| pre-miRNA Information | |
|---|---|
| pre-miRNA | hsa-mir-499a |
| Genomic Coordinates | chr20: 34990376 - 34990497 |
| Description | Homo sapiens miR-499a stem-loop |
| Comment | The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies . |
| RNA Secondary Structure |  |
| Associated Diseases |  |
| Mature miRNA Information | |||||||||||||||||||||||||||||||
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| Mature miRNA | hsa-miR-499a-3p | ||||||||||||||||||||||||||||||
| Sequence | 70| AACAUCACAGCAAGUCUGUGCU |91 | ||||||||||||||||||||||||||||||
| Evidence | Experimental | ||||||||||||||||||||||||||||||
| Experiments | Cloned | DRVs in miRNA |
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| SNPs in miRNA |
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| Putative Targets | |||||||||||||||||||||||||||||||
| miRNA Expression profile | |
|---|---|
| Human miRNA Tissue Atlas | |
| miRNAs in Extracellular Vesicles |
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| Circulating MicroRNA Expression Profiling | |
| Gene Information | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene Symbol | MYO1D | ||||||||||||||||||||
| Synonyms | PPP1R108, myr4 | ||||||||||||||||||||
| Description | myosin ID | ||||||||||||||||||||
| Transcript | NM_015194 | ||||||||||||||||||||
| Expression | |||||||||||||||||||||
| Putative miRNA Targets on MYO1D | |||||||||||||||||||||
| 3'UTR of MYO1D (miRNA target sites are highlighted) |
>MYO1D|NM_015194|3'UTR 1 CGCCCCGCGGAGGCCTGGCCCGGAGCCCGGCCACACTCCGAGTCCTGGGTCCCAGTCCAGCTGCTGCCTCCCAACCCATG 81 CCCGCTAGAAACCTGCTGCGAGGGCCCCTCCCAGAGGAGCCCCGCCCCTGTAAGATTTCCTTCCTGGTTTTCTGCCTTTG 161 GTATCATCTTCCTCTGTCCTTACTGTCCACGGTCCCTGTTCAATAAGCCAAAGACCCTGGTGCCCCGCCCAGACCCCTGG 241 GCTGACGTCCAGACCAATCTCACCCCAGAGGCAACTGGATGGTGCCTTTAGTTGGTGCGGATGCCCCGTGGCCAGGTCAA 321 GTCAGAGCACCTGGACAGGTGTCCTCCCTGCTGCTGACCCTGCAGAGGGAAGGGGTGGGGATGCAGGACCCCACTCTGCG 401 GGAGCCCCATAGCCACCTCTCTTGCCCAAGGTGAGCCAGCCCTGGGGACCCAGCTCAGGGAGGCTCTGCTCAGAGTTCGG 481 CGGACCCACCCCAACCCAACTCCCAGCCGCCAGCCAAAGCCACTGGGTGAGCAGAGTCACCCACAGGGCCAGCCCCTCAG 561 CCAGGAGCCAGTGGCAGGAGCGGAACAGCCCATCCAGCAGAGTGAGTCCATCCTTCCCAGGTTCTCCCCTGGGAGACTCC 641 CTTTGCCACCAAGGCCCCCACCAGGGCCTCTGACCACCGCTCTGGAGAGGACAGTGTGGCATGCTCCAAGGATCATCTTA 721 CTTAACTCGCAGCCTGTGGCTGTGGTCCTCTTATAGATACTTTCACCGTTTGCAGGGTTGCTAATCAGATACCTGCTGTC 801 ACCACACTTGGGTCAGGAACCCTAATGAGAACGGGGAGCTGCCAGGGTGAGGGCAGCCCTCAGGGTCGGCCGCTTTCCCT 881 CTGGACCACCTCCCGCTGCGTTTCCTACTCAGAGAAACAGCAAGGGCGGGGTCAAGACACGGGATGACGGGAAGCAGGAA 961 GCGGGGCAGCAGCACAGCGTGGGGTCCTGGCACTGCAGGCCAGGCCAGGATGCCCACCCCGCCCTCTACACGGCCCCTTG 1041 GGGCCTGCGCCCGTGAAACTGGTGCCAGGGAGCACTGCCAGCTTGCCAGTTTCTGCCCAGCAAAAGCACGTATGCTTCAG 1121 GGGCCTTCTGAGACCACCTTCCCCACTGAGCCCCAGCTGCTGAGAAGGCCTTGAGGGAAGTAGAGGCTGGGAGCAAATGC 1201 CCCATGCGGTGAGAGGATGAGGGGAGCCTACGCCTCAGGCATGTGGTGAGAGGATGAGGGGGAGGGAGCCAACGCCTCAG 1281 GTGGAGTGGGCAGAGGTGCAAGAGAGGGATGTACTGAAGCTTCTTCCCGTCCTGCCACAGACACTTCTCCTGCCTTCCCA 1361 CCCTGACCCGGCAGAACCCACCAAGTGCCTGTGTGCAGCCTCCTGTGCCTCACCCAGGGCCTGACCCCAGAGTGGTCCCA 1441 ACAACCCGGTCTCATGCCCACTCCCCATCCCTGCTTCCCAAAAATTGCACTGTGTGCAGTTTGCAACAAAGAATCCCGCT 1521 GGCATCCTGTCCTTGGGAACCCTTTCTCATTCTCCAAGCCTGGTCAGCTGCCTGCACAGGCAGAGGTGCCCTCAGCCCAG 1601 ATTAGCAACACTCATAGTTTTGCCAATTACCAGTAGACACTAGTGGAACCATCTAACTGGAACTTCCTCTCTCCTTCCAC 1681 TTATTTCCTCAAACTTGTTGCTTTACACTAGACACATGCAAATGTATGTTTTAAACACACCAAAACAGATCATGCCAAAT 1761 GAGTTGCCTGTCAAAGGCTGGAGGGCAGGAGGAGGGCCTGGGTTTGGGTTCTTTCCTCCCAGCCTTTGGATGGTGCCTTG 1841 GGCCCCTTAGCCCCAGCGCCAGGGCCTCCCAGCTGAGGCCACAGGACAAGCACTTTTTTATGATGTACTAAAAGCCACAG 1921 TATGTGGCAACTGCAAAAGGATCAGGAATTTAGGGTATGATCTCGGTCACGTGTCCCGGGCGCTGAGGGGAAAGGAAGCG 2001 GGCATGATTGTAGACAATGAGGGGGTTCTCTTGATGTAATGAAATGCAATTTTATGGTTTGGTGCAAAAACTCCTATTTT 2081 CCAGTAAATTAACTTTATTTCTAAAGCATATTTTGATTTGCCATCAAGAGCAATAAAGCATTAAATCTTATTTTTAAAGG 2161 TGTTCTGCTTATCTGTCACTGAAAACTTGGTGAAATTTTTGCTTAAATAAAGTCAACCATTATCTGGGAGGATAGAAAAA 2241 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 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 | |||||||
|---|---|---|---|---|---|---|---|
| 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 GSM1462573. RNA binding protein: AGO2. Condition:TZM-bl 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 GSM1462573 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | TZM-bl / TZM-bl BaL |
| Location of target site | ENST00000318217.5 | 3UTR | ACAAGCACUUUUUUAUG |
| 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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59 hsa-miR-499a-3p Target Genes:
Functional analysis:
ID |
Target | Description | Validation methods |
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| Strong evidence | Less strong evidence | |||||||||||
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| MIRT130131 | TXNIP | thioredoxin interacting protein |  |
|
2 | 2 | ||||||
| MIRT133678 | ETNK1 | ethanolamine kinase 1 | |
|
2 | 2 | ||||||
| MIRT252103 | NAPG | NSF attachment protein gamma | |
|
2 | 2 | ||||||
| MIRT260160 | IGFBP4 | insulin like growth factor binding protein 4 | |
|
2 | 2 | ||||||
| MIRT388009 | DR1 | down-regulator of transcription 1 | |
|
2 | 2 | ||||||
| MIRT441692 | ABLIM1 | actin binding LIM protein 1 | |
|
2 | 6 | ||||||
| MIRT447799 | EPC2 | enhancer of polycomb homolog 2 | |
|
2 | 2 | ||||||
| MIRT450657 | STYX | serine/threonine/tyrosine interacting protein | |
|
2 | 4 | ||||||
| MIRT456843 | ZNF460 | zinc finger protein 460 | |
|
2 | 2 | ||||||
| MIRT464134 | VPS35 | VPS35, retromer complex component | |
|
2 | 2 | ||||||
| MIRT465101 | TSC22D3 | TSC22 domain family member 3 | |
|
2 | 4 | ||||||
| MIRT470051 | PTGFRN | prostaglandin F2 receptor inhibitor | |
|
2 | 2 | ||||||
| MIRT474146 | LIMA1 | LIM domain and actin binding 1 | |
|
2 | 6 | ||||||
| MIRT474153 | LIFR | LIF receptor alpha | |
|
2 | 2 | ||||||
| MIRT485327 | MYO1D | myosin ID | |
|
2 | 2 | ||||||
| MIRT496403 | ZSCAN16 | zinc finger and SCAN domain containing 16 | |
|
2 | 2 | ||||||
| MIRT497280 | MAF | MAF bZIP transcription factor | |
|
2 | 2 | ||||||
| MIRT500970 | SPTSSA | serine palmitoyltransferase small subunit A | |
|
2 | 2 | ||||||
| MIRT501536 | POM121C | POM121 transmembrane nucleoporin C | |
|
2 | 6 | ||||||
| MIRT505174 | WDR76 | WD repeat domain 76 | |
|
2 | 4 | ||||||
| MIRT505203 | UQCRB | ubiquinol-cytochrome c reductase binding protein | |
|
2 | 4 | ||||||
| MIRT506745 | LIN54 | lin-54 DREAM MuvB core complex component | |
|
2 | 4 | ||||||
| MIRT506799 | KLHL15 | kelch like family member 15 | |
|
2 | 6 | ||||||
| MIRT525718 | DCAF12L2 | DDB1 and CUL4 associated factor 12 like 2 | |
|
2 | 2 | ||||||
| MIRT530014 | SRRM1 | serine and arginine repetitive matrix 1 | |
|
2 | 2 | ||||||
| MIRT531457 | PROSER2 | proline and serine rich 2 | |
|
2 | 2 | ||||||
| MIRT532272 | CD93 | CD93 molecule | |
|
2 | 2 | ||||||
| MIRT538715 | CAPRIN2 | caprin family member 2 | |
|
2 | 4 | ||||||
| MIRT547356 | NAT8L | N-acetyltransferase 8 like | |
|
2 | 2 | ||||||
| MIRT551468 | TRIM59 | tripartite motif containing 59 | |
|
2 | 2 | ||||||
| MIRT555444 | NT5C3A | 5'-nucleotidase, cytosolic IIIA | |
|
2 | 2 | ||||||
| MIRT555674 | PGAM4 | phosphoglycerate mutase family member 4 | |
|
2 | 4 | ||||||
| MIRT557816 | FOXO1 | forkhead box O1 | |
|
2 | 2 | ||||||
| MIRT557853 | FIGN | fidgetin, microtubule severing factor | |
|
2 | 2 | ||||||
| MIRT557880 | FEM1B | fem-1 homolog B | |
|
2 | 4 | ||||||
| MIRT562299 | GLO1 | glyoxalase I | |
|
2 | 2 | ||||||
| MIRT563245 | QRFPR | pyroglutamylated RFamide peptide receptor | |
|
2 | 2 | ||||||
| MIRT565571 | SLC7A2 | solute carrier family 7 member 2 | |
|
2 | 2 | ||||||
| MIRT566214 | PTMA | prothymosin, alpha | |
|
2 | 2 | ||||||
| MIRT575544 | Map4 | microtubule-associated protein 4 | |
|
2 | 2 | ||||||
| MIRT609316 | FXYD6 | FXYD domain containing ion transport regulator 6 | |
|
2 | 2 | ||||||
| MIRT609362 | ACOT2 | acyl-CoA thioesterase 2 | |
|
2 | 2 | ||||||
| MIRT611163 | BTLA | B and T lymphocyte associated | |
|
2 | 4 | ||||||
| MIRT611749 | CACNA1B | calcium voltage-gated channel subunit alpha1 B | |
|
2 | 2 | ||||||
| MIRT615019 | ELK4 | ELK4, ETS transcription factor | |
|
2 | 2 | ||||||
| MIRT623317 | MAPK1 | mitogen-activated protein kinase 1 | |
|
2 | 2 | ||||||
| MIRT624550 | BMPR1A | bone morphogenetic protein receptor type 1A | |
|
2 | 2 | ||||||
| MIRT633934 | DNAH9 | dynein axonemal heavy chain 9 | |
|
2 | 2 | ||||||
| MIRT635691 | BMP10 | bone morphogenetic protein 10 | |
|
2 | 2 | ||||||
| MIRT646438 | DNAH8 | dynein axonemal heavy chain 8 | |
|
2 | 2 | ||||||
| MIRT651940 | UBN1 | ubinuclein 1 | |
|
2 | 2 | ||||||
| MIRT663605 | TBC1D22A | TBC1 domain family member 22A | |
|
2 | 2 | ||||||
| MIRT689759 | PRR13 | proline rich 13 | |
|
2 | 2 | ||||||
| MIRT691916 | SRXN1 | sulfiredoxin 1 | |
|
2 | 2 | ||||||
| MIRT698678 | TEF | TEF, PAR bZIP transcription factor | |
|
2 | 2 | ||||||
| MIRT700924 | PDS5A | PDS5 cohesin associated factor A | |
|
2 | 2 | ||||||
| MIRT707970 | PDE12 | phosphodiesterase 12 | |
|
2 | 2 | ||||||
| MIRT715290 | CSTF1 | cleavage stimulation factor subunit 1 | |
|
2 | 2 | ||||||
| MIRT722414 | RARS2 | arginyl-tRNA synthetase 2, mitochondrial | |
|
2 | 2 | ||||||
| miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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