pre-miRNA Information
pre-miRNA hsa-mir-3911   
Genomic Coordinates chr9: 127690687 - 127690795
Description Homo sapiens miR-3911 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3911
Sequence 12| UGUGUGGAUCCUGGAGGAGGCA |33
Evidence Experimental
Experiments Illumina
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
431152 7 ClinVar
COSM3847691 15 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs943029638 2 dbSNP
rs780635543 3 dbSNP
rs371437556 6 dbSNP
rs1135401819 7 dbSNP
rs748706130 14 dbSNP
rs1403241180 15 dbSNP
rs779344153 17 dbSNP
rs755366929 21 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol IL1RAPL1   
Synonyms IL-1-RAPL-1, IL-1RAPL-1, IL1R8, IL1RAPL, IL1RAPL-1, MRX10, MRX21, MRX34, OPHN4, TIGIRR-2
Description interleukin 1 receptor accessory protein like 1
Transcript NM_014271   
Expression
Putative miRNA Targets on IL1RAPL1
3'UTR of IL1RAPL1
(miRNA target sites are highlighted)
>IL1RAPL1|NM_014271|3'UTR
   1 CAGAAAAGCAAGGGACATCCCGTCCCTGGGAGGTTGAGTGGAATCTGCAGTCCAGTGCCTGGAACTAAATCCTCGACTGC
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' acggaggagGUCCUAGGUGUgu 5'
                   ::| |||::||  
Target 5' gaggttgagTGGAATCTGCAgt 3'
30 - 51 97.00 -5.30
2
miRNA  3' acggaGGA----GGUCCUAGGUG-UGu 5'
               |||    |:|  |||| | || 
Target 5' cagtgCCTGGAACTA-AATCCTCGACt 3'
53 - 78 82.00 -10.40
3
miRNA  3' acggaggaGGUCC---UAGGugugu 5'
                  | |||   ||||     
Target 5' cagaaaagCAAGGGACATCCcgtcc 3'
1 - 25 70.00 -8.10
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1310025323 7 dbSNP
rs1475579994 9 dbSNP
rs1162709559 18 dbSNP
rs1239726288 19 dbSNP
rs766017219 23 dbSNP
rs751033164 29 dbSNP
rs369147232 32 dbSNP
rs781046009 34 dbSNP
rs1381778386 35 dbSNP
rs752671784 37 dbSNP
rs1330871009 44 dbSNP
rs371562657 49 dbSNP
rs1436204035 51 dbSNP
rs992914318 55 dbSNP
rs1220593930 56 dbSNP
rs1157474359 68 dbSNP
rs1024361427 71 dbSNP
rs1270984686 75 dbSNP
rs989577494 76 dbSNP
rs1465983819 88 dbSNP
rs1477584633 88 dbSNP
rs970600008 88 dbSNP
rs980990240 89 dbSNP
rs1195798851 94 dbSNP
rs1488548844 98 dbSNP
rs189952046 112 dbSNP
rs1474172979 116 dbSNP
rs1216033249 119 dbSNP
rs1183066883 121 dbSNP
rs941929882 138 dbSNP
rs1310070725 140 dbSNP
rs775345744 141 dbSNP
rs973078440 144 dbSNP
rs1281725876 146 dbSNP
rs1415200366 153 dbSNP
rs1341730153 164 dbSNP
rs918923068 166 dbSNP
rs772031005 174 dbSNP
rs1423696276 180 dbSNP
rs1163143343 182 dbSNP
rs1176344638 190 dbSNP
rs749020770 192 dbSNP
rs1422826725 193 dbSNP
rs1458092272 216 dbSNP
rs1478009554 220 dbSNP
rs761258776 223 dbSNP
rs928936589 231 dbSNP
rs1051517849 232 dbSNP
rs911605123 237 dbSNP
rs1311776480 252 dbSNP
rs943203407 252 dbSNP
rs1450341059 261 dbSNP
rs1261471523 266 dbSNP
rs1038857051 267 dbSNP
rs1319021489 280 dbSNP
rs1278137787 281 dbSNP
rs1051470630 286 dbSNP
rs1380754946 291 dbSNP
rs1284811434 292 dbSNP
rs1302872628 292 dbSNP
rs1446628238 292 dbSNP
rs1379830338 300 dbSNP
rs1227612632 301 dbSNP
rs1291215355 304 dbSNP
rs1331031976 305 dbSNP
rs1332943988 309 dbSNP
rs1465996406 312 dbSNP
rs773170703 318 dbSNP
rs1168445842 326 dbSNP
rs1209108006 327 dbSNP
rs911615978 341 dbSNP
rs943570935 342 dbSNP
rs1182567341 348 dbSNP
rs899105294 350 dbSNP
rs1241597045 358 dbSNP
rs994746336 358 dbSNP
rs1458498469 359 dbSNP
rs1257780448 362 dbSNP
rs532865583 376 dbSNP
rs747908685 380 dbSNP
rs904806470 381 dbSNP
rs1211648238 383 dbSNP
rs1000851039 396 dbSNP
rs1053324977 402 dbSNP
rs774520556 405 dbSNP
rs891808745 418 dbSNP
rs770914406 419 dbSNP
rs1186515180 420 dbSNP
rs1414824425 421 dbSNP
rs1014234675 429 dbSNP
rs762047654 431 dbSNP
rs1296189611 432 dbSNP
rs1473152956 442 dbSNP
rs1350439017 446 dbSNP
rs970528894 459 dbSNP
rs1002072726 462 dbSNP
rs1163976613 463 dbSNP
rs1423334834 465 dbSNP
rs1383389820 472 dbSNP
rs1180780353 479 dbSNP
rs1440505506 480 dbSNP
rs1021242381 484 dbSNP
rs1194483067 486 dbSNP
rs1489670456 499 dbSNP
rs1266602690 500 dbSNP
rs1221398668 501 dbSNP
rs1251364575 504 dbSNP
rs202241036 504 dbSNP
rs1287485226 505 dbSNP
rs1240451739 506 dbSNP
rs1160588303 509 dbSNP
rs1304372704 509 dbSNP
rs1363815704 509 dbSNP
rs1375755076 509 dbSNP
rs1420354381 509 dbSNP
rs765911053 509 dbSNP
rs879066952 509 dbSNP
rs867412129 510 dbSNP
rs1334938543 511 dbSNP
rs1435288026 513 dbSNP
rs1025015394 528 dbSNP
rs1191151795 529 dbSNP
rs1489987722 532 dbSNP
rs970761216 533 dbSNP
rs1445906944 535 dbSNP
rs1311052373 539 dbSNP
rs1258646867 545 dbSNP
rs1352229605 548 dbSNP
rs1312590408 559 dbSNP
rs1300276026 564 dbSNP
rs1402852944 568 dbSNP
rs1342339362 582 dbSNP
rs12854875 590 dbSNP
rs1228813409 597 dbSNP
rs1298731904 601 dbSNP
rs1287434782 609 dbSNP
rs1033923154 627 dbSNP
rs12855790 628 dbSNP
rs12855205 629 dbSNP
rs973298533 638 dbSNP
rs1400755035 639 dbSNP
rs919143959 640 dbSNP
rs12857717 641 dbSNP
rs12854891 642 dbSNP
rs1002357589 647 dbSNP
rs1467734402 648 dbSNP
rs775366175 652 dbSNP
rs987076288 656 dbSNP
rs1220529488 657 dbSNP
rs1195016436 658 dbSNP
rs1487679570 659 dbSNP
rs1259010235 660 dbSNP
rs1201846152 663 dbSNP
rs1483401407 665 dbSNP
rs1278891214 668 dbSNP
rs966971088 668 dbSNP
rs911672818 676 dbSNP
rs1208075718 680 dbSNP
rs1319723061 701 dbSNP
rs1278784404 724 dbSNP
rs943103282 725 dbSNP
rs1254647109 749 dbSNP
rs1217862009 752 dbSNP
rs1325958824 761 dbSNP
rs1033792602 762 dbSNP
rs1397832678 789 dbSNP
rs1403230542 795 dbSNP
rs1336316348 799 dbSNP
rs763151512 808 dbSNP
rs1039241680 809 dbSNP
rs1181931618 814 dbSNP
rs12855630 830 dbSNP
rs1172055894 834 dbSNP
rs1238038285 834 dbSNP
rs1475346117 835 dbSNP
rs1231473289 839 dbSNP
rs1479129338 844 dbSNP
rs1189070383 845 dbSNP
rs1173443893 847 dbSNP
rs1242213888 847 dbSNP
rs1201327423 848 dbSNP
rs1424709488 853 dbSNP
rs926115999 857 dbSNP
rs1170524977 861 dbSNP
rs1372356429 863 dbSNP
rs6630978 869 dbSNP
rs1247167974 873 dbSNP
rs1341125538 873 dbSNP
rs1327944286 876 dbSNP
rs1402938290 879 dbSNP
rs1450673936 879 dbSNP
rs1333837959 882 dbSNP
rs866509320 887 dbSNP
rs1395053176 888 dbSNP
rs1181399252 892 dbSNP
rs1384011213 892 dbSNP
rs1423367895 892 dbSNP
rs1472850036 892 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293S
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 GSM1084064. RNA binding protein: AGO2. Condition:CLIP_noemetine_AbnovaAb HITS-CLIP data was present in GSM1084069. RNA binding protein: AGO2. Condition:CLIP_emetine_SigmaAb HITS-CLIP data was present in GSM1084078. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep2_AbnovaAb ...

- Karginov FV; Hannon GJ, 2013, Genes & development.

Article - Karginov FV; Hannon GJ
- Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Cardiac Tissues
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 GSM2202478. RNA binding protein: AGO2. Condition:S3_LV_36yo_Male_AGO2_bound_RNA HITS-CLIP data was present in GSM2202477. RNA binding protein: AGO2. Condition:S2_LV_25yo_Male_AGO2_bound_RNA ...

- Spengler RM; Zhang X; Cheng C; McLendon JM; et al., 2016, Nucleic acids research.

Article - Spengler RM; Zhang X; Cheng C; McLendon JM; et al.
- Nucleic acids research, 2016
MicroRNAs (miRs) have emerged as key biological effectors in human health and disease. These small noncoding RNAs are incorporated into Argonaute (Ago) proteins, where they direct post-transcriptional gene silencing via base-pairing with target transcripts. Although miRs have become intriguing biological entities and attractive therapeutic targets, the translational impacts of miR research remain limited by a paucity of empirical miR targeting data, particularly in human primary tissues. Here, to improve our understanding of the diverse roles miRs play in cardiovascular function and disease, we applied high-throughput methods to globally profile miR:target interactions in human heart tissues. We deciphered Ago2:RNA interactions using crosslinking immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to generate the first transcriptome-wide map of miR targeting events in human myocardium, detecting 4000 cardiac Ago2 binding sites across >2200 target transcripts. Our initial exploration of this interactome revealed an abundance of miR target sites in gene coding regions, including several sites pointing to new miR-29 functions in regulating cardiomyocyte calcium, growth and metabolism. Also, we uncovered several clinically-relevant interactions involving common genetic variants that alter miR targeting events in cardiomyopathy-associated genes. Overall, these data provide a critical resource for bolstering translational miR research in heart, and likely beyond.
LinkOut: [PMID: 27418678]
CLIP-seq Support 1 for dataset GSM1084064
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_AbnovaAb
Location of target site ENST00000378993.1 | 3UTR | GGUGGCCACACACACACACACACACACACACAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1084069
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_SigmaAb
Location of target site ENST00000378993.1 | 3UTR | UGGCCACACACACACACACACA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1084078
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep2_AbnovaAb
Location of target site ENST00000378993.1 | 3UTR | GGUGGCCACACACACACACACACAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
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
LUSC -0.725 0.14 -0.800 0.1 4 Click to see details
BRCA -0.323 0.3 -0.200 0.37 5 Click to see details
HNSC -0.049 0.46 0.170 0.36 7 Click to see details
THCA -0.013 0.49 0.000 0.5 4 Click to see details
THCA -0.013 0.49 0.000 0.5 4 Click to see details
THCA -0.013 0.49 0.000 0.5 4 Click to see details
THCA -0.013 0.49 0.000 0.5 4 Click to see details
THCA -0.013 0.49 0.000 0.5 4 Click to see details
THCA -0.013 0.49 0.000 0.5 4 Click to see details
THCA -0.013 0.49 0.000 0.5 4 Click to see details
70 hsa-miR-3911 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT207399 MAT2A methionine adenosyltransferase 2A 2 6
MIRT284537 PDP2 pyruvate dehyrogenase phosphatase catalytic subunit 2 2 2
MIRT291946 TPM4 tropomyosin 4 2 2
MIRT293609 PVR poliovirus receptor 2 2
MIRT357688 PAIP2 poly(A) binding protein interacting protein 2 2 2
MIRT451607 MEIS3P1 Meis homeobox 3 pseudogene 1 2 2
MIRT452110 IFITM1 interferon induced transmembrane protein 1 2 2
MIRT457804 KLHL25 kelch like family member 25 2 2
MIRT462730 EFNB1 ephrin B1 2 2
MIRT463219 ZNF131 zinc finger protein 131 2 2
MIRT464141 VPS28 VPS28, ESCRT-I subunit 2 2
MIRT467582 SLC7A5 solute carrier family 7 member 5 2 6
MIRT470824 PLXND1 plexin D1 2 2
MIRT474230 LCLAT1 lysocardiolipin acyltransferase 1 2 2
MIRT478989 COLGALT1 collagen beta(1-O)galactosyltransferase 1 2 2
MIRT479462 CDK6 cyclin dependent kinase 6 2 2
MIRT483558 SYT2 synaptotagmin 2 2 2
MIRT484483 SLC9A1 solute carrier family 9 member A1 2 2
MIRT485224 PRICKLE1 prickle planar cell polarity protein 1 2 2
MIRT490356 DPYSL5 dihydropyrimidinase like 5 2 4
MIRT493177 MKNK2 MAP kinase interacting serine/threonine kinase 2 2 2
MIRT509802 CHAF1B chromatin assembly factor 1 subunit B 2 4
MIRT511815 HDGF heparin binding growth factor 2 2
MIRT512254 ARPP19 cAMP regulated phosphoprotein 19 2 6
MIRT513025 GPT2 glutamic--pyruvic transaminase 2 2 2
MIRT519640 ZNF772 zinc finger protein 772 2 4
MIRT531178 SIGLEC12 sialic acid binding Ig like lectin 12 (gene/pseudogene) 2 2
MIRT537870 EDA2R ectodysplasin A2 receptor 2 2
MIRT551914 IGLON5 IgLON family member 5 2 2
MIRT558359 DMTF1 cyclin D binding myb like transcription factor 1 2 2
MIRT559771 URGCP-MRPS24 URGCP-MRPS24 readthrough 2 4
MIRT559813 ZNF83 zinc finger protein 83 2 2
MIRT561999 LPP LIM domain containing preferred translocation partner in lipoma 2 2
MIRT565754 SERTAD2 SERTA domain containing 2 2 2
MIRT569423 DCAF8 DDB1 and CUL4 associated factor 8 2 2
MIRT569845 RGS5 regulator of G protein signaling 5 2 2
MIRT606928 CDK15 cyclin dependent kinase 15 2 2
MIRT607616 TMEM130 transmembrane protein 130 2 4
MIRT607629 TRIOBP TRIO and F-actin binding protein 2 2
MIRT607885 SATB1 SATB homeobox 1 2 2
MIRT607942 SSX2 SSX family member 2 2 4
MIRT608017 CARNS1 carnosine synthase 1 2 4
MIRT608036 UBLCP1 ubiquitin like domain containing CTD phosphatase 1 2 2
MIRT608063 SSX2B SSX family member 2B 2 4
MIRT608558 SBK1 SH3 domain binding kinase 1 2 6
MIRT608915 NCDN neurochondrin 2 6
MIRT615876 HIF1AN hypoxia inducible factor 1 alpha subunit inhibitor 2 4
MIRT618023 ELFN1 extracellular leucine rich repeat and fibronectin type III domain containing 1 2 2
MIRT620505 SNRPD1 small nuclear ribonucleoprotein D1 polypeptide 2 2
MIRT628101 IL1RAPL1 interleukin 1 receptor accessory protein like 1 2 2
MIRT628700 ZNF548 zinc finger protein 548 2 2
MIRT630658 POU2F1 POU class 2 homeobox 1 2 2
MIRT643508 ZNF28 zinc finger protein 28 2 2
MIRT646379 SLC22A6 solute carrier family 22 member 6 2 2
MIRT660041 C15orf61 chromosome 15 open reading frame 61 2 2
MIRT687700 KRR1 KRR1, small subunit processome component homolog 2 2
MIRT688858 CAMKK2 calcium/calmodulin dependent protein kinase kinase 2 2 2
MIRT690443 REPIN1 replication initiator 1 2 2
MIRT690456 ZNF33A zinc finger protein 33A 2 2
MIRT693796 RHOG ras homolog family member G 2 2
MIRT694274 ZNF529 zinc finger protein 529 2 4
MIRT697697 WAC WW domain containing adaptor with coiled-coil 2 2
MIRT700242 RCC2 regulator of chromosome condensation 2 2 2
MIRT701836 MRPL37 mitochondrial ribosomal protein L37 2 2
MIRT704255 DHCR24 24-dehydrocholesterol reductase 2 2
MIRT707203 SDK2 sidekick cell adhesion molecule 2 2 2
MIRT710365 CREB5 cAMP responsive element binding protein 5 2 2
MIRT711943 WDFY1 WD repeat and FYVE domain containing 1 2 2
MIRT715496 MAZ MYC associated zinc finger protein 2 2
MIRT719250 MS4A1 membrane spanning 4-domains A1 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-3911 5-Fluorouracil approved 3385 Microarray CNE cells 22614822 2012 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-3911 Ceritinib 57379345 NSC776422 approved resistant High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-miR-3911 Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-miR-3911 Dabrafenib 44462760 NSC764134 approved sensitive High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-3911 Vemurafenib 42611257 NSC761431 approved sensitive High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-3911 Fulvestrant 17756771 NSC719276 approved sensitive High Breast Cancer cell line (MCF-7)
hsa-mir-3911 Vincristine 5978 approved resistant cell line (W1)
hsa-mir-3911 Androstenedione+Letrozole sensitive cell line (MCF-7)
hsa-miR-3911 Palbociclib 5330286 NSC758247 approved resistant tissue (breast cancer)
hsa-miR-3911 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3911 Doxorubicin 31703 NSC123127 approved sensitive cell line (HS578T)
hsa-miR-3911 Tamoxifen+Fulvestrant sensitive cell line (LCC9)
hsa-miR-3911 Osimertinib 71496458 NSC779217 approved resistant cell line (H1975)
hsa-miR-3911 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3911 Ceritinib 57379345 NSC776422 approved resistant cell line (H3122)
hsa-miR-3911 Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide resistant cell line (Bads-200)

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