pre-miRNA Information | |
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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 | ||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-3911 | |||||||||||||||||||||||||||
Sequence | 12| UGUGUGGAUCCUGGAGGAGGCA |33 | |||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||
Experiments | Illumina | DRVs in miRNA |
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SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | CDK15 | ||||||||||||||||||||
Synonyms | ALS2CR7, PFTAIRE2, PFTK2 | ||||||||||||||||||||
Description | cyclin dependent kinase 15 | ||||||||||||||||||||
Transcript | NM_139158 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on CDK15 | |||||||||||||||||||||
3'UTR of CDK15 (miRNA target sites are highlighted) |
>CDK15|NM_139158|3'UTR 1 AAAGAAAGGGCGAGATCACCAAGGTTCTTCCAGGGCTGTATTTCTGCAGTTTCGGTTTTCATTTGCTTCAGCTTACTAAG 81 AAGCTTCAAATCTAACTCCATACTGAACAAGGGGCTTTATGTCCTCACCTATGACCTGGAATAGTTTAAATATGGTGTTC 161 AAGGCAATAGTACATAATAGTGGAAGAAAATTCAGTGGAAGGTTATTGCTATTGTCATTTGCATAGAATTTAAGTGATTG 241 ATTTAAAAAAACTGGACATAAACTAAGTCTAAGAAGAGGGCTTCTGAATAACTTCATTCATTTTGGCATTTGTTAAGAGA 321 TTCCTGGGCTAGAAGGTTGATTTCCCAAAAAGACAGATAAGAGACTGACAATTTAAAAGAATCTGGAGACAGAGCTGGTG 401 CTTACAGAGACCTGCCACTCCTGTGTTCACTTACAATTTCTCCCAACAAAAGGATTTCTGTGGCAAGGAGAAAACTAGCC 481 TAAAGTTTAGAAAAAGATGGTTTCTTGGATAACATTGTTAACAAAAGGACTTCCTGAGGACTATTTATTATTATTTTGTA 561 GGGGGCACTTCCTCCTTCACTAAACTGGATTATCAGAACGTATTACCACCCAACCCATATTTTAGAAGTTTGGATTTGGC 641 TGCTGATTAGAAATGAATTTCAGGCTATCTCCTCCTACTGAATCTTAATTGTCTGTGATGATGGCAACAGTGATGGGGAA 721 TCTAAGCGCTGGTTTGATGGTGGAGATATTGAATAAGTAGTTGGGAGCAGAGTTCCAAAGATGTAATTTAAGCCCTGTTG 801 CACCACCACACACACACACACACACACACACACACACACACACACACCCCTCAAGTAAAATGAGAGATCTGTCTTAGCTA 881 ACACGTGTGCCGTTTTATACAATGACTCCTTCTAAAAGCAGCCAGGGAAACTCAAATCGCTTCTGTCCAGGGATCATCTC 961 AGGAAATGTAGCAGCCTAGAAACCAGAGACCTCTGTATATCCTTTGGAAGAGCAAGGAGGAACTAATTAAGAGATAATTA 1041 AAAAATAGTAACTATCCCCCAATGTCTGAGATGGAAAAAGGAAAAAGACACATGGGTAGCCCAAATCAACCTGCCTGAGT 1121 AAGTATCTGATTTTAGTAAGGCATTTGACAAAGACTGTCCAGCTATACCTGAAAGATGAAACAGTGTAGGCTGGGTGATG 1201 GAGCAGATATATGTACTCAAATCATGGTGTTTATTTAACCCAGAGAAAGGCCAGCCGTGGTGTGCTACAAGGTTCAGTCT 1281 TGAGTCCTATTCTGGTCAAATATTTTTATTAATTACTCGAATAAATCAGAGTACATGGACAACTTTATACAACTCCTTGA 1361 AGTAAGTACTATTATTATTAATTTATGACTTCCATTTCACAAAAGAGGAGACTGAGGCTCAGTGAAGTTAGGTAACTCCT 1441 TCATAGTAGCATGCCAGAGTGAAGATGCAAACCTCAGACCTGGTTCTCCAATGTTCCTGACACCTATCGAATTTAGAGAA 1521 TACACAACTCTTGCAGAGGCAGCTGCTATTTAGTATTGGATCATGATTCAAAAGACACCTTGCTAGAAGCCAATGAACAG 1601 CAGGCCAAAACAACACTTACTTGCATCAAATTTCATCTGACTTAAATTCTTACACTTTGGGCTACAACTTAAAAAAGGCT 1681 ATGACTTAGTGGAAATTGGCACTTTTAAGTACAATATGAATTAATAGTATAATTTCGCTGTCCCCCAGAGATAATGCTAG 1761 TACCAATCGAAAGCTCAGGGATGCTACTGTTGACGCATCAGCAAGAGTTCTTGAGCAGTTTTACCTGTCCATCAATACAA 1841 AGAGTTCCCACAACAGTAGTGGGATTCCTCTGCCTCTCTGAAGATATGAGAGCTATAGGAGGGATTCCCATGTTGGAGGT 1921 TAGAAGAGCTGACCTCCAATGTCCCGTCTAATTCCAAGATTCTCCAATAATGACTTTGGAACAGCTGTGTACAGATTATA 2001 CTTGGAATTATGCTTAGATACTATTGCTGCAGGAATGAATAGACAAATTTTGTTATTAAAAAATTGATTTTATTAAGTGG 2081 AAGTTGACAGAATTATCCTCTTTATAATGGAGGAACATTATGCTTATGCATATGCATATACCTTATGCATATGATTATGC 2161 TTGTGCTTCCTTCTTTAATGGATTTACCTATTCAAAAGCTTAATAAATGTTATAAGACTCTAAAACATTTAAATCTTTCA 2241 TTTCTCAATTTTATCAAATAAACATTCCTGGAATTTGTGCATA Target sites
Provided by authors
Predicted by miRanda
DRVs
SNPs
DRVs & SNPs
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miRNA-target interactions (Predicted by miRanda) |
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DRVs in gene 3'UTRs | |||||||||||||||||||||
SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | BT474 , MDA-MB-231 |
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 GSM1395167. RNA binding protein: AGO. Condition:BT474 AGO HITS-CLIP Replicate 2
HITS-CLIP data was present in GSM1395170. RNA binding protein: AGO. Condition:MDA-MB-231 AGO HITS-CLIP Replicate 2
... - Pillai MM; Gillen AE; Yamamoto TM; Kline E; et al., 2014, Breast cancer research and treatment. |
Article |
- Pillai MM; Gillen AE; Yamamoto TM; Kline E; et al. - Breast cancer research and treatment, 2014
miRNAs regulate the expression of genes in both normal physiology and disease. While miRNAs have been demonstrated to play a pivotal role in aspects of cancer biology, these reports have generally focused on the regulation of single genes. Such single-gene approaches have significant limitations, relying on miRNA expression levels and heuristic predictions of mRNA-binding sites. This results in only circumstantial evidence of miRNA-target interaction and typically leads to large numbers of false positive predictions. Here, we used a genome-wide approach (high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation, HITS-CLIP) to define direct miRNA-mRNA interactions in three breast cancer subtypes (estrogen receptor positive, Her2 amplified, and triple negative). Focusing on steroid receptor signaling, we identified two novel regulators of the ER pathway (miR-9-5p and miR-193a/b-3p), which together target multiple genes involved in ER signaling. Moreover, this approach enabled the definition of miR-9-5p as a global regulator of steroid receptor signaling in breast cancer. We show that miRNA targets and networks defined by HITS-CLIP under physiologic conditions are predictive of patient outcomes and provide global insight into miRNA regulation in breast cancer.
LinkOut: [PMID: 24906430]
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Experimental Support 2 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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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 GSM2202480. RNA binding protein: AGO2. Condition:S5_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
HITS-CLIP data was present in GSM2202479. RNA binding protein: AGO2. Condition:S4_LV_29yo_Male_AGO2_bound_RNA
HITS-CLIP data was present in GSM2202478. RNA binding protein: AGO2. Condition:S3_LV_36yo_Male_AGO2_bound_RNA
... - Spengler RM; Zhang X; Cheng C; McLendon JM; et al., 2016, Nucleic acids research. |
Article |
Elucidation of transcriptome-wide microRNA binding sites in human cardiac tissues by Ago2 HITS-CLIP.
- 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]
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CLIP-seq Support 1 for dataset GSM1395167 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | BT474 / BT474 AGO HITS-CLIP Replicate 2 |
Location of target site | ENST00000450471.2 | 3UTR | CACCACACACACACACACACACACACACACACACACACACACACCCCUC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 24906430 / GSE57855 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM1395170 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | MDA-MB-231 / MDA-MB-231 AGO HITS-CLIP Replicate 2 |
Location of target site | ENST00000450471.2 | 3UTR | ACACACACACACACACACACACACACACACACACACCCCU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 24906430 / GSE57855 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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70 hsa-miR-3911 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT207399 | MAT2A | methionine adenosyltransferase 2A | ![]() |
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2 | 6 | ||||||
MIRT284537 | PDP2 | pyruvate dehyrogenase phosphatase catalytic subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT291946 | TPM4 | tropomyosin 4 | ![]() |
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2 | 2 | ||||||
MIRT293609 | PVR | poliovirus receptor | ![]() |
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2 | 2 | ||||||
MIRT357688 | PAIP2 | poly(A) binding protein interacting protein 2 | ![]() |
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2 | 2 | ||||||
MIRT451607 | MEIS3P1 | Meis homeobox 3 pseudogene 1 | ![]() |
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2 | 2 | ||||||
MIRT452110 | IFITM1 | interferon induced transmembrane protein 1 | ![]() |
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2 | 2 | ||||||
MIRT457804 | KLHL25 | kelch like family member 25 | ![]() |
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2 | 2 | ||||||
MIRT462730 | EFNB1 | ephrin B1 | ![]() |
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2 | 2 | ||||||
MIRT463219 | ZNF131 | zinc finger protein 131 | ![]() |
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2 | 2 | ||||||
MIRT464141 | VPS28 | VPS28, ESCRT-I subunit | ![]() |
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2 | 2 | ||||||
MIRT467582 | SLC7A5 | solute carrier family 7 member 5 | ![]() |
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2 | 6 | ||||||
MIRT470824 | PLXND1 | plexin D1 | ![]() |
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2 | 2 | ||||||
MIRT474230 | LCLAT1 | lysocardiolipin acyltransferase 1 | ![]() |
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2 | 2 | ||||||
MIRT478989 | COLGALT1 | collagen beta(1-O)galactosyltransferase 1 | ![]() |
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2 | 2 | ||||||
MIRT479462 | CDK6 | cyclin dependent kinase 6 | ![]() |
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2 | 2 | ||||||
MIRT483558 | SYT2 | synaptotagmin 2 | ![]() |
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2 | 2 | ||||||
MIRT484483 | SLC9A1 | solute carrier family 9 member A1 | ![]() |
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2 | 2 | ||||||
MIRT485224 | PRICKLE1 | prickle planar cell polarity protein 1 | ![]() |
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2 | 2 | ||||||
MIRT490356 | DPYSL5 | dihydropyrimidinase like 5 | ![]() |
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2 | 4 | ||||||
MIRT493177 | MKNK2 | MAP kinase interacting serine/threonine kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT509802 | CHAF1B | chromatin assembly factor 1 subunit B | ![]() |
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2 | 4 | ||||||
MIRT511815 | HDGF | heparin binding growth factor | ![]() |
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2 | 2 | ||||||
MIRT512254 | ARPP19 | cAMP regulated phosphoprotein 19 | ![]() |
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2 | 6 | ||||||
MIRT513025 | GPT2 | glutamic--pyruvic transaminase 2 | ![]() |
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2 | 2 | ||||||
MIRT519640 | ZNF772 | zinc finger protein 772 | ![]() |
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2 | 4 | ||||||
MIRT531178 | SIGLEC12 | sialic acid binding Ig like lectin 12 (gene/pseudogene) | ![]() |
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2 | 2 | ||||||
MIRT537870 | EDA2R | ectodysplasin A2 receptor | ![]() |
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2 | 2 | ||||||
MIRT551914 | IGLON5 | IgLON family member 5 | ![]() |
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2 | 2 | ||||||
MIRT558359 | DMTF1 | cyclin D binding myb like transcription factor 1 | ![]() |
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2 | 2 | ||||||
MIRT559771 | URGCP-MRPS24 | URGCP-MRPS24 readthrough | ![]() |
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2 | 4 | ||||||
MIRT559813 | ZNF83 | zinc finger protein 83 | ![]() |
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2 | 2 | ||||||
MIRT561999 | LPP | LIM domain containing preferred translocation partner in lipoma | ![]() |
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2 | 2 | ||||||
MIRT565754 | SERTAD2 | SERTA domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT569423 | DCAF8 | DDB1 and CUL4 associated factor 8 | ![]() |
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2 | 2 | ||||||
MIRT569845 | RGS5 | regulator of G protein signaling 5 | ![]() |
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2 | 2 | ||||||
MIRT606928 | CDK15 | cyclin dependent kinase 15 | ![]() |
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2 | 2 | ||||||
MIRT607616 | TMEM130 | transmembrane protein 130 | ![]() |
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2 | 4 | ||||||
MIRT607629 | TRIOBP | TRIO and F-actin binding protein | ![]() |
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2 | 2 | ||||||
MIRT607885 | SATB1 | SATB homeobox 1 | ![]() |
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2 | 2 | ||||||
MIRT607942 | SSX2 | SSX family member 2 | ![]() |
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2 | 4 | ||||||
MIRT608017 | CARNS1 | carnosine synthase 1 | ![]() |
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2 | 4 | ||||||
MIRT608036 | UBLCP1 | ubiquitin like domain containing CTD phosphatase 1 | ![]() |
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2 | 2 | ||||||
MIRT608063 | SSX2B | SSX family member 2B | ![]() |
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2 | 4 | ||||||
MIRT608558 | SBK1 | SH3 domain binding kinase 1 | ![]() |
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2 | 6 | ||||||
MIRT608915 | NCDN | neurochondrin | ![]() |
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2 | 6 | ||||||
MIRT615876 | HIF1AN | hypoxia inducible factor 1 alpha subunit inhibitor | ![]() |
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2 | 4 | ||||||
MIRT618023 | ELFN1 | extracellular leucine rich repeat and fibronectin type III domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT620505 | SNRPD1 | small nuclear ribonucleoprotein D1 polypeptide | ![]() |
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2 | 2 | ||||||
MIRT628101 | IL1RAPL1 | interleukin 1 receptor accessory protein like 1 | ![]() |
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2 | 2 | ||||||
MIRT628700 | ZNF548 | zinc finger protein 548 | ![]() |
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2 | 2 | ||||||
MIRT630658 | POU2F1 | POU class 2 homeobox 1 | ![]() |
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2 | 2 | ||||||
MIRT643508 | ZNF28 | zinc finger protein 28 | ![]() |
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2 | 2 | ||||||
MIRT646379 | SLC22A6 | solute carrier family 22 member 6 | ![]() |
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2 | 2 | ||||||
MIRT660041 | C15orf61 | chromosome 15 open reading frame 61 | ![]() |
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2 | 2 | ||||||
MIRT687700 | KRR1 | KRR1, small subunit processome component homolog | ![]() |
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2 | 2 | ||||||
MIRT688858 | CAMKK2 | calcium/calmodulin dependent protein kinase kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT690443 | REPIN1 | replication initiator 1 | ![]() |
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2 | 2 | ||||||
MIRT690456 | ZNF33A | zinc finger protein 33A | ![]() |
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2 | 2 | ||||||
MIRT693796 | RHOG | ras homolog family member G | ![]() |
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2 | 2 | ||||||
MIRT694274 | ZNF529 | zinc finger protein 529 | ![]() |
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2 | 4 | ||||||
MIRT697697 | WAC | WW domain containing adaptor with coiled-coil | ![]() |
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2 | 2 | ||||||
MIRT700242 | RCC2 | regulator of chromosome condensation 2 | ![]() |
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2 | 2 | ||||||
MIRT701836 | MRPL37 | mitochondrial ribosomal protein L37 | ![]() |
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2 | 2 | ||||||
MIRT704255 | DHCR24 | 24-dehydrocholesterol reductase | ![]() |
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2 | 2 | ||||||
MIRT707203 | SDK2 | sidekick cell adhesion molecule 2 | ![]() |
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2 | 2 | ||||||
MIRT710365 | CREB5 | cAMP responsive element binding protein 5 | ![]() |
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2 | 2 | ||||||
MIRT711943 | WDFY1 | WD repeat and FYVE domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT715496 | MAZ | MYC associated zinc finger protein | ![]() |
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2 | 2 | ||||||
MIRT719250 | MS4A1 | membrane spanning 4-domains A1 | ![]() |
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2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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