pre-miRNA Information | |
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pre-miRNA | hsa-mir-3529 |
Genomic Coordinates | chr15: 88611847 - 88611924 |
Description | Homo sapiens miR-3529 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | ||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-3529-3p | |||||||||||||||||||||||||||
Sequence | 46| AACAACAAAAUCACUAGUCUUCCA |69 | |||||||||||||||||||||||||||
Evidence | Not_experimental | |||||||||||||||||||||||||||
Experiments | ||||||||||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | FZD6 | ||||||||||||||||||||
Synonyms | FZ-6, FZ6, HFZ6, NDNC10 | ||||||||||||||||||||
Description | frizzled class receptor 6 | ||||||||||||||||||||
Transcript | NM_001164615 | ||||||||||||||||||||
Other Transcripts | NM_001164616 , NM_003506 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on FZD6 | |||||||||||||||||||||
3'UTR of FZD6 (miRNA target sites are highlighted) |
>FZD6|NM_001164615|3'UTR 1 AGAACATTTTCTCTCGTTACTCAGAAGCAAATTTGTGTTACACTGGAAGTGACCTATGCACTGTTTTGTAAGAATCACTG 81 TTACATTCTTCTTTTGCACTTAAAGTTGCATTGCCTACTGTTATACTGGAAAAAATAGAGTTCAAGAATAATATGACTCA 161 TTTCACACAAAGGTTAATGACAACAATATACCTGAAAACAGAAATGTGCAGGTTAATAATATTTTTTTAATAGTGTGGGA 241 GGACAGAGTTAGAGGAATCTTCCTTTTCTATTTATGAAGATTCTACTCTTGGTAAGAGTATTTTAAGATGTACTATGCTA 321 TTTTACTTTTTTGATATAAAATCAAGATATTTCTTTGCTGAAGTATTTAAATCTTATCCTTGTATCTTTTTATACATATT 401 TGAAAATAAGCTTATATGTATTTGAACTTTTTTGAAATCCTATTCAAGTATTTTTATCATGCTATTGTGATATTTTAGCA 481 CTTTGGTAGCTTTTACACTGAATTTCTAAGAAAATTGTAAAATAGTCTTCTTTTATACTGTAAAAAAAGATATACCAAAA 561 AGTCTTATAATAGGAATTTAACTTTAAAAACCCACTTATTGATACCTTACCATCTAAAATGTGTGATTTTTATAGTCTCG 641 TTTTAGGAATTTCACAGATCTAAATTATGTAACTGAAATAAGGTGCTTACTCAAAGAGTGTCCACTATTGATTGTATTAT 721 GCTGCTCACTGATCCTTCTGCATATTTAAAATAAAATGTCCTAAAGGGTTAGTAGACAAAATGTTAGTCTTTTGTATATT 801 AGGCCAAGTGCAATTGACTTCCCTTTTTTAATGTTTCATGACCACCCATTGATTGTATTATAACCACTTACAGTTGCTTA 881 TATTTTTTGTTTTAACTTTTGTTTTTTAACATTTAGAATATTACATTTTGTATTATACAGTACCTTTCTCAGACATTTTG 961 TAGAATTCATTTCGGCAGCTCACTAGGATTTTGCTGAACATTAAAAAGTGTGATAGCGATATTAGTGCCAATCAAATGGA 1041 AAAAAGGTAGTTTTAATAAACAAGACACAACGTTTTTATACAACATACTTTAAAATATTAAGGAGTTTTCTTAATTTTGT 1121 TTCCTATTAAGTATTATTCTTTGGGCAAGATTTTCTGATGCTTTTGATTTTCTCTCAATTTAGCATTTGCTTTTGGTTTT 1201 TTTCTCTATTTAGCATTCTGTTAAGGCACAAAAACTATGTACTGTATGGGAAATGTTGTAAATATTACCTTTTCCACATT 1281 TTAAACAGACAACTTTGAATACAAAAACTTTGTTTTGTGTGATCTTTTCATTAATAAAATTATCTTTGTATAAGAAAAAA 1361 AAAAAAAA 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 | 8323.0 |
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. |
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 GSM714644 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repA |
Location of target site | ENST00000358755.4 | 3UTR | AAGGCACAAAAACUAUGUACUGUAUGGGAAAU |
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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101 hsa-miR-3529-3p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT061395 | WEE1 | WEE1 G2 checkpoint kinase | 2 | 2 | ||||||||
MIRT066530 | HMGA2 | high mobility group AT-hook 2 | 2 | 6 | ||||||||
MIRT072699 | SMAD3 | SMAD family member 3 | 2 | 2 | ||||||||
MIRT080963 | LRRC8B | leucine rich repeat containing 8 VRAC subunit B | 2 | 2 | ||||||||
MIRT095081 | SAR1B | secretion associated Ras related GTPase 1B | 2 | 2 | ||||||||
MIRT104782 | FZD6 | frizzled class receptor 6 | 2 | 2 | ||||||||
MIRT161286 | U2SURP | U2 snRNP associated SURP domain containing | 2 | 2 | ||||||||
MIRT176138 | ATP7A | ATPase copper transporting alpha | 2 | 2 | ||||||||
MIRT221376 | DNAJB6 | DnaJ heat shock protein family (Hsp40) member B6 | 2 | 2 | ||||||||
MIRT260611 | SOX4 | SRY-box 4 | 2 | 4 | ||||||||
MIRT269640 | MDM4 | MDM4, p53 regulator | 2 | 4 | ||||||||
MIRT306853 | FYTTD1 | forty-two-three domain containing 1 | 2 | 2 | ||||||||
MIRT315027 | TFAP2A | transcription factor AP-2 alpha | 2 | 2 | ||||||||
MIRT367278 | CRKL | CRK like proto-oncogene, adaptor protein | 2 | 2 | ||||||||
MIRT444211 | TMPRSS4 | transmembrane protease, serine 4 | 2 | 2 | ||||||||
MIRT455829 | ZSWIM1 | zinc finger SWIM-type containing 1 | 2 | 2 | ||||||||
MIRT466299 | TM4SF1 | transmembrane 4 L six family member 1 | 2 | 2 | ||||||||
MIRT467332 | SPATA13 | spermatogenesis associated 13 | 2 | 4 | ||||||||
MIRT469830 | RAB14 | RAB14, member RAS oncogene family | 2 | 2 | ||||||||
MIRT470571 | POU2F1 | POU class 2 homeobox 1 | 2 | 2 | ||||||||
MIRT472094 | NOLC1 | nucleolar and coiled-body phosphoprotein 1 | 2 | 2 | ||||||||
MIRT482529 | ACTB | actin beta | 2 | 4 | ||||||||
MIRT495009 | KRTAP4-9 | keratin associated protein 4-9 | 2 | 4 | ||||||||
MIRT495562 | ZNF169 | zinc finger protein 169 | 2 | 2 | ||||||||
MIRT496742 | PBX2P1 | PBX homeobox 2 pseudogene 1 | 2 | 4 | ||||||||
MIRT500811 | THBS1 | thrombospondin 1 | 2 | 2 | ||||||||
MIRT500846 | SYPL1 | synaptophysin like 1 | 2 | 4 | ||||||||
MIRT504267 | C1orf147 | chromosome 1 open reading frame 147 | 2 | 4 | ||||||||
MIRT504320 | TUSC1 | tumor suppressor candidate 1 | 2 | 6 | ||||||||
MIRT505533 | SPATA2 | spermatogenesis associated 2 | 2 | 4 | ||||||||
MIRT505799 | RSBN1 | round spermatid basic protein 1 | 2 | 4 | ||||||||
MIRT518201 | CLEC4E | C-type lectin domain family 4 member E | 2 | 2 | ||||||||
MIRT520019 | YTHDF1 | YTH N6-methyladenosine RNA binding protein 1 | 2 | 4 | ||||||||
MIRT527321 | NCAM2 | neural cell adhesion molecule 2 | 2 | 2 | ||||||||
MIRT529005 | SIGLEC14 | sialic acid binding Ig like lectin 14 | 2 | 4 | ||||||||
MIRT530312 | TNFRSF10D | TNF receptor superfamily member 10d | 2 | 2 | ||||||||
MIRT532324 | DUSP4 | dual specificity phosphatase 4 | 2 | 2 | ||||||||
MIRT532497 | HOXA13 | homeobox A13 | 2 | 2 | ||||||||
MIRT533203 | WASF3 | WAS protein family member 3 | 2 | 4 | ||||||||
MIRT533376 | UBE2D4 | ubiquitin conjugating enzyme E2 D4 (putative) | 2 | 4 | ||||||||
MIRT534107 | SOWAHC | sosondowah ankyrin repeat domain family member C | 2 | 2 | ||||||||
MIRT537381 | FGF2 | fibroblast growth factor 2 | 2 | 2 | ||||||||
MIRT537487 | FAM169A | family with sequence similarity 169 member A | 2 | 2 | ||||||||
MIRT539210 | ANTXR2 | anthrax toxin receptor 2 | 2 | 4 | ||||||||
MIRT540299 | GFPT1 | glutamine--fructose-6-phosphate transaminase 1 | 2 | 2 | ||||||||
MIRT544610 | FCF1 | FCF1, rRNA-processing protein | 2 | 2 | ||||||||
MIRT547382 | MPRIP | myosin phosphatase Rho interacting protein | 2 | 2 | ||||||||
MIRT551195 | GAB2 | GRB2 associated binding protein 2 | 2 | 2 | ||||||||
MIRT554193 | SLC35D1 | solute carrier family 35 member D1 | 2 | 2 | ||||||||
MIRT554998 | RAB39B | RAB39B, member RAS oncogene family | 2 | 2 | ||||||||
MIRT557252 | CRAMP1L | cramped chromatin regulator homolog 1 | 2 | 2 | ||||||||
MIRT558440 | DDIT4 | DNA damage inducible transcript 4 | 2 | 3 | ||||||||
MIRT558687 | CMIP | c-Maf inducing protein | 2 | 2 | ||||||||
MIRT562111 | ITGB1 | integrin subunit beta 1 | 2 | 2 | ||||||||
MIRT562312 | GATAD2A | GATA zinc finger domain containing 2A | 2 | 2 | ||||||||
MIRT564781 | ZDHHC7 | zinc finger DHHC-type containing 7 | 2 | 2 | ||||||||
MIRT565536 | SON | SON DNA binding protein | 2 | 2 | ||||||||
MIRT567294 | HNRNPA2B1 | heterogeneous nuclear ribonucleoprotein A2/B1 | 2 | 2 | ||||||||
MIRT572337 | SOX5 | SRY-box 5 | 2 | 2 | ||||||||
MIRT572389 | MTX3 | metaxin 3 | 2 | 2 | ||||||||
MIRT575082 | Ddit4 | DNA-damage-inducible transcript 4 | 2 | 3 | ||||||||
MIRT576838 | Tgfbr3 | transforming growth factor, beta receptor III | 2 | 2 | ||||||||
MIRT607441 | SEMA6D | semaphorin 6D | 2 | 4 | ||||||||
MIRT609555 | TCEAL4 | transcription elongation factor A like 4 | 2 | 2 | ||||||||
MIRT612890 | HOOK3 | hook microtubule tethering protein 3 | 2 | 2 | ||||||||
MIRT613611 | TP53 | tumor protein p53 | 2 | 2 | ||||||||
MIRT614708 | TNFRSF21 | TNF receptor superfamily member 21 | 2 | 2 | ||||||||
MIRT616823 | HERC5 | HECT and RLD domain containing E3 ubiquitin protein ligase 5 | 2 | 2 | ||||||||
MIRT620652 | CXCL5 | C-X-C motif chemokine ligand 5 | 2 | 2 | ||||||||
MIRT626770 | CDC14B | cell division cycle 14B | 2 | 2 | ||||||||
MIRT633598 | IBA57 | IBA57 homolog, iron-sulfur cluster assembly | 2 | 2 | ||||||||
MIRT634853 | PTP4A2 | protein tyrosine phosphatase type IVA, member 2 | 2 | 2 | ||||||||
MIRT638138 | TTC26 | tetratricopeptide repeat domain 26 | 2 | 2 | ||||||||
MIRT639574 | GORASP1 | golgi reassembly stacking protein 1 | 2 | 2 | ||||||||
MIRT643710 | ZNF736 | zinc finger protein 736 | 2 | 2 | ||||||||
MIRT644969 | STEAP4 | STEAP4 metalloreductase | 2 | 2 | ||||||||
MIRT645427 | NINJ1 | ninjurin 1 | 2 | 2 | ||||||||
MIRT645939 | HIPK1 | homeodomain interacting protein kinase 1 | 2 | 2 | ||||||||
MIRT646142 | INTS7 | integrator complex subunit 7 | 2 | 2 | ||||||||
MIRT658015 | GABRA4 | gamma-aminobutyric acid type A receptor alpha4 subunit | 2 | 2 | ||||||||
MIRT658995 | DIP2C | disco interacting protein 2 homolog C | 2 | 2 | ||||||||
MIRT675003 | SLC22A17 | solute carrier family 22 member 17 | 2 | 2 | ||||||||
MIRT675553 | SIK1 | salt inducible kinase 1 | 2 | 2 | ||||||||
MIRT675621 | CSE1L | chromosome segregation 1 like | 2 | 2 | ||||||||
MIRT675952 | IDE | insulin degrading enzyme | 2 | 2 | ||||||||
MIRT692250 | POLR3F | RNA polymerase III subunit F | 2 | 2 | ||||||||
MIRT698738 | STX12 | syntaxin 12 | 2 | 2 | ||||||||
MIRT699001 | SPAG9 | sperm associated antigen 9 | 2 | 2 | ||||||||
MIRT703275 | GNG12 | G protein subunit gamma 12 | 2 | 2 | ||||||||
MIRT706268 | MKLN1 | muskelin 1 | 2 | 2 | ||||||||
MIRT707633 | TARDBP | TAR DNA binding protein | 2 | 2 | ||||||||
MIRT709622 | KBTBD6 | kelch repeat and BTB domain containing 6 | 2 | 2 | ||||||||
MIRT712931 | RPF2 | ribosome production factor 2 homolog | 2 | 2 | ||||||||
MIRT713807 | KCNK5 | potassium two pore domain channel subfamily K member 5 | 2 | 2 | ||||||||
MIRT714036 | SYDE2 | synapse defective Rho GTPase homolog 2 | 2 | 2 | ||||||||
MIRT714388 | PDP2 | pyruvate dehyrogenase phosphatase catalytic subunit 2 | 2 | 2 | ||||||||
MIRT714404 | FBXO31 | F-box protein 31 | 2 | 2 | ||||||||
MIRT714599 | HSPA4L | heat shock protein family A (Hsp70) member 4 like | 2 | 2 | ||||||||
MIRT714663 | TPCN2 | two pore segment channel 2 | 2 | 2 | ||||||||
MIRT714882 | GOLPH3 | golgi phosphoprotein 3 | 2 | 2 | ||||||||
MIRT725043 | NDUFAF7 | NADH:ubiquinone oxidoreductase complex assembly factor 7 | 2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||
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