| pre-miRNA Information | |
|---|---|
| pre-miRNA | hsa-mir-548t |
| Genomic Coordinates | chr4: 173268160 - 173268233 |
| Description | Homo sapiens miR-548t stem-loop |
| Comment | None |
| RNA Secondary Structure |  |
| Mature miRNA Information | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mature miRNA | hsa-miR-548t-3p | |||||||||||||||||||||||||||||||||||
| Sequence | 46| AAAAACCACAAUUACUUUUGCACCA |70 | |||||||||||||||||||||||||||||||||||
| Evidence | Not_experimental | |||||||||||||||||||||||||||||||||||
| Experiments | ||||||||||||||||||||||||||||||||||||
| Editing Events in miRNAs |
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| SNPs in miRNA |
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| Putative Targets | ||||||||||||||||||||||||||||||||||||
| Gene Information | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene Symbol | AKAP11 | ||||||||||||||||||||
| Synonyms | AKAP-11, AKAP220, PPP1R44, PRKA11 | ||||||||||||||||||||
| Description | A-kinase anchoring protein 11 | ||||||||||||||||||||
| Transcript | NM_016248 | ||||||||||||||||||||
| Expression | |||||||||||||||||||||
| Putative miRNA Targets on AKAP11 | |||||||||||||||||||||
| 3'UTR of AKAP11 (miRNA target sites are highlighted) |
>AKAP11|NM_016248|3'UTR 1 AGCAAACCCCAAACCAGTATATTTTAGTATTTGTTTGGGGAGGGGAACAAGCCAATAAAGATGTTTAGGATAAAATTTGA 81 ATAGTGAATATTAACATCGTAAGTCAGTTGGGAGGCAAGTAAATATAGCTTTCTGAGCGCTTTGTGTTATCACTCGGTGT 161 ATATAGTTCATACTTTTGTAATCTGTCAAAATACTACCTTCATTTATTCTTCTATACACATGTGTAGTGTGTCAAGACCC 241 TAAGAACATGTATTTGAAGGAAGGTCTAACCAGGGGGTTTTCAGGGGCATTGTCTGACCACATTCTTTTTGTATCCAAAT 321 AGTGCTGCTAGAAACTGCACTGAAGTGGCTGAGGATAGGTTCCAGTGATAGAGTTATAATTTTGCTCCTTTGCAAACAAA 401 TGGTATCTAATTAATAACTAGTCTGACATCAGAAAATAAAATTGAGGCTGATTTTTAAAAATTTCTAGTAGATTTTTGGC 481 CTTTCCTGTTTTTAAAAATCAGTTTCATTTTCATATTTCATAGATCAGCTATTGGTAGCTTTTTGATTTCCCCAAACTAT 561 TTAATTTCTTAGCAGAAACATTAGTATTTTAGGTTTCTATAAACACTATAAGTGATAGTTTCCCCCATCCTTTCATTGAC 641 ATTATTTGCCAATGCTGCCAGTCATTCTGGCATGAAAGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 721 GTAAGGGAGTACTTTAACCTTGCCAGTTTGTTCCCTCTTTTATTTTACTGTTTTCTTTTTAGAAACCCACTGTTAAAATT 801 TAAAAAGGTGCTTTAAAATAAAACGCCTATAAAGATTGTGCAGTAAGAATTTTTATTGACAATAATTAAAATTTTTTTTG 881 ACAATTTTGGGTTCCCAACTTATCTTACAAGTGAAAACTTAAATTGTAAAACATGTTGAAATTTTAAAAATTAATGTTAA 961 TATGGAAATGCATTTAGAGAAGCCCAGTAGTTTTTATTGTTGGATTTTTGAAAAAACCTCTACCAAGAATGTGGTGTTTT 1041 TTTTGTTTGTTTGTTTGTTTGTTTTAGAAAAATTGGGATTTCCCCCCACCCCGCCCCACCCAGATAAACTATATCTACAC 1121 TGTCTCGTCAAGTTCTCTGACACGATCTTTCTGGGCTCTACATTTCCTACTAGTTTGTGTCCAGAAACTGCAAGTTGACA 1201 TGAATAGAGGACAAAGGTTGTGTCTTGCTTTTGTCTCTCTCTTCCCTCCCTGCAACTCTCTCTCCCCTCCTCCCACTCTC 1281 TTCCCCCTCCCCCCTCCTCCCACTGTCTCTCACCTCCCCCACCCCCCACTCTCTCTCATCTCTCGCTGTGTCCTGTGTAT 1361 GTGTGGGTGTGTGTGTATTTGGGTGTGTAAATGTTGGTTCTTCCACTACTGGATTTTGTAATCTAGGATAAATCACTTTT 1441 TTTGGGGACTTTGATTTTGCTCCATTACGTTTTCATTTTTTCTGAGCACTGACTGTTCTGAAAGCTGCACAAAACGTAGA 1521 AAGAAGACATAGCGCCTGCCAGGGAATAGGAAATGAGGGCACTTACACATTAATGTGAATTAGTAATTGTGGTATAGAAA 1601 TGTTTTATAGTGAAAGATTCAAATTTGCTTTTCAAGAAAAATGCCAAAAGCTATTTAAATAATTCGAGGTTACATCGTAG 1681 GTTTTGATTTTTCTCAATTTAAGATACAGAAATACAGCAAGCCTTAATATAAAGTTTCCTAAAGTTTCTTCAAGTATTTT 1761 TTAAGGTGGAGAAATGCAGGAATTGTATAACCAGAATTGTTCCTGCCTTTAGCTTTTCAGAACTTGAGATGTGGCAGCAC 1841 TGGACTGGGTTTTTTTAAATGTTAGGACTAGGAATGTTTGCTCTTGTTAATTATGAATTAATTGATTATTAAGTTTAGAA 1921 TGCATTTTTACAAGTATCTAACTATCAAATTGTGTTTAGTAACTTGAGTGTATGCACAAGTTTGATCAACAGCAAAATAG 2001 AGTTCTGAATTTCTTTTAAAGTGATGATATATTATTTTGTGAAACTTTGTGTTTGAAAATGTTTATTTCTGTTTATGGTG 2081 TAATCATTCTGAGGTGAGGCTTTTCTTATTTCCTTTGCATTTTGCTAGAGCTGTGCTGAGTTCAGCATTTGCTTATTTAA 2161 CCACTACATAATGACAGACCAGTTATTAGGTATTAGCATGTGTGGTAATAATAATAGTGGAACTTCACACTTACATCAAT 2241 TCAGTGCAGGGGCATAGAATAAAATATTAAATATTGGCAGATGTATGAAAAGAAGTGTGAGTTAAAAATATTGAATATTG 2321 GCAGGTGTGAAAACAAGTGTCAAAATTCCTCATATAGAGAAAATAATTTTGAGTTTAGAGTATTATCTTTTAATTAAGTG 2401 TAGTCTAAACTTAACTTTCTGTAAAGGCACTTTGTGGTTTTTCCAAAGATGTTCTAGATCTATTTGGTTGCTCTATAGTC 2481 AAACAGCTCTTTTGAAGACAACTGTCTTATTTTATTACAAATTGGCTTGACATATTTATACTGTAACATTGTAATATTGC 2561 TGTGCTGTACATTTTGGCCCTTACGAAATACGTCTTTTTCAGAACTGTTAAAGTTTTGATGTACATCGAGCTGAATTCTG 2641 TTTTTACCAGTTTCAAAACCTTCAAGTGATATGTGGAAAAAAGTGAATGAGACCTCTGATAGGGGGTTTTCAGAACCTTG 2721 TTCACACCAAAATGTGACAGTTCTTTCATGTTTTCCTAAACCAAGTTAAAATTACATGTATATTTTGGTGTTAAGGTTGA 2801 TTTTTAAGATACTTCTGATTTGTACAAAAGGAATGTTTCCTTTATAAATCACAGAAGAAAATGACAATATCTGTTGGATA 2881 TTTGATATAATTTAATGGTGTTATAAAACCTTTAAGAGGATTCATGGTGAATATATGTGATAACATCTTTATACTTTGAA 2961 AAATGTTCCACTTACCCTTCAGATATTTGTTGTAAGTTAATTCAATTCTTAATACTTTAATTTTGCTCCAACAAGGGCTT 3041 TATGTTGCTGGTAAGAGAATTTATTTACTAAATGCACTATGTATAAAGTGAAAGATAGTTTACTTATCTGACTTTGATAT 3121 TAGATGGCTGACATTAGTGCACATAATGCAGAGTTTAACCTTGATTCTTCAACAGAGTCCAGATTTAAATGTCTACTTAG 3201 TTAATTAGTTAGCTGATATTCTTCCACAATTAATATATTCAATTTCCCATCAGTATATCACTTTAAATTTTATGTTTTTC 3281 TAAGGAAACTTTCCACAGAATTTTAAACAACTGATGCATCCATACTCAGGGTGTAGGGAGAATACTTTGCATTTAAAAAC 3361 CCTGTCCACCTGTCACCAGCACAAGAGAATTAGAGCTTCAGTGAGAATTTAGAAAAATTATACTAAAGTGAGATGCATTT 3441 TTTCTCATTTTCAGCAAGACTCCTCTAAGCATTTACTCATTTACTGTATTCCTGCTCTGAAGATGTGGATACAGAATTAG 3521 TCACTCTTGTCACTTTATTTATTTATTGGTTTTTTTTTAACCATCTGTGTACATTCCTTTCATAGGGTAGAGTTCTAGTT 3601 CTAGAAGTTCTTATTTTGTTTTTGTTGTAATGTTTGAATACTATTTAATATCCGGTTTTAATATTGCTGGATTTGCTACC 3681 TTTGGTTACTTGTGCAGTGTTAAAAGTAATCCACTTTCTTGTTTAATATACCAGATACATAGCAAAAGCAGCTTGGAATA 3761 ATTATAGCTGTTTATTTGGCTGTGCTCAGTTACTATATTAAGATCTTGTACTGTGTAACAGTAACTCTTTTTTGCTTTTC 3841 AGTAATTTAATATGTTCACTTAACAAAATACGAACTTTGAGATGCACTAAAGTTTTGTTTCAGCAGTGGCTCAAAAAATT 3921 TCAGAAATTACTTTTGTAATTATTTGCAATTAATTGTTCTTTTATCTTACAATTGTTTAAGCCTGTGATCTTTCTTCTCC 4001 CAGCTAAGAGTTCTTCAATAAATTTAAGAAATACCTGGTAAAAAA 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
... - 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 | 11215.0 |
| 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
... - 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 | 11215.0 |
| 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 | 11215.0 |
| 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 GSM1065668. 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 | C8166 |
| 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 GSM1462572. RNA binding protein: AGO2. Condition:C8166 NL4-3
... - 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 | HCT116 |
| 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 ERX177615. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_3_5
PAR-CLIP data was present in ERX177603. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_2_5
PAR-CLIP data was present in ERX177627. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_4_5
... - Krell J; Stebbing J; Carissimi C; Dabrowska et al., 2016, Genome research. |
| Article |
- Krell J; Stebbing J; Carissimi C; Dabrowska et al. - Genome research, 2016
DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.
LinkOut: [PMID: 26701625]
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| CLIP-seq Support 1 for dataset GSM714642 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO2 |
| Cell line / Condition | HEK293 / completeT1, repA |
| Location of target site | ENST00000025301.2 | 3UTR | AAUUAGUCACUCUUGUCACUUUAUUUAUUUAUUG |
| 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 | ENST00000025301.2 | 3UTR | UCACUCUUGUCACUUUAUUUAUUUAUU |
| 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 SRR359787 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | hESCs (WA-09) / 4-thiouridine, RNase T1 |
| Location of target site | ENST00000025301.2 | 3UTR | UCACUCUUGUCACUUUAUUUAUUUAUUG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 22012620 / SRX103431 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 4 for dataset GSM1065668 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO1 |
| Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_7 |
| Location of target site | ENST00000025301.2 | 3UTR | UCACUCUUGUCACUUUAUUUAUUUAUU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 23446348 / GSE43573 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 5 for dataset GSM1065670 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | HEK293 / 4-thiouridine, 3_ML_LG |
| Location of target site | ENST00000025301.2 | 3UTR | UCACUCUUGUCACUUUAUUUAUUUAUUG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 23446348 / GSE43573 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 6 for dataset GSM1462572 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | C8166 / C8166 NL4-3 |
| Location of target site | ENST00000025301.2 | 3UTR | UCACUCUUGUCACUUUAUUUAUUUAUUG |
| 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) | |||||||
|---|---|---|---|---|---|---|---|
|
168 hsa-miR-548t-3p Target Genes:
Functional analysis:
ID |
Target | Description | Validation methods |
 |
 |
|||||||
| Strong evidence | Less strong evidence | |||||||||||
 |
 |
 |
 |
 |
 |
 |
 |
|||||
| MIRT059365 | ANP32E | acidic nuclear phosphoprotein 32 family member E |  |
|
2 | 2 | ||||||
| MIRT072839 | ARIH1 | ariadne RBR E3 ubiquitin protein ligase 1 | |
|
2 | 6 | ||||||
| MIRT076945 | PCGF2 | polycomb group ring finger 2 | |
|
2 | 6 | ||||||
| MIRT083941 | TFAP2C | transcription factor AP-2 gamma | |
|
2 | 2 | ||||||
| MIRT085401 | ETS2 | ETS proto-oncogene 2, transcription factor | |
|
2 | 2 | ||||||
| MIRT109790 | KLHL15 | kelch like family member 15 | |
|
2 | 2 | ||||||
| MIRT114046 | AKAP11 | A-kinase anchoring protein 11 | |
|
2 | 10 | ||||||
| MIRT130165 | TXNIP | thioredoxin interacting protein | |
|
2 | 6 | ||||||
| MIRT150013 | MIDN | midnolin | |
|
2 | 2 | ||||||
| MIRT181258 | ASH1L | ASH1 like histone lysine methyltransferase | |
|
2 | 2 | ||||||
| MIRT205594 | NCL | nucleolin | |
|
2 | 2 | ||||||
| MIRT222253 | ACTB | actin beta | |
|
2 | 4 | ||||||
| MIRT245653 | EIF5AL1 | eukaryotic translation initiation factor 5A-like 1 | |
|
2 | 4 | ||||||
| MIRT250947 | CDK5R1 | cyclin dependent kinase 5 regulatory subunit 1 | |
|
2 | 4 | ||||||
| MIRT252497 | NWD1 | NACHT and WD repeat domain containing 1 | |
|
2 | 2 | ||||||
| MIRT271990 | ARF1 | ADP ribosylation factor 1 | |
|
2 | 4 | ||||||
| MIRT280804 | RNF11 | ring finger protein 11 | |
|
2 | 2 | ||||||
| MIRT293803 | FEM1A | fem-1 homolog A | |
|
2 | 2 | ||||||
| MIRT318231 | RREB1 | ras responsive element binding protein 1 | |
|
2 | 2 | ||||||
| MIRT341455 | ATP6V0B | ATPase H+ transporting V0 subunit b | |
|
2 | 2 | ||||||
| MIRT347413 | CEBPG | CCAAT/enhancer binding protein gamma | |
|
2 | 4 | ||||||
| MIRT351860 | PLEKHA3 | pleckstrin homology domain containing A3 | |
|
2 | 2 | ||||||
| MIRT357983 | GRPEL2 | GrpE like 2, mitochondrial | |
|
2 | 2 | ||||||
| MIRT377094 | PPP1CB | protein phosphatase 1 catalytic subunit beta | |
|
2 | 2 | ||||||
| MIRT407303 | IGFBP5 | insulin like growth factor binding protein 5 | |
|
2 | 2 | ||||||
| MIRT441564 | LMOD3 | leiomodin 3 | |
|
2 | 2 | ||||||
| MIRT442364 | ZC3H12C | zinc finger CCCH-type containing 12C | |
|
2 | 2 | ||||||
| MIRT443228 | ARL5B | ADP ribosylation factor like GTPase 5B | |
|
2 | 2 | ||||||
| MIRT443404 | HMX3 | H6 family homeobox 3 | |
|
2 | 2 | ||||||
| MIRT446055 | NR5A2 | nuclear receptor subfamily 5 group A member 2 | |
|
2 | 2 | ||||||
| MIRT448277 | ZNF652 | zinc finger protein 652 | |
|
2 | 2 | ||||||
| MIRT450822 | KCNB1 | potassium voltage-gated channel subfamily B member 1 | |
|
2 | 2 | ||||||
| MIRT453016 | CCDC115 | coiled-coil domain containing 115 | |
|
2 | 17 | ||||||
| MIRT454463 | PPP2R2B | protein phosphatase 2 regulatory subunit Bbeta | |
|
2 | 2 | ||||||
| MIRT456360 | CITED2 | Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 2 | |
|
2 | 2 | ||||||
| MIRT460007 | DNALI1 | dynein axonemal light intermediate chain 1 | |
|
2 | 2 | ||||||
| MIRT463154 | ZNF385A | zinc finger protein 385A | |
|
2 | 6 | ||||||
| MIRT463766 | YPEL2 | yippee like 2 | |
|
2 | 2 | ||||||
| MIRT468310 | SFT2D2 | SFT2 domain containing 2 | |
|
2 | 2 | ||||||
| MIRT470668 | POLR2D | RNA polymerase II subunit D | |
|
2 | 4 | ||||||
| MIRT478517 | CTTN | cortactin | |
|
2 | 2 | ||||||
| MIRT480507 | C11orf57 | chromosome 11 open reading frame 57 | |
|
2 | 2 | ||||||
| MIRT484718 | INHBA | inhibin beta A subunit | |
|
2 | 12 | ||||||
| MIRT485494 | HMGN2 | high mobility group nucleosomal binding domain 2 | |
|
2 | 2 | ||||||
| MIRT487302 | SLC38A9 | solute carrier family 38 member 9 | |
|
2 | 2 | ||||||
| MIRT487771 | ANKEF1 | ankyrin repeat and EF-hand domain containing 1 | |
|
2 | 16 | ||||||
| MIRT491876 | YWHAZ | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta | |
|
2 | 2 | ||||||
| MIRT494304 | CEP120 | centrosomal protein 120 | |
|
2 | 2 | ||||||
| MIRT495396 | TRIM24 | tripartite motif containing 24 | |
|
2 | 2 | ||||||
| MIRT495646 | CDK1 | cyclin dependent kinase 1 | |
|
2 | 2 | ||||||
| MIRT496665 | TMEM237 | transmembrane protein 237 | |
|
2 | 2 | ||||||
| MIRT496837 | ZNF460 | zinc finger protein 460 | |
|
2 | 2 | ||||||
| MIRT498638 | CHD4 | chromodomain helicase DNA binding protein 4 | |
|
2 | 10 | ||||||
| MIRT503928 | FBXL13 | F-box and leucine rich repeat protein 13 | |
|
2 | 4 | ||||||
| MIRT506063 | PPP2R2A | protein phosphatase 2 regulatory subunit Balpha | |
|
2 | 2 | ||||||
| MIRT506582 | MIER3 | MIER family member 3 | |
|
2 | 4 | ||||||
| MIRT506606 | MAT2A | methionine adenosyltransferase 2A | |
|
2 | 4 | ||||||
| MIRT506844 | KIF23 | kinesin family member 23 | |
|
2 | 6 | ||||||
| MIRT508536 | RPP14 | ribonuclease P/MRP subunit p14 | |
|
2 | 4 | ||||||
| MIRT509669 | ZNF354B | zinc finger protein 354B | |
|
2 | 10 | ||||||
| MIRT511170 | MBNL3 | muscleblind like splicing regulator 3 | |
|
2 | 6 | ||||||
| MIRT512147 | COX6B1 | cytochrome c oxidase subunit 6B1 | |
|
2 | 2 | ||||||
| MIRT512831 | ID4 | inhibitor of DNA binding 4, HLH protein | |
|
2 | 6 | ||||||
| MIRT514558 | XRCC3 | X-ray repair cross complementing 3 | |
|
2 | 4 | ||||||
| MIRT515856 | AJAP1 | adherens junctions associated protein 1 | |
|
2 | 4 | ||||||
| MIRT521848 | PNISR | PNN interacting serine and arginine rich protein | |
|
2 | 4 | ||||||
| MIRT525364 | SYNM | synemin | |
|
2 | 2 | ||||||
| MIRT527120 | ARHGAP15 | Rho GTPase activating protein 15 | |
|
2 | 2 | ||||||
| MIRT527271 | FBLN2 | fibulin 2 | |
|
2 | 2 | ||||||
| MIRT527439 | COL4A3 | collagen type IV alpha 3 chain | |
|
2 | 2 | ||||||
| MIRT527658 | CD300E | CD300e molecule | |
|
2 | 2 | ||||||
| MIRT528334 | TBC1D22B | TBC1 domain family member 22B | |
|
2 | 2 | ||||||
| MIRT529033 | EXOC8 | exocyst complex component 8 | |
|
2 | 2 | ||||||
| MIRT529321 | PDE5A | phosphodiesterase 5A | |
|
2 | 2 | ||||||
| MIRT529677 | TRPV2 | transient receptor potential cation channel subfamily V member 2 | |
|
2 | 2 | ||||||
| MIRT529846 | SMTN | smoothelin | |
|
2 | 2 | ||||||
| MIRT530385 | ZNF431 | zinc finger protein 431 | |
|
2 | 2 | ||||||
| MIRT530913 | GPR85 | G protein-coupled receptor 85 | |
|
2 | 2 | ||||||
| MIRT531794 | KDR | kinase insert domain receptor | |
|
2 | 2 | ||||||
| MIRT532246 | KLF2 | Kruppel like factor 2 | |
|
2 | 4 | ||||||
| MIRT532658 | CBX7 | chromobox 7 | |
|
2 | 2 | ||||||
| MIRT533630 | TMX3 | thioredoxin related transmembrane protein 3 | |
|
2 | 2 | ||||||
| MIRT534811 | RAB33B | RAB33B, member RAS oncogene family | |
|
2 | 2 | ||||||
| MIRT534975 | PSD3 | pleckstrin and Sec7 domain containing 3 | |
|
2 | 2 | ||||||
| MIRT536588 | ITPKB | inositol-trisphosphate 3-kinase B | |
|
2 | 2 | ||||||
| MIRT536779 | HNRNPD | heterogeneous nuclear ribonucleoprotein D | |
|
2 | 2 | ||||||
| MIRT538764 | CABLES1 | Cdk5 and Abl enzyme substrate 1 | |
|
2 | 2 | ||||||
| MIRT539294 | ANGEL2 | angel homolog 2 | |
|
2 | 2 | ||||||
| MIRT539621 | SHISA9 | shisa family member 9 | |
|
2 | 2 | ||||||
| MIRT539651 | BUB1 | BUB1 mitotic checkpoint serine/threonine kinase | |
|
2 | 2 | ||||||
| MIRT540347 | OPHN1 | oligophrenin 1 | |
|
2 | 2 | ||||||
| MIRT540413 | PITPNC1 | phosphatidylinositol transfer protein, cytoplasmic 1 | |
|
2 | 2 | ||||||
| MIRT541396 | CDC27 | cell division cycle 27 | |
|
2 | 2 | ||||||
| MIRT542916 | HSBP1 | heat shock factor binding protein 1 | |
|
2 | 2 | ||||||
| MIRT544710 | EIF5A | eukaryotic translation initiation factor 5A | |
|
2 | 4 | ||||||
| MIRT544998 | MFF | mitochondrial fission factor | |
|
2 | 4 | ||||||
| MIRT553289 | TSPAN3 | tetraspanin 3 | |
|
2 | 2 | ||||||
| MIRT553455 | TNRC6C | trinucleotide repeat containing 6C | |
|
2 | 2 | ||||||
| MIRT553782 | TAF13 | TATA-box binding protein associated factor 13 | |
|
2 | 2 | ||||||
| MIRT554656 | ROBO1 | roundabout guidance receptor 1 | |
|
2 | 2 | ||||||
| MIRT555104 | PURB | purine rich element binding protein B | |
|
2 | 2 | ||||||
| MIRT557235 | HNRNPA1 | heterogeneous nuclear ribonucleoprotein A1 | |
|
2 | 2 | ||||||
| MIRT560861 | GAL3ST3 | galactose-3-O-sulfotransferase 3 | |
|
2 | 2 | ||||||
| MIRT561545 | SON | SON DNA binding protein | |
|
2 | 2 | ||||||
| MIRT561554 | SLMO2 | PRELI domain containing 3B | |
|
2 | 2 | ||||||
| MIRT563764 | ZNF678 | zinc finger protein 678 | |
|
2 | 2 | ||||||
| MIRT565653 | SIX4 | SIX homeobox 4 | |
|
2 | 2 | ||||||
| MIRT568080 | CELF2 | CUGBP Elav-like family member 2 | |
|
2 | 2 | ||||||
| MIRT568759 | MYBL1 | MYB proto-oncogene like 1 | |
|
2 | 2 | ||||||
| MIRT569078 | CADM2 | cell adhesion molecule 2 | |
|
2 | 2 | ||||||
| MIRT569509 | THYN1 | thymocyte nuclear protein 1 | |
|
2 | 2 | ||||||
| MIRT571268 | CDKN2AIP | CDKN2A interacting protein | |
|
2 | 2 | ||||||
| MIRT571809 | PHF19 | PHD finger protein 19 | |
|
2 | 2 | ||||||
| MIRT572554 | DKK3 | dickkopf WNT signaling pathway inhibitor 3 | |
|
2 | 2 | ||||||
| MIRT573782 | SLC24A4 | solute carrier family 24 member 4 | |
|
2 | 4 | ||||||
| MIRT576441 | Ccdc115 | coiled-coil domain containing 115 | |
|
2 | 10 | ||||||
| MIRT576712 | Slc30a3 | solute carrier family 30 (zinc transporter), member 3 | |
|
2 | 3 | ||||||
| MIRT608377 | PIWIL2 | piwi like RNA-mediated gene silencing 2 | |
|
2 | 2 | ||||||
| MIRT608484 | NKTR | natural killer cell triggering receptor | |
|
2 | 6 | ||||||
| MIRT610186 | FAM49A | family with sequence similarity 49 member A | |
|
2 | 2 | ||||||
| MIRT611631 | EDIL3 | EGF like repeats and discoidin domains 3 | |
|
2 | 2 | ||||||
| MIRT613534 | TRA2B | transformer 2 beta homolog | |
|
2 | 2 | ||||||
| MIRT616221 | PTPN11 | protein tyrosine phosphatase, non-receptor type 11 | |
|
2 | 2 | ||||||
| MIRT622370 | SALL1 | spalt like transcription factor 1 | |
|
2 | 2 | ||||||
| MIRT624371 | CDK12 | cyclin dependent kinase 12 | |
|
2 | 2 | ||||||
| MIRT624995 | ZNF665 | zinc finger protein 665 | |
|
2 | 4 | ||||||
| MIRT626875 | AP3B1 | adaptor related protein complex 3 beta 1 subunit | |
|
2 | 2 | ||||||
| MIRT627737 | RAP2B | RAP2B, member of RAS oncogene family | |
|
2 | 4 | ||||||
| MIRT628490 | ADAT2 | adenosine deaminase, tRNA specific 2 | |
|
2 | 2 | ||||||
| MIRT633647 | PLEKHG7 | pleckstrin homology and RhoGEF domain containing G7 | |
|
2 | 4 | ||||||
| MIRT634028 | SLC30A3 | solute carrier family 30 member 3 | |
|
2 | 3 | ||||||
| MIRT635923 | GLTSCR2 | NOP53 ribosome biogenesis factor | |
|
2 | 2 | ||||||
| MIRT638287 | SERBP1 | SERPINE1 mRNA binding protein 1 | |
|
2 | 2 | ||||||
| MIRT641959 | RNF115 | ring finger protein 115 | |
|
2 | 2 | ||||||
| MIRT643573 | CTNNA3 | catenin alpha 3 | |
|
2 | 2 | ||||||
| MIRT645180 | NOL9 | nucleolar protein 9 | |
|
2 | 4 | ||||||
| MIRT647497 | ZNF639 | zinc finger protein 639 | |
|
2 | 2 | ||||||
| MIRT647682 | PCK1 | phosphoenolpyruvate carboxykinase 1 | |
|
2 | 2 | ||||||
| MIRT648422 | MYOZ3 | myozenin 3 | |
|
2 | 2 | ||||||
| MIRT650113 | ZCCHC9 | zinc finger CCHC-type containing 9 | |
|
2 | 2 | ||||||
| MIRT651076 | ZNF518B | zinc finger protein 518B | |
|
2 | 4 | ||||||
| MIRT651415 | ZADH2 | zinc binding alcohol dehydrogenase domain containing 2 | |
|
2 | 2 | ||||||
| MIRT651456 | XKR4 | XK related 4 | |
|
2 | 2 | ||||||
| MIRT653619 | SLC30A4 | solute carrier family 30 member 4 | |
|
2 | 2 | ||||||
| MIRT653637 | SLC30A1 | solute carrier family 30 member 1 | |
|
2 | 2 | ||||||
| MIRT654896 | POU2F1 | POU class 2 homeobox 1 | |
|
2 | 2 | ||||||
| MIRT656483 | MAP3K9 | mitogen-activated protein kinase kinase kinase 9 | |
|
2 | 2 | ||||||
| MIRT658016 | GABRA4 | gamma-aminobutyric acid type A receptor alpha4 subunit | |
|
2 | 2 | ||||||
| MIRT658041 | FZD10 | frizzled class receptor 10 | |
|
2 | 2 | ||||||
| MIRT660093 | BTBD3 | BTB domain containing 3 | |
|
2 | 2 | ||||||
| MIRT663923 | MAGEF1 | MAGE family member F1 | |
|
2 | 2 | ||||||
| MIRT665882 | TGIF2 | TGFB induced factor homeobox 2 | |
|
2 | 2 | ||||||
| MIRT669051 | CEP128 | centrosomal protein 128 | |
|
2 | 2 | ||||||
| MIRT669711 | AAGAB | alpha and gamma adaptin binding protein | |
|
2 | 2 | ||||||
| MIRT686812 | SNX2 | sorting nexin 2 | |
|
2 | 4 | ||||||
| MIRT689883 | SOD2 | superoxide dismutase 2 | |
|
2 | 2 | ||||||
| MIRT693274 | GLRX2 | glutaredoxin 2 | |
|
2 | 4 | ||||||
| MIRT697056 | BCAR1 | BCAR1, Cas family scaffolding protein | |
|
2 | 2 | ||||||
| MIRT703297 | GID4 | GID complex subunit 4 homolog | |
|
2 | 2 | ||||||
| MIRT704087 | DYRK2 | dual specificity tyrosine phosphorylation regulated kinase 2 | |
|
2 | 2 | ||||||
| MIRT707719 | CDC6 | cell division cycle 6 | |
|
2 | 2 | ||||||
| MIRT708136 | GK5 | glycerol kinase 5 (putative) | |
|
2 | 2 | ||||||
| MIRT709212 | KLHL30 | kelch like family member 30 | |
|
2 | 2 | ||||||
| MIRT710062 | RWDD2A | RWD domain containing 2A | |
|
2 | 2 | ||||||
| MIRT712770 | POU6F2 | POU class 6 homeobox 2 | |
|
2 | 2 | ||||||
| MIRT715073 | TMTC1 | transmembrane and tetratricopeptide repeat containing 1 | |
|
2 | 2 | ||||||
| MIRT715387 | TADA3 | transcriptional adaptor 3 | |
|
2 | 2 | ||||||
| MIRT717712 | NCKAP1 | NCK associated protein 1 | |
|
2 | 2 | ||||||
| miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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