pre-miRNA Information | |
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pre-miRNA | hsa-mir-2115 |
Genomic Coordinates | chr3: 48316360 - 48316459 |
Description | Homo sapiens miR-2115 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||
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Mature miRNA | hsa-miR-2115-3p | |||||||||
Sequence | 58| CAUCAGAAUUCAUGGAGGCUAG |79 | |||||||||
Evidence | Experimental | |||||||||
Experiments | 454 | DRVs in miRNA |
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SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | TRUB1 | ||||||||||||||||||||
Synonyms | PUS4 | ||||||||||||||||||||
Description | TruB pseudouridine synthase family member 1 | ||||||||||||||||||||
Transcript | NM_139169 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on TRUB1 | |||||||||||||||||||||
3'UTR of TRUB1 (miRNA target sites are highlighted) |
>TRUB1|NM_139169|3'UTR 1 GATTGGCCTGGGAATATCATCATTTTCTAGTTGACATTTGAATCCTGTGTGCAGATGCAGAATGACAAGCTGCATTCAAA 81 AGACAAACAATATGTCTTTTTTTTTTTTGCATGAAGAAAAATGTCTATCATTTACAGTTTCAATAGCACATAATTTATTT 161 TCTATGCATTATAAATGGCCTTGCAGTTGGCTCAGTTGTTTGTTGTGTTGTGAAATGTTTTAGGATTTTTTGTATTGTGA 241 AAATATGAATATGATTGGATTCAGAAAAATTAACTTTCTGAATTTGATCTGTCTTCAGTCTTGTGAAAAAGTTGAACAAA 321 TTTCCTAATCAAAGAAAAAAGTATGAGCTCCATGTTTCTTTAGTTTCACAAAAATGACCATAATTTAGTGTTATTTTTAC 401 TTTATTTAGGCTTCCTGGTGGCTTCATTTTATTGAAATTCTTTAAATTGTTTAAAGTGGCCATTATTGATCTCTTTCTTC 481 TGTTTTGGAGAGTTTATTATTAAAAACATTTCTTTGATAAAATGGCCATCATCTAGTAATACCTGTGTTTGTTTAGATCT 561 TGGAAATGAATAAGCTTTGATAATATTTGTAAATGAACCAAATTATTACTGCTACCACTAACAGGTTGTAAATAGAAGAC 641 TAATACTTAATTAAAGTCACCTTCCTACCATTAGAGCAGAAGACAGCTCCTATAGTTTTGTATTTTGGCAGCTATGAGAT 721 ATTTTCATGGTAATGTCAACATGGTCAAGCACTTTGTACCAAGTTATTAAGTAACATAATTTTTAAAATTTAAAGAATGT 801 GTCTTCAACTAAAAACTTTATTCTTTAGCATTTATTTATATTTCTCTGTAGGGTGTTCCCTGTGACATTGTCTCTTTAGT 881 TTGCTCTTTCAAGAGATACTTACAGATGTTGAGATGGCTGCCCTGCATTTCCAGCTAATCTCTTCTGCTCTAAATATTTA 961 AAAACAGTTCTTCTCAAACATTTTCATTCAGATAGCTTTCTGAAAGTTCCCTATCCCTCTTTACCATAATTTTTTAAATG 1041 TAGCCACATTGTAATAGTAAACTTCATATATAATGAGTGCTTCATATTTTTGTTATGGGAAAGCAATATATTATGCAGCC 1121 AGTCTGTAGAAACATTCAGATCCCTCTTCCTTTACTCAAATACAGTTTCAAAAGGAAGACTCATGAGAAATTTCATAAAA 1201 TACAAGTTTTTAGATGTTTATGCTTTGCCTTTCTTTTTAAAGGTGTTTTCCTGCTTTGTAGTCTCTAACTCTGAAATTTA 1281 AAATATGTAAACTAAAGTGGTTTTATTTGTGCTTAACCCAATTTAAACTCAATGTAAAATGTTATATATGCATCAGTACA 1361 GCATTTTCAACATATTGGCAACATATTTTAAATGAAAACACTAAAACAATTCTTAGTATGAGACAAAACTGTAAGGAAAA 1441 AGAGTGTTAATACCATGATGCATTAACATAAAATATCAAACACACAAAGTCATAAAATGAAAATTTACAGTTTTACCTGT 1521 TCATATCTAGTGCCCCACAGTGTGTGTCAACCAAAGGTGGCAGTGGCTACATCTGCCTGTTGGACTGGTACAGGTTACAA 1601 TATGTCCTCTTCCATTGCAAATTAAAGTCCAAATAGAGAAATACTTAGGTTTTAGAACACATCAGAGGTATTTCTGCTGT 1681 ATTTTTCACCTTAAAAATTGACACAGAGTTTACTAATAGAGGAGTAGAGATTGTTGACCATTTTTAAAAAACGATAGCCA 1761 CTCTTTTTCTTTTATGTTTAAAACTGAAGTTTTGCCAAATGGGAAAATTACTGTTACCTCTACCATCTTAATGTAGTAAC 1841 TTTAGAATTTAAATTTTTATATTACTATTTTCCTTTTTGTTGTTCACATAGTCTTAAGGCACCTATACTTTTAAATTGAC 1921 TTTTTCATTTGATATTATCTATATGTATGTAGTTGTGATAATGATTATTTTAATTATATTACTTTATACTCTTAATTTAT 2001 TTAGAGTATTTCTCTATTGCTGAATACTTAAGTAGTTTTAAATTTTATTATGATAAATTCCTGGGAGGGGGATTATTTAG 2081 TGAAATAATATGAAGAACTTTATGACTTATGTTTGCCTTATTGCATTCCCAAAGAGTTGTAACATTTTACAGTGTTACCA 2161 TTTGAGTAGGGGTTTTATATGTTGTTGCTAATTTAGTAAACATAGGAGAGAAATCAAAGTTTTTCTGATTTGCTTTTATG 2241 TGATTTATCTGTATACTTTGTTCATTTATATAAATAAATGTCTTAATGGTTTCTATACATA 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 | hESCs (WA-09) |
Disease | 142940.0 |
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]
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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 | Prostate Tissue |
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 SRX1760639. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP-MDV_A
... - Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al., 2016, Neoplasia (New York, N.Y.). |
Article |
- Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al. - Neoplasia (New York, N.Y.), 2016
MicroRNA (miRNA) deregulation in prostate cancer (PCa) contributes to PCa initiation and metastatic progression. To comprehensively define the cancer-associated changes in miRNA targeting and function in commonly studied models of PCa, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the Argonaute protein in a panel of PCa cell lines modeling different stages of PCa progression. Using this comprehensive catalogue of miRNA targets, we analyzed miRNA targeting on known drivers of PCa and examined tissue-specific and stage-specific pathway targeting by miRNAs. We found that androgen receptor is the most frequently targeted PCa oncogene and that miR-148a targets the largest number of known PCa drivers. Globally, tissue-specific and stage-specific changes in miRNA targeting are driven by homeostatic response to active oncogenic pathways. Our findings indicate that, even in advanced PCa, the miRNA pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. These findings are important because they are the first to globally characterize miRNA changes in PCa and demonstrate how the miRNA target spectrum responds to staged tumorigenesis.
LinkOut: [PMID: 27292025]
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CLIP-seq Support 1 for dataset SRR359787 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | hESCs (WA-09) / 4-thiouridine, RNase T1 |
Location of target site | ENST00000298746.3 | 3UTR | AGAGAAAUCAAAGUUUUUC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 22012620 / SRX103431 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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80 hsa-miR-2115-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT057089 | DDIT4 | DNA damage inducible transcript 4 | ![]() |
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2 | 2 | ||||||
MIRT071216 | FCF1 | FCF1, rRNA-processing protein | ![]() |
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2 | 2 | ||||||
MIRT226901 | RAD23B | RAD23 homolog B, nucleotide excision repair protein | ![]() |
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2 | 2 | ||||||
MIRT235961 | BACH1 | BTB domain and CNC homolog 1 | ![]() |
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2 | 2 | ||||||
MIRT294569 | ZNF460 | zinc finger protein 460 | ![]() |
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2 | 4 | ||||||
MIRT321046 | RAC1 | Rac family small GTPase 1 | ![]() |
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2 | 4 | ||||||
MIRT359666 | NUS1 | NUS1 dehydrodolichyl diphosphate synthase subunit | ![]() |
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2 | 8 | ||||||
MIRT366451 | KLHL15 | kelch like family member 15 | ![]() |
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2 | 2 | ||||||
MIRT405375 | ZBTB18 | zinc finger and BTB domain containing 18 | ![]() |
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2 | 2 | ||||||
MIRT441794 | TCEAL5 | transcription elongation factor A like 5 | ![]() |
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2 | 2 | ||||||
MIRT443295 | TCEAL3 | transcription elongation factor A like 3 | ![]() |
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2 | 2 | ||||||
MIRT455275 | DDX39B | DExD-box helicase 39B | ![]() |
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2 | 2 | ||||||
MIRT458523 | C5orf22 | chromosome 5 open reading frame 22 | ![]() |
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2 | 2 | ||||||
MIRT464960 | TWIST1 | twist family bHLH transcription factor 1 | ![]() |
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2 | 2 | ||||||
MIRT466848 | STX6 | syntaxin 6 | ![]() |
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2 | 2 | ||||||
MIRT469252 | RHOB | ras homolog family member B | ![]() |
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2 | 2 | ||||||
MIRT469825 | RAB14 | RAB14, member RAS oncogene family | ![]() |
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2 | 4 | ||||||
MIRT470047 | PTGFRN | prostaglandin F2 receptor inhibitor | ![]() |
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2 | 2 | ||||||
MIRT471420 | PDP2 | pyruvate dehyrogenase phosphatase catalytic subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT472024 | NPM1 | nucleophosmin 1 | ![]() |
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2 | 2 | ||||||
MIRT484156 | CENPN | centromere protein N | ![]() |
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2 | 2 | ||||||
MIRT485490 | HMGN2 | high mobility group nucleosomal binding domain 2 | ![]() |
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2 | 2 | ||||||
MIRT490462 | PROSER2 | proline and serine rich 2 | ![]() |
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2 | 2 | ||||||
MIRT493069 | MTCH1 | mitochondrial carrier 1 | ![]() |
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2 | 2 | ||||||
MIRT493573 | HSP90AA1 | heat shock protein 90 alpha family class A member 1 | ![]() |
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2 | 8 | ||||||
MIRT494919 | NDUFC2-KCTD14 | NDUFC2-KCTD14 readthrough | ![]() |
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2 | 2 | ||||||
MIRT500439 | ZMAT3 | zinc finger matrin-type 3 | ![]() |
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2 | 2 | ||||||
MIRT500931 | SRPR | SRP receptor alpha subunit | ![]() |
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2 | 4 | ||||||
MIRT501551 | POC1B-GALNT4 | POC1B-GALNT4 readthrough | ![]() |
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2 | 2 | ||||||
MIRT501809 | NEURL1B | neuralized E3 ubiquitin protein ligase 1B | ![]() |
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2 | 2 | ||||||
MIRT502415 | GALNT4 | polypeptide N-acetylgalactosaminyltransferase 4 | ![]() |
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2 | 2 | ||||||
MIRT506504 | MSANTD4 | Myb/SANT DNA binding domain containing 4 with coiled-coils | ![]() |
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2 | 2 | ||||||
MIRT507861 | CCNE2 | cyclin E2 | ![]() |
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2 | 2 | ||||||
MIRT510511 | YOD1 | YOD1 deubiquitinase | ![]() |
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2 | 6 | ||||||
MIRT516073 | RAB42 | RAB42, member RAS oncogene family | ![]() |
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2 | 2 | ||||||
MIRT519030 | KYNU | kynureninase | ![]() |
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2 | 6 | ||||||
MIRT521762 | PPIL1 | peptidylprolyl isomerase like 1 | ![]() |
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2 | 4 | ||||||
MIRT522898 | KCNJ3 | potassium voltage-gated channel subfamily J member 3 | ![]() |
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2 | 4 | ||||||
MIRT527370 | MGARP | mitochondria localized glutamic acid rich protein | ![]() |
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2 | 2 | ||||||
MIRT530691 | C8orf46 | chromosome 8 open reading frame 46 | ![]() |
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2 | 2 | ||||||
MIRT530867 | TRUB1 | TruB pseudouridine synthase family member 1 | ![]() |
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2 | 2 | ||||||
MIRT531832 | MTPAP | mitochondrial poly(A) polymerase | ![]() |
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2 | 4 | ||||||
MIRT533035 | ZBTB5 | zinc finger and BTB domain containing 5 | ![]() |
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2 | 2 | ||||||
MIRT533165 | WIPF2 | WAS/WASL interacting protein family member 2 | ![]() |
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2 | 2 | ||||||
MIRT533464 | TRIM71 | tripartite motif containing 71 | ![]() |
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2 | 2 | ||||||
MIRT534331 | SHCBP1 | SHC binding and spindle associated 1 | ![]() |
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2 | 2 | ||||||
MIRT539372 | ADSS | adenylosuccinate synthase | ![]() |
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2 | 6 | ||||||
MIRT545951 | ZBTB10 | zinc finger and BTB domain containing 10 | ![]() |
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2 | 2 | ||||||
MIRT553283 | TSR1 | TSR1, ribosome maturation factor | ![]() |
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2 | 2 | ||||||
MIRT553532 | TMEM185B | transmembrane protein 185B | ![]() |
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2 | 4 | ||||||
MIRT556480 | LIPA | lipase A, lysosomal acid type | ![]() |
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2 | 2 | ||||||
MIRT556975 | HSPA4L | heat shock protein family A (Hsp70) member 4 like | ![]() |
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2 | 2 | ||||||
MIRT557697 | GATA6 | GATA binding protein 6 | ![]() |
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2 | 2 | ||||||
MIRT558901 | CCDC58 | coiled-coil domain containing 58 | ![]() |
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2 | 2 | ||||||
MIRT559224 | BLMH | bleomycin hydrolase | ![]() |
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2 | 2 | ||||||
MIRT559827 | SLPI | secretory leukocyte peptidase inhibitor | ![]() |
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2 | 2 | ||||||
MIRT563435 | SLC3A2 | solute carrier family 3 member 2 | ![]() |
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2 | 2 | ||||||
MIRT569270 | PCDH11X | protocadherin 11 X-linked | ![]() |
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2 | 2 | ||||||
MIRT571386 | JKAMP | JNK1/MAPK8-associated membrane protein | ![]() |
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2 | 2 | ||||||
MIRT572567 | AFF1 | AF4/FMR2 family member 1 | ![]() |
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2 | 2 | ||||||
MIRT610400 | AR | androgen receptor | ![]() |
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2 | 2 | ||||||
MIRT611058 | ZNF621 | zinc finger protein 621 | ![]() |
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2 | 2 | ||||||
MIRT635118 | TMEM233 | transmembrane protein 233 | ![]() |
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2 | 2 | ||||||
MIRT641617 | DEFB118 | defensin beta 118 | ![]() |
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2 | 2 | ||||||
MIRT642146 | CHORDC1 | cysteine and histidine rich domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT647295 | C8orf33 | chromosome 8 open reading frame 33 | ![]() |
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2 | 2 | ||||||
MIRT648155 | MPLKIP | M-phase specific PLK1 interacting protein | ![]() |
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2 | 2 | ||||||
MIRT652780 | TENM3 | teneurin transmembrane protein 3 | ![]() |
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2 | 2 | ||||||
MIRT657356 | HNRNPA2B1 | heterogeneous nuclear ribonucleoprotein A2/B1 | ![]() |
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2 | 2 | ||||||
MIRT658718 | ELN | elastin | ![]() |
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2 | 2 | ||||||
MIRT662441 | RALGAPA1 | Ral GTPase activating protein catalytic alpha subunit 1 | ![]() |
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2 | 2 | ||||||
MIRT665302 | ZBTB38 | zinc finger and BTB domain containing 38 | ![]() |
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2 | 2 | ||||||
MIRT699898 | RUNX1 | runt related transcription factor 1 | ![]() |
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2 | 2 | ||||||
MIRT700921 | PDS5A | PDS5 cohesin associated factor A | ![]() |
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2 | 2 | ||||||
MIRT700992 | PDE3A | phosphodiesterase 3A | ![]() |
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2 | 2 | ||||||
MIRT707397 | DCAF4L1 | DDB1 and CUL4 associated factor 4 like 1 | ![]() |
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2 | 2 | ||||||
MIRT711895 | INSIG2 | insulin induced gene 2 | ![]() |
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2 | 2 | ||||||
MIRT712072 | XRCC5 | X-ray repair cross complementing 5 | ![]() |
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2 | 2 | ||||||
MIRT716121 | PTPLAD2 | 3-hydroxyacyl-CoA dehydratase 4 | ![]() |
1 | 1 | |||||||
MIRT724470 | SMAD2 | SMAD family member 2 | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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