pre-miRNA Information | |
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pre-miRNA | hsa-mir-6871 |
Genomic Coordinates | chr20: 41169023 - 41169078 |
Description | Homo sapiens miR-6871 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-6871-3p | |||||||||||||||||||||||||||
Sequence | 35| CAGCACCCUGUGGCUCCCACAG |56 | |||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||
Experiments | Meta-analysis | DRVs in miRNA |
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SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | DYNLT1 | ||||||||||||||||||||
Synonyms | CW-1, TCTEL1, tctex-1 | ||||||||||||||||||||
Description | dynein light chain Tctex-type 1 | ||||||||||||||||||||
Transcript | NM_006519 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on DYNLT1 | |||||||||||||||||||||
3'UTR of DYNLT1 (miRNA target sites are highlighted) |
>DYNLT1|NM_006519|3'UTR 1 CCTGCAGTCCAGCCTATGGCCTTTCTCCTTTTGTCTCTAGTTCATCCTCTAACCACCAGCCATGAATTCAGTGAACTCTT 81 TTCTCATTCTCTTTGTTTTGTGGCACTTTCACAATGTAGAGGAAAAAACCAAATGACCGCACTGTGATGTGAATGGCACC 161 GAAGTCAGATGAGTATCCCTGTAGGTCACCTGCAGCCTGCGTTGCCACTTGTCTTAACTCTGAATATTTCATTTCAAAGG 241 TGCTAAAATCTGAAATCTGCTAGTGTGAAACTTGCTCTACTCTCTGAAATGATTCAAATACACTAATTTTCCATACTTTA 321 TACTTTTGTTAGAATAAATTATTCAAATCTAAAAAAAAAAAAAAAAAA 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 | 6993.0 | ||||||
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 GSM714644. RNA binding protein: AGO2. Condition:completeT1
... - Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods. |
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miRNA-target interactions (Provided by authors) |
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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 2 for Functional miRNA-Target Interaction | |||||||
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miRNA:Target | ---- | ||||||
Validation Method |
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Conditions | HEK293 | ||||||
Disease | 6993.0 | ||||||
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
... - 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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CLIP-seq Support 1 for dataset GSM714644 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repA |
Location of target site | ENST00000367088.1 | 3UTR | AAUAUUUCAUUUCAAAGGUGCUAAAAUCUG |
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 GSM1065667 | |
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Method / RBP | PAR-CLIP / AGO1 |
Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_6 |
Location of target site | ENST00000367088.1 | 3UTR | AAUAUUUCAUUUCAAAGGUGCUAAAAUCUG |
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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88 hsa-miR-6871-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT061678 | BTG2 | BTG anti-proliferation factor 2 | ![]() |
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2 | 4 | ||||||
MIRT116181 | NUFIP2 | NUFIP2, FMR1 interacting protein 2 | ![]() |
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2 | 2 | ||||||
MIRT150139 | MIDN | midnolin | ![]() |
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2 | 2 | ||||||
MIRT197058 | NKIRAS2 | NFKB inhibitor interacting Ras like 2 | ![]() |
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2 | 2 | ||||||
MIRT225108 | GOLGA7 | golgin A7 | ![]() |
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2 | 2 | ||||||
MIRT376288 | CALM3 | calmodulin 3 | ![]() |
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2 | 2 | ||||||
MIRT454810 | NEDD9 | neural precursor cell expressed, developmentally down-regulated 9 | ![]() |
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2 | 2 | ||||||
MIRT464228 | VEGFA | vascular endothelial growth factor A | ![]() |
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2 | 6 | ||||||
MIRT466961 | STAT3 | signal transducer and activator of transcription 3 | ![]() |
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2 | 2 | ||||||
MIRT468219 | SGK1 | serum/glucocorticoid regulated kinase 1 | ![]() |
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2 | 2 | ||||||
MIRT472460 | NASP | nuclear autoantigenic sperm protein | ![]() |
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2 | 2 | ||||||
MIRT474203 | LEPRE1 | prolyl 3-hydroxylase 1 | ![]() |
1 | 1 | |||||||
MIRT475836 | HDGF | heparin binding growth factor | ![]() |
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2 | 4 | ||||||
MIRT478667 | CTC1 | CST telomere replication complex component 1 | ![]() |
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2 | 14 | ||||||
MIRT478707 | CSRNP2 | cysteine and serine rich nuclear protein 2 | ![]() |
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2 | 2 | ||||||
MIRT478982 | COMMD2 | COMM domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT479693 | CCNT2 | cyclin T2 | ![]() |
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2 | 6 | ||||||
MIRT488440 | ULBP2 | UL16 binding protein 2 | ![]() |
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2 | 2 | ||||||
MIRT492511 | RAET1L | retinoic acid early transcript 1L | ![]() |
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2 | 2 | ||||||
MIRT492975 | NCS1 | neuronal calcium sensor 1 | ![]() |
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2 | 2 | ||||||
MIRT494158 | COL4A1 | collagen type IV alpha 1 chain | ![]() |
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2 | 6 | ||||||
MIRT495934 | SLC7A5P2 | solute carrier family 7 member 5 pseudogene 2 | ![]() |
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2 | 2 | ||||||
MIRT496210 | PLEKHG2 | pleckstrin homology and RhoGEF domain containing G2 | ![]() |
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2 | 2 | ||||||
MIRT496356 | PPY | pancreatic polypeptide | ![]() |
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2 | 2 | ||||||
MIRT496385 | ZC3H6 | zinc finger CCCH-type containing 6 | ![]() |
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2 | 2 | ||||||
MIRT496463 | DCTN5 | dynactin subunit 5 | ![]() |
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2 | 2 | ||||||
MIRT497642 | GLDN | gliomedin | ![]() |
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2 | 2 | ||||||
MIRT498496 | FRK | fyn related Src family tyrosine kinase | ![]() |
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2 | 2 | ||||||
MIRT501928 | MCL1 | MCL1, BCL2 family apoptosis regulator | ![]() |
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2 | 8 | ||||||
MIRT513286 | PDPK1 | 3-phosphoinositide dependent protein kinase 1 | ![]() |
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2 | 2 | ||||||
MIRT514767 | RBM4B | RNA binding motif protein 4B | ![]() |
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2 | 2 | ||||||
MIRT514916 | MDM2 | MDM2 proto-oncogene | ![]() |
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2 | 6 | ||||||
MIRT515669 | LRRC27 | leucine rich repeat containing 27 | ![]() |
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2 | 2 | ||||||
MIRT520367 | UBE2G2 | ubiquitin conjugating enzyme E2 G2 | ![]() |
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2 | 2 | ||||||
MIRT523960 | DYNLT1 | dynein light chain Tctex-type 1 | ![]() |
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2 | 4 | ||||||
MIRT526859 | KIFC1 | kinesin family member C1 | ![]() |
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2 | 2 | ||||||
MIRT527673 | CASP8 | caspase 8 | ![]() |
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2 | 2 | ||||||
MIRT527828 | TMEM74B | transmembrane protein 74B | ![]() |
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2 | 2 | ||||||
MIRT529553 | EI24 | EI24, autophagy associated transmembrane protein | ![]() |
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2 | 2 | ||||||
MIRT530547 | SYNPO | synaptopodin | ![]() |
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2 | 2 | ||||||
MIRT531725 | TARS | threonyl-tRNA synthetase | ![]() |
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2 | 2 | ||||||
MIRT533340 | UNC119B | unc-119 lipid binding chaperone B | ![]() |
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2 | 2 | ||||||
MIRT533620 | TNFRSF13C | TNF receptor superfamily member 13C | ![]() |
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2 | 2 | ||||||
MIRT537226 | GAN | gigaxonin | ![]() |
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2 | 2 | ||||||
MIRT544430 | ZNF460 | zinc finger protein 460 | ![]() |
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2 | 4 | ||||||
MIRT546905 | PTP4A1 | protein tyrosine phosphatase type IVA, member 1 | ![]() |
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2 | 2 | ||||||
MIRT547102 | PLAG1 | PLAG1 zinc finger | ![]() |
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2 | 2 | ||||||
MIRT547820 | ISG20L2 | interferon stimulated exonuclease gene 20 like 2 | ![]() |
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2 | 2 | ||||||
MIRT548236 | FEM1B | fem-1 homolog B | ![]() |
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2 | 2 | ||||||
MIRT550034 | WWTR1 | WW domain containing transcription regulator 1 | ![]() |
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2 | 2 | ||||||
MIRT554337 | SH3GLB1 | SH3 domain containing GRB2 like, endophilin B1 | ![]() |
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2 | 4 | ||||||
MIRT565483 | SPRTN | SprT-like N-terminal domain | ![]() |
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2 | 2 | ||||||
MIRT568200 | CBX6 | chromobox 6 | ![]() |
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2 | 2 | ||||||
MIRT569754 | C2orf71 | chromosome 2 open reading frame 71 | ![]() |
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2 | 2 | ||||||
MIRT571369 | ZNF45 | zinc finger protein 45 | ![]() |
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2 | 2 | ||||||
MIRT609886 | CLASP1 | cytoplasmic linker associated protein 1 | ![]() |
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2 | 4 | ||||||
MIRT640543 | C3orf36 | chromosome 3 open reading frame 36 | ![]() |
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2 | 2 | ||||||
MIRT640885 | ENTPD1 | ectonucleoside triphosphate diphosphohydrolase 1 | ![]() |
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2 | 2 | ||||||
MIRT643494 | LRCH3 | leucine rich repeats and calponin homology domain containing 3 | ![]() |
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2 | 2 | ||||||
MIRT643627 | YY2 | YY2 transcription factor | ![]() |
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2 | 2 | ||||||
MIRT644384 | ZNF286A | zinc finger protein 286A | ![]() |
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2 | 2 | ||||||
MIRT646126 | SLC26A9 | solute carrier family 26 member 9 | ![]() |
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2 | 2 | ||||||
MIRT655939 | NDUFA4P1 | NDUFA4, mitochondrial complex associated pseudogene 1 | ![]() |
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2 | 2 | ||||||
MIRT656057 | MYLK4 | myosin light chain kinase family member 4 | ![]() |
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2 | 2 | ||||||
MIRT658767 | EIF4EBP2 | eukaryotic translation initiation factor 4E binding protein 2 | ![]() |
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2 | 2 | ||||||
MIRT661583 | EPHX2 | epoxide hydrolase 2 | ![]() |
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2 | 2 | ||||||
MIRT664285 | RNMTL1 | mitochondrial rRNA methyltransferase 3 | ![]() |
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2 | 2 | ||||||
MIRT689391 | ZNF850 | zinc finger protein 850 | ![]() |
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2 | 2 | ||||||
MIRT694530 | TRIM72 | tripartite motif containing 72 | ![]() |
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2 | 2 | ||||||
MIRT694626 | ZFPM1 | zinc finger protein, FOG family member 1 | ![]() |
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2 | 2 | ||||||
MIRT695133 | PRY2 | PTPN13-like, Y-linked 2 | ![]() |
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2 | 2 | ||||||
MIRT695150 | PRY | PTPN13-like, Y-linked | ![]() |
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2 | 2 | ||||||
MIRT697468 | ZC3H4 | zinc finger CCCH-type containing 4 | ![]() |
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2 | 2 | ||||||
MIRT701919 | MLXIP | MLX interacting protein | ![]() |
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2 | 2 | ||||||
MIRT704548 | CNBP | CCHC-type zinc finger nucleic acid binding protein | ![]() |
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2 | 2 | ||||||
MIRT704791 | CDK6 | cyclin dependent kinase 6 | ![]() |
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2 | 2 | ||||||
MIRT705696 | ANKRD13A | ankyrin repeat domain 13A | ![]() |
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2 | 2 | ||||||
MIRT707992 | OTUD4 | OTU deubiquitinase 4 | ![]() |
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2 | 2 | ||||||
MIRT708739 | FAM71F2 | family with sequence similarity 71 member F2 | ![]() |
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2 | 2 | ||||||
MIRT713401 | FAM179A | TOG array regulator of axonemal microtubules 2 | ![]() |
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2 | 2 | ||||||
MIRT713846 | FAM3D | family with sequence similarity 3 member D | ![]() |
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2 | 2 | ||||||
MIRT716998 | ARL6IP4 | ADP ribosylation factor like GTPase 6 interacting protein 4 | ![]() |
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2 | 2 | ||||||
MIRT718511 | DIRAS1 | DIRAS family GTPase 1 | ![]() |
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2 | 2 | ||||||
MIRT718698 | BTBD9 | BTB domain containing 9 | ![]() |
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2 | 2 | ||||||
MIRT719578 | TYRO3 | TYRO3 protein tyrosine kinase | ![]() |
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2 | 2 | ||||||
MIRT720892 | CSGALNACT1 | chondroitin sulfate N-acetylgalactosaminyltransferase 1 | ![]() |
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2 | 2 | ||||||
MIRT722633 | C8A | complement C8 alpha chain | ![]() |
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2 | 2 | ||||||
MIRT723333 | DGAT1 | diacylglycerol O-acyltransferase 1 | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||
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