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 ZNF76   
Synonyms D6S229E, ZNF523, Zfp523
Description zinc finger protein 76
Transcript NM_003427   
Expression
Putative miRNA Targets on ZNF76
3'UTR of ZNF76
(miRNA target sites are highlighted)
>ZNF76|NM_003427|3'UTR
   1 GTCCAAGAGGGCTGGGTCCCACACCATGCTGGAGGAAGTGCCATCTGCATGGCCACTCTTGCCCCCAAGGGCCCAGGCTG
  81 TGGCTGACACATAGAAGGTGGCCACATAGGTCTCTGGGGTGAGAAGACAGCAAGAAAACTGCCTAACTGAAGGGAATGGG
 161 GGCCCTGCTCAAGAAGGGGGCCAGGCAGCTGGAATCAGGGGAGTGCATCATCCTCGGGAGCTGACAACAGCCAGGCTACA
 241 CCAGGGCACCCGCCTCTCAAAATCAGCTGGGCGCCCACTCTCCTCCTAAAGAACACCCTTCTGGCCCTCAGTCTGTTCCC
 321 CTTCTCAGGTAGAGATTGGGGCTGCTATGGGGACTGGCCCTGTAGGGTTGAGCCACAGACAGCTCTTCAGCCCAGTAGCA
 401 GTGGAGCAGGCCCTGTCCTGCCCTCCCAGCAATAACCACCTCCCTGGAGGCCAGCTGAGATGCCTGGCTACTTGGCACCA
 481 GGGACTTCCTGACACCACAGTCAATTAATTCCTCAGGGGCCTGTGGCTGAAGAAAAGGTGCCCAGCCCCCACCACTCCTC
 561 AGCTGCCCCCCAACCTCTCTATGGCAGAGAGGCAGGGAGTGGCCCTGTACATAGACTGCTGGGGATTGGGTTTGATTTGT
 641 TTTGTTTTTTTTAATTCCATTTTGATAATTTTTTTCCTGCTCTGGGTGGTGGTGGCACATGGATGAATGAGTATTTAATA
 721 AAAGTTCCAAATTTCCACCAAAAAAAAAAAAAA
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' aaaCCAGUGUGGUCAGGUGUAa 5'
             ||  :::||| ||::||| 
Target 5' ggaGGAAGTGCCA-TCTGCATg 3'
31 - 51 122.00 -9.70
2
miRNA  3' aaACC-AGUGUG-GU------CAGGUGUAa 5'
            ||| | |||| :|      | |||||| 
Target 5' tgTGGCTGACACATAGAAGGTGGCCACATa 3'
79 - 108 122.00 -14.90
3
miRNA  3' aaaccAGUGUGGUC-AGGUGUAa 5'
               | |:|  || |||| || 
Target 5' gtattTAATAAAAGTTCCAAATt 3'
711 - 733 117.00 -5.50
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN28874736 113 COSMIC
COSN2160464 155 COSMIC
COSN28879993 228 COSMIC
COSN31580131 232 COSMIC
COSN20075788 249 COSMIC
COSN31555600 253 COSMIC
COSN9312277 371 COSMIC
COSN28216078 372 COSMIC
COSN8400602 473 COSMIC
COSN28834205 531 COSMIC
COSN27111703 593 COSMIC
COSN30175652 602 COSMIC
COSN31519007 606 COSMIC
rs1194 531 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs780560323 1 dbSNP
rs1256806667 3 dbSNP
rs749041041 4 dbSNP
rs1424999768 8 dbSNP
rs1190836268 11 dbSNP
rs1422353260 15 dbSNP
rs370498815 18 dbSNP
rs754332339 19 dbSNP
rs755359520 20 dbSNP
rs560665926 23 dbSNP
rs1303899641 27 dbSNP
rs747786557 31 dbSNP
rs73745179 33 dbSNP
rs1428193000 35 dbSNP
rs1277627745 39 dbSNP
rs1341275493 62 dbSNP
rs777584156 65 dbSNP
rs1037970810 66 dbSNP
rs543320740 69 dbSNP
rs965342504 75 dbSNP
rs770382663 78 dbSNP
rs1209201119 83 dbSNP
rs1256407487 84 dbSNP
rs1486598077 92 dbSNP
rs1001727077 93 dbSNP
rs1220979891 103 dbSNP
rs1035436439 111 dbSNP
rs769519983 111 dbSNP
rs1261755282 118 dbSNP
rs975058930 124 dbSNP
rs1276210598 125 dbSNP
rs1195334773 133 dbSNP
rs959812786 136 dbSNP
rs1306365034 144 dbSNP
rs936013399 149 dbSNP
rs1177218775 154 dbSNP
rs1368108242 158 dbSNP
rs1388086405 158 dbSNP
rs1009998523 161 dbSNP
rs561443943 163 dbSNP
rs531695435 164 dbSNP
rs945150720 165 dbSNP
rs1361178898 170 dbSNP
rs1169083165 177 dbSNP
rs745802031 178 dbSNP
rs1371337050 192 dbSNP
rs571831666 197 dbSNP
rs906399636 200 dbSNP
rs1002528146 202 dbSNP
rs549915480 205 dbSNP
rs1197679040 206 dbSNP
rs1055074755 207 dbSNP
rs146773223 208 dbSNP
rs994476274 211 dbSNP
rs1205026291 215 dbSNP
rs16874216 217 dbSNP
rs1256253159 221 dbSNP
rs775046777 229 dbSNP
rs547523102 232 dbSNP
rs1282450869 234 dbSNP
rs148591752 236 dbSNP
rs73745181 243 dbSNP
rs1390688212 247 dbSNP
rs114752944 248 dbSNP
rs958578027 249 dbSNP
rs1458813495 250 dbSNP
rs375055882 252 dbSNP
rs1019525752 253 dbSNP
rs964949053 259 dbSNP
rs1047825775 273 dbSNP
rs907838435 274 dbSNP
rs1411885834 277 dbSNP
rs1413075996 278 dbSNP
rs1181740255 280 dbSNP
rs1417846618 283 dbSNP
rs975384648 288 dbSNP
rs1446106328 289 dbSNP
rs1201651221 298 dbSNP
rs926237240 300 dbSNP
rs957333899 302 dbSNP
rs369175747 311 dbSNP
rs1038340346 312 dbSNP
rs192199819 313 dbSNP
rs913284859 315 dbSNP
rs548746995 316 dbSNP
rs927768976 319 dbSNP
rs537011002 323 dbSNP
rs1055424010 325 dbSNP
rs1469095142 329 dbSNP
rs899102149 330 dbSNP
rs1188800077 331 dbSNP
rs1057288707 335 dbSNP
rs1241922506 336 dbSNP
rs1181429898 337 dbSNP
rs1413004050 338 dbSNP
rs372217846 340 dbSNP
rs895991407 347 dbSNP
rs558271722 348 dbSNP
rs1267181122 352 dbSNP
rs1246543313 357 dbSNP
rs1226554525 365 dbSNP
rs1008600780 367 dbSNP
rs768317681 368 dbSNP
rs1010380141 370 dbSNP
rs1205478450 381 dbSNP
rs1393243454 389 dbSNP
rs1164355773 393 dbSNP
rs576960350 398 dbSNP
rs1020047375 403 dbSNP
rs1161102052 405 dbSNP
rs1450998882 408 dbSNP
rs1242361603 412 dbSNP
rs1191977525 416 dbSNP
rs1445075543 418 dbSNP
rs996375458 424 dbSNP
rs1033638454 430 dbSNP
rs773737250 433 dbSNP
rs989096113 441 dbSNP
rs1020293504 444 dbSNP
rs999901249 446 dbSNP
rs1018138036 462 dbSNP
rs151112379 463 dbSNP
rs1484437676 464 dbSNP
rs1212418403 468 dbSNP
rs1333249066 471 dbSNP
rs971411083 479 dbSNP
rs1256160565 483 dbSNP
rs976639331 497 dbSNP
rs981920422 515 dbSNP
rs927413454 520 dbSNP
rs1431139395 522 dbSNP
rs922415579 523 dbSNP
rs1307123100 524 dbSNP
rs1194 531 dbSNP
rs983930342 541 dbSNP
rs182782667 547 dbSNP
rs942024832 552 dbSNP
rs973463101 553 dbSNP
rs927289196 555 dbSNP
rs920480223 562 dbSNP
rs1199850684 566 dbSNP
rs937538574 567 dbSNP
rs1057409005 571 dbSNP
rs1490110339 574 dbSNP
rs1451679424 580 dbSNP
rs775061774 582 dbSNP
rs572648785 588 dbSNP
rs1169532232 595 dbSNP
rs1207122965 600 dbSNP
rs571158758 602 dbSNP
rs930556256 603 dbSNP
rs1394722615 607 dbSNP
rs1213099502 613 dbSNP
rs111803945 614 dbSNP
rs886090369 615 dbSNP
rs1041853149 617 dbSNP
rs187281495 619 dbSNP
rs1304696238 622 dbSNP
rs904304403 632 dbSNP
rs372477409 636 dbSNP
rs540758461 636 dbSNP
rs1316096912 641 dbSNP
rs199763785 644 dbSNP
rs1000359561 645 dbSNP
rs1040501683 645 dbSNP
rs1327601872 645 dbSNP
rs900251160 646 dbSNP
rs868320064 652 dbSNP
rs8205 653 dbSNP
rs1345296242 664 dbSNP
rs1184331108 665 dbSNP
rs1232413355 669 dbSNP
rs755946686 669 dbSNP
rs1033172519 679 dbSNP
rs893346883 680 dbSNP
rs1264025858 682 dbSNP
rs1203197712 688 dbSNP
rs752790419 693 dbSNP
rs1290590292 694 dbSNP
rs1224896321 701 dbSNP
rs1373210488 707 dbSNP
rs565122948 712 dbSNP
rs1256095468 721 dbSNP
rs1485245106 728 dbSNP
rs1384275321 733 dbSNP
rs1336992378 736 dbSNP
rs1205097583 737 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions hESCs (WA-09)
Disease 7629.0
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.

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 ENST00000373953.3 | 3UTR | CUGACACAUAGAAGGUGGCCA
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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