pre-miRNA Information
pre-miRNA hsa-mir-4291   
Genomic Coordinates chr9: 93819357 - 93819421
Description Homo sapiens miR-4291 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4291
Sequence 11| UUCAGCAGGAACAGCU |26
Evidence Experimental
Experiments SOLiD
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1265713434 9 dbSNP
rs1433969451 12 dbSNP
rs1372852268 16 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol HOMER2   
Synonyms ACPD, CPD, DFNA68, HOMER-2, VESL-2
Description homer scaffolding protein 2
Transcript NM_004839   
Other Transcripts NM_199330   
Expression
Putative miRNA Targets on HOMER2
3'UTR of HOMER2
(miRNA target sites are highlighted)
>HOMER2|NM_004839|3'UTR
   1 GGCTGGCCGAGGCCCAGGCCCCGCCCGTGAGTCCCAAGCGTGTGTGCGAGACCAGATAGCTCTAGGACGTTCTTCTGTGT
  81 GCATTGCTTCTGTAAATGCAGGCGCAGTTTGTCGTGTTTCCAAACCAGTTGTGCCGTCCACTCACTCCTTTTCAGAATAG
 161 AAATCTCCTCTCGCTTCTCTGGCCTTGTGAGGTTGTGGACAACTGGAAGATTCTGACTCAGGAATCCAGAACTAGGTCTA
 241 CCTTCAACATTTATGCAGTCAGGGCAGGGATGTTTATATCTTTCATAAGGGCTGTTGCAACCATATGAACTGAAAAAACA
 321 CGCATTTTGTAATCCAAATATTGATATTCTTTACACCAAGCCATCAGGCTCCTTTTATCAAATAGCATTCAGAGTATTTG
 401 AATGTCCACCAGACACCAGCCCCGGGGGGCACAGAGAGAACAACATTCCTCTCTGTCAACATCGAGAGGCTTTAAAACAA
 481 CTGTTTAGTGGAAACTTTCTGAGAGATGGAAAACAAGCTTCTGGTGGGTGCATTTTCTGGCCCGGAGTTGCCTGCATCCA
 561 CGCTACTGCCCCCTGCCCCCCGCCCCCCCAGTTTGTACGGTTGCAACAGTGTTCCTTTTCTTGGTTTTAATTTCTGAGCA
 641 GATGATTGTGCTGTGGGAACAGCACACAGTGAGGGTGCCTAGCACAATGTCTGGCACAAAGTAGGTGCTTAATAAATATT
 721 TGTTCAATTAAATGTGTAAAAAAAAAAAAAAAAAA
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' ucgacaagGACGACuu 5'
                  |||:||  
Target 5' cataagggCTGTTGca 3'
284 - 299 104.00 -6.96
2
miRNA  3' ucgACAAGGACGACuu 5'
             || |: |||||  
Target 5' agaTGATTGTGCTGtg 3'
640 - 655 101.00 -7.50
3
miRNA  3' ucgaCAAGGACGACUu 5'
              | |:||| ||: 
Target 5' acaaGCTTCTGGTGGg 3'
513 - 528 100.00 -10.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30146598 9 COSMIC
COSN30193446 26 COSMIC
COSN30461801 34 COSMIC
COSN30120287 69 COSMIC
COSN9091204 87 COSMIC
COSN8590528 127 COSMIC
COSN17530770 133 COSMIC
COSN30174059 170 COSMIC
COSN22295731 486 COSMIC
COSN1181052 544 COSMIC
COSN1181051 553 COSMIC
COSN24850360 590 COSMIC
COSN21166892 598 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs368315318 2 dbSNP
rs1298561101 4 dbSNP
rs747264854 6 dbSNP
rs576146765 8 dbSNP
rs772280916 9 dbSNP
rs748289039 13 dbSNP
rs757019204 13 dbSNP
rs938541913 14 dbSNP
rs778944756 15 dbSNP
rs755521915 16 dbSNP
rs1331042875 18 dbSNP
rs749719535 19 dbSNP
rs1440420038 20 dbSNP
rs753554437 21 dbSNP
rs562749296 22 dbSNP
rs375278051 23 dbSNP
rs750095599 24 dbSNP
rs779001466 26 dbSNP
rs756947554 27 dbSNP
rs1385819133 34 dbSNP
rs1177701607 37 dbSNP
rs1176830763 38 dbSNP
rs368134483 39 dbSNP
rs374705092 40 dbSNP
rs762967810 42 dbSNP
rs765081496 47 dbSNP
rs370317385 48 dbSNP
rs1333136100 53 dbSNP
rs1359332032 55 dbSNP
rs754514079 57 dbSNP
rs1454166536 62 dbSNP
rs76267893 64 dbSNP
rs944949174 65 dbSNP
rs912168000 68 dbSNP
rs1281143188 69 dbSNP
rs573435618 72 dbSNP
rs1218377434 76 dbSNP
rs1007111505 77 dbSNP
rs553641670 83 dbSNP
rs754906921 84 dbSNP
rs1196899459 91 dbSNP
rs1243996804 97 dbSNP
rs950708100 99 dbSNP
rs553472749 101 dbSNP
rs1418254747 103 dbSNP
rs973486752 104 dbSNP
rs1011607366 111 dbSNP
rs114462449 113 dbSNP
rs185414724 114 dbSNP
rs1168019499 118 dbSNP
rs1398922035 126 dbSNP
rs1236644161 135 dbSNP
rs1315920554 136 dbSNP
rs1002707190 148 dbSNP
rs906997098 148 dbSNP
rs1315359544 152 dbSNP
rs558159230 163 dbSNP
rs1044222522 167 dbSNP
rs1435547072 171 dbSNP
rs79958469 172 dbSNP
rs1347684519 173 dbSNP
rs909158454 175 dbSNP
rs1257591624 176 dbSNP
rs1380013570 189 dbSNP
rs906431295 189 dbSNP
rs554512917 199 dbSNP
rs1048700270 203 dbSNP
rs1451509049 207 dbSNP
rs1387791110 220 dbSNP
rs1200107775 221 dbSNP
rs1157139996 224 dbSNP
rs1477006036 229 dbSNP
rs1453530147 231 dbSNP
rs1422403197 235 dbSNP
rs1386056099 236 dbSNP
rs1462094138 240 dbSNP
rs929000481 242 dbSNP
rs919014255 248 dbSNP
rs1020885059 256 dbSNP
rs549635597 257 dbSNP
rs893478400 258 dbSNP
rs1442856440 260 dbSNP
rs1053432964 262 dbSNP
rs1397866455 264 dbSNP
rs965828870 265 dbSNP
rs536074331 269 dbSNP
rs912691024 276 dbSNP
rs566940182 280 dbSNP
rs1229758718 285 dbSNP
rs1282499684 289 dbSNP
rs985643683 298 dbSNP
rs1210961222 299 dbSNP
rs1447463368 301 dbSNP
rs1263808460 302 dbSNP
rs1203128134 303 dbSNP
rs547116090 304 dbSNP
rs533322105 306 dbSNP
rs1292032915 307 dbSNP
rs755834966 321 dbSNP
rs193161482 322 dbSNP
rs1366219122 334 dbSNP
rs750025047 341 dbSNP
rs1164167393 344 dbSNP
rs1367316699 347 dbSNP
rs1227546643 348 dbSNP
rs1031679677 353 dbSNP
rs1297326203 354 dbSNP
rs1003341008 357 dbSNP
rs1316887522 361 dbSNP
rs1381984743 367 dbSNP
rs189800573 371 dbSNP
rs1384124835 379 dbSNP
rs907305004 391 dbSNP
rs912100362 392 dbSNP
rs1044192419 400 dbSNP
rs146174181 402 dbSNP
rs1317833295 405 dbSNP
rs887690249 407 dbSNP
rs1168530031 414 dbSNP
rs1287171842 416 dbSNP
rs1476456401 418 dbSNP
rs535238754 420 dbSNP
rs1191006449 421 dbSNP
rs184521004 423 dbSNP
rs918881255 424 dbSNP
rs1183648694 425 dbSNP
rs973440867 427 dbSNP
rs959426666 429 dbSNP
rs1364163007 430 dbSNP
rs1489690423 430 dbSNP
rs757636067 432 dbSNP
rs944428199 436 dbSNP
rs542379394 446 dbSNP
rs141923876 448 dbSNP
rs970606654 452 dbSNP
rs932839725 455 dbSNP
rs1375401837 456 dbSNP
rs1340920848 457 dbSNP
rs1446711617 459 dbSNP
rs1268934576 461 dbSNP
rs1218496569 463 dbSNP
rs559774556 464 dbSNP
rs1021254266 468 dbSNP
rs539978280 469 dbSNP
rs1456030953 470 dbSNP
rs149401837 478 dbSNP
rs1251091469 482 dbSNP
rs1420701754 484 dbSNP
rs577562061 486 dbSNP
rs1470418014 487 dbSNP
rs1178780121 492 dbSNP
rs1031963145 495 dbSNP
rs191907343 501 dbSNP
rs1465135322 505 dbSNP
rs1365158675 509 dbSNP
rs981491059 511 dbSNP
rs1385493719 512 dbSNP
rs1329851160 522 dbSNP
rs137932772 524 dbSNP
rs1223766726 525 dbSNP
rs1264571345 527 dbSNP
rs1023041528 531 dbSNP
rs1012702872 533 dbSNP
rs1251854020 534 dbSNP
rs1802494 537 dbSNP
rs1189310554 541 dbSNP
rs1167413565 543 dbSNP
rs1480602024 544 dbSNP
rs1201903713 550 dbSNP
rs546046407 561 dbSNP
rs1429932810 562 dbSNP
rs1040811066 563 dbSNP
rs1201261881 566 dbSNP
rs1477564749 567 dbSNP
rs1009456021 571 dbSNP
rs1027450163 574 dbSNP
rs890631873 574 dbSNP
rs993790790 575 dbSNP
rs897758029 576 dbSNP
rs368314308 577 dbSNP
rs1337917245 579 dbSNP
rs1295656753 581 dbSNP
rs572089618 581 dbSNP
rs764605010 581 dbSNP
rs1490459105 582 dbSNP
rs556584421 582 dbSNP
rs1479355482 583 dbSNP
rs929541885 584 dbSNP
rs187099919 587 dbSNP
rs373097657 588 dbSNP
rs1353700388 589 dbSNP
rs879337911 589 dbSNP
rs990351166 589 dbSNP
rs1289018758 590 dbSNP
rs1429605473 590 dbSNP
rs934888992 590 dbSNP
rs1363492445 591 dbSNP
rs1226071682 593 dbSNP
rs924916049 595 dbSNP
rs938009502 596 dbSNP
rs981840129 598 dbSNP
rs560028629 599 dbSNP
rs1283609083 602 dbSNP
rs1446157182 603 dbSNP
rs1222044561 606 dbSNP
rs1022922151 609 dbSNP
rs1482343780 611 dbSNP
rs1183026873 613 dbSNP
rs982222703 614 dbSNP
rs115909263 624 dbSNP
rs1280355095 634 dbSNP
rs146939144 639 dbSNP
rs1346574094 655 dbSNP
rs553495938 657 dbSNP
rs957928849 667 dbSNP
rs1335493624 668 dbSNP
rs1383513140 674 dbSNP
rs1027423929 675 dbSNP
rs1306906729 678 dbSNP
rs1349732685 679 dbSNP
rs1224105346 681 dbSNP
rs1286657340 683 dbSNP
rs1310659533 685 dbSNP
rs1328205740 687 dbSNP
rs1203173537 691 dbSNP
rs1032247442 693 dbSNP
rs1453509005 694 dbSNP
rs996438310 699 dbSNP
rs1177347478 704 dbSNP
rs897725417 705 dbSNP
rs963763996 705 dbSNP
rs1019742516 711 dbSNP
rs1179288634 719 dbSNP
rs539971221 719 dbSNP
rs1409795776 727 dbSNP
rs140182603 732 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_ControlB_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell Control B ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

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_ControlB_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell Control B
Location of target site ENST00000225719.4 | 3UTR | GUAUGAGAAACAGACUC
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
82 hsa-miR-4291 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT102445 CALU calumenin 2 4
MIRT108677 ZBTB33 zinc finger and BTB domain containing 33 2 4
MIRT125969 SHOC2 SHOC2, leucine rich repeat scaffold protein 2 6
MIRT179018 PAFAH1B2 platelet activating factor acetylhydrolase 1b catalytic subunit 2 2 4
MIRT379033 CDK6 cyclin dependent kinase 6 2 6
MIRT442473 CPEB4 cytoplasmic polyadenylation element binding protein 4 2 2
MIRT442910 PCBD2 pterin-4 alpha-carbinolamine dehydratase 2 2 2
MIRT442979 ZNF736 zinc finger protein 736 2 2
MIRT445663 TNFSF15 TNF superfamily member 15 2 2
MIRT446237 FZD6 frizzled class receptor 6 2 2
MIRT448860 FAM49B family with sequence similarity 49 member B 2 2
MIRT455559 TRAF1 TNF receptor associated factor 1 2 2
MIRT459704 ZNF641 zinc finger protein 641 2 2
MIRT460608 FEM1A fem-1 homolog A 2 2
MIRT462251 LAMA4 laminin subunit alpha 4 2 2
MIRT462469 FIZ1 FLT3 interacting zinc finger 1 2 2
MIRT466656 TAF1D TATA-box binding protein associated factor, RNA polymerase I subunit D 2 6
MIRT466841 STX6 syntaxin 6 2 2
MIRT471403 PDP2 pyruvate dehyrogenase phosphatase catalytic subunit 2 2 2
MIRT471517 PCGF3 polycomb group ring finger 3 2 2
MIRT471681 PABPN1 poly(A) binding protein nuclear 1 2 2
MIRT472858 MTHFD2 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase 2 2
MIRT474813 KIAA0226 RUN and cysteine rich domain containing beclin 1 interacting protein 2 2
MIRT474931 KCTD15 potassium channel tetramerization domain containing 15 2 2
MIRT475814 HDGF heparin binding growth factor 2 2
MIRT480434 C17orf49 chromosome 17 open reading frame 49 2 2
MIRT480903 BCL2L2-PABPN1 BCL2L2-PABPN1 readthrough 2 2
MIRT481478 ARL8B ADP ribosylation factor like GTPase 8B 2 2
MIRT484982 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 8
MIRT485019 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 8
MIRT485036 TMEM189 transmembrane protein 189 2 8
MIRT495074 HEYL hes related family bHLH transcription factor with YRPW motif-like 2 2
MIRT496004 CD180 CD180 molecule 2 2
MIRT500675 TRIM37 tripartite motif containing 37 2 2
MIRT504544 ZNF417 zinc finger protein 417 2 6
MIRT506782 KLHL15 kelch like family member 15 2 6
MIRT507256 FGF2 fibroblast growth factor 2 2 6
MIRT507386 EN2 engrailed homeobox 2 2 2
MIRT512505 BTBD19 BTB domain containing 19 2 2
MIRT516903 CTSB cathepsin B 2 2
MIRT528124 PPP1R10 protein phosphatase 1 regulatory subunit 10 2 2
MIRT528874 ATF3 activating transcription factor 3 2 2
MIRT536091 MBOAT2 membrane bound O-acyltransferase domain containing 2 2 2
MIRT541079 RLIM ring finger protein, LIM domain interacting 2 2
MIRT541099 RAF1 Raf-1 proto-oncogene, serine/threonine kinase 2 2
MIRT545360 LIN7C lin-7 homolog C, crumbs cell polarity complex component 2 2
MIRT545831 ZNF367 zinc finger protein 367 2 4
MIRT547115 PHLPP2 PH domain and leucine rich repeat protein phosphatase 2 2 2
MIRT547312 NPTN neuroplastin 2 2
MIRT547959 HIGD1A HIG1 hypoxia inducible domain family member 1A 2 4
MIRT549943 RPL7L1 ribosomal protein L7 like 1 2 2
MIRT550749 ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 2 2
MIRT565145 TUBB2A tubulin beta 2A class IIa 2 2
MIRT571050 POLQ DNA polymerase theta 2 2
MIRT571361 ZNF45 zinc finger protein 45 2 2
MIRT610133 FOXI2 forkhead box I2 2 2
MIRT613145 DSE dermatan sulfate epimerase 2 2
MIRT613379 ABCC12 ATP binding cassette subfamily C member 12 2 2
MIRT615752 C6 complement C6 2 2
MIRT616460 ADRA2B adrenoceptor alpha 2B 2 2
MIRT616719 FEM1B fem-1 homolog B 2 2
MIRT618312 IPP intracisternal A particle-promoted polypeptide 2 2
MIRT631491 RASSF4 Ras association domain family member 4 2 2
MIRT643134 PLCXD2 phosphatidylinositol specific phospholipase C X domain containing 2 2 2
MIRT643482 DISC1 disrupted in schizophrenia 1 2 2
MIRT649715 TWSG1 twisted gastrulation BMP signaling modulator 1 2 2
MIRT653542 SLC38A7 solute carrier family 38 member 7 2 2
MIRT666307 SLC22A3 solute carrier family 22 member 3 2 2
MIRT692005 NAP1L4 nucleosome assembly protein 1 like 4 2 2
MIRT696838 ARL2BP ADP ribosylation factor like GTPase 2 binding protein 2 2
MIRT698204 TMEM248 transmembrane protein 248 2 2
MIRT703316 GDPD5 glycerophosphodiester phosphodiesterase domain containing 5 2 2
MIRT709376 FAM13A family with sequence similarity 13 member A 2 2
MIRT710112 MED23 mediator complex subunit 23 2 2
MIRT711975 HOMER2 homer scaffolding protein 2 2 2
MIRT712275 PPIP5K2 diphosphoinositol pentakisphosphate kinase 2 2 2
MIRT714108 TMED9 transmembrane p24 trafficking protein 9 2 2
MIRT719113 MAML1 mastermind like transcriptional coactivator 1 2 2
MIRT719727 SLC39A11 solute carrier family 39 member 11 2 2
MIRT720018 TFAP2C transcription factor AP-2 gamma 2 2
MIRT720358 ZBTB8B zinc finger and BTB domain containing 8B 2 2
MIRT720372 NUDT3 nudix hydrolase 3 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-4291 Platinum-based doublet chemotherapy resistant High Lung Adenocarcinoma tissue
hsa-miR-4291 Platinum 23939 resistant High Ovarian Cancer tissue
hsa-miR-4291 Paclitaxel 36314 NSC125973 approved resistant High Prostate Cancer cell line (DU-145, PC-3)
hsa-miR-4291 Doxorubicin 31703 NSC123127 approved resistant High Chronic Myelogenous Leukemia cell line (K562)
hsa-miR-4291 Radioactivity Iodine resistant High Papillary Thyroid Cancer tissue
hsa-miR-4291 Cisplatin 5460033 NSC119875 approved resistant High Hypopharyngeal Cancer cell line (FaDu)
hsa-miR-4291 Gefitinib 123631 NSC715055 approved resistant cell line (PC9)
hsa-miR-4291 Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-4291 Cisplatin 5460033 NSC119875 approved sensitive cell line (CAL-27) (cytosolic RNA)
hsa-miR-4291 Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-4291 Platinum-based doublet chemotherapy resistant tissue (lung adenocarcinoma)
hsa-miR-4291 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4291 Gemcitabine 60750 NSC613327 approved resistant cell line (Panc1-GR3)
hsa-miR-4291 Gemcitabine 60750 NSC613327 approved resistant cell line (Panc1-GR4)

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