pre-miRNA Information | |
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pre-miRNA | hsa-mir-4260 |
Genomic Coordinates | chr1: 209623444 - 209623510 |
Description | Homo sapiens miR-4260 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | |||||||||||||
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Mature miRNA | hsa-miR-4260 | ||||||||||||
Sequence | 11| CUUGGGGCAUGGAGUCCCA |29 | ||||||||||||
Evidence | Experimental | ||||||||||||
Experiments | SOLiD | DRVs in miRNA |
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SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | DYNAP | ||||||||||||||||||||
Synonyms | C18orf26 | ||||||||||||||||||||
Description | dynactin associated protein | ||||||||||||||||||||
Transcript | NM_173629 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on DYNAP | |||||||||||||||||||||
3'UTR of DYNAP (miRNA target sites are highlighted) |
>DYNAP|NM_173629|3'UTR 1 TTTGAACAGCCATAGCCATCACTTCAACTGAAACTTCAACCTCTACCACTTCAACTCAGTTTGCAACTATAATAGCTACT 81 CCTATCACTTCAAGTGGAATCATGGCTGCAGTCACTTTAACAGACTCTATAACCGTTACAACTTCAACAAAATCAAGTCC 161 TACTTCAACTTAAACTTACTTGACAACTCAAATAATCACCACTTCGACCATCTCTTTGACTGAATCAACAACTACATTCC 241 CTTCAACTGAATCTGCAACCACTTCCACTTAACCTATAACTACTGTAACTTCTACTTAGCCTACAGTAACAATGCTCATC 321 ACTCTTTTCCAACAATGTATAATCTCCACCTATTCATCTGAGGACTAAGCTCTGATTTTTCATCTTGCCCAAATTCCTTT 401 CTAAGGGGTATGGGGAGTCATGCCCTACAAACCATAAATTCTCATCAGATGGGTTTTATTTAACCCTGTATATTGTGACT 481 TACTTTCTAATCTGACTCTGGCATAACAAGGGAAAAAAATCAAAATGTTTTACCCCAAAATATATTTCCTTGCCATACCT 561 TGAAATTGTCCTGCAAAGTCTCTTGTGGAGAAACTCCACATTCTGTAGAGAATATCCTTTCCCCTTTGTTTTCCTTCCTT 641 TCTTTCCAGATCCAGGAGATAATCAACTAAGAGCCAGGCACCCTTTTAGGTCTAATAAGAAACACTTTACAACCTGCTCT 721 CTCTCTGAAGTCTGCTTTCTGAGAGATTCCTCTGCACAATAAAACTTGATCTCCACAATCCTTTATCTTAACCTGAACAT 801 TCCTTTCCATGGATCTCAGGTCTTCAGATAAACTAAACCAATTGTCAACCAGAACATGTTTAAATTTACCTATAGCCTGG 881 AAGCCCCAACTTTGAGTTGTCCTGCCTTTCTGAACCAAGCCAATGTATTTCTTAAATGTATTTGATTGATGTCTCATGTC 961 TCCCTAAAAATATATAAAACCAAACTGTACCTTAGCCACTTTGGACACATGTTCTCAGGACCTCCTGAGGGCTATGTCAT 1041 GAGCCATGGTCACTCATATTTGGCTCAGAATTAATCTCTTAAAATATTTTACAGAGTTTGACTCTTTTTGTCAACACATC 1121 CGAACCTGCAACTACAAATGCCACCATTACCACTTAAAACTTGATAGAACTAGCATCAGTCATCAAAATAACCTGTTCTA 1201 TATTAAGTTAACTTTTAGTTATCACCAGTAATACTAGCCTACAACTACTCGCCACACTGGCTCTTCCCCAAAATTGAAAT 1281 TGTACAATATGTGAGTCTAATTCTTGCTAACATAACATTATTGCCTACATTAAAAGCTTCTGCAAAGC 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 | ||||||
Disease | 284254.0 | ||||||
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. |
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miRNA-target interactions (Provided by authors) |
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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 2 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) |
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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. |
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miRNA-target interactions (Provided by authors) |
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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 GSM1065668 | |
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Method / RBP | PAR-CLIP / AGO1 |
Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_7 |
Location of target site | ENST00000321600.1 | 3UTR | GCCACACUGGCUCUUCCC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23446348 / GSE43573 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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66 hsa-miR-4260 Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT074404 | TNRC6A | trinucleotide repeat containing 6A | 2 | 2 | ||||||||
MIRT289774 | PER1 | period circadian clock 1 | 2 | 2 | ||||||||
MIRT442576 | HOXD9 | homeobox D9 | 2 | 2 | ||||||||
MIRT443878 | CNKSR3 | CNKSR family member 3 | 2 | 2 | ||||||||
MIRT449080 | XPO6 | exportin 6 | 2 | 2 | ||||||||
MIRT450294 | DRAXIN | dorsal inhibitory axon guidance protein | 2 | 2 | ||||||||
MIRT461785 | FXR2 | FMR1 autosomal homolog 2 | 2 | 2 | ||||||||
MIRT463931 | WNT10B | Wnt family member 10B | 2 | 2 | ||||||||
MIRT464860 | UBB | ubiquitin B | 2 | 8 | ||||||||
MIRT467619 | SLC7A5 | solute carrier family 7 member 5 | 2 | 2 | ||||||||
MIRT469649 | RAC1 | Rac family small GTPase 1 | 2 | 2 | ||||||||
MIRT473421 | MDM4 | MDM4, p53 regulator | 2 | 2 | ||||||||
MIRT473646 | MARCKSL1 | MARCKS like 1 | 2 | 2 | ||||||||
MIRT474213 | LCOR | ligand dependent nuclear receptor corepressor | 2 | 2 | ||||||||
MIRT474335 | KMT2D | lysine methyltransferase 2D | 2 | 2 | ||||||||
MIRT474871 | KDELR1 | KDEL endoplasmic reticulum protein retention receptor 1 | 2 | 2 | ||||||||
MIRT477440 | ELOVL5 | ELOVL fatty acid elongase 5 | 2 | 2 | ||||||||
MIRT478432 | DAZAP2 | DAZ associated protein 2 | 2 | 2 | ||||||||
MIRT479851 | CCDC6 | coiled-coil domain containing 6 | 2 | 2 | ||||||||
MIRT482507 | ACTB | actin beta | 2 | 2 | ||||||||
MIRT485473 | IGF1R | insulin like growth factor 1 receptor | 2 | 8 | ||||||||
MIRT485670 | CCDC64 | BICD family like cargo adaptor 1 | 2 | 4 | ||||||||
MIRT485902 | PGPEP1 | pyroglutamyl-peptidase I | 2 | 4 | ||||||||
MIRT488143 | PRRC2B | proline rich coiled-coil 2B | 2 | 4 | ||||||||
MIRT489455 | MSC | musculin | 2 | 2 | ||||||||
MIRT509568 | HIST2H2AB | histone cluster 2 H2A family member b | 2 | 4 | ||||||||
MIRT513093 | DYNAP | dynactin associated protein | 2 | 2 | ||||||||
MIRT513256 | CALM3 | calmodulin 3 | 2 | 2 | ||||||||
MIRT514356 | UBBP4 | ubiquitin B pseudogene 4 | 2 | 6 | ||||||||
MIRT522019 | PAQR3 | progestin and adipoQ receptor family member 3 | 2 | 4 | ||||||||
MIRT523164 | HIST3H3 | histone cluster 3 H3 | 2 | 2 | ||||||||
MIRT523297 | HIST1H1B | histone cluster 1 H1 family member b | 2 | 2 | ||||||||
MIRT524782 | BAG5 | BCL2 associated athanogene 5 | 2 | 2 | ||||||||
MIRT530921 | SCIN | scinderin | 2 | 2 | ||||||||
MIRT533302 | USP44 | ubiquitin specific peptidase 44 | 2 | 2 | ||||||||
MIRT552782 | YIPF4 | Yip1 domain family member 4 | 2 | 4 | ||||||||
MIRT553981 | SRPR | SRP receptor alpha subunit | 2 | 2 | ||||||||
MIRT563126 | ZNF215 | zinc finger protein 215 | 2 | 2 | ||||||||
MIRT569025 | IL21R | interleukin 21 receptor | 2 | 2 | ||||||||
MIRT573413 | RPL18A | ribosomal protein L18a | 2 | 2 | ||||||||
MIRT574877 | Dnajc6 | DnaJ heat shock protein family (Hsp40) member C6 | 2 | 3 | ||||||||
MIRT607538 | GLI2 | GLI family zinc finger 2 | 2 | 2 | ||||||||
MIRT607682 | MAPK10 | mitogen-activated protein kinase 10 | 2 | 3 | ||||||||
MIRT623791 | GK5 | glycerol kinase 5 (putative) | 2 | 2 | ||||||||
MIRT628834 | FAM151B | family with sequence similarity 151 member B | 2 | 2 | ||||||||
MIRT635547 | LEPREL1 | prolyl 3-hydroxylase 2 | 2 | 2 | ||||||||
MIRT635698 | NMNAT2 | nicotinamide nucleotide adenylyltransferase 2 | 2 | 2 | ||||||||
MIRT635906 | ARPC1B | actin related protein 2/3 complex subunit 1B | 2 | 2 | ||||||||
MIRT649985 | MSI1 | musashi RNA binding protein 1 | 2 | 2 | ||||||||
MIRT654900 | POMGNT1 | protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) | 2 | 2 | ||||||||
MIRT655116 | PHF7 | PHD finger protein 7 | 2 | 2 | ||||||||
MIRT658958 | DNAJC6 | DnaJ heat shock protein family (Hsp40) member C6 | 2 | 3 | ||||||||
MIRT659665 | CDC42EP4 | CDC42 effector protein 4 | 2 | 2 | ||||||||
MIRT668946 | CNBP | CCHC-type zinc finger nucleic acid binding protein | 2 | 2 | ||||||||
MIRT691164 | APOL6 | apolipoprotein L6 | 2 | 2 | ||||||||
MIRT692696 | MEAF6 | MYST/Esa1 associated factor 6 | 2 | 2 | ||||||||
MIRT693245 | HBS1L | HBS1 like translational GTPase | 2 | 2 | ||||||||
MIRT695203 | SCAMP3 | secretory carrier membrane protein 3 | 2 | 2 | ||||||||
MIRT701957 | MINK1 | misshapen like kinase 1 | 2 | 2 | ||||||||
MIRT706802 | APOL4 | apolipoprotein L4 | 2 | 2 | ||||||||
MIRT716899 | CACNB2 | calcium voltage-gated channel auxiliary subunit beta 2 | 2 | 2 | ||||||||
MIRT717632 | HLX | H2.0 like homeobox | 2 | 2 | ||||||||
MIRT719052 | ZNF281 | zinc finger protein 281 | 2 | 2 | ||||||||
MIRT722973 | GDE1 | glycerophosphodiester phosphodiesterase 1 | 2 | 2 | ||||||||
MIRT723643 | RPTN | repetin | 2 | 2 | ||||||||
MIRT734708 | NR3C2 | nuclear receptor subfamily 3 group C member 2 | 4 | 0 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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