pre-miRNA Information | |
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pre-miRNA | hsa-mir-4480 |
Genomic Coordinates | chr10: 12578753 - 12578823 |
Description | Homo sapiens miR-4480 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||||||||||||||
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Mature miRNA | hsa-miR-4480 | |||||||||||||||||||||
Sequence | 44| AGCCAAGUGGAAGUUACUUUA |64 | |||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||
Experiments | Illumina | |||||||||||||||||||||
Editing Events in miRNAs |
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SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | PHLDA2 | ||||||||||||||||||||
Synonyms | BRW1C, BWR1C, HLDA2, IPL, TSSC3 | ||||||||||||||||||||
Description | pleckstrin homology like domain family A member 2 | ||||||||||||||||||||
Transcript | NM_003311 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on PHLDA2 | |||||||||||||||||||||
3'UTR of PHLDA2 (miRNA target sites are highlighted) |
>PHLDA2|NM_003311|3'UTR 1 GCCCGCCGCGGGCCATACGCTGGACGAGTCGGACCGAGGCTAGGACGTGGCCGGCGCTCTCCAGCCCTGCAGCAGAAGAA 81 CTTCCCGTGCGCGCGGATCCTCGCTCCGTTGCACGGGCGCCTTAAGTTATTGGACTATCTAATATCTATGTATTTATTTC 161 GCTGGTTCTTTGTAGTCACATATTTTATAGTCTTAATATCTTGTTTTTGCATCACTGTGCCCATTGCAAATAAATCACTT 241 GGCCAGTTTGCTTTTCTACCATCCGGCTGTGGCTCAGTGAGACTCCTGCTGGGAGGGTGGAGGCCCAGGAATGGGCGGGC 321 AGGACACCCTCATCCAGTCCTGCGGGGCTGGTGTGAAAGGCGCTGGGAACCGGCTTTGAATGAATAAATGAATCGTGTCA 401 TCTGCAAAAAAAAAAAAAAAAA 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 | TZM-bl | ||||||
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 GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL
... - 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 GSM1462574 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | TZM-bl / TZM-bl ami BaL |
Location of target site | ENST00000314222.4 | 3UTR | CAAAUAAAUCACUUGGCCAGUUUG |
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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117 hsa-miR-4480 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT056040 | MLLT10 | MLLT10, histone lysine methyltransferase DOT1L cofactor | ![]() |
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2 | 2 | ||||||
MIRT091259 | FXR1 | FMR1 autosomal homolog 1 | ![]() |
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2 | 4 | ||||||
MIRT117347 | MAPRE2 | microtubule associated protein RP/EB family member 2 | ![]() |
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2 | 2 | ||||||
MIRT234960 | ZNF439 | zinc finger protein 439 | ![]() |
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2 | 4 | ||||||
MIRT441356 | ZNF75A | zinc finger protein 75a | ![]() |
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2 | 2 | ||||||
MIRT441426 | STXBP2 | syntaxin binding protein 2 | ![]() |
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2 | 2 | ||||||
MIRT441455 | ZNF488 | zinc finger protein 488 | ![]() |
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2 | 4 | ||||||
MIRT441524 | ZBTB10 | zinc finger and BTB domain containing 10 | ![]() |
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2 | 2 | ||||||
MIRT441576 | EXOC5 | exocyst complex component 5 | ![]() |
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2 | 2 | ||||||
MIRT441597 | ABCB5 | ATP binding cassette subfamily B member 5 | ![]() |
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2 | 6 | ||||||
MIRT441610 | ATP13A4 | ATPase 13A4 | ![]() |
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2 | 2 | ||||||
MIRT441698 | CIT | citron rho-interacting serine/threonine kinase | ![]() |
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2 | 2 | ||||||
MIRT441714 | FGF9 | fibroblast growth factor 9 | ![]() |
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2 | 2 | ||||||
MIRT441784 | MAPK8 | mitogen-activated protein kinase 8 | ![]() |
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2 | 4 | ||||||
MIRT441795 | EXOSC2 | exosome component 2 | ![]() |
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2 | 2 | ||||||
MIRT441868 | RNASEL | ribonuclease L | ![]() |
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2 | 2 | ||||||
MIRT441900 | SLC9A8 | solute carrier family 9 member A8 | ![]() |
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2 | 6 | ||||||
MIRT441919 | FAM217B | family with sequence similarity 217 member B | ![]() |
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2 | 2 | ||||||
MIRT441928 | C1orf109 | chromosome 1 open reading frame 109 | ![]() |
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2 | 2 | ||||||
MIRT441938 | RIMKLB | ribosomal modification protein rimK like family member B | ![]() |
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2 | 2 | ||||||
MIRT442157 | DPY19L1 | dpy-19 like C-mannosyltransferase 1 | ![]() |
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2 | 2 | ||||||
MIRT442172 | AZF1 | azoospermia factor 1 | ![]() |
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2 | 2 | ||||||
MIRT442208 | IRS1 | insulin receptor substrate 1 | ![]() |
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2 | 2 | ||||||
MIRT442237 | DDX19A | DEAD-box helicase 19A | ![]() |
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2 | 2 | ||||||
MIRT442366 | ZC3HAV1L | zinc finger CCCH-type containing, antiviral 1 like | ![]() |
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2 | 2 | ||||||
MIRT442572 | SDC1 | syndecan 1 | ![]() |
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2 | 2 | ||||||
MIRT442604 | ZNF391 | zinc finger protein 391 | ![]() |
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2 | 2 | ||||||
MIRT442609 | MRC1 | mannose receptor C-type 1 | ![]() |
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2 | 2 | ||||||
MIRT442647 | POP4 | POP4 homolog, ribonuclease P/MRP subunit | ![]() |
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2 | 2 | ||||||
MIRT442658 | OIP5 | Opa interacting protein 5 | ![]() |
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2 | 6 | ||||||
MIRT442686 | COX15 | COX15, cytochrome c oxidase assembly homolog | ![]() |
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2 | 2 | ||||||
MIRT442773 | JAG1 | jagged 1 | ![]() |
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2 | 2 | ||||||
MIRT442785 | CHD8 | chromodomain helicase DNA binding protein 8 | ![]() |
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2 | 2 | ||||||
MIRT442895 | PLCB3 | phospholipase C beta 3 | ![]() |
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2 | 2 | ||||||
MIRT442941 | C17orf105 | chromosome 17 open reading frame 105 | ![]() |
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2 | 2 | ||||||
MIRT442959 | SGCD | sarcoglycan delta | ![]() |
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2 | 2 | ||||||
MIRT442998 | EDAR | ectodysplasin A receptor | ![]() |
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2 | 2 | ||||||
MIRT443017 | C21orf91 | chromosome 21 open reading frame 91 | ![]() |
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2 | 2 | ||||||
MIRT443064 | CASP5 | caspase 5 | ![]() |
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2 | 2 | ||||||
MIRT443069 | ABLIM1 | actin binding LIM protein 1 | ![]() |
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2 | 2 | ||||||
MIRT443208 | VPS36 | vacuolar protein sorting 36 homolog | ![]() |
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2 | 2 | ||||||
MIRT443237 | ANKRD26 | ankyrin repeat domain 26 | ![]() |
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2 | 2 | ||||||
MIRT443253 | A1CF | APOBEC1 complementation factor | ![]() |
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2 | 2 | ||||||
MIRT443329 | JUN | Jun proto-oncogene, AP-1 transcription factor subunit | ![]() |
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2 | 2 | ||||||
MIRT443333 | NRAS | NRAS proto-oncogene, GTPase | ![]() |
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2 | 2 | ||||||
MIRT443349 | STX7 | syntaxin 7 | ![]() |
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2 | 2 | ||||||
MIRT443452 | CLIC5 | chloride intracellular channel 5 | ![]() |
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2 | 2 | ||||||
MIRT443547 | GPR35 | G protein-coupled receptor 35 | ![]() |
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2 | 2 | ||||||
MIRT443616 | AVPR1A | arginine vasopressin receptor 1A | ![]() |
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2 | 2 | ||||||
MIRT443626 | CPSF2 | cleavage and polyadenylation specific factor 2 | ![]() |
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2 | 2 | ||||||
MIRT443730 | ALPK3 | alpha kinase 3 | ![]() |
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2 | 2 | ||||||
MIRT443786 | ST13 | ST13, Hsp70 interacting protein | ![]() |
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2 | 2 | ||||||
MIRT443852 | RGS6 | regulator of G protein signaling 6 | ![]() |
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2 | 2 | ||||||
MIRT445483 | KLF5 | Kruppel like factor 5 | ![]() |
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2 | 2 | ||||||
MIRT471105 | PHLDA2 | pleckstrin homology like domain family A member 2 | ![]() |
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2 | 2 | ||||||
MIRT472329 | NETO2 | neuropilin and tolloid like 2 | ![]() |
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2 | 4 | ||||||
MIRT472391 | NDRG3 | NDRG family member 3 | ![]() |
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2 | 2 | ||||||
MIRT473522 | MAX | MYC associated factor X | ![]() |
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2 | 2 | ||||||
MIRT473874 | MAFK | MAF bZIP transcription factor K | ![]() |
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2 | 6 | ||||||
MIRT476021 | GTF2A1 | general transcription factor IIA subunit 1 | ![]() |
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2 | 2 | ||||||
MIRT478320 | DDN | dendrin | ![]() |
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2 | 2 | ||||||
MIRT492049 | TNFSF9 | TNF superfamily member 9 | ![]() |
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2 | 2 | ||||||
MIRT494851 | ANKRD24 | ankyrin repeat domain 24 | ![]() |
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2 | 2 | ||||||
MIRT494991 | TSSC1 | EARP complex and GARP complex interacting protein 1 | ![]() |
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2 | 2 | ||||||
MIRT495034 | RASSF2 | Ras association domain family member 2 | ![]() |
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2 | 2 | ||||||
MIRT495111 | NOL10 | nucleolar protein 10 | ![]() |
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2 | 2 | ||||||
MIRT495113 | TRADD | TNFRSF1A associated via death domain | ![]() |
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2 | 2 | ||||||
MIRT495131 | METTL24 | methyltransferase like 24 | ![]() |
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2 | 2 | ||||||
MIRT495147 | STAC2 | SH3 and cysteine rich domain 2 | ![]() |
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2 | 2 | ||||||
MIRT495297 | NUP54 | nucleoporin 54 | ![]() |
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2 | 2 | ||||||
MIRT495341 | RTN2 | reticulon 2 | ![]() |
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2 | 2 | ||||||
MIRT495347 | ATP5S | ATP synthase, H+ transporting, mitochondrial Fo complex subunit s (factor B) | ![]() |
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2 | 2 | ||||||
MIRT496682 | DUSP18 | dual specificity phosphatase 18 | ![]() |
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2 | 2 | ||||||
MIRT496743 | TGFBR1 | transforming growth factor beta receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT496841 | KCNIP2 | potassium voltage-gated channel interacting protein 2 | ![]() |
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2 | 2 | ||||||
MIRT496852 | GPAM | glycerol-3-phosphate acyltransferase, mitochondrial | ![]() |
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2 | 2 | ||||||
MIRT496889 | FOXP1 | forkhead box P1 | ![]() |
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2 | 2 | ||||||
MIRT496922 | CLMN | calmin | ![]() |
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2 | 2 | ||||||
MIRT496990 | TMEM231 | transmembrane protein 231 | ![]() |
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2 | 2 | ||||||
MIRT497002 | SNAP25 | synaptosome associated protein 25 | ![]() |
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2 | 2 | ||||||
MIRT497058 | C6orf223 | chromosome 6 open reading frame 223 | ![]() |
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2 | 2 | ||||||
MIRT500529 | YWHAZ | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta | ![]() |
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2 | 6 | ||||||
MIRT506048 | PPP6C | protein phosphatase 6 catalytic subunit | ![]() |
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2 | 4 | ||||||
MIRT512163 | CD164 | CD164 molecule | ![]() |
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2 | 6 | ||||||
MIRT527051 | RDH13 | retinol dehydrogenase 13 | ![]() |
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2 | 2 | ||||||
MIRT532282 | TNFSF14 | TNF superfamily member 14 | ![]() |
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2 | 2 | ||||||
MIRT534083 | SPRY4 | sprouty RTK signaling antagonist 4 | ![]() |
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2 | 2 | ||||||
MIRT534605 | RNASEH1 | ribonuclease H1 | ![]() |
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2 | 4 | ||||||
MIRT539509 | ACSS3 | acyl-CoA synthetase short chain family member 3 | ![]() |
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2 | 2 | ||||||
MIRT543069 | ARID4B | AT-rich interaction domain 4B | ![]() |
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2 | 2 | ||||||
MIRT544233 | CCBL2 | kynurenine aminotransferase 3 | ![]() |
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2 | 2 | ||||||
MIRT544686 | ZNF224 | zinc finger protein 224 | ![]() |
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2 | 4 | ||||||
MIRT546269 | TMEM30A | transmembrane protein 30A | ![]() |
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2 | 4 | ||||||
MIRT559069 | C19orf47 | chromosome 19 open reading frame 47 | ![]() |
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2 | 2 | ||||||
MIRT562768 | RMI2 | RecQ mediated genome instability 2 | ![]() |
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2 | 2 | ||||||
MIRT563974 | HCFC1 | host cell factor C1 | ![]() |
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2 | 2 | ||||||
MIRT564086 | NSA2 | NSA2, ribosome biogenesis homolog | ![]() |
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2 | 2 | ||||||
MIRT564525 | PDXP | pyridoxal phosphatase | ![]() |
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2 | 2 | ||||||
MIRT564613 | ZNF703 | zinc finger protein 703 | ![]() |
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2 | 2 | ||||||
MIRT566252 | PTBP1 | polypyrimidine tract binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT614420 | ZNF440 | zinc finger protein 440 | ![]() |
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2 | 2 | ||||||
MIRT618789 | MTHFR | methylenetetrahydrofolate reductase | ![]() |
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2 | 2 | ||||||
MIRT619160 | PPDPF | pancreatic progenitor cell differentiation and proliferation factor | ![]() |
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2 | 2 | ||||||
MIRT641778 | ZDHHC7 | zinc finger DHHC-type containing 7 | ![]() |
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2 | 4 | ||||||
MIRT653680 | SLC25A36 | solute carrier family 25 member 36 | ![]() |
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2 | 2 | ||||||
MIRT657861 | GJD2 | gap junction protein delta 2 | ![]() |
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2 | 2 | ||||||
MIRT660879 | ADCYAP1R1 | ADCYAP receptor type I | ![]() |
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2 | 2 | ||||||
MIRT668781 | DAAM1 | dishevelled associated activator of morphogenesis 1 | ![]() |
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2 | 4 | ||||||
MIRT688559 | DCAF16 | DDB1 and CUL4 associated factor 16 | ![]() |
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2 | 2 | ||||||
MIRT695393 | WDR41 | WD repeat domain 41 | ![]() |
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2 | 2 | ||||||
MIRT698680 | TCEA1 | transcription elongation factor A1 | ![]() |
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2 | 2 | ||||||
MIRT700974 | PDIA6 | protein disulfide isomerase family A member 6 | ![]() |
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2 | 2 | ||||||
MIRT705055 | C5orf15 | chromosome 5 open reading frame 15 | ![]() |
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2 | 2 | ||||||
MIRT705864 | AFF1 | AF4/FMR2 family member 1 | ![]() |
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2 | 2 | ||||||
MIRT710586 | CDCA4 | cell division cycle associated 4 | ![]() |
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2 | 2 | ||||||
MIRT713904 | IGF2R | insulin like growth factor 2 receptor | ![]() |
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2 | 2 | ||||||
MIRT717133 | SKI | SKI proto-oncogene | ![]() |
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2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||
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