| pre-miRNA Information | |
|---|---|
| pre-miRNA | hsa-mir-4650-1 |
| Genomic Coordinates | chr7: 67114322 - 67114397 |
| Description | Homo sapiens miR-4650-1 stem-loop |
| Comment | None |
| RNA Secondary Structure |  |
| pre-miRNA | hsa-mir-4650-2 |
| Genomic Coordinates | chr7: 72697903 - 72697978 |
| Description | Homo sapiens miR-4650-2 stem-loop |
| Comment | None |
| RNA Secondary Structure | |
| Mature miRNA Information | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mature miRNA | hsa-miR-4650-5p | |||||||||||||||
| Sequence | 15| UCAGGCCUCUUUCUACCUU |33 | |||||||||||||||
| Evidence | Experimental | |||||||||||||||
| Experiments | Illumina | |||||||||||||||
| SNPs in miRNA |
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| Putative Targets | ||||||||||||||||
| miRNA Expression profile | |
|---|---|
| Human miRNA Tissue Atlas | |
| Circulating MicroRNA Expression Profiling | |
| Gene Information | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene Symbol | C15orf52 | ||||||||||||||||||||
| Synonyms | - | ||||||||||||||||||||
| Description | chromosome 15 open reading frame 52 | ||||||||||||||||||||
| Transcript | NM_207380 | ||||||||||||||||||||
| Expression | |||||||||||||||||||||
| Putative miRNA Targets on C15orf52 | |||||||||||||||||||||
| 3'UTR of C15orf52 (miRNA target sites are highlighted) |
>C15orf52|NM_207380|3'UTR 1 ACACAGCTCCTGGGAGCTGGGGAGTCCCCGGGGAGAGGAAAAGGGAATCACTCTGTTAAAGGCCCTCCGCGTGATGGCCA 81 TGTGGTTGCCGGTGGCTTGCGCCATTGTCACTGAGCAGTGTGGCAAACTCTCCAGCATGGCGACCTTGTGAGGGCAAGGA 161 GTGGCCTCCCTGCACCTCACACGCTCATCTCTGTGCACATGTGTGTTTTCACGCACGGGCACAGCCCCTGGTGTATTCCT 241 GTACTAGTATCTGGCATCTGAGGCTGGTGCACCCTGACCTGGGCCTACTGCTGCCCAGGCCACAAGCCTTCTCCACTATG 321 ATGAGAGAACAAGGCTTGGTGGCACCCAGCACCTGGCTCTCCTGGCTCCCCGTCACCCCCCCAGGGCCTGGCCTCCCTCT 401 CCAGCTGCAGGCTTTCACCTCTTGCCTGGGCTGGATTCCCCCAGTCCCAGATTCCCAGGATGCCCAACCAGGGGAATCCC 481 AGTAACCATGCGCCAGCCTCCTGCCTCTCCTGAGTGGTGGCTGAGGCCTGGAGGAGGAGAGGCCACACAGCTGGCAGGGT 561 CTGGCCTGGGCAAAGAAGAGTAGAGCTCACGTCTTCTTGGTGAAAAGGAGGATCTCTGGAAAGTCCTCCTCTCTGAAATG 641 GGTTGGGATGGGGAGCGACAACCTCCTCTTCCCACAGCAGGATGGGAGAGCTTACTCCCAGGCCCCCACACCCAGGTCAG 721 ACATCACGTGCACCCTGAATGTAGGCAAGGGCCTGGCCCTGCAGCCCAGGGTCATTTCCTGCTCTTTCCACTTCCTCTTT 801 CCCCACCGTCCTGCACTAGCACCAGGGCCAGGCCAAGGCAAGAATCAGACAGCTACTCCACAGACAGAGAAACAACTTCC 881 AGCTAAGTATGACATCAGGACTTGTCTTTCCTACTAAGCCTCCATCCCCGCCCCTCCCCTGAGGCCCACGTCTGCTGAAT 961 TATCCGGACTCCGCACAAGCTGTGGCTTCCTCTCAGTTCAACAAACATTTCCTGAGCACCCACTACCAGTAATCCAGCCG 1041 GTAGGCGACGGAGACTGCCAGCAGGAGGGAGGGAAGAAAGCCAGTCATCCGGCAGATCTGGGCTGTTCTGGGCGGGAGCT 1121 GTTCTGGGCCACAGGTGCCCTACAGGGCTGGGGGCAGGATGGCGGTAGGAGCCCCAGGGGACCCTCCCACCTCTGCCTGG 1201 CAGAAGCAAGTGCCCTTCTTTCTTGTTATGTGTGCCTTCTGCTCCTGAGCCCTAGTGTGGACCTCACCGCATGGTCCCCT 1281 CTGCCCCCTCCTTCTGGTCCTGCCATGGCTGCTGCTCTCTGCTGAAGGCTGTGGGGCTCTAGGGAGAGTCCAGATCACCC 1361 TGGGATTTCTCCACTGCCCAATGTGAAGCCTAAACTGTGGGGTCCCAGCTCAGCCTTCCTCACTGGCTCTCAACTCCACC 1441 CCACCCCTCTATTCAGGAAGGTGAGGGGCATCTCTTTAGCAGACCAGACTGTTTTGAGAAGTGTCTCTCATACTTTAACT 1521 GAAGAGTCATGCAGATTCTAATGGTCTGGGGAGGGCCTGAGAGTTCGTCTTTTTTTTTTTTTTTTTTTTTTAGTTAGGGT 1601 CCTGCTGTTATCACCTAGGCTGGAGTGCAGTGGCACAATCATGGCTCACTGCAGCCTCGAACCCTCCAGGCTCAGGCGAT 1681 CCTCTCACATCAACCTCTTGAGTAGCCGGGACTACAGGTGTGCCACCACACCTGGCTAATTTTTGTATTTTTTGTAGAGG 1761 CAGGGTTTCACCATGTTGCCCAGGCTGGTCTCCAACTCCTGGGCTCAAGCAATCTGCTCGCCTTGGCCTCCTAAACTGCT 1841 GGGATTACAGGCATGAGCCACCACACCTGGCCGAGAATTCGTATTTCTAAGAGGCTTCAGGTGAAGCCCATGCTGGTTCC 1921 TGGACCATGGTTTTGAGTAGTTAAGGGTTTGGACTAGAATATATGAAGGGCTGGGGGTGAAGACAGACTCTAGACTCTAA 2001 AGGTTGGTGGCTGGCTATGTAGGGGATGGGGGAGTGCTACCCCTGTCAGGTGGTGGGGGCTTCCTGGCTGCAGAGTTGGG 2081 TGGGAGACTTGGGGAAGATGCTTTGGAAGGCAGTGAGTGGGTGGTGTCAACTTCTAGTAGTGCAGTGGGAGAGCTGGTCA 2161 GGGATGGGATGGAGTGAAGGGGGCAGAGGCATTTGGTGTGGGGTTGATCAGAGGAATTTTGGAAAGGCTTGGAAACATTC 2241 CTATGTATGTGAGACACACCTATGCCAGGGCAAAGACTCCAAGCTCAAGTTTTTCTCTTGCCTTCTAGTCACAAGAACAT 2321 GGCTTTGGAGTGTGACACTGGCCTAGGAATCCATGACTCCCAAAGGACGGGGCTAGGGGTAGAGGAGGTTCAGGCAAAGC 2401 CCTTAGATTTTGGAGACATCAGGCAGATGTCTCCAAAAATGATTGTGATCAAGAATCTGAATTATAAGATTCACAGTCTG 2481 CTCCCCAACCCAGTGCTGCCAACTGTACAGCTGCGCCTCCACGAAGGGGCATATGCCAGGCTCGTCTGACCCTGGAATGA 2561 GGATGTAGGAAGCAGGCAGAGCTCGGGTTCAGCCCTCACAATGGGACTGAAGCAGGAGAGAAGGCTGGGCAGAAGGGCTG 2641 TGGGGAAGTAGGGCTTGTCTCCATGGATGACGTCCAGAAGGATGTCAGGAGGAGGAATATCACAGGAGTTATAGACATTG 2721 GAGGGAACAGAGACTGGCACAGGACCTCTTCATTGCAGGAAGATGGTAGTGTAGGCAGGTAACATTGAGCTCTTTTCAAA 2801 AAAGGAGAGCTCTTCTTCAAGATAAGGAAGTGGTAGTTATGGTGGTAACCCCCGGCTATCAGTCCGGATGGTTGCCACCC 2881 CTCCTGCTGTAGGATGGAAGCAGCCATGGAGTGGGAGGGAGGCGCAATAAGACACCCCTCCACAGAGCTTGGCATCATGG 2961 GAAGCTGGTTCTACCTCTTCCTGGCTCCTTTGTTTAAAGGCCTGGCTGGGAGCCTTCCTTTTGGGTGTCTTTCTCTTCTC 3041 CAACCAACAGAAAAGACTGCTCTTCAAAGGTGGAGGGTCTTCATGAAACACAGCTGCCAGGAGCCCAGGCACAGGGCTGG 3121 GGGCCTGGAAAAAGGAGGGCACACAGGAGGAGGGAGGAGCTGGTAGGGAGATGCTGGCTTTACCTAAGGTCTCGAAACAA 3201 GGAGGGCAGAATAGGCAGAGGCCTCTCCGTCCCAGGCCCATTTTTGACAGATGGCGGGACGGAAATGCAATAGACCAGCC 3281 TGCAAGAAAGACATGTGTTTTGATGACAGGCAGTGTGGCCGGGTGGAACAAGCACAGGCCTTGGAATCCAATGGACTGAA 3361 TCAGAACCCTAGGCCTGCCATCTGTCAGCCGGGTGACCTGGGTCAATTTTAGCCTCTAAAAGCCTCAGTCTCCTTATCTG 3441 CAAAATGAGGCTTGTGATACCTGTTTTGAAGGGTTGCTGAGAAAATTAAAGATAAGGGTATCCAAAATAGTCTACGGCCA 3521 TACCACCCTGAACGTGCCTAATCTCGTAAGCTAAGCAGGGTCAGGCCTGGTTAGTACCTGGATGGGGAGAGTATGGAAAA 3601 CATACCTGCCCGCAGTTGGAGTTGGACTCTGTCTTAACAGTAGCGTGGCACACAGAAGGCACTCAGTAAATACTTGTTGA 3681 ATAAATGAAGTAGCGATTTGGTGTGAAAAAAAAAAAAAAAAAA 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 | HeLa |
| 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 Chi_124B_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell miR-124 + B
HITS-CLIP data was present in Chi_ControlA_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell Control A
HITS-CLIP data was present in Chi_ControlB_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell Control B
... - Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature. |
| Article |
- Chi SW; Zang JB; Mele A; Darnell RB - Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
|
| Experimental Support 2 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 GSM545213. RNA binding protein: AGO2. 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 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 3 for Functional miRNA-Target Interaction | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
|
| Conditions | HEK293 |
| Disease | 388115.0 |
| 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 GSM714643. 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 4 for Functional miRNA-Target Interaction | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
|
| Conditions | HEK293 |
| Disease | 388115.0 |
| 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
... - 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]
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| 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 GSM1462573. RNA binding protein: AGO2. Condition:TZM-bl 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]
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| 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) |
...
HITS-CLIP data was present in GSM1395165. RNA binding protein: AGO. Condition:MCF7 AGO HITS-CLIP Replicate 3
... - 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 7 for Functional miRNA-Target Interaction | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
|
| 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 SRX1760630. RNA binding protein: AGO2. Condition:AGO-CLIP-22RV1_A
PAR-CLIP data was present in SRX1760591. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP_B
PAR-CLIP data was present in SRX1760639. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP-MDV_A
PAR-CLIP data was present in SRX1760632. RNA binding protein: AGO2. Condition:AGO-CLIP-22RV1_C
PAR-CLIP data was present in SRX1760641. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP-MDV_B
... - 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 GSM4903833 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | Dermal fibroblasts / CTL_TD_21_a |
| Location of target site | NM_207380 | 3UTR | AAUAGACCAGCCUGCAAGAAAGACAUGUGUUUUGAUGACAGGCAGUGUGGCCGGGUGGAACAAGCACAGGCCUUGGAAUCCAAUGGACUGAAUCAGAACCCUAGGCCUGCCAU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Accession Series | GSE161239 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 2 for dataset GSM4903834 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | Dermal fibroblasts / CTL_TD_21_b |
| Location of target site | NM_207380 | 3UTR | CCUGCAAGAAAGACAUGUGUUUUGAUGACAGGCAGUGUGGCCGGGUGGAACAAGCACAGGCCUUGGAAUCCAAUGGACUGAAUCAGAACCCUAGGCCUGCCAU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Accession Series | GSE161239 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 3 for dataset GSM4903835 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | Dermal fibroblasts / CTL_TD_21_c |
| Location of target site | NM_207380 | 3UTR | AGCCUGCAAGAAAGACAUGUGUUUUGAUGACAGGCAGUGUGGCCGGGUGGAACAAGCACAGGCCUUGGAAUCCAAUGGACUGAAUCAGAACCCUAGGCCUGCCAU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Accession Series | GSE161239 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 4 for dataset GSM4903836 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | Dermal fibroblasts / 124_TD_21_a |
| Location of target site | NM_207380 | 3UTR | GCAAUAGACCAGCCUGCAAGAAAGACAUGUGUUUUGAUGACAGGCAGUGUGGCCGGGUGGAACAAGCACAGGCCUUGGAAUCCAAUGGACUGAAUCAGAACCCUAGGCCUGCCAU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Accession Series | GSE161239 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 5 for dataset GSM4903837 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | Dermal fibroblasts / 124_TD_21_b |
| Location of target site | NM_207380 | 3UTR | AGUGUGGCCGGGUGGAACAAGCACAGGCCUUGGAAUCCAAUGGACUGAAUCAGAACCCUAGGCCUGCCAU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Accession Series | GSE161239 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 6 for dataset GSM4903838 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | Dermal fibroblasts / 124_TD_21_c |
| Location of target site | NM_207380 | 3UTR | CAAGCACAGGCCUUGGAAUCCAAUGGACUGAAUCAGAACCCUAGGCCUGCCAU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Accession Series | GSE161239 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 7 for dataset Chi_124B_2A8_130_50 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | HeLa / HeLa cell miR-124 + B |
| Location of target site | ENST00000397536.2 | 3UTR | GCCUGGUUAGUACCUGGAUGG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 19536157 / Chi_HITSCLIP |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 8 for dataset Chi_ControlA_2A8_130_50 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | HeLa / HeLa cell Control A |
| Location of target site | ENST00000397536.2 | 3UTR | GCCUGGUUAGUACCUGGAUG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 19536157 / Chi_HITSCLIP |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 9 for dataset Chi_ControlB_2A8_130_50 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | HeLa / HeLa cell Control B |
| Location of target site | ENST00000397536.2 | 3UTR | GGCCUGGUUAGUACCUGGAUGGG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 19536157 / Chi_HITSCLIP |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 10 for dataset GSM714643 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO2 |
| Cell line / Condition | HEK293 / completeT1, repB |
| Location of target site | ENST00000397536.2 | 3UTR | UCUCGUAAGCUAAGCAGGGUCAGGCCUGGUUAGUACCUGGAUGGG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 21572407 / GSE28865 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 11 for dataset GSM1395165 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | MCF7 / MCF7 AGO HITS-CLIP Replicate 3 |
| Location of target site | ENST00000397536.2 | 3UTR | AUCUCGUAAGCUAAGCAGGGUCAGGCCUGGUUA |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 24906430 / GSE57855 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 12 for dataset GSM1013111 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | HUVEC / HUVEC-replicate-2 |
| Location of target site | ENST00000397536.2 | 3UTR | AUCUCGUAAGCUAAGCAGGGUCAGGCCUGGUUAGUA |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 24038734 / GSE41272 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 13 for dataset GSM1013113 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | hMSC / hMSC-replicate-2 |
| Location of target site | ENST00000397536.2 | 3UTR | UCUCGUAAGCUAAGCAGGGUCAGGCCUGGUUAGUA |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 24038734 / GSE41272 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 14 for dataset GSM1013116 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | hMSC / hMSC-replicate-5 |
| Location of target site | ENST00000397536.2 | 3UTR | UCUCGUAAGCUAAGCAGGGUCAGGCCUGGUU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 24038734 / GSE41272 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 15 for dataset GSM545212 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO1 |
| Cell line / Condition | HEK293 / Control |
| Location of target site | ENST00000397536.2 | 3UTR | AUCUCGUAAGCUAAGCAGGGUCAGGCCUGGUUAGUACCUGGAUGGG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 16 for dataset GSM545213 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | HEK293 / Control |
| Location of target site | ENST00000397536.2 | 3UTR | GUCUACGGCCAUACCACCCUGAACGUGCCUAAUCUCGUAAGCUAAGCAGGGUCAGGCCUGGUUAG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 17 for dataset GSM545214 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO3 |
| Cell line / Condition | HEK293 / Control |
| Location of target site | ENST00000397536.2 | 3UTR | AUCUCGUAAGCUAAGCAGGGUCAGGCCUGGUUAGUACCUGGAUGGG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 18 for dataset GSM545215 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO4 |
| Cell line / Condition | HEK293 / Control |
| Location of target site | ENST00000397536.2 | 3UTR | GUCUACGGCCAUACCACCCUGAACGUGCCUAAUCUCGUAAGCUAAGCAGGGUCAGGCCUGGUUAGUACCUGGAUGGG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 19 for dataset GSM545217 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | HEK293 / miR-7 transfection |
| Location of target site | ENST00000397536.2 | 3UTR | AUCUCGUAAGCUAAGCAGGGUCAGGCCUGGUUAGU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 20 for dataset GSM1065668 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO1 |
| Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_7 |
| Location of target site | ENST00000397536.2 | 3UTR | AUCUCGUAAGCUAAGCAGGGUCAGGCCUGGUUAGU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 23446348 / GSE43573 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 21 for dataset GSM1462573 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | TZM-bl / TZM-bl BaL |
| Location of target site | ENST00000397536.2 | 3UTR | GUCUACGGCCAUACCACCCUGAACGUGCCUAAUCUCGUAAGCUAAGCAGGGUCAGGCCUGGUUAGUACC |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 23592263 / GSE59944 |
| CLIP-seq Viewer | Link |
| MiRNA-Target Expression Profile | |||||||
|---|---|---|---|---|---|---|---|
|
| MiRNA-Target Expression Profile (TCGA) | |||||||
|---|---|---|---|---|---|---|---|
|
62 hsa-miR-4650-5p Target Genes:
Functional analysis:
ID |
Target | Description | Validation methods |
 |
 |
|||||||
| Strong evidence | Less strong evidence | |||||||||||
 |
 |
 |
 |
 |
 |
 |
 |
|||||
| MIRT064263 | KIAA1804 | mitogen-activated protein kinase kinase kinase 21 |  |
|
2 | 2 | ||||||
| MIRT082508 | CALM3 | calmodulin 3 | |
|
2 | 10 | ||||||
| MIRT456061 | SLC25A28 | solute carrier family 25 member 28 | |
|
2 | 2 | ||||||
| MIRT463521 | ZBTB7B | zinc finger and BTB domain containing 7B | |
|
2 | 2 | ||||||
| MIRT465449 | TP53 | tumor protein p53 | |
|
2 | 2 | ||||||
| MIRT469517 | RBFOX2 | RNA binding protein, fox-1 homolog 2 | |
|
2 | 8 | ||||||
| MIRT470967 | PKM | pyruvate kinase, muscle | |
|
2 | 2 | ||||||
| MIRT471902 | NUAK2 | NUAK family kinase 2 | |
|
2 | 2 | ||||||
| MIRT479924 | CBX5 | chromobox 5 | |
|
2 | 2 | ||||||
| MIRT483045 | C15orf52 | chromosome 15 open reading frame 52 | |
|
2 | 13 | ||||||
| MIRT493184 | MKNK2 | MAP kinase interacting serine/threonine kinase 2 | |
|
2 | 2 | ||||||
| MIRT496615 | IKZF2 | IKAROS family zinc finger 2 | |
|
2 | 2 | ||||||
| MIRT496980 | DNAJC27 | DnaJ heat shock protein family (Hsp40) member C27 | |
|
2 | 2 | ||||||
| MIRT522489 | MFSD9 | major facilitator superfamily domain containing 9 | |
|
2 | 2 | ||||||
| MIRT527859 | SMOC1 | SPARC related modular calcium binding 1 | |
|
2 | 2 | ||||||
| MIRT528540 | TTC22 | tetratricopeptide repeat domain 22 | |
|
2 | 2 | ||||||
| MIRT528860 | PKP1 | plakophilin 1 | |
|
2 | 2 | ||||||
| MIRT529389 | NSFL1C | NSFL1 cofactor | |
|
2 | 2 | ||||||
| MIRT533523 | TRIM13 | tripartite motif containing 13 | |
|
2 | 2 | ||||||
| MIRT538056 | DNAH3 | dynein axonemal heavy chain 3 | |
|
2 | 2 | ||||||
| MIRT541480 | ARF3 | ADP ribosylation factor 3 | |
|
2 | 6 | ||||||
| MIRT576737 | Wars | tryptophanyl-tRNA synthetase | |
|
2 | 2 | ||||||
| MIRT610462 | SYNPO2L | synaptopodin 2 like | |
|
2 | 4 | ||||||
| MIRT614189 | GGT7 | gamma-glutamyltransferase 7 | |
|
2 | 2 | ||||||
| MIRT626341 | PCSK7 | proprotein convertase subtilisin/kexin type 7 | |
|
2 | 2 | ||||||
| MIRT627547 | SNIP1 | Smad nuclear interacting protein 1 | |
|
2 | 2 | ||||||
| MIRT628605 | TMEM251 | transmembrane protein 251 | |
|
2 | 2 | ||||||
| MIRT630827 | YTHDC1 | YTH domain containing 1 | |
|
2 | 4 | ||||||
| MIRT633419 | TMEM120B | transmembrane protein 120B | |
|
2 | 2 | ||||||
| MIRT635354 | CSMD2 | CUB and Sushi multiple domains 2 | |
|
2 | 2 | ||||||
| MIRT636418 | MTHFD2 | methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase | |
|
2 | 2 | ||||||
| MIRT637031 | SPTLC3 | serine palmitoyltransferase long chain base subunit 3 | |
|
2 | 2 | ||||||
| MIRT638032 | TMEM109 | transmembrane protein 109 | |
|
2 | 2 | ||||||
| MIRT642847 | ZBTB7C | zinc finger and BTB domain containing 7C | |
|
2 | 2 | ||||||
| MIRT644389 | CD59 | CD59 molecule (CD59 blood group) | |
|
2 | 2 | ||||||
| MIRT645167 | NOL9 | nucleolar protein 9 | |
|
2 | 2 | ||||||
| MIRT645601 | MRPS15 | mitochondrial ribosomal protein S15 | |
|
2 | 2 | ||||||
| MIRT649169 | IQSEC1 | IQ motif and Sec7 domain 1 | |
|
2 | 2 | ||||||
| MIRT659166 | DCTN5 | dynactin subunit 5 | |
|
2 | 4 | ||||||
| MIRT660814 | AHCY | adenosylhomocysteinase | |
|
2 | 2 | ||||||
| MIRT663640 | HM13 | histocompatibility minor 13 | |
|
2 | 2 | ||||||
| MIRT663848 | TRIM72 | tripartite motif containing 72 | |
|
2 | 2 | ||||||
| MIRT666535 | RNF157 | ring finger protein 157 | |
|
2 | 2 | ||||||
| MIRT667885 | IP6K1 | inositol hexakisphosphate kinase 1 | |
|
2 | 2 | ||||||
| MIRT671613 | C6orf25 | megakaryocyte and platelet inhibitory receptor G6b | |
|
2 | 2 | ||||||
| MIRT673800 | MALL | mal, T-cell differentiation protein like | |
|
2 | 2 | ||||||
| MIRT676281 | ZNF260 | zinc finger protein 260 | |
|
2 | 2 | ||||||
| MIRT687008 | RPL35 | ribosomal protein L35 | |
|
2 | 2 | ||||||
| MIRT689090 | ACVR1 | activin A receptor type 1 | |
|
2 | 2 | ||||||
| MIRT689259 | WDR83OS | WD repeat domain 83 opposite strand | |
|
2 | 2 | ||||||
| MIRT697458 | ZC3H4 | zinc finger CCCH-type containing 4 | |
|
2 | 2 | ||||||
| MIRT699223 | SLCO3A1 | solute carrier organic anion transporter family member 3A1 | |
|
2 | 2 | ||||||
| MIRT710222 | JMJD4 | jumonji domain containing 4 | |
|
2 | 2 | ||||||
| MIRT710935 | ING5 | inhibitor of growth family member 5 | |
|
2 | 2 | ||||||
| MIRT715830 | ZNF598 | zinc finger protein 598 | |
|
2 | 2 | ||||||
| MIRT716134 | THOC5 | THO complex 5 | |
|
2 | 2 | ||||||
| MIRT717518 | HRNR | hornerin | |
|
2 | 2 | ||||||
| MIRT717918 | LRRC15 | leucine rich repeat containing 15 | |
|
2 | 2 | ||||||
| MIRT718307 | XPOT | exportin for tRNA | |
|
2 | 2 | ||||||
| MIRT721350 | LIF | LIF, interleukin 6 family cytokine | |
|
2 | 2 | ||||||
| MIRT724503 | MSMO1 | methylsterol monooxygenase 1 | |
|
2 | 2 | ||||||
| MIRT724993 | FSTL3 | follistatin like 3 | |
|
2 | 2 | ||||||
| miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||
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