pre-miRNA Information | |
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pre-miRNA | hsa-mir-569 |
Genomic Coordinates | chr3: 171106664 - 171106759 |
Synonyms | MIRN569, hsa-mir-569, MIR569 |
Description | Homo sapiens miR-569 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Associated Diseases | ![]() |
Mature miRNA Information | ||||||||||||||||
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Mature miRNA | hsa-miR-569 | |||||||||||||||
Sequence | 61| AGUUAAUGAAUCCUGGAAAGU |81 | |||||||||||||||
Evidence | Experimental | |||||||||||||||
Experiments | SAGE | DRVs in miRNA |
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SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | RNF6 | ||||||||||||||||||||
Synonyms | - | ||||||||||||||||||||
Description | ring finger protein 6 | ||||||||||||||||||||
Transcript | NM_183043 | ||||||||||||||||||||
Other Transcripts | NM_005977 , NM_183044 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on RNF6 | |||||||||||||||||||||
3'UTR of RNF6 (miRNA target sites are highlighted) |
>RNF6|NM_183043|3'UTR 1 GGTGATGGGATCTACTCAAATACTGTTTTTTAGTAGAACTGAATGTTCAAGCATTGTTTTGCTGAGTTATTTGTGATTAG 81 CTAACCAGGATGAAAAATAACAGATTATATATAGTTTGAACTATTTTTCGTGTGCTTTTTTAAACTTGTTAAAAAGAAAT 161 TTATATAAAATTTAAAATACAAATGTTAAATTATCCAGAAATACAGAATAGTTAATATTGCTAGAACCAAATAACCTCTA 241 AAATGTTTTTATTTTGGTAATTTTGTCATGCTAAGCACTTTTGTATCTGCACAATTCAGTAGGTTAAGAATCAATCTTCT 321 TTTTCTTAATAGTACAGCAGACTTTAGCTTCAAGTTTCATAGGCTTAGTACTTATATCTAGACATTTGTGTCTAAATAAG 401 CTTTTCATTAACTTTTTATTTTAAGGACAGTATCTTTTCATGAAAGAGTATTTGGCTGAATGTTTGCTATATATATGTTA 481 CTTGAAATGTTAAATTTAATATGCAGCATACCATAGGTGTATATATAGGTATATAATTTTAAGGTTAAAATATTCAGTCT 561 ACAAGTTTGGTTCTTATTTAAGCTTTTGGGCTAATACTGCATATGGCACAATGTTTAATATTGGCAAGTTCATCTCAGAG 641 AAAGGGGATTCAGATATAATTTTAAAGTAGAGATAATTTACTGAAGCGTCTCTGACAATCTAACTTATTAGACAGCAAGC 721 AATATATAATACTGAAAAAGTATTCAGAAATGGAAAATTTACATCATATAGGTTATTTAACTTGTGTTCAGCCTTTTTGT 801 AACTTTTTTGAAAGTGCAAACAATTCTTTGGATTATTAAATAAGGTATACAGTATGCATGGTTTCTCAAATTTAGTTTTA 881 AAATCTAAAAGTCTATAAAGAATCAGATGCATAGGCAATATGTTAAGTTCACTTGGAGGCTAAAAATCTCCAGTGAAAAC 961 AAAACGAAAACCTTTAAGAGAATGTAGAGTTTATATAAACACAAAGTATGCATTGAAGATCTGTTTCTACCAATAAACAT 1041 TAAAACAAAGACTGTAAAAAAAAAAAAAAA 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 | 6049.0 | ||||||
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. |
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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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CLIP-seq Support 1 for dataset GSM714645 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repB |
Location of target site | ENST00000346166.3 | 3UTR | CUUUUCAUUAACUUUUUAUUUUAAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 21572407 / GSE28865 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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58 hsa-miR-569 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT004827 | SPI1 | Spi-1 proto-oncogene | ![]() |
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2 | 1 | ||||||
MIRT086537 | HSPE1-MOB4 | HSPE1-MOB4 readthrough | ![]() |
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2 | 2 | ||||||
MIRT086545 | MOB4 | MOB family member 4, phocein | ![]() |
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2 | 2 | ||||||
MIRT154349 | PARD6B | par-6 family cell polarity regulator beta | ![]() |
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2 | 4 | ||||||
MIRT182174 | POU2F1 | POU class 2 homeobox 1 | ![]() |
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2 | 2 | ||||||
MIRT190452 | EIF5 | eukaryotic translation initiation factor 5 | ![]() |
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2 | 2 | ||||||
MIRT191410 | NAA30 | N(alpha)-acetyltransferase 30, NatC catalytic subunit | ![]() |
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2 | 2 | ||||||
MIRT199846 | CSNK1G2 | casein kinase 1 gamma 2 | ![]() |
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2 | 2 | ||||||
MIRT208376 | SLC25A36 | solute carrier family 25 member 36 | ![]() |
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2 | 2 | ||||||
MIRT275677 | CARKD | NAD(P)HX dehydratase | ![]() |
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2 | 2 | ||||||
MIRT275764 | TFDP1 | transcription factor Dp-1 | ![]() |
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2 | 2 | ||||||
MIRT280470 | UBR7 | ubiquitin protein ligase E3 component n-recognin 7 (putative) | ![]() |
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2 | 2 | ||||||
MIRT296592 | FAM217B | family with sequence similarity 217 member B | ![]() |
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2 | 4 | ||||||
MIRT306847 | FYTTD1 | forty-two-three domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT443764 | HLF | HLF, PAR bZIP transcription factor | ![]() |
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2 | 2 | ||||||
MIRT448026 | GSR | glutathione-disulfide reductase | ![]() |
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2 | 2 | ||||||
MIRT448659 | NCALD | neurocalcin delta | ![]() |
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2 | 2 | ||||||
MIRT449142 | UQCRB | ubiquinol-cytochrome c reductase binding protein | ![]() |
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2 | 2 | ||||||
MIRT449225 | RAD51B | RAD51 paralog B | ![]() |
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2 | 2 | ||||||
MIRT462421 | TWISTNB | TWIST neighbor | ![]() |
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2 | 2 | ||||||
MIRT468478 | SESN3 | sestrin 3 | ![]() |
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2 | 4 | ||||||
MIRT478170 | DENND5B | DENN domain containing 5B | ![]() |
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2 | 2 | ||||||
MIRT478577 | VSIG2 | V-set and immunoglobulin domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT481300 | ATP5G3 | ATP synthase, H+ transporting, mitochondrial Fo complex subunit C3 (subunit 9) | ![]() |
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2 | 16 | ||||||
MIRT485894 | ZFP36 | ZFP36 ring finger protein | ![]() |
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2 | 2 | ||||||
MIRT497242 | FITM2 | fat storage inducing transmembrane protein 2 | ![]() |
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2 | 2 | ||||||
MIRT500282 | ZNF703 | zinc finger protein 703 | ![]() |
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2 | 8 | ||||||
MIRT509536 | RSBN1L | round spermatid basic protein 1 like | ![]() |
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2 | 4 | ||||||
MIRT511835 | GPATCH8 | G-patch domain containing 8 | ![]() |
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2 | 4 | ||||||
MIRT522437 | MON1B | MON1 homolog B, secretory trafficking associated | ![]() |
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2 | 2 | ||||||
MIRT523538 | GLO1 | glyoxalase I | ![]() |
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2 | 4 | ||||||
MIRT527631 | MYBPC1 | myosin binding protein C, slow type | ![]() |
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2 | 4 | ||||||
MIRT528059 | OLAH | oleoyl-ACP hydrolase | ![]() |
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2 | 2 | ||||||
MIRT532549 | TXNL1 | thioredoxin like 1 | ![]() |
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2 | 2 | ||||||
MIRT545503 | NAP1L1 | nucleosome assembly protein 1 like 1 | ![]() |
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2 | 2 | ||||||
MIRT546724 | RNF6 | ring finger protein 6 | ![]() |
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2 | 2 | ||||||
MIRT546737 | RNF141 | ring finger protein 141 | ![]() |
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2 | 2 | ||||||
MIRT550889 | ACTA1 | actin, alpha 1, skeletal muscle | ![]() |
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2 | 2 | ||||||
MIRT554180 | SLC35E2B | solute carrier family 35 member E2B | ![]() |
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2 | 2 | ||||||
MIRT555878 | PAFAH1B2 | platelet activating factor acetylhydrolase 1b catalytic subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT558458 | DCUN1D1 | defective in cullin neddylation 1 domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT560375 | TIMM8A | translocase of inner mitochondrial membrane 8A | ![]() |
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2 | 2 | ||||||
MIRT562672 | AKT3 | AKT serine/threonine kinase 3 | ![]() |
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2 | 2 | ||||||
MIRT563810 | TUBA1B | tubulin alpha 1b | ![]() |
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2 | 2 | ||||||
MIRT564607 | ZNF711 | zinc finger protein 711 | ![]() |
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2 | 2 | ||||||
MIRT564881 | YWHAE | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon | ![]() |
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2 | 2 | ||||||
MIRT566724 | MSL2 | MSL complex subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT566900 | CSRP3 | cysteine and glycine rich protein 3 | ![]() |
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2 | 2 | ||||||
MIRT570002 | COL1A2 | collagen type I alpha 2 chain | ![]() |
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2 | 2 | ||||||
MIRT612300 | ZFP14 | ZFP14 zinc finger protein | ![]() |
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2 | 2 | ||||||
MIRT618334 | ZNF813 | zinc finger protein 813 | ![]() |
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2 | 2 | ||||||
MIRT627658 | RSBN1 | round spermatid basic protein 1 | ![]() |
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2 | 2 | ||||||
MIRT630660 | PLAG1 | PLAG1 zinc finger | ![]() |
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2 | 2 | ||||||
MIRT640802 | MYCL1 | MYCL proto-oncogene, bHLH transcription factor | ![]() |
1 | 1 | |||||||
MIRT651370 | ZBTB21 | zinc finger and BTB domain containing 21 | ![]() |
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2 | 2 | ||||||
MIRT709227 | GPSM2 | G protein signaling modulator 2 | ![]() |
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2 | 2 | ||||||
MIRT712058 | ZBTB34 | zinc finger and BTB domain containing 34 | ![]() |
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2 | 2 | ||||||
MIRT725006 | ZPBP | zona pellucida binding protein | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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