pre-miRNA Information | |
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pre-miRNA | hsa-mir-124-1 |
Genomic Coordinates | chr8: 9903388 - 9903472 |
Description | Homo sapiens miR-124-1 stem-loop |
Comment | miR-124 was first identified by cloning studies in mouse . The 5' end of the miRNA may be offset with respect to previous annotations. |
RNA Secondary Structure | |
Associated Diseases | |
pre-miRNA | hsa-mir-124-2 |
Genomic Coordinates | chr8: 64379149 - 64379257 |
Description | Homo sapiens miR-124-2 stem-loop |
Comment | miR-124 was first identified by cloning studies in mouse . The 5' end of the miRNA may be offset with respect to previous annotations. |
RNA Secondary Structure | |
Associated Diseases | |
pre-miRNA | hsa-mir-124-3 |
Genomic Coordinates | chr20: 63178500 - 63178586 |
Description | Homo sapiens miR-124-3 stem-loop |
Comment | miR-124 was first identified by cloning studies in mouse . The 5' end of the miRNA may be offset with respect to previous annotations. |
RNA Secondary Structure | |
Associated Diseases |
Mature miRNA Information | |||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-124-5p | ||||||||||||||||||||||||||||||
Sequence | 14| CGUGUUCACAGCGGACCUUGAU |35 | ||||||||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||||||||
Experiments | Cloned | ||||||||||||||||||||||||||||||
Editing Events in miRNAs |
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SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Biomarker Information |
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Gene Information | |||||||||||||||||||||
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Gene Symbol | HLA-DRA | ||||||||||||||||||||
Synonyms | HLA-DRA1 | ||||||||||||||||||||
Description | major histocompatibility complex, class II, DR alpha | ||||||||||||||||||||
Transcript | NM_019111 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on HLA-DRA | |||||||||||||||||||||
3'UTR of HLA-DRA (miRNA target sites are highlighted) |
>HLA-DRA|NM_019111|3'UTR 1 GGCACATGGAGGTGATGGTGTTTCTTAGAGAGAAGATCACTGAAGAAACTTCTGCTTTAATGGCTTTACAAAGCTGGCAA 81 TATTACAATCCTTGACCTCAGTGAAAGCAGTCATCTTCAGCATTTTCCAGCCCTATAGCCACCCCAAGTGTGGATATGCC 161 TCTTCGATTGCTCCGTACTCTAACATCTAGCTGGCTTCCCTGTCTATTGCCTTTTCCTGTATCTATTTTCCTCTATTTCC 241 TATCATTTTATTATCACCATGCAATGCCTCTGGAATAAAACATACAGGAGTCTGTCTCTGCTATGGAATGCCCCATGGGG 321 CATCTCTTGTGTACTTATTGTTTAAGGTTTCCTCAAACTGTGATTTTTCTGAACACAATAAACTATTTTGATGATCTTGG 401 GTGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 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 | C8166 | ||||||
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 GSM1462572. RNA binding protein: AGO2. Condition:C8166 NL4-3
... - Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Whisnant AW; Bogerd HP; Flores O; Ho P; et al. - mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
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CLIP-seq Support 1 for dataset GSM1462572 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | C8166 / C8166 NL4-3 |
Location of target site | ENST00000395388.2 | 3UTR | UUUCCUCAAACUGUGAUUUUUCUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23592263 / GSE59944 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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MiRNA-Target Expression Profile (TCGA) | ||||||||||||||||||||||||||||
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65 hsa-miR-124-5p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT064177 | KIAA1804 | mitogen-activated protein kinase kinase kinase 21 | 2 | 2 | ||||||||
MIRT069736 | FOXG1 | forkhead box G1 | 2 | 4 | ||||||||
MIRT086429 | NABP1 | nucleic acid binding protein 1 | 2 | 6 | ||||||||
MIRT105334 | SLC7A2 | solute carrier family 7 member 2 | 2 | 4 | ||||||||
MIRT110455 | PLEKHA1 | pleckstrin homology domain containing A1 | 2 | 2 | ||||||||
MIRT172998 | YTHDF3 | YTH N6-methyladenosine RNA binding protein 3 | 2 | 2 | ||||||||
MIRT196428 | TAOK1 | TAO kinase 1 | 2 | 14 | ||||||||
MIRT325704 | CSTF2 | cleavage stimulation factor subunit 2 | 2 | 2 | ||||||||
MIRT365670 | TSC22D3 | TSC22 domain family member 3 | 2 | 4 | ||||||||
MIRT365873 | XIAP | X-linked inhibitor of apoptosis | 2 | 2 | ||||||||
MIRT404126 | ASB1 | ankyrin repeat and SOCS box containing 1 | 2 | 2 | ||||||||
MIRT404626 | LCOR | ligand dependent nuclear receptor corepressor | 2 | 2 | ||||||||
MIRT405284 | ARF1 | ADP ribosylation factor 1 | 2 | 2 | ||||||||
MIRT406099 | PAGR1 | PAXIP1 associated glutamate rich protein 1 | 2 | 2 | ||||||||
MIRT446627 | SDC3 | syndecan 3 | 2 | 2 | ||||||||
MIRT446906 | RGS5 | regulator of G protein signaling 5 | 2 | 2 | ||||||||
MIRT461790 | FXR2 | FMR1 autosomal homolog 2 | 2 | 2 | ||||||||
MIRT463982 | WEE1 | WEE1 G2 checkpoint kinase | 2 | 4 | ||||||||
MIRT464204 | VGLL4 | vestigial like family member 4 | 2 | 2 | ||||||||
MIRT472790 | MTMR4 | myotubularin related protein 4 | 2 | 4 | ||||||||
MIRT473485 | MCFD2 | multiple coagulation factor deficiency 2 | 2 | 2 | ||||||||
MIRT481124 | AZIN1 | antizyme inhibitor 1 | 2 | 4 | ||||||||
MIRT485060 | SUCO | SUN domain containing ossification factor | 2 | 2 | ||||||||
MIRT487343 | HLA-DRA | major histocompatibility complex, class II, DR alpha | 2 | 2 | ||||||||
MIRT491948 | VPS52 | VPS52, GARP complex subunit | 2 | 2 | ||||||||
MIRT497208 | CDH7 | cadherin 7 | 2 | 2 | ||||||||
MIRT497476 | TOR1AIP2 | torsin 1A interacting protein 2 | 2 | 2 | ||||||||
MIRT528203 | NELFE | negative elongation factor complex member E | 2 | 2 | ||||||||
MIRT529255 | TRIM4 | tripartite motif containing 4 | 2 | 4 | ||||||||
MIRT530096 | PSAPL1 | prosaposin like 1 (gene/pseudogene) | 2 | 2 | ||||||||
MIRT530597 | C7orf33 | chromosome 7 open reading frame 33 | 2 | 4 | ||||||||
MIRT534980 | PSAT1 | phosphoserine aminotransferase 1 | 2 | 4 | ||||||||
MIRT538326 | CSGALNACT1 | chondroitin sulfate N-acetylgalactosaminyltransferase 1 | 2 | 2 | ||||||||
MIRT561237 | ZNF652 | zinc finger protein 652 | 2 | 2 | ||||||||
MIRT562035 | KRAS | KRAS proto-oncogene, GTPase | 2 | 2 | ||||||||
MIRT563120 | THAP5 | THAP domain containing 5 | 2 | 2 | ||||||||
MIRT563538 | RBM41 | RNA binding motif protein 41 | 2 | 2 | ||||||||
MIRT566037 | REV3L | REV3 like, DNA directed polymerase zeta catalytic subunit | 2 | 2 | ||||||||
MIRT566505 | PAWR | pro-apoptotic WT1 regulator | 2 | 2 | ||||||||
MIRT566745 | MRPL35 | mitochondrial ribosomal protein L35 | 2 | 2 | ||||||||
MIRT566850 | LRRC58 | leucine rich repeat containing 58 | 2 | 2 | ||||||||
MIRT568077 | CELF2 | CUGBP Elav-like family member 2 | 2 | 2 | ||||||||
MIRT576826 | Tgfbr3 | transforming growth factor, beta receptor III | 2 | 2 | ||||||||
MIRT608870 | NR2E1 | nuclear receptor subfamily 2 group E member 1 | 2 | 4 | ||||||||
MIRT611997 | VAC14 | Vac14, PIKFYVE complex component | 2 | 2 | ||||||||
MIRT614054 | FAM89A | family with sequence similarity 89 member A | 2 | 2 | ||||||||
MIRT618800 | SPATA21 | spermatogenesis associated 21 | 2 | 2 | ||||||||
MIRT619389 | RSPH3 | radial spoke head 3 homolog | 2 | 2 | ||||||||
MIRT622282 | SH3TC2 | SH3 domain and tetratricopeptide repeats 2 | 2 | 2 | ||||||||
MIRT624026 | EN2 | engrailed homeobox 2 | 2 | 2 | ||||||||
MIRT626000 | MPEG1 | macrophage expressed 1 | 2 | 2 | ||||||||
MIRT641792 | USP32 | ubiquitin specific peptidase 32 | 2 | 2 | ||||||||
MIRT651599 | WDFY2 | WD repeat and FYVE domain containing 2 | 2 | 2 | ||||||||
MIRT659662 | CDC73 | cell division cycle 73 | 2 | 2 | ||||||||
MIRT663010 | KIAA1586 | KIAA1586 | 2 | 2 | ||||||||
MIRT663561 | ASTN2 | astrotactin 2 | 2 | 2 | ||||||||
MIRT669312 | C16orf72 | chromosome 16 open reading frame 72 | 2 | 2 | ||||||||
MIRT685216 | POTED | POTE ankyrin domain family member D | 2 | 2 | ||||||||
MIRT695757 | ZNF117 | zinc finger protein 117 | 2 | 2 | ||||||||
MIRT697909 | TXNRD1 | thioredoxin reductase 1 | 2 | 2 | ||||||||
MIRT707181 | RPH3A | rabphilin 3A | 2 | 2 | ||||||||
MIRT707214 | TRIM13 | tripartite motif containing 13 | 2 | 2 | ||||||||
MIRT707478 | SLCO4C1 | solute carrier organic anion transporter family member 4C1 | 2 | 2 | ||||||||
MIRT719507 | LMAN2L | lectin, mannose binding 2 like | 2 | 2 | ||||||||
MIRT755814 | PARP1 | poly(ADP-ribose) polymerase 1 | 2 | 1 |
miRNA-Drug Associations | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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