pre-miRNA Information | |
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pre-miRNA | hsa-mir-8067 |
Genomic Coordinates | chr15: 62304658 - 62304734 |
Description | Homo sapiens miR-8067 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||||||||
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Mature miRNA | hsa-miR-8067 | |||||||||||||||
Sequence | 11| CCUAGAAACUGUAAACUUAGUC |32 | |||||||||||||||
Evidence | Experimental | |||||||||||||||
Experiments | Illumina | |||||||||||||||
SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | PPP1R3D | ||||||||||||||||||||
Synonyms | PPP1R6 | ||||||||||||||||||||
Description | protein phosphatase 1 regulatory subunit 3D | ||||||||||||||||||||
Transcript | NM_006242 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on PPP1R3D | |||||||||||||||||||||
3'UTR of PPP1R3D (miRNA target sites are highlighted) |
>PPP1R3D|NM_006242|3'UTR 1 GCCGCGCGGGGACCGGCCACCTGGAGCCTCCACACCTAAGCTGCGCCTCCTGTCATTTCCCTGCTGGGCTCTCACATCTA 81 TCTGGTTGTTCTTCACCACCCTCCAAGTCCTCTGACCTAATTTTCTGCTGCAAGGTCCCCTGGCAGTGGCCCATCCTGTC 161 TTCTACTTGAAACGTCTGAGTCACTTGGTCTAAAAAGTAGCCTCAGGTGGCCAGAAGGCCGAGTTGTGTAATGAGTTGGG 241 GCAGGGTGGTGGGGTAGGTGCATGGGAGGGTGGGCCCTCTGGGGAGGCCCAAGCAGCTTGTTTTGCAAAGGCCCAAGTCC 321 TCCTGCTAGGAAAAGCTTTTGCATGTGTCCTGAATGTGTCTCTGTAAACATAGCTGTTATTTATTATTGTGATGTTGGGA 401 CCTTTAGCCCATAGCGGATGCCTCCTCAGGAATATTCTCGATTTAATAAGCTAAAAAAAAAAAGTTCTGTGTTTGTGCCC 481 ACAGTAAACAGAATGTACAGTGTGACCCACATCGTGGTCCCTCCAGGCATTCCTGCCCCAGGATAAGGAAAACCTGAGCC 561 CACATCTGATTGCCAACGGCTGTAGCCTTCTAACAGTGGGAAACTATTAATAGGCAAGAAATTTCTGCTTTATCAGTCAT 641 CACACAACCATTCCTGGGCATTGAGACTGTCCTGGTTAGGCTGTGTGTCTCCTACATTAACAGCTGGGGAGGAGGGAAAA 721 GCTTCAGACTTTTAAACTAGCAAAACAGTTATTTCTCTGCATTCACAATTCTGATTTCATGTATTTCTCTGTACATGTTT 801 GATCATTATCAGGCCATTCTGTTTAAGTTTGAAACTAAGCATTTTAAGAAGTCTTGCCTCAGTTATTTCAGTTTTCAGGT 881 GACTAGAGAATTTCAGGCAACAGTGCCCTTTGCAATTACCTTTTTGATGATTAAGGTGACTATTTTTATTTCTTGTTAAG 961 CATCAGAAGATGTCAGCATTCATCTTTTGGGAGTCCAGTTACAAGGTGGAACTAGAAGGTGTTTTCAGCAATAGCCAGAG 1041 CACTGGAGGAAAAATAATTGACAAATATTTATACTTTTAAATTGTTTTGAACTGTATTTACATACATCATGTTTTATCAG 1121 GTACCCACCAACTTTATACTTTCTGCCTTCAGATAGAGTTTCTAACATTTTCTAGTTTGTCAGTTTTAAAATATAAAATT 1201 CTTTTATGTTTTTAAACCGTCAACCAAGAAGTCAAGACCACTGTCCCCTGCTGAGTTAGGCAATCACTTAAAACTCCAAA 1281 GAACTCCAGGCTGAGGAGTTCTTTTGGTGCTGAACAGTGGTCTGACAACAGGTGCTAGAATTAAGGTGTGGGAAAAAAAA 1361 AAAAACAGCCAGGAAGGACAAGATCTCCAATTTGTGAAGCTTATGATACAGCTGAAACCAGTCTGATCAATTTTATGCTA 1441 CCTGTCACCAAGAAATTAACTCTAAATTTTTGAATGCTTGTTGGCATCTGTCAAATCAATACTGAAAGGATGCATTTCGG 1521 CTTTTAACCAGTTTGGTTCTGATCATTGCAACCTCTGTGCTTTTATAATTCAAAGAACAAGGATAGCTTTCTTCGGTATC 1601 TTTTAATATAAGAACACTGAATTTTGGCTTGAAATATTGTGACTAAATTGCACAATCTCTGGCTATTAGCACTGTTCACT 1681 ACATTAACATGCAAGAGAGAGAGAAGCCTTGTTACATTTCCTGCTATTTAACAAACTGTCCAATTAGGTCAGCAAGCCTG 1761 TTAGGGCCTTCACTGCTACGCCCCTGGCCCCAAAACAGAGAGCAAGACAGTTGTCCAGAGAATTTAGATATGAGTTAAGA 1841 GCTGCCAGATTTATTTTAAGGCATGTAGAGAATCTCATAATCTATGTGAAAGTCACTTGCCAAAAAGGTTTTGGTTATGA 1921 AAGTGAATGTTATATATTTAATATTAAGTGAACCTCCCGTGCCTTTTAAAAAATACCAACATTATGAAATTTAAAAGCTT 2001 AAATATATTTGCCTAGTTGATAAAGAGGCTGTGGAACAACTGAAGGAGAACTTTCAGACCCTAAAACAGTTATATTACTT 2081 AGATGTTAAAATTTTCTAGTGGGCTGTGCAATTGCTGGGTTGTCCCCCCAAACATATTTTAATATGTTATTTAAAATGAT 2161 TTTACCCAAGCCTAAGTATTAAAGTATATGTGCAAAAACAAAAAAAAAAAAAAAA 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 | 5509.0 |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
...
"HITS-CLIP data was present in GSM714642. 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 GSM714642 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repA |
Location of target site | ENST00000370996.3 | 3UTR | UUAAAAUUUUCUAGUGGGCUGUGCAAUUG |
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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68 hsa-miR-8067 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT084581 | BCL2L11 | BCL2 like 11 | ![]() |
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2 | 4 | ||||||
MIRT088215 | NUP50 | nucleoporin 50 | ![]() |
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2 | 2 | ||||||
MIRT092085 | ABHD5 | abhydrolase domain containing 5 | ![]() |
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2 | 2 | ||||||
MIRT135269 | TMBIM6 | transmembrane BAX inhibitor motif containing 6 | ![]() |
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2 | 8 | ||||||
MIRT175259 | PSAT1 | phosphoserine aminotransferase 1 | ![]() |
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2 | 6 | ||||||
MIRT182508 | KLHL20 | kelch like family member 20 | ![]() |
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2 | 2 | ||||||
MIRT286224 | TMEM97 | transmembrane protein 97 | ![]() |
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2 | 4 | ||||||
MIRT301718 | TEF | TEF, PAR bZIP transcription factor | ![]() |
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2 | 2 | ||||||
MIRT329381 | CCNG1 | cyclin G1 | ![]() |
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2 | 2 | ||||||
MIRT362146 | MTRNR2L6 | MT-RNR2-like 6 | ![]() |
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2 | 4 | ||||||
MIRT366561 | EIF2S3 | eukaryotic translation initiation factor 2 subunit gamma | ![]() |
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2 | 2 | ||||||
MIRT442002 | NDUFV3 | NADH:ubiquinone oxidoreductase subunit V3 | ![]() |
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2 | 2 | ||||||
MIRT442039 | TRPV2 | transient receptor potential cation channel subfamily V member 2 | ![]() |
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2 | 2 | ||||||
MIRT443045 | HPS4 | HPS4, biogenesis of lysosomal organelles complex 3 subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT446861 | SAMD9L | sterile alpha motif domain containing 9 like | ![]() |
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2 | 2 | ||||||
MIRT450346 | LHFPL3 | LHFPL tetraspan subfamily member 3 | ![]() |
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2 | 2 | ||||||
MIRT454306 | ZNF134 | zinc finger protein 134 | ![]() |
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2 | 2 | ||||||
MIRT481951 | ANKRD11 | ankyrin repeat domain 11 | ![]() |
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2 | 2 | ||||||
MIRT484816 | ZNFX1 | zinc finger NFX1-type containing 1 | ![]() |
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2 | 2 | ||||||
MIRT497596 | EBAG9 | estrogen receptor binding site associated, antigen, 9 | ![]() |
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2 | 2 | ||||||
MIRT498620 | MTRNR2L10 | MT-RNR2-like 10 | ![]() |
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2 | 12 | ||||||
MIRT501852 | MTRNR2L8 | MT-RNR2-like 8 | ![]() |
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2 | 15 | ||||||
MIRT502628 | DDX3X | DEAD-box helicase 3, X-linked | ![]() |
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2 | 8 | ||||||
MIRT503298 | GTF2A1 | general transcription factor IIA subunit 1 | ![]() |
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2 | 6 | ||||||
MIRT506789 | KLHL15 | kelch like family member 15 | ![]() |
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2 | 6 | ||||||
MIRT515069 | PLA2G2C | phospholipase A2 group IIC | ![]() |
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2 | 2 | ||||||
MIRT521334 | RPRD2 | regulation of nuclear pre-mRNA domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT523692 | FHL2 | four and a half LIM domains 2 | ![]() |
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2 | 4 | ||||||
MIRT524416 | CNOT6L | CCR4-NOT transcription complex subunit 6 like | ![]() |
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2 | 4 | ||||||
MIRT525526 | FSIP2 | fibrous sheath interacting protein 2 | ![]() |
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2 | 2 | ||||||
MIRT525771 | SOD2 | superoxide dismutase 2 | ![]() |
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2 | 2 | ||||||
MIRT526262 | CCDC169 | coiled-coil domain containing 169 | ![]() |
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2 | 2 | ||||||
MIRT526545 | MDM2 | MDM2 proto-oncogene | ![]() |
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2 | 2 | ||||||
MIRT527522 | CD59 | CD59 molecule (CD59 blood group) | ![]() |
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2 | 2 | ||||||
MIRT530875 | TRUB1 | TruB pseudouridine synthase family member 1 | ![]() |
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2 | 4 | ||||||
MIRT532991 | ZKSCAN8 | zinc finger with KRAB and SCAN domains 8 | ![]() |
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2 | 2 | ||||||
MIRT535581 | NUP35 | nucleoporin 35 | ![]() |
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2 | 2 | ||||||
MIRT536922 | HEPHL1 | hephaestin like 1 | ![]() |
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2 | 2 | ||||||
MIRT540004 | NT5DC3 | 5'-nucleotidase domain containing 3 | ![]() |
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2 | 2 | ||||||
MIRT540779 | SCO1 | SCO1, cytochrome c oxidase assembly protein | ![]() |
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2 | 2 | ||||||
MIRT541006 | ZNF136 | zinc finger protein 136 | ![]() |
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2 | 2 | ||||||
MIRT542072 | ASS1 | argininosuccinate synthase 1 | ![]() |
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2 | 6 | ||||||
MIRT544103 | IPMK | inositol polyphosphate multikinase | ![]() |
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2 | 2 | ||||||
MIRT547669 | KPNA1 | karyopherin subunit alpha 1 | ![]() |
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2 | 4 | ||||||
MIRT549914 | MRPS30 | mitochondrial ribosomal protein S30 | ![]() |
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2 | 2 | ||||||
MIRT551741 | HIST1H2BD | histone cluster 1 H2B family member d | ![]() |
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2 | 2 | ||||||
MIRT556374 | LUZP1 | leucine zipper protein 1 | ![]() |
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2 | 2 | ||||||
MIRT557320 | HIC2 | HIC ZBTB transcriptional repressor 2 | ![]() |
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2 | 2 | ||||||
MIRT561442 | TOB2 | transducer of ERBB2, 2 | ![]() |
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2 | 2 | ||||||
MIRT563938 | TAF7 | TATA-box binding protein associated factor 7 | ![]() |
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2 | 2 | ||||||
MIRT622315 | SEH1L | SEH1 like nucleoporin | ![]() |
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2 | 2 | ||||||
MIRT622334 | SEC63 | SEC63 homolog, protein translocation regulator | ![]() |
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2 | 2 | ||||||
MIRT627928 | KANSL1 | KAT8 regulatory NSL complex subunit 1 | ![]() |
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2 | 2 | ||||||
MIRT636122 | YPEL1 | yippee like 1 | ![]() |
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2 | 2 | ||||||
MIRT644871 | C2orf48 | chromosome 2 open reading frame 48 | ![]() |
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2 | 2 | ||||||
MIRT645105 | LANCL3 | LanC like 3 | ![]() |
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2 | 2 | ||||||
MIRT650430 | BBS9 | Bardet-Biedl syndrome 9 | ![]() |
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2 | 2 | ||||||
MIRT653330 | SMIM18 | small integral membrane protein 18 | ![]() |
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2 | 2 | ||||||
MIRT658101 | FOXN3 | forkhead box N3 | ![]() |
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2 | 2 | ||||||
MIRT690032 | CCDC90B | coiled-coil domain containing 90B | ![]() |
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2 | 2 | ||||||
MIRT697283 | ZNF800 | zinc finger protein 800 | ![]() |
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2 | 2 | ||||||
MIRT700266 | RAP2B | RAP2B, member of RAS oncogene family | ![]() |
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2 | 2 | ||||||
MIRT700310 | RABGEF1 | RAB guanine nucleotide exchange factor 1 | ![]() |
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2 | 2 | ||||||
MIRT705431 | ATP11A | ATPase phospholipid transporting 11A | ![]() |
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2 | 2 | ||||||
MIRT706193 | MED24 | mediator complex subunit 24 | ![]() |
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2 | 2 | ||||||
MIRT707928 | PPP1R3D | protein phosphatase 1 regulatory subunit 3D | ![]() |
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2 | 2 | ||||||
MIRT716123 | RPL24 | ribosomal protein L24 | ![]() |
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2 | 2 | ||||||
MIRT720940 | PPP1R3E | protein phosphatase 1 regulatory subunit 3E | ![]() |
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2 | 2 |