pre-miRNA Information | |
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pre-miRNA | hsa-mir-4708 |
Genomic Coordinates | chr14: 65335117 - 65335183 |
Description | Homo sapiens miR-4708 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||
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Mature miRNA | hsa-miR-4708-5p | ||||||||||||
Sequence | 9| AGAGAUGCCGCCUUGCUCCUU |29 | ||||||||||||
Evidence | Experimental | ||||||||||||
Experiments | Illumina | ||||||||||||
SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
Circulating MicroRNA Expression Profiling |
Gene Information | ||||||||||||||||
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Gene Symbol | GJD2 | |||||||||||||||
Synonyms | CX36, GJA9 | |||||||||||||||
Description | gap junction protein delta 2 | |||||||||||||||
Transcript | NM_020660 | |||||||||||||||
Expression | ||||||||||||||||
Putative miRNA Targets on GJD2 | ||||||||||||||||
3'UTR of GJD2 (miRNA target sites are highlighted) |
>GJD2|NM_020660|3'UTR 1 GAGGGCAGGTTTCATGAAGGTCTGGGGGATGGCAAGG 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. |
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miRNA-target interactions (Provided by authors) |
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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 | ENST00000454994.2 | 3UTR | GACUCCAUCUCAAAA |
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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94 hsa-miR-4708-5p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT095681 | RBM27 | RNA binding motif protein 27 | ![]() |
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2 | 4 | ||||||
MIRT104033 | USP42 | ubiquitin specific peptidase 42 | ![]() |
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2 | 6 | ||||||
MIRT114773 | CMPK1 | cytidine/uridine monophosphate kinase 1 | ![]() |
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2 | 2 | ||||||
MIRT246923 | CCND1 | cyclin D1 | ![]() |
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2 | 2 | ||||||
MIRT392569 | ORAI2 | ORAI calcium release-activated calcium modulator 2 | ![]() |
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2 | 2 | ||||||
MIRT443949 | LRIT3 | leucine rich repeat, Ig-like and transmembrane domains 3 | ![]() |
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2 | 2 | ||||||
MIRT446695 | PAPPA | pappalysin 1 | ![]() |
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2 | 2 | ||||||
MIRT447383 | VOPP1 | vesicular, overexpressed in cancer, prosurvival protein 1 | ![]() |
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2 | 2 | ||||||
MIRT449321 | FAM120AOS | family with sequence similarity 120A opposite strand | ![]() |
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2 | 2 | ||||||
MIRT449717 | C1orf61 | chromosome 1 open reading frame 61 | ![]() |
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2 | 2 | ||||||
MIRT449738 | TAB2 | TGF-beta activated kinase 1/MAP3K7 binding protein 2 | ![]() |
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2 | 2 | ||||||
MIRT450531 | PGLS | 6-phosphogluconolactonase | ![]() |
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2 | 2 | ||||||
MIRT455650 | YARS | tyrosyl-tRNA synthetase | ![]() |
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2 | 2 | ||||||
MIRT458036 | MRPL12 | mitochondrial ribosomal protein L12 | ![]() |
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2 | 2 | ||||||
MIRT463468 | ZC3HAV1L | zinc finger CCCH-type containing, antiviral 1 like | ![]() |
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2 | 2 | ||||||
MIRT466677 | TAF1D | TATA-box binding protein associated factor, RNA polymerase I subunit D | ![]() |
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2 | 4 | ||||||
MIRT467789 | SLC2A14 | solute carrier family 2 member 14 | ![]() |
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2 | 2 | ||||||
MIRT468167 | SGPL1 | sphingosine-1-phosphate lyase 1 | ![]() |
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2 | 2 | ||||||
MIRT468652 | SECISBP2L | SECIS binding protein 2 like | ![]() |
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2 | 6 | ||||||
MIRT469380 | RER1 | retention in endoplasmic reticulum sorting receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT470346 | PPP2R5E | protein phosphatase 2 regulatory subunit B'epsilon | ![]() |
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2 | 2 | ||||||
MIRT472418 | NCKAP1 | NCK associated protein 1 | ![]() |
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2 | 2 | ||||||
MIRT474612 | KLF3 | Kruppel like factor 3 | ![]() |
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2 | 2 | ||||||
MIRT478703 | CSRNP2 | cysteine and serine rich nuclear protein 2 | ![]() |
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2 | 2 | ||||||
MIRT481008 | BBC3 | BCL2 binding component 3 | ![]() |
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2 | 4 | ||||||
MIRT483098 | TFPI | tissue factor pathway inhibitor | ![]() |
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2 | 2 | ||||||
MIRT485113 | SHISA6 | shisa family member 6 | ![]() |
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2 | 2 | ||||||
MIRT497533 | ZNF607 | zinc finger protein 607 | ![]() |
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2 | 2 | ||||||
MIRT500644 | TUBB2A | tubulin beta 2A class IIa | ![]() |
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2 | 6 | ||||||
MIRT500890 | STRN | striatin | ![]() |
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2 | 4 | ||||||
MIRT501900 | MED13 | mediator complex subunit 13 | ![]() |
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2 | 2 | ||||||
MIRT506646 | MAPK1 | mitogen-activated protein kinase 1 | ![]() |
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2 | 4 | ||||||
MIRT512675 | ENO4 | enolase family member 4 | ![]() |
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2 | 2 | ||||||
MIRT516977 | OR7D2 | olfactory receptor family 7 subfamily D member 2 | ![]() |
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2 | 2 | ||||||
MIRT528754 | RPS27 | ribosomal protein S27 | ![]() |
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2 | 6 | ||||||
MIRT539670 | ZBTB44 | zinc finger and BTB domain containing 44 | ![]() |
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2 | 2 | ||||||
MIRT544129 | PPIL1 | peptidylprolyl isomerase like 1 | ![]() |
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2 | 2 | ||||||
MIRT546382 | STOX2 | storkhead box 2 | ![]() |
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2 | 4 | ||||||
MIRT562143 | IGFBP5 | insulin like growth factor binding protein 5 | ![]() |
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2 | 2 | ||||||
MIRT568713 | TMEM30B | transmembrane protein 30B | ![]() |
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2 | 2 | ||||||
MIRT571029 | CENPP | centromere protein P | ![]() |
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2 | 2 | ||||||
MIRT572781 | ZNF277 | zinc finger protein 277 | ![]() |
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2 | 2 | ||||||
MIRT573162 | SLC30A9 | solute carrier family 30 member 9 | ![]() |
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2 | 2 | ||||||
MIRT609126 | NUDT3 | nudix hydrolase 3 | ![]() |
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2 | 2 | ||||||
MIRT609284 | OAS3 | 2'-5'-oligoadenylate synthetase 3 | ![]() |
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2 | 2 | ||||||
MIRT613430 | GALNT6 | polypeptide N-acetylgalactosaminyltransferase 6 | ![]() |
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2 | 2 | ||||||
MIRT613770 | TTC38 | tetratricopeptide repeat domain 38 | ![]() |
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2 | 2 | ||||||
MIRT616645 | LRAT | lecithin retinol acyltransferase | ![]() |
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2 | 4 | ||||||
MIRT630892 | SLC25A33 | solute carrier family 25 member 33 | ![]() |
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2 | 2 | ||||||
MIRT636526 | FAXC | failed axon connections homolog | ![]() |
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2 | 4 | ||||||
MIRT641394 | NUBPL | nucleotide binding protein like | ![]() |
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2 | 2 | ||||||
MIRT641412 | SCN2B | sodium voltage-gated channel beta subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT642528 | CERS4 | ceramide synthase 4 | ![]() |
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2 | 2 | ||||||
MIRT643186 | HYPK | huntingtin interacting protein K | ![]() |
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2 | 2 | ||||||
MIRT647800 | FRMD8 | FERM domain containing 8 | ![]() |
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2 | 2 | ||||||
MIRT652150 | TRIM71 | tripartite motif containing 71 | ![]() |
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2 | 2 | ||||||
MIRT652602 | TIMM8A | translocase of inner mitochondrial membrane 8A | ![]() |
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2 | 2 | ||||||
MIRT661606 | C2orf15 | chromosome 2 open reading frame 15 | ![]() |
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2 | 2 | ||||||
MIRT666339 | SKAP2 | src kinase associated phosphoprotein 2 | ![]() |
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2 | 2 | ||||||
MIRT670414 | ELP2 | elongator acetyltransferase complex subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT671122 | ZNF573 | zinc finger protein 573 | ![]() |
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2 | 2 | ||||||
MIRT671155 | ANKRD9 | ankyrin repeat domain 9 | ![]() |
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2 | 2 | ||||||
MIRT671338 | FAM71F2 | family with sequence similarity 71 member F2 | ![]() |
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2 | 2 | ||||||
MIRT671869 | ZNF429 | zinc finger protein 429 | ![]() |
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2 | 2 | ||||||
MIRT671974 | IKZF3 | IKAROS family zinc finger 3 | ![]() |
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2 | 2 | ||||||
MIRT672064 | KIAA0930 | KIAA0930 | ![]() |
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2 | 2 | ||||||
MIRT672654 | SLC25A16 | solute carrier family 25 member 16 | ![]() |
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2 | 4 | ||||||
MIRT672673 | GTF2H5 | general transcription factor IIH subunit 5 | ![]() |
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2 | 2 | ||||||
MIRT672771 | UBE2V2 | ubiquitin conjugating enzyme E2 V2 | ![]() |
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2 | 2 | ||||||
MIRT672929 | LRRC2 | leucine rich repeat containing 2 | ![]() |
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2 | 2 | ||||||
MIRT673159 | C1orf50 | chromosome 1 open reading frame 50 | ![]() |
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2 | 2 | ||||||
MIRT673272 | RUNDC1 | RUN domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT673332 | THAP1 | THAP domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT673351 | SLC35F6 | solute carrier family 35 member F6 | ![]() |
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2 | 2 | ||||||
MIRT673667 | ZNF440 | zinc finger protein 440 | ![]() |
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2 | 2 | ||||||
MIRT673904 | DCTN6 | dynactin subunit 6 | ![]() |
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2 | 2 | ||||||
MIRT674096 | PLEKHA1 | pleckstrin homology domain containing A1 | ![]() |
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2 | 2 | ||||||
MIRT674401 | MYCBP | MYC binding protein | ![]() |
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2 | 2 | ||||||
MIRT674525 | PRR23A | proline rich 23A | ![]() |
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2 | 2 | ||||||
MIRT674793 | NPR1 | natriuretic peptide receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT674833 | ADAMTS4 | ADAM metallopeptidase with thrombospondin type 1 motif 4 | ![]() |
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2 | 2 | ||||||
MIRT675066 | FGD6 | FYVE, RhoGEF and PH domain containing 6 | ![]() |
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2 | 2 | ||||||
MIRT675080 | CCR6 | C-C motif chemokine receptor 6 | ![]() |
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2 | 2 | ||||||
MIRT675126 | FSD2 | fibronectin type III and SPRY domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT679401 | IL10RB | interleukin 10 receptor subunit beta | ![]() |
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2 | 2 | ||||||
MIRT689229 | RPS19 | ribosomal protein S19 | ![]() |
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2 | 2 | ||||||
MIRT694008 | PPIL4 | peptidylprolyl isomerase like 4 | ![]() |
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2 | 2 | ||||||
MIRT699671 | SFT2D2 | SFT2 domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT706213 | ACOT9 | acyl-CoA thioesterase 9 | ![]() |
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2 | 2 | ||||||
MIRT706548 | GJD2 | gap junction protein delta 2 | ![]() |
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2 | 2 | ||||||
MIRT707418 | RRP7A | ribosomal RNA processing 7 homolog A | ![]() |
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2 | 2 | ||||||
MIRT710648 | GLUL | glutamate-ammonia ligase | ![]() |
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2 | 2 | ||||||
MIRT719393 | NPCA1 | Nasopharyngeal carcinoma 1 | ![]() |
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2 | 2 | ||||||
MIRT720166 | PNPO | pyridoxamine 5'-phosphate oxidase | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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