| pre-miRNA Information | |
|---|---|
| pre-miRNA | hsa-mir-4524b |
| Genomic Coordinates | chr17: 69099542 - 69099656 |
| Description | Homo sapiens miR-4524b stem-loop |
| Comment | None |
| RNA Secondary Structure |  |
| Mature miRNA Information | |||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mature miRNA | hsa-miR-4524b-5p | ||||||||||||||||||||||||
| Sequence | 29| AUAGCAGCAUAAGCCUGUCUC |49 | ||||||||||||||||||||||||
| Evidence | Experimental | ||||||||||||||||||||||||
| Experiments | SOLiD | ||||||||||||||||||||||||
| SNPs in miRNA |
|
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| Putative Targets | |||||||||||||||||||||||||
| Gene Information | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene Symbol | NAPG | ||||||||||||||||||||
| Synonyms | GAMMASNAP | ||||||||||||||||||||
| Description | NSF attachment protein gamma | ||||||||||||||||||||
| Transcript | NM_003826 | ||||||||||||||||||||
| Expression | |||||||||||||||||||||
| Putative miRNA Targets on NAPG | |||||||||||||||||||||
| 3'UTR of NAPG (miRNA target sites are highlighted) |
>NAPG|NM_003826|3'UTR 1 TATTTTGCTTGCTGAAAAGAAAAGGGAAACAAAGGTAAAATCCTGACATGCCATTTCAAGGACTTGGGAATAGATTAGGG 81 ATATCCGTACTTCATTACAGTCATGATTTTGGATCCTAATAAAGACTAGTTTTTAGTTACCATCTTCCCAAATCACTCAT 161 TGTATCCATTACCTGTGAAGCATATCTTTTTCTTTCCATAAGAGCTTTTCTAAGACACCAGCAGGAATTAACAGAAAATG 241 TACTGTCATGTTTTAATACATTGATTAAAAAATTTGCAAGCCAAATTATACATAAATTATGTTCTAAACAAAAGGGGTAA 321 TAAGCATAGGTATTCTCTCTTGGACACTTGTAAGTTACTGTTAGTGAATTGTTTTTTACGTTTCATTTAATAATTGCTGC 401 TAAAGGTGATGTTTACTGATAAATCATTTTAAAATTTTTTTGTTTTGAAAAGTAAATTTATCCCCCATGATGTTAGATAC 481 ATTTAAATTATTAAGTCTTTTCAGAGATGAGATGGGGACAGGAAGTTATTTTGAGCCTTACAATATTATTTAGCCCAATA 561 AAAGATGCATTGAAGCTCTTATATATTATGAGTTTGAAAAATTTTGAAGGTAGCATATTGAAGTGATCTATAAATATCTT 641 CAGTCCTCTCTGAAGTGTGGGTATTTCTTCTATCTAAAAAATACATACAGTGACTGTCTTCAAATCTACTTGGTTCTTGA 721 CCAAATAGGAGCTAATGGGTAATGAATACCTTTTTGTTTGTTTGTTTGTTTGTTTTGTTTTTTGTTTTTTTTTTTAAGGG 801 TCTCACTCTTTTGCCCAGGCTGGAGTGCAGTGGCACAATCACGGCTCCCAGGCTAATGTTTTTATTTTTAATTTGTAATT 881 TTTTTTTTATTTTTTTTGTTGAGATGGAGTTGCTCCATGTTGCACAGGCTGTTCTCAAACTCCTAAGCTCAAGCCATCTG 961 CCTGCCTTGGCCTCCCAAAGTGCTGGGATTGTAGACATAAGCCACCTCACCCAGCCTATGAATATCTTTCTAACATTGTA 1041 AGAATGAGGTAATGTTTCCATCAGTCTAATACAGATATATTTCTTCCCTCCAAAACAGTTTATTTTGATTGTTTATTTTA 1121 TTTTGATTGTAACTCCGTCATAACTTGACATGGAAAATGCTATATACTATGAAAACTTAGCTGAAAGGGAAGAATTGTTT 1201 TAGAAAGACAATATTTAAAACACCGCACTGCCAATATATTGATCCTTTATAGTTATTTCCTAAAATGCTGTTTTCGAAAC 1281 ATTCCTTTTTCACCCTGTTGTGTGGCTTAGACCCATCTCGTAATCTGTTAATTGGAAAGAGGCTACAGACACCAGCAGTG 1361 TGCGTTCTGCAGGTACACGCTGCCAAAGTAATTCCTGCTCATCCATGCCCTGTCTCTGTCTCTTTTAGAGTCATACCTTA 1441 TTTGAGTATAGGTTGCTTAATTTTGCTAGACTTCCTGAAAACACTAAGGTGGAGTATCAGAAGTGATTTTAGTCACAGTT 1521 CTGCGGGAGAGCTTAGAATAACATCCTCCTTTGGGAGGTGGTCTCGGGTGCGTGGATGTTGGTATACAGTCTTTATTGTA 1601 AGTCTGATACAAAATGCTAATAAATTTAATGTTTTTCTTCCTTAATTTATTGGCATAGTTCTTCAGGTAGCACCTCATTT 1681 TTATTAATGATATTGGGATTAACTATGAACAAGCTATATGTAGACATTTGCATTTAAGGACATTGCAGTGTTTCAAAGAT 1761 CCCATCATTGCAGCTTGTATCCTTTAGATCCAATCGGAAACTTCTGGAGTCTTACATTAATGCTCATTTGAGCTAATTAG 1841 TAATCTGTTTAAACAGATTTGGCAATACTTTAAAGATACTGTAGACTATTTATGTATAGATAGATCATATTACCCATTAA 1921 AGTCTGGGGGAAAAAATTTTTTAATTTTACTCTTCTTATGTACTGAAAACTTTTTTTAAAAAAGGTGATGATGAAGTGCA 2001 TTCTGTAGCAGCAGCGCAGCTATGCTTTAAACCACACAAAAGGCTGTGTCCAGGTGCAGCCTCCTTCACCCTTCCTGCCC 2081 ACGGTGAGGATTGAATAACCAGGACTTGGGGATATTGTTTGTTGTCAGGGTTATTCTGTGTGGTAAGGAATATTTGTTTC 2161 ACATTTATACATTTTCTTTTTCCACTCACGTAAGTTTCTATCTTGAGAGCATAGTCCAAAGTGCAAAACTTGGTGTTTAC 2241 AAGGAAAATTGTCTTCCAGAACTCCACTGTCATCACTTTCACCAAAGTGGAAGTTTGCATGAATATGCTCAGAATCTAAT 2321 ATTCAATGTTCTGTTACATTGTAAGTGAAGTCCAGCTACAAAATAGATTTAATATATTGAATTTATTTGTACATATGCAG 2401 AGTACGGTATTTCTGTATGGAATCTGCTTTATTCCTATTTTTCCCAACTCTGATGAGTAGAATATTAAATGTGTTGTTAT 2481 GGAAATACAGATTATTGCTTCTATAGGAAGATAATTATGAAAATAAAACCTGAAACTATATAAATATAAAAAAAAAAAAA 2561 AAA 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 | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
|
| Conditions | HEK293 |
| 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 GSM545212. RNA binding protein: AGO1. Condition:Control
PAR-CLIP data was present in GSM545214. RNA binding protein: AGO3. Condition:Control
PAR-CLIP data was present in GSM545215. RNA binding protein: AGO4. Condition:Control
PAR-CLIP data was present in GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection
PAR-CLIP data was present in GSM545217. RNA binding protein: AGO2. Condition:miR-7 transfection
... - Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell. |
| Article |
- Hafner M; Landthaler M; Burger L; Khorshid et al. - Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
|
| Experimental Support 2 for Functional miRNA-Target Interaction | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
|
| Conditions | HEK293 |
| Disease | 8774.0 |
| 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 GSM714642. RNA binding protein: AGO2. Condition:completeT1
"PAR-CLIP data was present in GSM714644. RNA binding protein: AGO2. Condition:completeT1
"PAR-CLIP data was present in GSM714645. RNA binding protein: AGO2. Condition:completeT1
... - Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods. |
| Article |
- Kishore S; Jaskiewicz L; Burger L; Hausser et al. - Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
|
| Experimental Support 3 for Functional miRNA-Target Interaction | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
|
| Conditions | hESCs (WA-09) |
| Disease | 8774.0 |
| 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]
|
| Experimental Support 4 for Functional miRNA-Target Interaction | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
|
| Conditions | HEK293 |
| Disease | 8774.0 |
| 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 GSM1065667. RNA binding protein: AGO1. Condition:4-thiouridine
"PAR-CLIP data was present in GSM1065668. RNA binding protein: AGO1. Condition:4-thiouridine
"PAR-CLIP data was present in GSM1065669. RNA binding protein: AGO1. Condition:4-thiouridine
"PAR-CLIP data was present in GSM1065670. RNA binding protein: AGO2. Condition:4-thiouridine
... - Memczak S; Jens M; Elefsinioti A; Torti F; et al., 2013, Nature. |
| Article |
- Memczak S; Jens M; Elefsinioti A; Torti F; et al. - Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
|
| Experimental Support 5 for Functional miRNA-Target Interaction | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
|
| Conditions | TZM-bl |
| 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 GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL
... - Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio. |
| Article |
- Whisnant AW; Bogerd HP; Flores O; Ho P; et al. - mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
|
| Experimental Support 6 for Functional miRNA-Target Interaction | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
|
| Conditions | MCF7 |
| 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 SRR1045082. RNA binding protein: AGO2. Condition:Untreated
... - Farazi TA; Ten Hoeve JJ; Brown M; et al., 2014, Genome biology. |
| Article |
- Farazi TA; Ten Hoeve JJ; Brown M; et al. - Genome biology, 2014
BACKGROUND: Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired miRNA-mRNA expression data with a set of validated miRNA targets and pathway inference. RESULTS: To generate a biochemically-validated set of miRNA-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (AGO2-PAR-CLIP) in MCF7 cells. We then defined putative miRNA-target interactions using a computational model, which ranked and selected additional TargetScan-predicted interactions based on features of our AGO2-PAR-CLIP binding-site data. We subselected modeled interactions according to the abundance of their constituent miRNA and mRNA transcripts in tumors, and we took advantage of the variability of miRNA expression within molecular subtypes to detect miRNA repression. Interestingly, our data suggest that miRNA families control subtype-specific pathways; for example, miR-17, miR-19a, miR-25, and miR-200b show high miRNA regulatory activity in the triple-negative, basal-like subtype, whereas miR-22 and miR-24 do so in the HER2 subtype. An independent dataset validated our findings for miR-17 and miR-25, and showed a correlation between the expression levels of miR-182 targets and overall patient survival. Pathway analysis associated miR-17, miR-19a, and miR-200b with leukocyte transendothelial migration. CONCLUSIONS: We combined PAR-CLIP data with patient expression data to predict regulatory miRNAs, revealing potential therapeutic targets and prognostic markers in breast cancer.
LinkOut: [PMID: 24398324]
|
| CLIP-seq Support 1 for dataset GSM714642 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO2 |
| Cell line / Condition | HEK293 / completeT1, repA |
| Location of target site | ENST00000322897.6 | 3UTR | UUUCAUUUAAUAAUUGCUGCUAAAG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 21572407 / GSE28865 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 2 for dataset GSM545212 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO1 |
| Cell line / Condition | HEK293 / Control |
| Location of target site | ENST00000322897.6 | 3UTR | UUUCAUUUAAUAAUUGCUGCUAAAG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 3 for dataset GSM545214 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO3 |
| Cell line / Condition | HEK293 / Control |
| Location of target site | ENST00000322897.6 | 3UTR | UUUCAUUUAAUAAUUGCUGCUAAA |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 4 for dataset GSM545215 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO4 |
| Cell line / Condition | HEK293 / Control |
| Location of target site | ENST00000322897.6 | 3UTR | UUUCAUUUAAUAAUUGCUGCUAA |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 5 for dataset GSM545216 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | HEK293 / miR-124 transfection |
| Location of target site | ENST00000322897.6 | 3UTR | UUUCAUUUAAUAAUUGCUGCUAAA |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 6 for dataset GSM545217 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | HEK293 / miR-7 transfection |
| Location of target site | ENST00000322897.6 | 3UTR | UUUCAUUUAAUAAUUGCUGCUAA |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 7 for dataset GSM714644 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | HEK293 / completeT1, repA |
| Location of target site | ENST00000322897.6 | 3UTR | GUUUCAUUUAAUAAUUGCUGCUAAAGGUGAUGUUUACUG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 21572407 / GSE28865 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 8 for dataset GSM714645 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | HEK293 / completeT1, repB |
| Location of target site | ENST00000322897.6 | 3UTR | UUUCAUUUAAUAAUUGCUGCUAAAG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 21572407 / GSE28865 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 9 for dataset SRR359787 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | hESCs (WA-09) / 4-thiouridine, RNase T1 |
| Location of target site | ENST00000322897.6 | 3UTR | UUUCAUUUAAUAAUUGCUGCUAAAG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 22012620 / SRX103431 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 10 for dataset GSM1065667 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO1 |
| Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_6 |
| Location of target site | ENST00000322897.6 | 3UTR | UUUCAUUUAAUAAUUGCUGCUAAAG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 23446348 / GSE43573 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 11 for dataset GSM1065668 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO1 |
| Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_7 |
| Location of target site | ENST00000322897.6 | 3UTR | UUCAUUUAAUAAUUGCUGCUAA |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 23446348 / GSE43573 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 12 for dataset GSM1065669 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO1 |
| Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_8 |
| Location of target site | ENST00000322897.6 | 3UTR | UUUCAUUUAAUAAUUGCUGCUAAAG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 23446348 / GSE43573 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 13 for dataset GSM1065670 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | HEK293 / 4-thiouridine, 3_ML_LG |
| Location of target site | ENST00000322897.6 | 3UTR | UUUCAUUUAAUAAUUGCUGCUAAAG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 23446348 / GSE43573 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 14 for dataset SRR1045082 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | MCF7 / Untreated |
| Location of target site | ENST00000322897.6 | 3UTR | UUUCAUUUAAUAAUUGCUGCUAAAG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 24398324 / SRX388831 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 15 for dataset GSM1462574 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | TZM-bl / TZM-bl ami BaL |
| Location of target site | ENST00000322897.6 | 3UTR | UUUCAUUUAAUAAUUGCUGCUAAAG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 23592263 / GSE59944 |
| CLIP-seq Viewer | Link |
| MiRNA-Target Expression Profile | |||||||
|---|---|---|---|---|---|---|---|
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| MiRNA-Target Expression Profile (TCGA) | |||||||
|---|---|---|---|---|---|---|---|
|
181 hsa-miR-4524b-5p Target Genes:
Functional analysis:
ID |
Target | Description | Validation methods |
 |
 |
|||||||
| Strong evidence | Less strong evidence | |||||||||||
 |
 |
 |
 |
 |
 |
 |
 |
|||||
| MIRT055253 | CNNM2 | cyclin and CBS domain divalent metal cation transport mediator 2 |  |
|
2 | 2 | ||||||
| MIRT055828 | PLEKHA1 | pleckstrin homology domain containing A1 | |
|
2 | 2 | ||||||
| MIRT060575 | CCND1 | cyclin D1 | |
|
2 | 2 | ||||||
| MIRT061015 | C1ORF21 | chromosome 1 open reading frame 21 | |
|
2 | 6 | ||||||
| MIRT064695 | CCND2 | cyclin D2 | |
|
2 | 4 | ||||||
| MIRT075269 | SNTB2 | syntrophin beta 2 | |
|
2 | 4 | ||||||
| MIRT079670 | NAPG | NSF attachment protein gamma | |
|
2 | 12 | ||||||
| MIRT081653 | CCNE1 | cyclin E1 | |
|
2 | 4 | ||||||
| MIRT083002 | PNPLA6 | patatin like phospholipase domain containing 6 | |
|
2 | 2 | ||||||
| MIRT083465 | RALGAPB | Ral GTPase activating protein non-catalytic beta subunit | |
|
2 | 4 | ||||||
| MIRT085756 | RIF1 | replication timing regulatory factor 1 | |
|
2 | 2 | ||||||
| MIRT086024 | UBR3 | ubiquitin protein ligase E3 component n-recognin 3 (putative) | |
|
2 | 2 | ||||||
| MIRT087433 | ZNRF3 | zinc and ring finger 3 | |
|
2 | 2 | ||||||
| MIRT088789 | SOCS5 | suppressor of cytokine signaling 5 | |
|
2 | 2 | ||||||
| MIRT089223 | ACTR2 | ARP2 actin related protein 2 homolog | |
|
2 | 2 | ||||||
| MIRT093698 | PI4K2B | phosphatidylinositol 4-kinase type 2 beta | |
|
2 | 6 | ||||||
| MIRT095093 | SEC24A | SEC24 homolog A, COPII coat complex component | |
|
2 | 4 | ||||||
| MIRT096251 | CANX | calnexin | |
|
2 | 2 | ||||||
| MIRT100219 | PPP1R11 | protein phosphatase 1 regulatory inhibitor subunit 11 | |
|
2 | 2 | ||||||
| MIRT100748 | VEGFA | vascular endothelial growth factor A | |
|
2 | 12 | ||||||
| MIRT100905 | CD2AP | CD2 associated protein | |
|
2 | 2 | ||||||
| MIRT102650 | UBN2 | ubinuclein 2 | |
|
2 | 10 | ||||||
| MIRT103886 | FOXK1 | forkhead box K1 | |
|
2 | 2 | ||||||
| MIRT104249 | DMTF1 | cyclin D binding myb like transcription factor 1 | |
|
2 | 2 | ||||||
| MIRT106311 | ZFHX4 | zinc finger homeobox 4 | |
|
2 | 6 | ||||||
| MIRT107698 | RECK | reversion inducing cysteine rich protein with kazal motifs | |
|
2 | 2 | ||||||
| MIRT114946 | CHAC1 | ChaC glutathione specific gamma-glutamylcyclotransferase 1 | |
|
2 | 2 | ||||||
| MIRT117674 | SCAMP4 | secretory carrier membrane protein 4 | |
|
2 | 2 | ||||||
| MIRT133806 | SKI | SKI proto-oncogene | |
|
2 | 2 | ||||||
| MIRT140171 | SPRED1 | sprouty related EVH1 domain containing 1 | |
|
2 | 2 | ||||||
| MIRT142281 | DCTN5 | dynactin subunit 5 | |
|
2 | 8 | ||||||
| MIRT143297 | N4BP1 | NEDD4 binding protein 1 | |
|
2 | 2 | ||||||
| MIRT165945 | CREBRF | CREB3 regulatory factor | |
|
2 | 2 | ||||||
| MIRT175255 | PSAT1 | phosphoserine aminotransferase 1 | |
|
2 | 6 | ||||||
| MIRT186383 | PNRC2 | proline rich nuclear receptor coactivator 2 | |
|
2 | 2 | ||||||
| MIRT191472 | PPM1A | protein phosphatase, Mg2+/Mn2+ dependent 1A | |
|
2 | 2 | ||||||
| MIRT196481 | TAOK1 | TAO kinase 1 | |
|
2 | 2 | ||||||
| MIRT201472 | SNRPB2 | small nuclear ribonucleoprotein polypeptide B2 | |
|
2 | 8 | ||||||
| MIRT204619 | HSPE1-MOB4 | HSPE1-MOB4 readthrough | |
|
2 | 8 | ||||||
| MIRT204650 | MOB4 | MOB family member 4, phocein | |
|
2 | 8 | ||||||
| MIRT204751 | BZW1 | basic leucine zipper and W2 domains 1 | |
|
2 | 12 | ||||||
| MIRT206032 | NUP50 | nucleoporin 50 | |
|
2 | 6 | ||||||
| MIRT211197 | FGF2 | fibroblast growth factor 2 | |
|
2 | 4 | ||||||
| MIRT229356 | ZNF449 | zinc finger protein 449 | |
|
2 | 2 | ||||||
| MIRT247139 | WEE1 | WEE1 G2 checkpoint kinase | |
|
2 | 4 | ||||||
| MIRT249464 | ZNF691 | zinc finger protein 691 | |
|
2 | 4 | ||||||
| MIRT256318 | CDC42SE2 | CDC42 small effector 2 | |
|
2 | 2 | ||||||
| MIRT258420 | WIPI2 | WD repeat domain, phosphoinositide interacting 2 | |
|
2 | 2 | ||||||
| MIRT265085 | CHEK1 | checkpoint kinase 1 | |
|
2 | 2 | ||||||
| MIRT270562 | SETD1B | SET domain containing 1B | |
|
2 | 2 | ||||||
| MIRT274751 | RAB3IP | RAB3A interacting protein | |
|
2 | 2 | ||||||
| MIRT277517 | PPP2R5C | protein phosphatase 2 regulatory subunit B'gamma | |
|
2 | 4 | ||||||
| MIRT289644 | CBX2 | chromobox 2 | |
|
2 | 2 | ||||||
| MIRT301002 | MTMR3 | myotubularin related protein 3 | |
|
2 | 2 | ||||||
| MIRT307150 | CTDSPL | CTD small phosphatase like | |
|
2 | 4 | ||||||
| MIRT309026 | USP53 | ubiquitin specific peptidase 53 | |
|
2 | 2 | ||||||
| MIRT314102 | PIK3R1 | phosphoinositide-3-kinase regulatory subunit 1 | |
|
2 | 8 | ||||||
| MIRT319339 | CAPZA2 | capping actin protein of muscle Z-line alpha subunit 2 | |
|
2 | 2 | ||||||
| MIRT320624 | ZNRF2 | zinc and ring finger 2 | |
|
2 | 2 | ||||||
| MIRT324286 | LURAP1L | leucine rich adaptor protein 1 like | |
|
2 | 2 | ||||||
| MIRT446497 | ASCC1 | activating signal cointegrator 1 complex subunit 1 | |
|
2 | 2 | ||||||
| MIRT448436 | TLL1 | tolloid like 1 | |
|
2 | 2 | ||||||
| MIRT461536 | ACTR3B | ARP3 actin related protein 3 homolog B | |
|
2 | 2 | ||||||
| MIRT463161 | ZNF367 | zinc finger protein 367 | |
|
2 | 10 | ||||||
| MIRT463492 | ZC3H10 | zinc finger CCCH-type containing 10 | |
|
2 | 2 | ||||||
| MIRT465153 | TSC22D2 | TSC22 domain family member 2 | |
|
2 | 2 | ||||||
| MIRT466417 | TFAP2A | transcription factor AP-2 alpha | |
|
2 | 8 | ||||||
| MIRT468277 | SFT2D2 | SFT2 domain containing 2 | |
|
2 | 2 | ||||||
| MIRT469398 | REL | REL proto-oncogene, NF-kB subunit | |
|
2 | 6 | ||||||
| MIRT471940 | NR6A1 | nuclear receptor subfamily 6 group A member 1 | |
|
2 | 2 | ||||||
| MIRT473687 | MAPK8 | mitogen-activated protein kinase 8 | |
|
2 | 4 | ||||||
| MIRT479617 | CDC25A | cell division cycle 25A | |
|
2 | 2 | ||||||
| MIRT482097 | AKT3 | AKT serine/threonine kinase 3 | |
|
2 | 4 | ||||||
| MIRT483994 | ATAD5 | ATPase family, AAA domain containing 5 | |
|
2 | 12 | ||||||
| MIRT485204 | PRKAR2A | protein kinase cAMP-dependent type II regulatory subunit alpha | |
|
2 | 8 | ||||||
| MIRT498762 | C3orf38 | chromosome 3 open reading frame 38 | |
|
2 | 8 | ||||||
| MIRT498960 | ORC4 | origin recognition complex subunit 4 | |
|
2 | 8 | ||||||
| MIRT499439 | ODF2L | outer dense fiber of sperm tails 2 like | |
|
2 | 8 | ||||||
| MIRT500079 | L2HGDH | L-2-hydroxyglutarate dehydrogenase | |
|
2 | 8 | ||||||
| MIRT500303 | ZNF622 | zinc finger protein 622 | |
|
2 | 8 | ||||||
| MIRT500409 | ZMAT3 | zinc finger matrin-type 3 | |
|
2 | 8 | ||||||
| MIRT500788 | TLK1 | tousled like kinase 1 | |
|
2 | 6 | ||||||
| MIRT500929 | SRPR | SRP receptor alpha subunit | |
|
2 | 6 | ||||||
| MIRT500942 | SREK1 | splicing regulatory glutamic acid and lysine rich protein 1 | |
|
2 | 8 | ||||||
| MIRT501067 | SMAD7 | SMAD family member 7 | |
|
2 | 8 | ||||||
| MIRT501710 | PARD6B | par-6 family cell polarity regulator beta | |
|
2 | 2 | ||||||
| MIRT502626 | DDX3X | DEAD-box helicase 3, X-linked | |
|
2 | 8 | ||||||
| MIRT502909 | CDCA4 | cell division cycle associated 4 | |
|
2 | 8 | ||||||
| MIRT502934 | CDC37L1 | cell division cycle 37 like 1 | |
|
2 | 8 | ||||||
| MIRT504530 | ZNF620 | zinc finger protein 620 | |
|
2 | 6 | ||||||
| MIRT505105 | YTHDC1 | YTH domain containing 1 | |
|
2 | 6 | ||||||
| MIRT505336 | TMEM245 | transmembrane protein 245 | |
|
2 | 6 | ||||||
| MIRT505382 | TMEM100 | transmembrane protein 100 | |
|
2 | 2 | ||||||
| MIRT505677 | SESTD1 | SEC14 and spectrin domain containing 1 | |
|
2 | 6 | ||||||
| MIRT506156 | PLAG1 | PLAG1 zinc finger | |
|
2 | 8 | ||||||
| MIRT506182 | PHKA1 | phosphorylase kinase regulatory subunit alpha 1 | |
|
2 | 6 | ||||||
| MIRT506474 | MYO5A | myosin VA | |
|
2 | 6 | ||||||
| MIRT506825 | KIF23 | kinesin family member 23 | |
|
2 | 6 | ||||||
| MIRT507159 | GAS2L3 | growth arrest specific 2 like 3 | |
|
2 | 2 | ||||||
| MIRT507510 | DYNLL2 | dynein light chain LC8-type 2 | |
|
2 | 4 | ||||||
| MIRT507844 | CCNE2 | cyclin E2 | |
|
2 | 6 | ||||||
| MIRT510402 | ZNF507 | zinc finger protein 507 | |
|
2 | 2 | ||||||
| MIRT518077 | TRIM35 | tripartite motif containing 35 | |
|
2 | 2 | ||||||
| MIRT518981 | NNT | nicotinamide nucleotide transhydrogenase | |
|
2 | 4 | ||||||
| MIRT521044 | SLC2A3 | solute carrier family 2 member 3 | |
|
2 | 4 | ||||||
| MIRT521189 | SBNO1 | strawberry notch homolog 1 | |
|
2 | 6 | ||||||
| MIRT522087 | NUFIP2 | NUFIP2, FMR1 interacting protein 2 | |
|
2 | 4 | ||||||
| MIRT524845 | ARPP19 | cAMP regulated phosphoprotein 19 | |
|
2 | 2 | ||||||
| MIRT527786 | TMEM44 | transmembrane protein 44 | |
|
2 | 4 | ||||||
| MIRT537802 | EFNB2 | ephrin B2 | |
|
2 | 4 | ||||||
| MIRT540829 | GNAT1 | G protein subunit alpha transducin 1 | |
|
2 | 4 | ||||||
| MIRT541139 | PISD | phosphatidylserine decarboxylase | |
|
2 | 2 | ||||||
| MIRT541418 | CBX4 | chromobox 4 | |
|
2 | 2 | ||||||
| MIRT543516 | PRSS21 | protease, serine 21 | |
|
2 | 2 | ||||||
| MIRT543823 | GSG1 | germ cell associated 1 | |
|
2 | 2 | ||||||
| MIRT544958 | UGT2B4 | UDP glucuronosyltransferase family 2 member B4 | |
|
2 | 2 | ||||||
| MIRT545178 | MAP4K2 | mitogen-activated protein kinase kinase kinase kinase 2 | |
|
2 | 4 | ||||||
| MIRT545333 | CCDC83 | coiled-coil domain containing 83 | |
|
2 | 2 | ||||||
| MIRT545517 | RSL24D1 | ribosomal L24 domain containing 1 | |
|
2 | 2 | ||||||
| MIRT545668 | DECR1 | 2,4-dienoyl-CoA reductase 1 | |
|
2 | 2 | ||||||
| MIRT545930 | ZBTB44 | zinc finger and BTB domain containing 44 | |
|
2 | 4 | ||||||
| MIRT546101 | USP48 | ubiquitin specific peptidase 48 | |
|
2 | 4 | ||||||
| MIRT546597 | SALL1 | spalt like transcription factor 1 | |
|
2 | 4 | ||||||
| MIRT546625 | RTN4 | reticulon 4 | |
|
2 | 2 | ||||||
| MIRT547650 | KPNA3 | karyopherin subunit alpha 3 | |
|
2 | 2 | ||||||
| MIRT547986 | HCFC2 | host cell factor C2 | |
|
2 | 4 | ||||||
| MIRT548716 | CRK | CRK proto-oncogene, adaptor protein | |
|
2 | 2 | ||||||
| MIRT548930 | CDK17 | cyclin dependent kinase 17 | |
|
2 | 2 | ||||||
| MIRT549066 | CACUL1 | CDK2 associated cullin domain 1 | |
|
2 | 2 | ||||||
| MIRT549265 | ASH1L | ASH1 like histone lysine methyltransferase | |
|
2 | 2 | ||||||
| MIRT550458 | OSCAR | osteoclast associated, immunoglobulin-like receptor | |
|
2 | 4 | ||||||
| MIRT550805 | FAM229B | family with sequence similarity 229 member B | |
|
2 | 2 | ||||||
| MIRT552023 | DNAJC10 | DnaJ heat shock protein family (Hsp40) member C10 | |
|
2 | 2 | ||||||
| MIRT552333 | ZNF704 | zinc finger protein 704 | |
|
2 | 2 | ||||||
| MIRT552731 | YRDC | yrdC N6-threonylcarbamoyltransferase domain containing | |
|
2 | 2 | ||||||
| MIRT553794 | SZRD1 | SUZ RNA binding domain containing 1 | |
|
2 | 4 | ||||||
| MIRT554693 | RNF149 | ring finger protein 149 | |
|
2 | 2 | ||||||
| MIRT555131 | PTPRD | protein tyrosine phosphatase, receptor type D | |
|
2 | 2 | ||||||
| MIRT555263 | PRDM4 | PR/SET domain 4 | |
|
2 | 2 | ||||||
| MIRT556847 | KANK1 | KN motif and ankyrin repeat domains 1 | |
|
2 | 4 | ||||||
| MIRT557473 | GPR27 | G protein-coupled receptor 27 | |
|
2 | 4 | ||||||
| MIRT558017 | EXT1 | exostosin glycosyltransferase 1 | |
|
2 | 2 | ||||||
| MIRT558497 | CYP26B1 | cytochrome P450 family 26 subfamily B member 1 | |
|
2 | 4 | ||||||
| MIRT558578 | CREBL2 | cAMP responsive element binding protein like 2 | |
|
2 | 4 | ||||||
| MIRT558609 | COX6B1 | cytochrome c oxidase subunit 6B1 | |
|
2 | 4 | ||||||
| MIRT558649 | CNKSR3 | CNKSR family member 3 | |
|
2 | 2 | ||||||
| MIRT558984 | CA8 | carbonic anhydrase 8 | |
|
2 | 2 | ||||||
| MIRT559140 | BTN3A3 | butyrophilin subfamily 3 member A3 | |
|
2 | 2 | ||||||
| MIRT559326 | ATP5G3 | ATP synthase, H+ transporting, mitochondrial Fo complex subunit C3 (subunit 9) | |
|
2 | 2 | ||||||
| MIRT562020 | LANCL1 | LanC like 1 | |
|
2 | 2 | ||||||
| MIRT562868 | KIAA1456 | KIAA1456 | |
|
2 | 2 | ||||||
| MIRT563073 | SLC25A12 | solute carrier family 25 member 12 | |
|
2 | 2 | ||||||
| MIRT563495 | DLGAP3 | DLG associated protein 3 | |
|
2 | 2 | ||||||
| MIRT563889 | RAPH1 | Ras association (RalGDS/AF-6) and pleckstrin homology domains 1 | |
|
2 | 2 | ||||||
| MIRT564310 | CCNT1 | cyclin T1 | |
|
2 | 2 | ||||||
| MIRT564941 | XKR7 | XK related 7 | |
|
2 | 2 | ||||||
| MIRT564978 | WNK3 | WNK lysine deficient protein kinase 3 | |
|
2 | 2 | ||||||
| MIRT565422 | TEF | TEF, PAR bZIP transcription factor | |
|
2 | 2 | ||||||
| MIRT566823 | MAP3K7 | mitogen-activated protein kinase kinase kinase 7 | |
|
2 | 2 | ||||||
| MIRT571960 | KIF5B | kinesin family member 5B | |
|
2 | 2 | ||||||
| MIRT575876 | Cask | calcium/calmodulin-dependent serine protein kinase (MAGUK family) | |
|
2 | 3 | ||||||
| MIRT576522 | Txlna | taxilin alpha | |
|
2 | 2 | ||||||
| MIRT614692 | TRAK1 | trafficking kinesin protein 1 | |
|
2 | 2 | ||||||
| MIRT616064 | ZC3H14 | zinc finger CCCH-type containing 14 | |
|
2 | 2 | ||||||
| MIRT618837 | ASAH2B | N-acylsphingosine amidohydrolase 2B | |
|
2 | 2 | ||||||
| MIRT624625 | ATXN2 | ataxin 2 | |
|
2 | 2 | ||||||
| MIRT624651 | ASAH2 | N-acylsphingosine amidohydrolase 2 | |
|
2 | 2 | ||||||
| MIRT640313 | MMAB | methylmalonic aciduria (cobalamin deficiency) cblB type | |
|
2 | 2 | ||||||
| MIRT659247 | CUL3 | cullin 3 | |
|
2 | 2 | ||||||
| MIRT680971 | DCAF17 | DDB1 and CUL4 associated factor 17 | |
|
2 | 2 | ||||||
| MIRT682260 | RS1 | retinoschisin 1 | |
|
2 | 2 | ||||||
| MIRT682504 | GLP2R | glucagon like peptide 2 receptor | |
|
2 | 2 | ||||||
| MIRT693903 | HNRNPA1L2 | heterogeneous nuclear ribonucleoprotein A1-like 2 | |
|
2 | 2 | ||||||
| MIRT699213 | SLCO3A1 | solute carrier organic anion transporter family member 3A1 | |
|
2 | 2 | ||||||
| MIRT699372 | SLC30A6 | solute carrier family 30 member 6 | |
|
2 | 2 | ||||||
| MIRT699450 | SLC16A9 | solute carrier family 16 member 9 | |
|
2 | 2 | ||||||
| MIRT701229 | OCRL | OCRL, inositol polyphosphate-5-phosphatase | |
|
2 | 2 | ||||||
| MIRT702848 | HNRNPA1 | heterogeneous nuclear ribonucleoprotein A1 | |
|
2 | 2 | ||||||
| MIRT706162 | CASK | calcium/calmodulin dependent serine protein kinase | |
|
2 | 3 | ||||||
| MIRT718989 | UTP15 | UTP15, small subunit processome component | |
|
2 | 2 | ||||||
| MIRT755921 | ALDH1A3 | aldehyde dehydrogenase 1 family member A3 | 1 | 1 | ||||||||