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 | MED24 | ||||||||||||||||||||
Synonyms | ARC100, CRSP100, CRSP4, DRIP100, MED5, THRAP4, TRAP100 | ||||||||||||||||||||
Description | mediator complex subunit 24 | ||||||||||||||||||||
Transcript | NM_001079518 | ||||||||||||||||||||
Other Transcripts | NM_014815 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on MED24 | |||||||||||||||||||||
3'UTR of MED24 (miRNA target sites are highlighted) |
>MED24|NM_001079518|3'UTR 1 GGGGCTTGGCATGGCCGCAGTGGGGGCTGGGGACTGGCGCAGCCCCAGGCGCCTCCAAGGGAAGCAGTGAGGAAAGATGA 81 GGCATCGTGCCTCACATCCGCTCCACATGGTGCAAGAGCCTCTAGCGGCTTCCAGTTCCCCGCTCCTGACTCCTGACCTC 161 CAGGATGTCTCCCGGTTTCTTCTTTCAAAATTTCCTCTCCATCTGCTGGCACCTGAGGAGAGTGAGCAGCCTGGACCACA 241 AGCCCAGTGGTCACCCCTGTGTGCGCCCGCCCCAGCCCAGGAGTAGTCTTACCTCTGAGGAACTTTCTAGATGCAAAGTG 321 TGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGTGTGTATTTTGTAATATGTGAGGGAAATCTACCTTCGTTCATGT 401 ATAAATAAAGCTCCTCGTGGCTCCCTTTGTGAAAAAAAAAAAAAAAAAAAAA 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 | BCBL-1 |
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 GSM1015448. RNA binding protein: AGO2. Condition:BCBL-1 mRNA
... - Haecker I; Gay LA; Yang Y; Hu J; Morse AM; et al., 2012, PLoS pathogens. |
Article |
- Haecker I; Gay LA; Yang Y; Hu J; Morse AM; et al. - PLoS pathogens, 2012
KSHV is the etiological agent of Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), and a subset of multicentricCastleman's disease (MCD). The fact that KSHV-encoded miRNAs are readily detectable in all KSHV-associated tumors suggests a potential role in viral pathogenesis and tumorigenesis. MiRNA-mediated regulation of gene expression is a complex network with each miRNA having many potential targets, and to date only few KSHV miRNA targets have been experimentally determined. A detailed understanding of KSHV miRNA functions requires high-through putribonomics to globally analyze putative miRNA targets in a cell type-specific manner. We performed Ago HITS-CLIP to identify viral and cellular miRNAs and their cognate targets in two latently KSHV-infected PEL cell lines. Ago HITS-CLIP recovered 1170 and 950 cellular KSHV miRNA targets from BCBL-1 and BC-3, respectively. Importantly, enriched clusters contained KSHV miRNA seed matches in the 3'UTRs of numerous well characterized targets, among them THBS1, BACH1, and C/EBPbeta. KSHV miRNA targets were strongly enriched for genes involved in multiple pathways central for KSHV biology, such as apoptosis, cell cycle regulation, lymphocyte proliferation, and immune evasion, thus further supporting a role in KSHV pathogenesis and potentially tumorigenesis. A limited number of viral transcripts were also enriched by HITS-CLIP including vIL-6 expressed only in a subset of PEL cells during latency. Interestingly, Ago HITS-CLIP revealed extremely high levels of Ago-associated KSHV miRNAs especially in BC-3 cells where more than 70% of all miRNAs are of viral origin. This suggests that in addition to seed match-specific targeting of cellular genes, KSHV miRNAs may also function by hijacking RISCs, thereby contributing to a global de-repression of cellular gene expression due to the loss of regulation by human miRNAs. In summary, we provide an extensive list of cellular and viral miRNA targets representing an important resource to decipher KSHV miRNA function.
LinkOut: [PMID: 22927820]
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CLIP-seq Support 1 for dataset GSM1015448 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | BCBL-1 / BCBL-1 mRNA |
Location of target site | ENST00000394126.1 | 3UTR | UUCUAGAUGCAAAGUGUGUAUGUGUGUGUGUGUGUGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 22927820 / GSE41357 |
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 |