pre-miRNA Information | |
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pre-miRNA | hsa-mir-4280 |
Genomic Coordinates | chr5: 87114879 - 87114954 |
Description | Homo sapiens miR-4280 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||||||||
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Mature miRNA | hsa-miR-4280 | ||||||||||||||||||
Sequence | 11| GAGUGUAGUUCUGAGCAGAGC |31 | ||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||
Experiments | SOLiD | ||||||||||||||||||
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 | FAM127B |
Experimental Support 1 for Functional miRNA-Target Interaction | |||||||
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miRNA:Target | ---- | ||||||
Validation Method |
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Conditions | HEK293 | ||||||
Disease | 26071.0 | ||||||
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 GSM1065669. RNA binding protein: AGO1. Condition:4-thiouridine
... - Memczak S; Jens M; Elefsinioti A; Torti F; et al., 2013, Nature. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Memczak S; Jens M; Elefsinioti A; Torti F; et al. - Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
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Experimental Support 2 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 GSM4903833 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_a |
Location of target site | NM_001134321 | 3UTR | GCCUUUUGUUCAACACAGUAAGCCCUGCUCCCUUCCCUGCUCUAAUACACUACCUGUACAAAGGUUUUUUCCUUAUUUUUAAUAA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM4903835 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_c |
Location of target site | NM_001134321 | 3UTR | CUUUUGUUCAACACAGUAAGCCCUGCUCCCUUCCCUGCUCUAAUACACUACCUGUACAAAGGUUUUUUCCUUAUUUUUAAUAA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset GSM4903836 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_a |
Location of target site | NM_001134321 | 3UTR | UCUCUCUGAUGGGUGCCUUUUGUUCAACACAGUAAGCCCUGCUCCCUUCCCUGCUCUAAUACACUACCUGUACAAAGGUUUUUUCCUUAUUUUUAAUAA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 for dataset GSM4903837 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_b |
Location of target site | NM_001134321 | 3UTR | UUCAACACAGUAAGCCCUGCUCCCUUCCCUGCUCUAAUACACUACCUGUACAAAGGUUUUUUCCUUAUUUUUAAUAA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 5 for dataset GSM4903838 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_c |
Location of target site | NM_001134321 | 3UTR | AGCUGUCUCUCUGAUGGGUGCCUUUUGUUCAACACAGUAAGCCCUGCUCCCUUCCCUGCUCUAAUACACUACCUGUACAAAGGUUUUUUCCUUAUUUUUAAUAA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 6 for dataset GSM1065669 | |
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Method / RBP | PAR-CLIP / AGO1 |
Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_8 |
Location of target site | ENST00000370775.2 | 3UTR | CUCCCUUCCCUGCUCUAAUACACUACCUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23446348 / GSE43573 |
CLIP-seq Viewer | Link |
CLIP-seq Support 7 for dataset GSM1462572 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | C8166 / C8166 NL4-3 |
Location of target site | ENST00000370775.2 | 3UTR | CUCCCUUCCCUGCUCUAAUACACUACCUG |
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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67 hsa-miR-4280 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT065612 | DAZAP2 | DAZ associated protein 2 | ![]() |
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2 | 10 | ||||||
MIRT084985 | BACH1 | BTB domain and CNC homolog 1 | ![]() |
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2 | 2 | ||||||
MIRT088053 | UBXN2A | UBX domain protein 2A | ![]() |
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2 | 4 | ||||||
MIRT097327 | SCAMP1 | secretory carrier membrane protein 1 | ![]() |
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2 | 2 | ||||||
MIRT099148 | MYLIP | myosin regulatory light chain interacting protein | ![]() |
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2 | 12 | ||||||
MIRT127042 | FAM208B | family with sequence similarity 208 member B | ![]() |
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2 | 4 | ||||||
MIRT140479 | BNIP2 | BCL2 interacting protein 2 | ![]() |
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2 | 6 | ||||||
MIRT154889 | GNAS | GNAS complex locus | ![]() |
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2 | 4 | ||||||
MIRT187983 | MBD6 | methyl-CpG binding domain protein 6 | ![]() |
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2 | 2 | ||||||
MIRT190440 | EIF5 | eukaryotic translation initiation factor 5 | ![]() |
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2 | 2 | ||||||
MIRT240673 | GAPVD1 | GTPase activating protein and VPS9 domains 1 | ![]() |
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2 | 2 | ||||||
MIRT295049 | EVI5L | ecotropic viral integration site 5 like | ![]() |
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2 | 2 | ||||||
MIRT324749 | ACER2 | alkaline ceramidase 2 | ![]() |
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2 | 2 | ||||||
MIRT366075 | FAM127A | retrotransposon Gag like 8C | ![]() |
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2 | 4 | ||||||
MIRT442625 | LOX | lysyl oxidase | ![]() |
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2 | 2 | ||||||
MIRT445224 | TYRP1 | tyrosinase related protein 1 | ![]() |
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2 | 2 | ||||||
MIRT448967 | CCNT2 | cyclin T2 | ![]() |
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2 | 4 | ||||||
MIRT450137 | PFN4 | profilin family member 4 | ![]() |
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2 | 2 | ||||||
MIRT464350 | USP46 | ubiquitin specific peptidase 46 | ![]() |
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2 | 2 | ||||||
MIRT470460 | PPP1R15B | protein phosphatase 1 regulatory subunit 15B | ![]() |
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2 | 2 | ||||||
MIRT473691 | MAPK8 | mitogen-activated protein kinase 8 | ![]() |
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2 | 4 | ||||||
MIRT480188 | CALM2 | calmodulin 2 | ![]() |
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2 | 6 | ||||||
MIRT486355 | PCBD2 | pterin-4 alpha-carbinolamine dehydratase 2 | ![]() |
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2 | 2 | ||||||
MIRT486708 | TROVE2 | TROVE domain family member 2 | ![]() |
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2 | 4 | ||||||
MIRT488337 | SCD | stearoyl-CoA desaturase | ![]() |
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2 | 2 | ||||||
MIRT489322 | PEX26 | peroxisomal biogenesis factor 26 | ![]() |
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2 | 2 | ||||||
MIRT491791 | ZNF24 | zinc finger protein 24 | ![]() |
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2 | 2 | ||||||
MIRT491970 | USP37 | ubiquitin specific peptidase 37 | ![]() |
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2 | 2 | ||||||
MIRT492029 | TWF1 | twinfilin actin binding protein 1 | ![]() |
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2 | 4 | ||||||
MIRT492063 | TMEM245 | transmembrane protein 245 | ![]() |
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2 | 2 | ||||||
MIRT492247 | SLC39A9 | solute carrier family 39 member 9 | ![]() |
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2 | 2 | ||||||
MIRT492254 | SLC35F5 | solute carrier family 35 member F5 | ![]() |
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2 | 2 | ||||||
MIRT492592 | PPIL4 | peptidylprolyl isomerase like 4 | ![]() |
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2 | 2 | ||||||
MIRT493436 | KAT7 | lysine acetyltransferase 7 | ![]() |
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2 | 2 | ||||||
MIRT493470 | IPMK | inositol polyphosphate multikinase | ![]() |
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2 | 2 | ||||||
MIRT493639 | HECTD1 | HECT domain E3 ubiquitin protein ligase 1 | ![]() |
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2 | 2 | ||||||
MIRT493919 | FAM127B | retrotransposon Gag like 8A | ![]() |
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2 | 4 | ||||||
MIRT494639 | ARNTL | aryl hydrocarbon receptor nuclear translocator like | ![]() |
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2 | 2 | ||||||
MIRT500032 | ABCF2 | ATP binding cassette subfamily F member 2 | ![]() |
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2 | 8 | ||||||
MIRT504589 | ADH1B | alcohol dehydrogenase 1B (class I), beta polypeptide | ![]() |
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2 | 4 | ||||||
MIRT505535 | SP4 | Sp4 transcription factor | ![]() |
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2 | 6 | ||||||
MIRT507539 | DNAJB6 | DnaJ heat shock protein family (Hsp40) member B6 | ![]() |
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2 | 6 | ||||||
MIRT508846 | TMCO1 | transmembrane and coiled-coil domains 1 | ![]() |
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2 | 4 | ||||||
MIRT510488 | YWHAZ | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta | ![]() |
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2 | 2 | ||||||
MIRT511402 | IFNAR2 | interferon alpha and beta receptor subunit 2 | ![]() |
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2 | 6 | ||||||
MIRT523252 | HIST1H2AH | histone cluster 1 H2A family member h | ![]() |
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2 | 2 | ||||||
MIRT525939 | C11orf74 | chromosome 11 open reading frame 74 | ![]() |
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2 | 2 | ||||||
MIRT531453 | HSD17B12 | hydroxysteroid 17-beta dehydrogenase 12 | ![]() |
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2 | 2 | ||||||
MIRT533317 | UNKL | unkempt family like zinc finger | ![]() |
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2 | 2 | ||||||
MIRT541034 | STRBP | spermatid perinuclear RNA binding protein | ![]() |
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2 | 8 | ||||||
MIRT546734 | RNF217 | ring finger protein 217 | ![]() |
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2 | 2 | ||||||
MIRT555125 | PTPRJ | protein tyrosine phosphatase, receptor type J | ![]() |
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2 | 2 | ||||||
MIRT556105 | MOAP1 | modulator of apoptosis 1 | ![]() |
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2 | 2 | ||||||
MIRT560205 | AK4 | adenylate kinase 4 | ![]() |
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2 | 2 | ||||||
MIRT561087 | LLPH | LLP homolog, long-term synaptic facilitation | ![]() |
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2 | 2 | ||||||
MIRT566967 | LBR | lamin B receptor | ![]() |
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2 | 2 | ||||||
MIRT567344 | H3F3B | H3 histone family member 3B | ![]() |
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2 | 2 | ||||||
MIRT567863 | DCAF12 | DDB1 and CUL4 associated factor 12 | ![]() |
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2 | 2 | ||||||
MIRT574449 | SCML2 | Scm polycomb group protein like 2 | ![]() |
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2 | 2 | ||||||
MIRT575700 | Map1b | microtubule-associated protein 1B | ![]() |
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2 | 2 | ||||||
MIRT651432 | YIPF6 | Yip1 domain family member 6 | ![]() |
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2 | 2 | ||||||
MIRT659728 | CCDC93 | coiled-coil domain containing 93 | ![]() |
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2 | 2 | ||||||
MIRT686937 | SFT2D3 | SFT2 domain containing 3 | ![]() |
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2 | 2 | ||||||
MIRT699385 | SLC30A6 | solute carrier family 30 member 6 | ![]() |
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2 | 2 | ||||||
MIRT710287 | CSNK1G3 | casein kinase 1 gamma 3 | ![]() |
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2 | 2 | ||||||
MIRT715123 | PANK3 | pantothenate kinase 3 | ![]() |
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2 | 2 | ||||||
MIRT721847 | VLDLR | very low density lipoprotein receptor | ![]() |
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2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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