miRTarBase - #MIRT532624


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pre-miRNA Information
pre-miRNA hsa-mir-4540   
Genomic Coordinates chr9: 36864254 - 36864308
Description Homo sapiens miR-4540 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4540
Sequence 35| UUAGUCCUGCCUGUAGGUUUA |55
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs937122950 4 dbSNP
rs143699849 7 dbSNP
Putative Targets

Gene Information
Gene Symbol PHF5A   
Synonyms INI, Rds3, SAP14b, SF3B7, SF3b14b, bK223H9.2
Description PHD finger protein 5A
Transcript NM_032758   
Expression
Putative miRNA Targets on PHF5A
3'UTR of PHF5A
(miRNA target sites are highlighted)		 
>PHF5A|NM_032758|3'UTR
   1 TTGGTGGGTGGCCCCTTCCTCCCCCCAACATCAGTCTGCTGCAGCTGCCAGAAAACATGCCTACTACTACCAGCAGAAAG
  81 GGAGCAGAGCCCAGAGCATCACCAGGAGTGCCTGCTAGTGTACTGGCAGCTTGCCACCCCCTCCTCTCCCTTCACCCAGA
 161 CACGTGGTAGGGATGGAAAAGGATTCTTCACAGAGCACTCTGGCACACCATATCGGAGAAAACTTGATAGATTAGTTAAT
 241 GGTTTTTCTTGAATTCGAGAAGCAAAGATCTGTTCTCCATATTGGTATGTTCTCCCTCAACCAAGATCTTCTAAAAAGAA
 321 ATAATATTTTAGTCTTCTGCTTGAGGAACTGACTGTGAAGCGACGCCCAGTGAAAAACATGTTCTTGCAGCAGCTCTGGT
 401 GGCAGCTGTCCTTGAGGAACCTTTGGTGTGTGGTGGGAAGCTATCAGAACAAGAAATGTAGGCATTTCCCGTTTTTTTTG
 481 GGGGGGGGGTGGGGGGGCAGGGCTCTGCCCTCTTGAAAGGCATTTACTTGTTTAACACTTGTCCAGCTACAGTGGGGTAC
 561 AGTAGCTGGCTATTCACAGGCATCATCATAGCCCACTAGTCTCATATTATTTTCCTTTTGAGAAATTGGAAACTCTTTCT
 641 GTTGCTATTATATTAATAAAGTTGGTGTTTATTTTCTGGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 721 A
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' auuuggaugUCCGUCCUGAuu 5'
                   :||||||:||  
Target 5' ggggtggggGGGCAGGGCTct 3'
 486 - 506 120.00 -16.50
2 
miRNA  3' auuuggauguccgUCCUGAuu 5'
                       ||||:|  
Target 5' gtagggatggaaaAGGATTct 3'
 167 - 187 104.00 -6.60
3 
miRNA  3' auUUGGAUGUC-----CGUCCUGAUu 5'
            |:|| | ||      ||||| |: 
Target 5' agAGCCCAGAGCATCACCAGGAGTGc 3'
 86 - 111 103.00 -9.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN32063182 3 COSMIC
COSN30527245 16 COSMIC
COSN30116169 36 COSMIC
COSN31558272 48 COSMIC
COSN30153129 51 COSMIC
COSN26988860 54 COSMIC
COSN31542630 64 COSMIC
COSN30144642 115 COSMIC
COSN18744257 122 COSMIC
COSN28679702 129 COSMIC
COSN30466202 153 COSMIC
COSN30109281 176 COSMIC
COSN30514511 204 COSMIC
COSN20670209 343 COSMIC
COSN27307998 472 COSMIC
rs5758364 490 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs574375738 5 dbSNP
rs779356066 6 dbSNP
rs757348271 11 dbSNP
rs753836588 12 dbSNP
rs1369794493 14 dbSNP
rs1420842877 15 dbSNP
rs764412268 18 dbSNP
rs764027890 20 dbSNP
rs375345370 21 dbSNP
rs752594319 22 dbSNP
rs201597741 25 dbSNP
rs768434018 27 dbSNP
rs372071367 29 dbSNP
rs1202684012 30 dbSNP
rs964081097 44 dbSNP
rs1302870496 49 dbSNP
rs1456369912 51 dbSNP
rs1016996065 56 dbSNP
rs984064430 64 dbSNP
rs1004588232 67 dbSNP
rs1239779229 71 dbSNP
rs886147322 73 dbSNP
rs1288448646 75 dbSNP
rs951428592 87 dbSNP
rs1048820730 93 dbSNP
rs995048301 94 dbSNP
rs546374204 102 dbSNP
rs577362560 111 dbSNP
rs765844652 112 dbSNP
rs907154307 127 dbSNP
rs1054988789 130 dbSNP
rs1419157772 133 dbSNP
rs1042939 137 dbSNP
rs1383023111 138 dbSNP
rs1042940 141 dbSNP
rs1393056346 143 dbSNP
rs559200755 148 dbSNP
rs1163386293 149 dbSNP
rs1366557846 154 dbSNP
rs927898920 162 dbSNP
rs1296965119 163 dbSNP
rs1373171714 164 dbSNP
rs1012785001 166 dbSNP
rs1046109929 169 dbSNP
rs534456060 182 dbSNP
rs1432884514 186 dbSNP
rs762580395 200 dbSNP
rs894211992 206 dbSNP
rs1323279050 207 dbSNP
rs1377530822 208 dbSNP
rs1042943 209 dbSNP
rs1042944 210 dbSNP
rs370458271 212 dbSNP
rs913285059 214 dbSNP
rs1480887760 218 dbSNP
rs1362406741 221 dbSNP
rs1042947 223 dbSNP
rs149294656 233 dbSNP
rs1257360276 234 dbSNP
rs1386639276 237 dbSNP
rs1186633102 242 dbSNP
rs1042952 256 dbSNP
rs1462918118 257 dbSNP
rs191483313 259 dbSNP
rs202639 265 dbSNP
rs922087941 268 dbSNP
rs974923873 272 dbSNP
rs1259233342 277 dbSNP
rs966260902 279 dbSNP
rs1019164719 281 dbSNP
rs1294530054 284 dbSNP
rs1042958 285 dbSNP
rs4822029 286 dbSNP
rs922873698 287 dbSNP
rs1200428008 290 dbSNP
rs1349763429 294 dbSNP
rs950424899 296 dbSNP
rs765030725 303 dbSNP
rs1027761031 327 dbSNP
rs1203685819 330 dbSNP
rs1474201888 332 dbSNP
rs1185183104 334 dbSNP
rs1258738584 336 dbSNP
rs13766 339 dbSNP
rs975531805 340 dbSNP
rs569192944 343 dbSNP
rs894936274 348 dbSNP
rs1033504926 349 dbSNP
rs557479641 351 dbSNP
rs57259696 351 dbSNP
rs1469366298 355 dbSNP
rs17002469 361 dbSNP
rs186918522 362 dbSNP
rs183695146 364 dbSNP
rs951420876 365 dbSNP
rs906408572 368 dbSNP
rs1281315423 369 dbSNP
rs1025643536 371 dbSNP
rs1223633091 382 dbSNP
rs1280088540 384 dbSNP
rs1444973625 387 dbSNP
rs982556503 388 dbSNP
rs535977723 390 dbSNP
rs1488823372 391 dbSNP
rs192793191 393 dbSNP
rs1267407354 398 dbSNP
rs946009443 401 dbSNP
rs891781644 402 dbSNP
rs1173270163 405 dbSNP
rs1381857898 409 dbSNP
rs1382979588 410 dbSNP
rs1054889689 413 dbSNP
rs936086315 414 dbSNP
rs922055533 419 dbSNP
rs974848757 436 dbSNP
rs1345954894 450 dbSNP
rs1042972 453 dbSNP
rs944893073 456 dbSNP
rs1301023820 458 dbSNP
rs1454586989 468 dbSNP
rs1405463705 471 dbSNP
rs1417815836 471 dbSNP
rs76744137 472 dbSNP
rs1347922908 477 dbSNP
rs1163366305 478 dbSNP
rs1425723937 478 dbSNP
rs1491214661 479 dbSNP
rs9423 479 dbSNP
rs1491254821 480 dbSNP
rs1491265943 480 dbSNP
rs780059894 480 dbSNP
rs865871235 480 dbSNP
rs1364724135 481 dbSNP
rs1491131579 481 dbSNP
rs1419374869 482 dbSNP
rs1199909329 483 dbSNP
rs1187903615 484 dbSNP
rs1243292991 485 dbSNP
rs958535984 485 dbSNP
rs1292672834 486 dbSNP
rs1359166805 486 dbSNP
rs1203964572 487 dbSNP
rs1446074465 487 dbSNP
rs1181976830 488 dbSNP
rs1384773365 488 dbSNP
rs1473012873 489 dbSNP
rs1164727797 490 dbSNP
rs1199738083 490 dbSNP
rs5758364 490 dbSNP
rs1286291602 491 dbSNP
rs1383007435 491 dbSNP
rs1259165568 496 dbSNP
rs1258875995 498 dbSNP
rs1276630459 498 dbSNP
rs751852522 498 dbSNP
rs1340659153 499 dbSNP
rs1371103205 499 dbSNP
rs35777353 503 dbSNP
rs1206699687 504 dbSNP
rs559991943 506 dbSNP
rs1272518794 507 dbSNP
rs1171292560 509 dbSNP
rs1231362827 511 dbSNP
rs999945259 518 dbSNP
rs1337126564 529 dbSNP
rs1335447425 530 dbSNP
rs1402522682 534 dbSNP
rs1397396210 548 dbSNP
rs113800666 551 dbSNP
rs1336622689 553 dbSNP
rs902963427 561 dbSNP
rs1253644564 570 dbSNP
rs1284857178 573 dbSNP
rs1320563713 575 dbSNP
rs769031354 577 dbSNP
rs774216439 585 dbSNP
rs1226706589 588 dbSNP
rs1041368420 590 dbSNP
rs1259479421 590 dbSNP
rs1042993 595 dbSNP
rs998280365 596 dbSNP
rs1394423182 599 dbSNP
rs1324232008 601 dbSNP
rs1265288840 605 dbSNP
rs1463347035 608 dbSNP
rs1175151617 619 dbSNP
rs1419113172 620 dbSNP
rs951055697 634 dbSNP
rs1156453278 639 dbSNP
rs1467325038 639 dbSNP
rs1383727017 641 dbSNP
rs1399807512 647 dbSNP
rs1299140916 650 dbSNP
rs1027319200 652 dbSNP
rs1342976246 656 dbSNP
rs973099143 671 dbSNP
rs1300742505 678 dbSNP
rs1312842237 679 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions hESCs (WA-09)
Disease 84844.0
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' auUUGGAUGUCCG--UCCUGAUu 5'
            ::|| |::| |  ||||||| 
Target 5' --GGCC-AUGGCCAUAGGACUA- 3'
 		1 - 19
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 ENST00000216252.3 | 3UTR | GGCCAUGGCCAUAGGACUA
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
29 hsa-miR-4540 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT154897 GNAS GNAS complex locus 2 2
MIRT444915 PSG11 pregnancy specific beta-1-glycoprotein 11 2 2
MIRT446718 PSG3 pregnancy specific beta-1-glycoprotein 3 2 2
MIRT464587 UBN2 ubinuclein 2 2 2
MIRT468816 RSRC2 arginine and serine rich coiled-coil 2 2 6
MIRT469397 REL REL proto-oncogene, NF-kB subunit 2 6
MIRT491901 YWHAE tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon 2 2
MIRT498959 ORC4 origin recognition complex subunit 4 2 8
MIRT499438 ODF2L outer dense fiber of sperm tails 2 like 2 8
MIRT506234 PEX13 peroxisomal biogenesis factor 13 2 4
MIRT527911 B3GALT5 beta-1,3-galactosyltransferase 5 2 2
MIRT532624 PHF5A PHD finger protein 5A 2 2
MIRT538103 DDX6 DEAD-box helicase 6 2 2
MIRT549032 CASZ1 castor zinc finger 1 2 2
MIRT559870 ATXN3 ataxin 3 2 2
MIRT575888 Ablim1 actin-binding LIM protein 1 2 4
MIRT608663 ABLIM1 actin binding LIM protein 1 2 5
MIRT616515 C9orf170 chromosome 9 open reading frame 170 2 2
MIRT624063 EID1 EP300 interacting inhibitor of differentiation 1 2 2
MIRT625533 RALGAPB Ral GTPase activating protein non-catalytic beta subunit 2 2
MIRT637169 TMEM50A transmembrane protein 50A 2 2
MIRT639274 KLHL23 kelch like family member 23 2 2
MIRT642924 CCDC90B coiled-coil domain containing 90B 2 2
MIRT649085 FBXO25 F-box protein 25 2 2
MIRT655089 PI4K2A phosphatidylinositol 4-kinase type 2 alpha 2 2
MIRT700888 PER2 period circadian clock 2 2 2
MIRT705966 ACBD5 acyl-CoA binding domain containing 5 2 2
MIRT709418 FBXL20 F-box and leucine rich repeat protein 20 2 2
MIRT723921 ADAMTS15 ADAM metallopeptidase with thrombospondin type 1 motif 15 2 2
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
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4540 Topotecan 60699 NSC609699 approved resistant cell line (W1)
hsa-miR-4540 Tamoxifen 2733525 NSC180973 approved resistant cell line (LCC2)
hsa-miR-4540 Platinum 23939 resistant tissue (non-small cell lung cancer)

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