbSNP
rs1419316801 425 dbSNP
rs1467243517 432 dbSNP
rs887520733 437 dbSNP
rs1327240552 438 dbSNP
rs1400191292 448 dbSNP
rs1476722068 463 dbSNP
rs1257965105 464 dbSNP
rs763210834 464 dbSNP
rs1182112349 466 dbSNP
rs1033331701 478 dbSNP
rs1253857305 486 dbSNP
rs1300227289 497 dbSNP
rs959321281 506 dbSNP
rs1013268929 507 dbSNP
rs1317922256 516 dbSNP
rs898540780 526 dbSNP
rs1024944773 535 dbSNP
rs1218516984 538 dbSNP
rs1374373776 553 dbSNP
rs995085881 557 dbSNP
rs1396941340 560 dbSNP
rs1026188285 563 dbSNP
rs886255192 569 dbSNP
rs560993420 578 dbSNP
rs1014202761 583 dbSNP
rs1449107861 584 dbSNP
rs546105646 590 dbSNP
rs1024149954 598 dbSNP
rs771181407 600 dbSNP
rs977557063 606 dbSNP
rs774657754 607 dbSNP
rs1423028964 631 dbSNP
rs957440926 641 dbSNP
rs759911845 642 dbSNP
rs1457844384 645 dbSNP
rs1236980348 652 dbSNP
rs1032731340 658 dbSNP
rs1315963064 659 dbSNP
rs957179319 660 dbSNP
rs1338058610 663 dbSNP
rs1267752948 668 dbSNP
rs1246060867 673 dbSNP
rs1321438961 676 dbSNP
rs910657756 677 dbSNP
rs1449228088 679 dbSNP
rs1377774864 681 dbSNP
rs1389714579 688 dbSNP
rs1392882454 688 dbSNP
rs913423093 688 dbSNP
rs1233193756 692 dbSNP
rs1482731898 694 dbSNP
rs1457218318 699 dbSNP
rs1366454210 702 dbSNP
rs934139364 708 dbSNP
rs943337399 709 dbSNP
rs1439970947 715 dbSNP
rs1379270774 719 dbSNP
rs563066464 723 dbSNP
rs771419664 723 dbSNP
rs777027817 723 dbSNP
rs777015170 728 dbSNP
rs184691461 730 dbSNP
rs1488377041 734 dbSNP
rs1475280346 751 dbSNP
rs1040381992 756 dbSNP
rs923140455 761 dbSNP
rs1423590475 763 dbSNP
rs2515691 764 dbSNP
rs546658641 765 dbSNP
rs1308801144 776 dbSNP
rs1237052969 778 dbSNP
rs1173022843 781 dbSNP
rs1355424823 783 dbSNP
rs1447582284 784 dbSNP
rs929245268 786 dbSNP
rs15260 787 dbSNP
rs930100987 795 dbSNP
rs1386093127 797 dbSNP
rs531921949 798 dbSNP
rs1047585171 805 dbSNP
rs1420075375 809 dbSNP
rs886290187 814 dbSNP
rs767950731 825 dbSNP
rs1478727429 834 dbSNP
rs1014480814 841 dbSNP
rs1024179396 845 dbSNP
rs887638445 858 dbSNP
rs1005955986 860 dbSNP
rs571270203 863 dbSNP
rs1267346077 879 dbSNP
rs1055258574 880 dbSNP
rs1001400480 890 dbSNP
rs1277611213 892 dbSNP
rs1316024733 893 dbSNP
rs894907797 895 dbSNP
rs1203569890 908 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions hESCs (WA-09)
Disease 4613.0
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... "PAR-CLIP data was present in SRR359787. RNA binding protein: AGO2. Condition:4-thiouridine ...

- Lipchina I; Elkabetz Y; Hafner M; Sheridan et al., 2011, Genes & development.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' aaacCAGUGUGGUC-A-GGUGUAa 5'
              ||: || ||| | |||||| 
Target 5' uuaaGUUCCAGCAGAUGCCACAU- 3'
26 - 48
Article - Lipchina I; Elkabetz Y; Hafner M; Sheridan et al.
- Genes & development, 2011
MicroRNAs are important regulators in many cellular processes, including stem cell self-renewal. Recent studies demonstrated their function as pluripotency factors with the capacity for somatic cell reprogramming. However, their role in human embryonic stem (ES) cells (hESCs) remains poorly understood, partially due to the lack of genome-wide strategies to identify their targets. Here, we performed comprehensive microRNA profiling in hESCs and in purified neural and mesenchymal derivatives. Using a combination of AGO cross-linking and microRNA perturbation experiments, together with computational prediction, we identified the targets of the miR-302/367 cluster, the most abundant microRNAs in hESCs. Functional studies identified novel roles of miR-302/367 in maintaining pluripotency and regulating hESC differentiation. We show that in addition to its role in TGF-beta signaling, miR-302/367 promotes bone morphogenetic protein (BMP) signaling by targeting BMP inhibitors TOB2, DAZAP2, and SLAIN1. This study broadens our understanding of microRNA function in hESCs and is a valuable resource for future studies in this area.
LinkOut: [PMID: 22012620]
CLIP-seq Support 1 for dataset SRR359787
Method / RBP PAR-CLIP / AGO2
Cell line / Condition hESCs (WA-09) / 4-thiouridine, RNase T1
Location of target site ENST00000281043.3 | 3UTR | UCAUUCCUUCUUUUUAAAAUGGUGCUUAAGUUCCAGCAGAUGCCACAU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22012620 / SRX103431
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
67 hsa-miR-4491 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT056779 ARID5B AT-rich interaction domain 5B 2 2
MIRT061577 BTG2 BTG anti-proliferation factor 2 2 2
MIRT063828 SRP9 signal recognition particle 9 2 4
MIRT102306 DNAJB9 DnaJ heat shock protein family (Hsp40) member B9 2 10
MIRT186634 COX20 COX20, cytochrome c oxidase assembly factor 2 8
MIRT191243 STYX serine/threonine/tyrosine interacting protein 2 2
MIRT195908 SRSF11 serine and arginine rich splicing factor 11 2 4
MIRT240343 UBXN2B UBX domain protein 2B 2 2
MIRT271178 PTPN14 protein tyrosine phosphatase, non-receptor type 14 2 2
MIRT286219 TMEM97 transmembrane protein 97 2 4
MIRT314182 OCLN occludin 2 4
MIRT323938 AKAP2 A-kinase anchoring protein 2 2 4
MIRT323940 PALM2-AKAP2 PALM2-AKAP2 readthrough 2 4
MIRT340113 TXLNA taxilin alpha 2 2
MIRT450333 LRWD1 leucine rich repeats and WD repeat domain containing 1 2 2
MIRT451283 ZNF101 zinc finger protein 101 2 2
MIRT451879 SOD2 superoxide dismutase 2 2 8
MIRT453577 CRCP CGRP receptor component 2 2
MIRT454366 ASAH2 N-acylsphingosine amidohydrolase 2 2 2
MIRT454797 STOML3 stomatin like 3 2 2
MIRT459801 POTED POTE ankyrin domain family member D 2 10
MIRT460911 POLQ DNA polymerase theta 2 2
MIRT468082 SHOC2 SHOC2, leucine rich repeat scaffold protein 2 6
MIRT470281 PRKAA1 protein kinase AMP-activated catalytic subunit alpha 1 2 2
MIRT471876 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 2
MIRT476147 GPR137C G protein-coupled receptor 137C 2 8
MIRT478056 DNAJC10 DnaJ heat shock protein family (Hsp40) member C10 2 10
MIRT501054 SMCR8 Smith-Magenis syndrome chromosome region, candidate 8 2 4
MIRT501732 OVOL1 ovo like transcriptional repressor 1 2 2
MIRT502214 HSPB8 heat shock protein family B (small) member 8 2 2
MIRT505243 UBE2D3 ubiquitin conjugating enzyme E2 D3 2 2
MIRT505957 RAN RAN, member RAS oncogene family 2 6
MIRT507996 BCL2L13 BCL2 like 13 2 4
MIRT510433 ZNF207 zinc finger protein 207 2 6
MIRT510827 SBNO1 strawberry notch homolog 1 2 4
MIRT511493 HNRNPA0 heterogeneous nuclear ribonucleoprotein A0 2 4
MIRT512129 CREBL2 cAMP responsive element binding protein like 2 2 8
MIRT514512 SHISA9 shisa family member 9 2 4
MIRT516482 RAB32 RAB32, member RAS oncogene family 2 4
MIRT519514 RBM22 RNA binding motif protein 22 2 4
MIRT523367 GTF2A1 general transcription factor IIA subunit 1 2 2
MIRT524217 DDI2 DNA damage inducible 1 homolog 2 2 6
MIRT524649 C4orf32 family with sequence similarity 241 member A 2 2
MIRT528297 ZNF76 zinc finger protein 76 2 2
MIRT528577 ITGB3BP integrin subunit beta 3 binding protein 2 2
MIRT530458 SULT1B1 sulfotransferase family 1B member 1 2 2
MIRT535774 MYCN MYCN proto-oncogene, bHLH transcription factor 2 2
MIRT544239 CCBL2 kynurenine aminotransferase 3 2 2
MIRT546733 RNF217 ring finger protein 217 2 2
MIRT550360 INCENP inner centromere protein 2 4
MIRT553343 TRPC3 transient receptor potential cation channel subfamily C member 3 2 4
MIRT556629 LAPTM4A lysosomal protein transmembrane 4 alpha 2 2
MIRT558006 FAM122B family with sequence similarity 122B 2 2
MIRT558994 CA8 carbonic anhydrase 8 2 2
MIRT560418 ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 2 2
MIRT565717 SESN3 sestrin 3 2 2
MIRT566271 PTAR1 protein prenyltransferase alpha subunit repeat containing 1 2 2
MIRT568161 CCDC6 coiled-coil domain containing 6 2 2
MIRT569753 C2orf71 chromosome 2 open reading frame 71 2 2
MIRT573959 FIGNL1 fidgetin like 1 2 2
MIRT574530 PEG10 paternally expressed 10 2 2
MIRT609453 CCDC149 coiled-coil domain containing 149 2 2
MIRT614047 THBS2 thrombospondin 2 2 2
MIRT628418 ATMIN ATM interactor 2 2
MIRT689556 XPO6 exportin 6 2 2
MIRT725598 CDH7 cadherin 7 2 2
MIRT735561 TRIM7 tripartite motif containing 7 3 0
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-4 Dexamethasone approved 5743 Microarray primary rat thymocytes 20847043 2010 up-regulated

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