pre-miRNA Information | |
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pre-miRNA | hsa-mir-520g |
Genomic Coordinates | chr19: 53722166 - 53722255 |
Description | Homo sapiens miR-520g stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Associated Diseases | ![]() |
Mature miRNA Information | |||||||||||||||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-520g-3p | ||||||||||||||||||||||||||||||||||||||||||
Sequence | 55| ACAAAGUGCUUCCCUUUAGAGUGU |78 | ||||||||||||||||||||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||||||||||||||||||||
Experiments | Array-cloned | ||||||||||||||||||||||||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | PTPN4 | ||||||||||||||||||||
Synonyms | MEG, PTPMEG, PTPMEG1 | ||||||||||||||||||||
Description | protein tyrosine phosphatase, non-receptor type 4 | ||||||||||||||||||||
Transcript | NM_002830 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on PTPN4 | |||||||||||||||||||||
3'UTR of PTPN4 (miRNA target sites are highlighted) |
>PTPN4|NM_002830|3'UTR 1 GAAAGCAAAAAGATCTGGGATATGTGTTGGAAAACTGCTTTCCCTTATGTTCACTGTGCCATAATGCTGCTCGCAGGAAA 81 TGGCATTTTACAAAAAAAAAATGAAGAACTCAAAAAAACTTTGAAAACTTCAGCACTGTTGCACTTTATGTTTTAAAAAA 161 TGTCACTCTTTCAAAATCTATAACTCATGTATTTGAAGACTGTTTCATGCTTTGCTCCGAACAAATAGTAAATAACTGAG 241 TATGTTCAGGGTAATTTATGAAATTTTGTGGTGGTGCCATGCAATCCCCTTTTGGTAGAATTGCCACAAACAAGGCTCAA 321 AATTCTCATCATCTCTGTTATACACCTGTATCATGAAAGCAAAAAGAAGTAAACATCAGGAGTCAGCTCTGGTCTTTTGC 401 AGTGGTTTGCGTACTTACTATACTGATTACCAGATTTTATTTTTAAAATTTTAGCAATATCGTTCTTAATATTAGCCAAT 481 ACACTGCCTATGGATGCAGCACATTTTTCCCTGCACACCCCCTGTAGAGACCTGCCTGCTGCTCAGAAGAAGAAAGATGG 561 AATTTGCTGTTCCCAGGAAATGCTGCACATTGTCCATTTACCAGCATCTTATAGAAAATATAAATATGAATCTACAAATT 641 CTCTTGGATTTAATAATGTAACTTATATTTATCATAAGGTTGGCTTATTCCAAATCATGTGATTTCACATACTTGATGTA 721 AAGGAATGCATGCATTGTGTCTTAACCCCTTAAGTGCCTTGAGACGTCCTTGTATGTCTAACGAAAAGGCACTCATTTGA 801 CCCCACTAGGAGGTATATATGTATATTGTACATTCGTATATTTTTATGCATTTTGAATAAGTTCACATTTTAAAAAACAG 881 CTATATTGAGTGTTATACAGTCAAAGAAGGGTAAGGAAATTCTGTTTCTTACTCAGTACTCGTGATTTGCTATAAGAAGC 961 AAAGATAATTTGTGTTCTACTGAGTGCACACTGCTGCTATGGAATTGTTCAAAATCTGCACATTCCTTTACTTGAGGGAC 1041 TGAGGGGTTACGGTTTAGCAGCTCAACTTTAAAAGATGCTTTTATGCTTCAAATTTCATATTTATTTCATCCCTAACTTT 1121 AGGAAGACATCTAACATGCAGATTAATGTTAAACATATTGATAATCTAAGCTAAAGTTAGAGCAAATAATTGTGATTTAT 1201 TCATGTCCATAACTAAAATATTATTCTTTAGCACTCATTTCAGTTAATATCAAGCTTTGTTCACACTGATATATTGATTG 1281 GGATTCTTCAAACGAAGAATGAAACATTATTGACTTATTTCTAAGTGTAATAACTCAATAACTAAATTGAGAATTTTCTT 1361 GTTTTTTTGTGTACAATTAAATTATTCCATTTTATATATACTTATTAAGTTATAAGCATGTTAATAAGGAGACTTTTGAC 1441 TGTCCAGCCTAATGGAGGATCTGATTCCCATTAAGGATGTGGGAATTCCCGTATTTTCCTCTTCAGGTTTTTTTGTTTTT 1521 AAGTCTACAGAGAGATAGAACCTTAACATTGCCCAGTTTGATAAAAGTGAAAATTTGCTCACCTATACAAATGTTATTTT 1601 ACACAATTATTTTATGTGGATTGGGGTTTTAAAAGATTCATTTCCTAGCAGTTTCTGAATATTTCTGTAAGATCTTGATA 1681 AAGTTTAGAGTCAAATGGCAGATATTTTGGAAAGCCATTTAGTATGAGGGGAAGAGTACACATTTTAAATCTTTGGTATA 1761 ATCTAAACGATGTCATTTCAGACATTCAAAACTCATAATAATAAATTTCAGGAAATCAAGCTCCTAAACATTAATAGCCA 1841 AGATACCAAATAAATTATCATATTAAAATATTTAAGTTTATTTAAAGAGAGAAGTAAACATAAACTTATGTCAAAGAGAA 1921 ATTCTCTTAATCTATTTCCTGACTTCACAGTCAAAACAGTATAAGATAGTGAAGTAACTTATAATCTTATTTGGTCATTC 2001 TGTTCTATAAACAGACAAATATAATTTAGGCTGCTATATGACATGATAAATTAAAAACTGAGAAAGTAAAATTATGTCGG 2081 GGTCTACACATTAAATGACTGTTTTGGCAGTTTTTCACCTGAATTTAAAAATAAAATTTGTCTGTTCTATCTGTATGGAC 2161 AGAATATGACAACCATAGACCAAAAGATATCATTGTATAGATGTAAAGAGACAAAAGTCATGGTTGGCATGTTCTTTAAT 2241 TTAGGGCCTTGTTTATACTTGTGAGTTTAATAATTTCTTGGCAATGAGCACTGCTGCCTTTTTAAATCATCAATGCCTGT 2321 CTTTAAATGCCAATCATTAGAAGTTTAGAATTACATTTAAATTTCTCATATATGAATTTTTCATCTGGGAACTACCCACT 2401 GTCGTCATTTTTATGTGCAGAAAAGATCCTTTTTGAAAACCATATTTATTGGGATCTTATTTAAATTTAAATTATCCTTT 2481 ACAACTTCTTAAAATGAATATGCTAATAGATAAGACTTTATCCATTACATCTAAGAACTTTTTAACCTGTATATCAATCT 2561 AAATAGGTTTCTAGAAATAATCCTAGCTTTCATACACCATGTAGTTCTAGACTCCGTCCATATCAGTGTAACATTGTGTG 2641 ATAAAATGCCAAATGTCTTGTATCTAAGCTACGCTCCCACTCTTCCAGCCACCCCTACCTCCCACCTTGACACCCTTAAG 2721 AAAGCAATGCTGACTTTTATTCTGACAAGTGGAAATCAATAGTGGTTAATCAAGTGGATTTTGTAAATGCTAAGAAGTGT 2801 TTGTGAAAACCTTCCCTTTCTGAGTTAGGATTGTTTTTTCCTGTTCATTTCAGGTGTTTTATTGAGCATCTGATTTGTGT 2881 CAGCACCATGTAAATATGATGAGGAGTATTTGGAATAGACTTTACATTCACCAGAAAATTGATAGTATTTGTTAAACCAA 2961 TGCATCCATTCAAAATAGAGGCAGAGTAAACAGCCTAAGAAATGATTTCCTTTCTACAGTCTGCTAGGAGAAAGAGGTGA 3041 GAGGGGAGTGGTTGATGATTTTAATCAAGAGTAAAGGGAACATTTATTACATGAAATCTGACTTCAGTTGTGCAAAGGTA 3121 TGTTAAGACATTAAGACAATTGCTGGAAGGTTTCAAATATGTGTACACACACATAGAGCTACTTTTGTGTGTTTATTTAT 3201 ATGTATATTTCACAAAGGCTAATGCCCACAGAGGAAAATGATTATTTTAACTTCTGGGTTATCATCTGCTGGCAGGGTCT 3281 GATCAGGTCTAGAGTATTTAAGGAAAAGTCTCCTGTCTTCTATCTCCACTAGAAGTACTGCAGCTTGAGAGCTGAAAGGA 3361 ACTTGAAAAATGTTATCCAGTCTTCACTTAGCCCATTTTTATCGGCATTAGGAAATAGGGTTCAGCAATGGTTATTGATT 3441 TAGCAGTCTGGTCTTATATGATCTGCTTTCTAATTATCTATCTAGTATTCCTATATTATACTGGAACTTCAATAAATTAT 3521 AACCTATGTGAATATCATAAATTCTTGTGAATTTTTGTCTATTTCCAGTAGAGAAGCATACTCAGCCAATGTTTTCACTT 3601 AATAACTATGACAACCTTAAAGGATGTCACTTAAGTTAGAAAATAAGCAGGCTTAAGAAGTGATTCTAATTAGGACCCCC 3681 ACTCAGTTTGCTAGTCATGCCTGCCTGACAGAACATAAGCTTTTGTAAAGTATTTAGACTGATAACACATGCAGTATGAA 3761 AACATTATAGACTGCAGTTAGAAGACTAATTTTTTAAAAGCACTCAAAACATAGAACTAAGATTTAGAATATATGTCCAT 3841 TTATAATGAAATAATTTGTGTTCATAATGTGAACATGTAAGATAAGTAAATAAAGCATTACTTGTTTTATAATATCAGGA 3921 AGAGAGAAGGAAACATTAGTTTATAACAATGTGCTATTTAATATCTGTATTTTGAACATTTAAAATACTCTGATGGTAAG 4001 GTTGCCAAAGTAATTTTGAATTCATAAAAATTGTTTATACCACAATAATGTGGGATATGTTTACAGGCTCTTTTATTTTG 4081 TGGTAGTTACTTTATAGTTCAGATGAATTTGCATTTCAGTCACTTATAGTAAATAAAGTATATTAAATATTTGTTGGAAT 4161 AAAAATCTCAATGTAATAGGACATAGATAAATTATGCAACAGCCTGCTTTGATGAAAGCTGGTGCATTATGTGAGCTGCC 4241 ACAGTTAATACTTTGTATTAACATTGCTTACTTCCCCCATTTGCTTCACCTATCTGACTACAATTGCTGGAATCATTCTT 4321 TTTGTGGTGCTTCCTCCAAGTGAAATAACTATGTTATTAAAACCTACTGGATTAATTTTATCAAATATCAGACTTACTGA 4401 TCTCTTGGCAGAGATTTATTGGTGTCTCAGTGTGATCACAATACAAGTTGTAGCAACCATTTTATAAAACTCTTAGAGAA 4481 TTATGTAGATAAAATGGAAATTACATAATCCTAAAACATTTTTGAGGGCTAATTGATAATAATTTCAGCAATTTTATTAA 4561 GAACCCAGTAAATTAATCCCTAATTTGTATGTTTTTTGTTCAACTTACCGTGTCTGCAACCATTATATAGACTTCATTGA 4641 TACTCAGCAATTACTACAGTGTGTCTTACAATGTTATAAAAAACAAACAGCAATCTCTGTTTCTGCCAGAAGTTAGATAT 4721 TTTTTTATAGTCCTGATGAATTTGTTGTGAGTAGACACCACATAGTTATTTCTGTTTGCATATAAATTTGCTGCTATTTA 4801 TTTGTATGTTTTTCTACTGTAGTATGCTATTGATTTCTGAAGTTATAATCATAATTTTTATTTTAGTAATCCAAGCTAAA 4881 TGGGCAACCAGAAGTAATATCTGCTAGGGTGCAATCCATCAGCATTGGTTCAGTGCATATACATAAGTAAACCAGTTTAA 4961 AAAAATTTTACTAAGCAAAAGGTAGTAGCAATATTGCTAGTTAAAGATTACCATTTTAGGGGAAAGTTCAAAGGTTTAAC 5041 TTCCTGAAACCTTTTAAACTTTTCAGTGCAAGAATGAAAATGTTTGAAAGCCTTGTTAAGCTCATAAAAGTTTCATTTAA 5121 ACACTGTAGAGTTTCCTACCTTTGTTGTGTAAAGGATATAGAAAATATTTTTCTATGGACAGAAGGTTGAAACTGTTAAC 5201 TTCTTTAATTTCATTGTTTAAAGGAGATAAAATGTTATTTGTGTGTCTTTCATGCTGTAAAGAAAATGAATGTATCTTTC 5281 AAATGTCATTAGAATTATGGCTTGATTCTAAGGATACTCTATTTGTTTTAAAGTCTACACGGGATTGAAAAGAAAGGGAA 5361 GAGTATTACACTTCATTGTACAAAATGTAATTTTAGAAGAAAAACATTTTCATTATAAACAAGAGCAATCATTGAAGCAT 5441 TTTCAGATATAATGTACATTCTTTTTCATTTTGCTTTGCCTCTAGAATAGAAACTTTTCAGAAAATTTGCACATACTGTT 5521 TGTAAGTATAAAATAATTGAATTCTAGACTTTTGGAGTGTGGAAGGGTGTTTGTGTGTGAAGGTAATAAATGTGTTGCTG 5601 CATGTGTTTACCATAGAGAACGTTGCCAGGCTTTGTCAAATGAGGACATTGTTGTGAGGGTGTGACTTTTGTGAAGCCAG 5681 AAAACTGTGCCTAAGATTCATTACAGTGAGTATGTGCAGAGGCCCCTGACCCAGTAAATGCTTTTTGCCTTTTTATTCCC 5761 AATGTCTTGGACAGTTGAGACAACTTGGCCCAACTCTGAATTGTAGCAGTGATGTCTTATATGCTTACGAGTTTATATTA 5841 ATTCAGCTGAACAAGAACTACATCTTAAACCACCTTTGTAGGTATGATTAATACGTGCAACAGCTGCTTTAAAAGGTGGT 5921 ATTTATTATTCATCACTCATGAAACTTGACTCAGTGAGGACTTCATTATTTTTATTTCTCTTTCCACGTCTCCAACTTTT 6001 TAAAAATCACTAATTTAACTCTTTGTTAAGTACTCAAGTACAAAGTGATCTCTTCTTTCATGAACTTTGCTATAACTGTT 6081 GAAAGGATTGGTGTCAGGCTCTCTCAACCCTGGGAGTTTCCAAAATTTAGCAAATATTACTTGTGATAAGCTTAAATGCC 6161 ACATCGCTAAGTACAATTATTACCAGGAATCCGTCAAGGGGGAGATAGCCCCGCTCACACCCTTAGACCCAAACAGGTGC 6241 TGGTTCATGCTTTCTCCACAAATTGGCAGTTGGGTACTTCCCCACTGTCATCACAGTTGAGCTCATTTTAACATATATTC 6321 AAAGAAGCTTTTTAGTTTCTACTCCTGAATTGTAGTGTTCAAGTTATTTGCCTTCCTGGGTAAGAAAATTTTAACCCAAG 6401 TCTGGGATTCTCTGGCACCTGTCTTTTCCCATCTTTTAATGAGTTGGCAAGATTAGGTCAAATTTCAATGCTAAATTTGA 6481 TTTTTTGAATTTTAAATAGTTGCACTTTATTTCATGCTGACCACCAACTTAATTTATACATTTTAAAATAAAATTATCCT 6561 AGAAGTGTTGTAAACGTGGGAAAATTTTAATTAGTGTTGGAGGTCATTAGATTGGACCCAGGTTTAAATATAATGATCTC 6641 TTCACAGCTTATTTGATGTTTAAGAGCAACTTGTGTGATCTTAGCTTTGCAGGTTTTCTGTAATTTATGTAGCACAATAA 6721 AGGATAACCAGTTGACTGTGTTACTGGACTCTGAGTTCTCACAGCTAGTTTCATCTAAGCTTGGTTTATTATCATTTCTG 6801 CTTTGGATTTTTTTGTGCATCACATGAATACTTAGAAATCCATTTGTTTTCAGTGTAGTACCTAGGGTGAAGTAGATGCT 6881 GCACAAGTAAGTTTAAGGGAATAAAAGTCCCGACACTTTATATACATGTTGAGGGGCACGATTTAAGAGACTGAAACAGT 6961 TTACATTAAACTGTTTTTATTTTCTGCCAGTAGACTCTATCTGCTTAAAAAAATAAAAATTGTTCAACCCAGTGTTCTCC 7041 AGCATCAGGACATTACAGTTGTAATCTATGTTGTAATCTTTTCAAATAAGAAAAGCTACTCCTTATTCTCTACAGTGTAG 7121 GCTTAATTTTAGAACCGATAATTTACTATATCTGCATTATTGATATTTTTAAGTAGTAGTTTTAAAAATAATTATTTCTA 7201 TGTGGAGGGTGTTTTAATTTGGGATTTTTTTTTTCTTGTAACAGGTGCTATTTGTAAATATGAAGGGGAAAAGTCACTTA 7281 GTTAAAAGTCTAGCTTATGTCATAATTAAGATACAATTATTCATTTCATGTTTGATTCTATTAAACTAGTGGCAAAACAG 7361 AATTGGTCCCTTAGTTTTTTAGATTACCTTTCCCCCTATATCACAAAAATATCTCTTTCCATATGATCTCATAATTGAGG 7441 CAAAGAAGCTAAGGGTTTATTTAAAATGTGTATAAGCTTGAATTTGGTCAACACTGCATAATTTGAAATCACTCTGCATT 7521 TGTCACTGCAGCTTACTGTATGCTTGAAAGGCCTTGTGTGTTTGTCTTAATTTTAGTGAAAAAATTAGAATTTCTGCCAT 7601 TCATGTACAAAAAAATTACAACTACAGCAAACAAGATAAAAATGCTGGTTTGCATTAATACTGTTTTAGTCTTAAGAGCA 7681 ATTTATATTATGTGAAATGCTGTTACACATATTTTGTTGGCCATATTTCATTTTGAGAAACAGTTGTTCAGGTACAAACA 7761 TGACAAACAACTCTAGCTATGACTCTTAATGTTCAATTGCAAAATAAAGATGTGCTTTAGTAATCTAAA Target sites
Provided by authors
Predicted by miRanda
DRVs
SNPs
DRVs & SNPs
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miRNA-target interactions (Predicted by miRanda) |
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DRVs in gene 3'UTRs | |||||||||||||||||||||
SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | 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 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]
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Experimental Support 2 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | HEK293 |
Disease | 5775.0 |
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 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]
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Experimental Support 3 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | HEK293 |
Disease | 5775.0 |
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]
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Experimental Support 4 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | MCF7 |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
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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]
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Experimental Support 5 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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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 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 GSM545212 | |
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Method / RBP | PAR-CLIP / AGO1 |
Cell line / Condition | HEK293 / Control |
Location of target site | ENST00000263708.2 | 3UTR | AAAACUUCAGCACUGUUGCACUUUAUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 20371350 / GSE21578 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM545214 | |
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Method / RBP | PAR-CLIP / AGO3 |
Cell line / Condition | HEK293 / Control |
Location of target site | ENST00000263708.2 | 3UTR | AAAACUUCAGCACUGUUGCACUUUAUG |
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 GSM545216 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / miR-124 transfection |
Location of target site | ENST00000263708.2 | 3UTR | AAAACUUCAGCACUGUUGCACUUUAUGUUUUA |
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 GSM545217 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / miR-7 transfection |
Location of target site | ENST00000263708.2 | 3UTR | AAAACUUCAGCACUGUUGCACUUUAUG |
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 GSM714645 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repB |
Location of target site | ENST00000263708.2 | 3UTR | AAAACUUCAGCACUGUUGCACUUUAUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 21572407 / GSE28865 |
CLIP-seq Viewer | Link |
CLIP-seq Support 6 for dataset GSM1065667 | |
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Method / RBP | PAR-CLIP / AGO1 |
Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_6 |
Location of target site | ENST00000263708.2 | 3UTR | AAAACUUCAGCACUGUUGCACUUUAUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23446348 / GSE43573 |
CLIP-seq Viewer | Link |
CLIP-seq Support 7 for dataset GSM1065668 | |
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Method / RBP | PAR-CLIP / AGO1 |
Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_7 |
Location of target site | ENST00000263708.2 | 3UTR | AAAACUUCAGCACUGUUGCACUUUAUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23446348 / GSE43573 |
CLIP-seq Viewer | Link |
CLIP-seq Support 8 for dataset GSM1065669 | |
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Method / RBP | PAR-CLIP / AGO1 |
Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_8 |
Location of target site | ENST00000263708.2 | 3UTR | AAAACUUCAGCACUGUUGCACUUUAUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23446348 / GSE43573 |
CLIP-seq Viewer | Link |
CLIP-seq Support 9 for dataset GSM1065670 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / 4-thiouridine, 3_ML_LG |
Location of target site | ENST00000263708.2 | 3UTR | AAAACUUCAGCACUGUUGCACUUUAUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23446348 / GSE43573 |
CLIP-seq Viewer | Link |
CLIP-seq Support 10 for dataset SRR1045082 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | MCF7 / Untreated |
Location of target site | ENST00000263708.2 | 3UTR | AAAACUUCAGCACUGUUGCACUUUAUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 24398324 / SRX388831 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||||||||||||||||||||||||||||||||||||||||||||
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362 hsa-miR-520g-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT004276 | VEGFA | vascular endothelial growth factor A | ![]() |
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2 | 1 | ||||||
MIRT061377 | WEE1 | WEE1 G2 checkpoint kinase | ![]() |
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2 | 2 | ||||||
MIRT070863 | EIF2S1 | eukaryotic translation initiation factor 2 subunit alpha | ![]() |
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2 | 4 | ||||||
MIRT074319 | TNRC6A | trinucleotide repeat containing 6A | ![]() |
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2 | 4 | ||||||
MIRT081126 | LDLR | low density lipoprotein receptor | ![]() |
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2 | 6 | ||||||
MIRT093444 | MSMO1 | methylsterol monooxygenase 1 | ![]() |
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2 | 2 | ||||||
MIRT103397 | CBX3 | chromobox 3 | ![]() |
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2 | 2 | ||||||
MIRT107536 | VLDLR | very low density lipoprotein receptor | ![]() |
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2 | 2 | ||||||
MIRT109624 | KLHL15 | kelch like family member 15 | ![]() |
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2 | 4 | ||||||
MIRT119717 | TNRC6B | trinucleotide repeat containing 6B | ![]() |
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2 | 2 | ||||||
MIRT130126 | TXNIP | thioredoxin interacting protein | ![]() |
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2 | 2 | ||||||
MIRT133699 | SKI | SKI proto-oncogene | ![]() |
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2 | 2 | ||||||
MIRT140155 | SPRED1 | sprouty related EVH1 domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT153990 | PRNP | prion protein | ![]() |
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2 | 2 | ||||||
MIRT161898 | FXR1 | FMR1 autosomal homolog 1 | ![]() |
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2 | 2 | ||||||
MIRT164670 | WHSC1 | nuclear receptor binding SET domain protein 2 | ![]() |
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2 | 4 | ||||||
MIRT178073 | SAMD8 | sterile alpha motif domain containing 8 | ![]() |
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2 | 2 | ||||||
MIRT193026 | TMOD3 | tropomodulin 3 | ![]() |
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2 | 2 | ||||||
MIRT216879 | MSH3 | mutS homolog 3 | ![]() |
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2 | 2 | ||||||
MIRT230977 | PRRG4 | proline rich and Gla domain 4 | ![]() |
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2 | 2 | ||||||
MIRT242752 | FNBP1L | formin binding protein 1 like | ![]() |
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2 | 2 | ||||||
MIRT249018 | PABPC3 | poly(A) binding protein cytoplasmic 3 | ![]() |
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2 | 8 | ||||||
MIRT254769 | XRCC6 | X-ray repair cross complementing 6 | ![]() |
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2 | 6 | ||||||
MIRT266862 | SLC25A44 | solute carrier family 25 member 44 | ![]() |
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2 | 2 | ||||||
MIRT275453 | TMPO | thymopoietin | ![]() |
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2 | 2 | ||||||
MIRT285530 | CDT1 | chromatin licensing and DNA replication factor 1 | ![]() |
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2 | 2 | ||||||
MIRT286959 | SOCS7 | suppressor of cytokine signaling 7 | ![]() |
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2 | 2 | ||||||
MIRT301219 | SH3BP4 | SH3 domain binding protein 4 | ![]() |
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2 | 2 | ||||||
MIRT325706 | CSTF2 | cleavage stimulation factor subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT437832 | SMAD7 | SMAD family member 7 | ![]() |
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3 | 1 | |||||
MIRT442639 | TBC1D12 | TBC1 domain family member 12 | ![]() |
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2 | 2 | ||||||
MIRT443433 | MAPT | microtubule associated protein tau | ![]() |
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2 | 2 | ||||||
MIRT446289 | RIMKLB | ribosomal modification protein rimK like family member B | ![]() |
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2 | 2 | ||||||
MIRT447962 | WDR77 | WD repeat domain 77 | ![]() |
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2 | 2 | ||||||
MIRT454271 | PSMA1 | proteasome subunit alpha 1 | ![]() |
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2 | 2 | ||||||
MIRT454809 | NEDD9 | neural precursor cell expressed, developmentally down-regulated 9 | ![]() |
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2 | 2 | ||||||
MIRT456031 | CRYZ | crystallin zeta | ![]() |
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2 | 8 | ||||||
MIRT462068 | CCDC77 | coiled-coil domain containing 77 | ![]() |
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2 | 4 | ||||||
MIRT463549 | ZBTB5 | zinc finger and BTB domain containing 5 | ![]() |
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2 | 4 | ||||||
MIRT470351 | PPP2R5E | protein phosphatase 2 regulatory subunit B'epsilon | ![]() |
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2 | 2 | ||||||
MIRT474452 | KLHL11 | kelch like family member 11 | ![]() |
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2 | 10 | ||||||
MIRT476644 | G2E3 | G2/M-phase specific E3 ubiquitin protein ligase | ![]() |
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2 | 2 | ||||||
MIRT481110 | B2M | beta-2-microglobulin | ![]() |
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2 | 2 | ||||||
MIRT481790 | APEX1 | apurinic/apyrimidinic endodeoxyribonuclease 1 | ![]() |
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2 | 2 | ||||||
MIRT482106 | AKT3 | AKT serine/threonine kinase 3 | ![]() |
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2 | 4 | ||||||
MIRT482526 | ACTB | actin beta | ![]() |
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2 | 4 | ||||||
MIRT485571 | FOXQ1 | forkhead box Q1 | ![]() |
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2 | 2 | ||||||
MIRT486010 | LPAR2 | lysophosphatidic acid receptor 2 | ![]() |
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2 | 2 | ||||||
MIRT493607 | HMGB3 | high mobility group box 3 | ![]() |
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2 | 6 | ||||||
MIRT495181 | MUC20 | mucin 20, cell surface associated | ![]() |
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2 | 2 | ||||||
MIRT496046 | MORC1 | MORC family CW-type zinc finger 1 | ![]() |
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2 | 2 | ||||||
MIRT496734 | TRIM31 | tripartite motif containing 31 | ![]() |
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2 | 2 | ||||||
MIRT497421 | FAM46A | family with sequence similarity 46 member A | ![]() |
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2 | 2 | ||||||
MIRT497493 | RGS17 | regulator of G protein signaling 17 | ![]() |
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2 | 2 | ||||||
MIRT497751 | OXGR1 | oxoglutarate receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT498355 | ABHD17B | abhydrolase domain containing 17B | ![]() |
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2 | 2 | ||||||
MIRT501454 | PTPN4 | protein tyrosine phosphatase, non-receptor type 4 | ![]() |
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2 | 8 | ||||||
MIRT501584 | PLEKHA1 | pleckstrin homology domain containing A1 | ![]() |
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2 | 10 | ||||||
MIRT501781 | NRBF2 | nuclear receptor binding factor 2 | ![]() |
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2 | 6 | ||||||
MIRT506503 | MSANTD4 | Myb/SANT DNA binding domain containing 4 with coiled-coils | ![]() |
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2 | 2 | ||||||
MIRT507414 | ELK4 | ELK4, ETS transcription factor | ![]() |
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2 | 2 | ||||||
MIRT508557 | CEP72 | centrosomal protein 72 | ![]() |
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2 | 4 | ||||||
MIRT508726 | ZNF682 | zinc finger protein 682 | ![]() |
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2 | 4 | ||||||
MIRT508762 | IPP | intracisternal A particle-promoted polypeptide | ![]() |
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2 | 2 | ||||||
MIRT508818 | GPR155 | G protein-coupled receptor 155 | ![]() |
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2 | 2 | ||||||
MIRT509112 | BMP8B | bone morphogenetic protein 8b | ![]() |
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2 | 6 | ||||||
MIRT509273 | NPM3 | nucleophosmin/nucleoplasmin 3 | ![]() |
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2 | 6 | ||||||
MIRT511537 | HMGB1 | high mobility group box 1 | ![]() |
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2 | 6 | ||||||
MIRT514118 | SERF2 | small EDRK-rich factor 2 | ![]() |
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2 | 2 | ||||||
MIRT514302 | FXYD5 | FXYD domain containing ion transport regulator 5 | ![]() |
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2 | 6 | ||||||
MIRT514962 | SIGLEC11 | sialic acid binding Ig like lectin 11 | ![]() |
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2 | 2 | ||||||
MIRT515557 | TMEM134 | transmembrane protein 134 | ![]() |
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2 | 2 | ||||||
MIRT516042 | MED18 | mediator complex subunit 18 | ![]() |
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2 | 2 | ||||||
MIRT516540 | MIXL1 | Mix paired-like homeobox | ![]() |
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2 | 2 | ||||||
MIRT516992 | COX19 | COX19, cytochrome c oxidase assembly factor | ![]() |
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2 | 4 | ||||||
MIRT517169 | SLC28A1 | solute carrier family 28 member 1 | ![]() |
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2 | 2 | ||||||
MIRT517242 | PRIM1 | DNA primase subunit 1 | ![]() |
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2 | 4 | ||||||
MIRT517722 | KIF1C | kinesin family member 1C | ![]() |
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2 | 2 | ||||||
MIRT517797 | EFCAB11 | EF-hand calcium binding domain 11 | ![]() |
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2 | 4 | ||||||
MIRT517997 | SLC16A13 | solute carrier family 16 member 13 | ![]() |
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2 | 2 | ||||||
MIRT518033 | ABHD15 | abhydrolase domain containing 15 | ![]() |
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2 | 4 | ||||||
MIRT518843 | NEK8 | NIMA related kinase 8 | ![]() |
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2 | 2 | ||||||
MIRT518874 | NKD1 | naked cuticle homolog 1 | ![]() |
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2 | 2 | ||||||
MIRT520138 | WSB1 | WD repeat and SOCS box containing 1 | ![]() |
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2 | 2 | ||||||
MIRT521531 | QSOX1 | quiescin sulfhydryl oxidase 1 | ![]() |
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2 | 4 | ||||||
MIRT522855 | KIAA1551 | KIAA1551 | ![]() |
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2 | 2 | ||||||
MIRT522976 | INTU | inturned planar cell polarity protein | ![]() |
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2 | 2 | ||||||
MIRT523064 | HYPK | huntingtin interacting protein K | ![]() |
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2 | 2 | ||||||
MIRT523421 | GPR157 | G protein-coupled receptor 157 | ![]() |
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2 | 2 | ||||||
MIRT524077 | DNAJC10 | DnaJ heat shock protein family (Hsp40) member C10 | ![]() |
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2 | 2 | ||||||
MIRT524277 | CYCS | cytochrome c, somatic | ![]() |
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2 | 2 | ||||||
MIRT524326 | CRLF3 | cytokine receptor like factor 3 | ![]() |
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2 | 4 | ||||||
MIRT524374 | CREB1 | cAMP responsive element binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT524439 | CNKSR3 | CNKSR family member 3 | ![]() |
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2 | 2 | ||||||
MIRT524756 | BCL2L2 | BCL2 like 2 | ![]() |
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2 | 2 | ||||||
MIRT526621 | NME6 | NME/NM23 nucleoside diphosphate kinase 6 | ![]() |
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2 | 2 | ||||||
MIRT529610 | H1F0 | H1 histone family member 0 | ![]() |
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2 | 2 | ||||||
MIRT529984 | TNFAIP8L1 | TNF alpha induced protein 8 like 1 | ![]() |
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2 | 6 | ||||||
MIRT530605 | C7orf33 | chromosome 7 open reading frame 33 | ![]() |
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2 | 4 | ||||||
MIRT531759 | TXK | TXK tyrosine kinase | ![]() |
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2 | 4 | ||||||
MIRT532031 | FHDC1 | FH2 domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT532107 | RRP8 | ribosomal RNA processing 8 | ![]() |
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2 | 2 | ||||||
MIRT532920 | ZNF385A | zinc finger protein 385A | ![]() |
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2 | 2 | ||||||
MIRT533005 | ZFHX3 | zinc finger homeobox 3 | ![]() |
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2 | 4 | ||||||
MIRT533102 | YOD1 | YOD1 deubiquitinase | ![]() |
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2 | 2 | ||||||
MIRT534262 | SLC12A7 | solute carrier family 12 member 7 | ![]() |
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2 | 2 | ||||||
MIRT534458 | SCML2 | Scm polycomb group protein like 2 | ![]() |
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2 | 4 | ||||||
MIRT534982 | PRR11 | proline rich 11 | ![]() |
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2 | 2 | ||||||
MIRT536679 | IKZF5 | IKAROS family zinc finger 5 | ![]() |
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2 | 2 | ||||||
MIRT537431 | FBXL7 | F-box and leucine rich repeat protein 7 | ![]() |
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2 | 2 | ||||||
MIRT538035 | DNAJB6 | DnaJ heat shock protein family (Hsp40) member B6 | ![]() |
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2 | 2 | ||||||
MIRT539717 | EIF3H | eukaryotic translation initiation factor 3 subunit H | ![]() |
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2 | 2 | ||||||
MIRT540260 | FAM89A | family with sequence similarity 89 member A | ![]() |
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2 | 2 | ||||||
MIRT540372 | MASTL | microtubule associated serine/threonine kinase like | ![]() |
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2 | 2 | ||||||
MIRT540519 | CXCL10 | C-X-C motif chemokine ligand 10 | ![]() |
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2 | 2 | ||||||
MIRT540651 | ZNF514 | zinc finger protein 514 | ![]() |
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2 | 2 | ||||||
MIRT540921 | KCNA7 | potassium voltage-gated channel subfamily A member 7 | ![]() |
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2 | 2 | ||||||
MIRT541156 | PABPC1 | poly(A) binding protein cytoplasmic 1 | ![]() |
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2 | 4 | ||||||
MIRT541745 | ZC3HAV1 | zinc finger CCCH-type containing, antiviral 1 | ![]() |
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2 | 2 | ||||||
MIRT542029 | PEX2 | peroxisomal biogenesis factor 2 | ![]() |
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2 | 2 | ||||||
MIRT542036 | PTRF | caveolae associated protein 1 | ![]() |
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2 | 2 | ||||||
MIRT542127 | DIS3L | DIS3 like exosome 3'-5' exoribonuclease | ![]() |
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2 | 2 | ||||||
MIRT542252 | HSPA4L | heat shock protein family A (Hsp70) member 4 like | ![]() |
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2 | 2 | ||||||
MIRT542354 | MED16 | mediator complex subunit 16 | ![]() |
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2 | 2 | ||||||
MIRT542466 | AKR7A2 | aldo-keto reductase family 7 member A2 | ![]() |
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2 | 2 | ||||||
MIRT542505 | WDR13 | WD repeat domain 13 | ![]() |
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2 | 2 | ||||||
MIRT542712 | RPS15A | ribosomal protein S15a | ![]() |
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2 | 2 | ||||||
MIRT542958 | FOXK1 | forkhead box K1 | ![]() |
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2 | 2 | ||||||
MIRT543179 | FICD | FIC domain containing | ![]() |
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2 | 2 | ||||||
MIRT552884 | WASL | Wiskott-Aldrich syndrome like | ![]() |
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2 | 4 | ||||||
MIRT554997 | RAB39B | RAB39B, member RAS oncogene family | ![]() |
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2 | 2 | ||||||
MIRT555187 | PRUNE2 | prune homolog 2 | ![]() |
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2 | 2 | ||||||
MIRT555236 | PRICKLE2 | prickle planar cell polarity protein 2 | ![]() |
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2 | 2 | ||||||