| pre-miRNA Information | |
|---|---|
| pre-miRNA | mmu-mir-1839 |
| Genomic Coordinates | chr7: 81529916 - 81529988 |
| Synonyms | mmu-mir-1839, Mir1839 |
| Description | Mus musculus miR-1839 stem-loop |
| Comment | This sequence was named mmu-mir-1980 in , but is a clear ortholog of the mir-1839 sequence published in dog (MIR:MI0008087), so is renamed here. |
| RNA Secondary Structure |  |
| Mature miRNA Information | |
|---|---|
| Mature miRNA | mmu-miR-1839-3p |
| Sequence | 43| AGACCUACUUAUCUACCAACAGC |65 |
| Evidence | Experimental |
| Experiments | Illumina |
| Putative Targets | |
| Gene Information | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene Symbol | Reep3 | ||||||||||||||||||||
| Synonyms | D10Ucla1 | ||||||||||||||||||||
| Description | receptor accessory protein 3 | ||||||||||||||||||||
| Transcript | NM_178606 | ||||||||||||||||||||
| Expression | |||||||||||||||||||||
| Putative miRNA Targets on Reep3 | |||||||||||||||||||||
| 3'UTR of Reep3 (miRNA target sites are highlighted) |
>Reep3|NM_178606|3'UTR 1 TGTCTACACCTTGCCCTTCCCAAGATGAATAAACCGCTAACAGATCAACTTCATTTTCTAACCTGATGTATTCAGGGCTT 81 AACACTTTAAATCTTCAGAGTGTGGCAGGGATGGGATTTACGCAATGACTTTAAATGGTCTGTGTTTCTTTAACAATTAC 161 TTTTAGATGTTTAACTGCTAAACTTAGTTATGTAAGGTTTGTAAATGTACGTGTAGATAACAAAAGTGACCGAGAATCGC 241 GTCCCTGATGTCAGCAGCAACACTGAGTGCCTAGGGCCTAAGGATAAAGCCTAGCTAGACCCAGGGCAGACTTCAAAAGT 321 CTCTGCTCCAGGACACACCTGCCTGCCGTTCTGGTGTTGCATTCTGTTTACATCATCTTGCCTGCATCTATCACAGGAGA 401 GTGGTGACAGCCCCTGAGGAGCCAGTGTCATTGCCATAGGAGGGGGCTGTGTCCTTCCTTAAGCCTTAGACGCTGAAAGT 481 TTTTTAAACAAATGATTTGAAAACCAGGTGTCCACATAGCACTTTCCTGGCTAGTTTTGCACACTTGAAAATTGTTTACT 561 TATTTTACAACTGTACATTTACATTTTCCTGATGCTGTCTGTTTTGTTGTCTGTCATATTCCGACATGTCAAGATCATGC 641 CTTGAAACCGCGTCATCTCCTTTTCCTATGGGTTTGTTTCGTTTGGTAAATCCATTCAGCCCATTATAGACACATAACTG 721 TTAAGTTTGTAGTCTTTTGTTTTGTTTTATTGAGGTAGGGTCTCTTCCCTGATCCTCGTCCTGCTTCCACTTCGCCATTG 801 CTGGGATAACAGACGTTATCACACTTGGCTCATTTTAAATGCCCTTCAGTTATATTCCGGACATCTGAGAAGTTATCTTA 881 AACATTAACCAGTTTCCATCATTGAATTTGATGTGGTTTTTCTCAACAGCAAATTATTCTAGGTTATTCTAGGTTAAAAA 961 AAAAAAAGCTTTTGGGGGCTGGAGAGGTGGCTCAGAGGTAAAGAGCACTGGCTGCTCTTCCAGAGGTCCTGAGTTCAAAT 1041 CCCATCACCCACGTGGCAGCTCACAACTGTCTGCAATCCAGCTCCAAGTGATTTGACACCCTCACACAGATATGCGTACA 1121 GGCAAAACACCAATGCACATTAGATAGAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA 1201 TTAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATTGATTTTGTGGAAGCGTCACAGACCA 1281 ATGTAGCACTTAGTGTTTTCTAACTCATGGACTTCCCAATGCCCACACTCAGCTCCTGAGCTCGGCAGAGGCCTATGCTG 1361 CCTTACAGACCCAGCAATGACTAACATCTTTTAGATCTTTTTCTGCCTGAGATTATTCTCTGAAAATGAGTGTCAGGGTA 1441 AAACACAAACACCATTGATGCTACGTAACAGGCTTCCAGAAAAATGCCATCTTTTATTTTATTTTATTTTATTTTATTTT 1521 TGGGTTTTTTTTTTTCGAGACAGGGTTTCTCTGTATAGCCCTGGCTCTCCTGGAACTCACTCTGGAGACCAGGCTAAAGG 1601 CCTTCTTTTTAATCTAACAGATTTAGAGGGATTGAACTCAGCTCCTTTTAGGTTGCCCTACTAACTGGACATTGTGGACA 1681 CTAAATCATATTGGGGTGATGAATAATCAAATTTTCAATATCAAACAATGCTTACATGGGGGTGCCTGAATGGCCCACAC 1761 ACACAATGACCTCTTGATACTACGAATATTTTCTACACAGAATCACATTGTTAATATTTTTAACACGAAATAAAAATTCA 1841 ATCTTTTTCCTCCCCAATTTAATCTTGTATCTCCATCTACTTTGCTTTGACTAATAGCCTCTTCCTTTCGAAAAGGATTC 1921 TTTAATTTCTATTCAAACATCTATAAAGTCCCACAATAAATTATTGGACAGGATGTATTCATTTCTCATGAACCAGACCT 2001 GCTCTGAACCAATGCTGTGCGGCATGGGTGGTTTTCCCTGCAGAGGCCGTGTTACCTGATAAGGTGATGTGATAAGTACA 2081 GTAAGTTACTTTGTCTCCATGGGGACAAATTGGCAAGATTGTATCATATTCAAGTCCAGTATCAGTATTAAACTTACCCT 2161 TAGGAGCTAAGGATAGACACCATGCTTGAGGTACACAAGGCCTTGAGTTCAATCCCAAAACCAAAAAAAAAAAAAAAAAA 2241 GATAGTTAAAACAAACTTATTATTATTTAATGAGTTTGTATACTATTTGTTTCTTCTTTTGACTTTTGTTTGTTTGGGTG 2321 GAGGGTGTTTTGTTTTGTGAGACAGAGTCTCTCTGTGTAGCCCTGGCTGTCCTGGAATTCACTCTGTAGGTCAGGCTGGC 2401 CTCAAACTCACAAAGCTCCACCTGCCGCTGCCTCCCAGATGCTGCCATTAGAGGTGTGTCCCACCATGCCCAAGTTGTTT 2481 TGAGACTAAGCCTCACTCTAGCCAGCCTGAAATGCACTGTGTAGCCCAGGCTTACTTCCAGTATATGGTCACTCTGGATG 2561 CCTCCGCCGCCTTTTTTTTTTAAATATTTTTTATTATTATGTATTTTCCTCAATTACATTTGGAATGCTATCCCAAAGGT 2641 CCCCCATACCCTCCCCCCCCCCCACTTCCCTACCCACCCATTCCCATTTTTTGGCTCTGGCATTCCCCTGTATTGGGGCA 2721 TATAAAGTTTGCGTGTCCAATGGGCCTCTCTTTCCAGTGATGGCCGACTAGGCCATCTTTTGATACATATGCAGCTAGAG 2801 TCAACAACATTATGCCTCCGCCTTCTAAGTGCTGAGATTACAGGTGTGTGGCTCCATACCCTACTTCACAGGCGTTTTAA 2881 ATTGGGAGAAATATCACGTTCTAGAATCAAAATTCTCAAGCAAAGATACCGCCTGACTCGGAGCTAAAGTTGGCTGACCT 2961 GCTCACTGCCGTTCACCCTCCCGGTCCTGGTCCCTGCTCGGGCTTGTCCCTGCTGTAGACATGCTCATATGCGCTTGATG 3041 ACTGTCCTACCCCGCTTTGTTTCTGTCCCCAAGGTCTCATGTCATAGCATGCCCTTTTCTTTGAACTCTGTATGCTGAGC 3121 TAAAGCGCTGTTTTGTTCTGTTTCTCTTAAAGAGGACCGGGTCACCTTGTTTGTTTCTGCTTTTGAGCATGCTGATTTTT 3201 TCAAGAGATGTAAATTTATTCATAGACCACAGTGCCTTGACTTAACCCACACTGCCAACTGGAGCACCAGCACGCGAATG 3281 CACAAACCGGTTTAAGGCACTGTTTCTCTCTGCCTTTTGACATGTATCCAAAAATTATAGCCTACTAGCATTTCATCTTA 3361 GTATCCAGTCGTTCAGCATGATCACTAACATTCCCCGTACTTAGCTGTTGTTTAAGTATAAAAATTGATATGTCTATACT 3441 GTGTCTTTCTTTTTCCTTTCTGGTATTAAGAAGAGCCATAGCTGGAGAGATGGCTCTGTTTTAAGAATGCATACTGCTCT 3521 TACAGAGGACCTGGATTCAGTTCTTAGTGCCTAAGCCAGGTGTTTAGTTCACTGCAGCCTGCAGTGCCAGCTCCTGGGGG 3601 TACAATACCTTCCTCTGATTTCCAAGGGCACCTACGTGCATGTGAACATTCTTTCTCACGGATACACATACACACATCAT 3681 TTGAAATTAAAAAAAAAAAATCCTGTGAAAAACAAAAAGGAACCAGAAATAAGCTGATTACTACATAAACAATTGTCTAC 3761 GGCCACCTCAGTTCCTCATAGGTCCCCTCCACACACACTGTGTGTGTTTTCTAGGGCTAAAAAAATGAGATCTTGCTATC 3841 GTTTCTAGCAATAAACACTTTAGCACATAGAGGTCTGGGACAGAACTAACTCCTCATGTGTTTTCAGGGATCTTATTCCA 3921 TGTGTCACCACCAAAGACTTCCACAGTATTATAAAACATGTAACTACTCTAAAATGACGTCAGCCCTTGGCTACATCGTC 4001 TTCTTTCTCTTTTGTACATTTGGAGAAATGCCTGAACCTTAATGGTATTACTATAATACTGTCTTATATTAACTGTAGGG 4081 TTTTTTCATTGGAATATTGTCTGCCATTGGAGGGGCGGGGGAGACAACGAATGAAGATCTAAATACAGAAATCTGAACAC 4161 AAGTTCCAAAGCGTGTCCTCTGACCTCTCCCTTTTAGGTTGACTTATTTGTGAAACAGGTAAAATTTGAGAGGGTCATTG 4241 TTTTGTGGTTTGTACTATTTCTTAAGAAACATACCCTAAGATTAAATTTTTTCTGAAAAGAAAGTATCTTTTTTTCCTAA 4321 GTACTTCTCAAGTTAGTCTTTTAGTGGGAATTCTGCCGATTAACCTTGACTTAACATTTTTTTCCTTCTAATATATATTT 4401 TTTAACTCTGTGTACTTTAATACTTTAAGTGGAAATAATTTTATAAAATCTCTGTTAAATCTCAAGCCCCAAATGTGGGT 4481 GGCTCTGCATGTGTGTTTTGGGAAACTTTTACAATAAAGTAAACTCATTTTATTAGTGGCA 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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| Experimental Support 1 for Functional miRNA-Target Interaction | |||||||
|---|---|---|---|---|---|---|---|
| miRNA:Target | ---- | ||||||
| Validation Method |
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| Conditions | C2C12 | ||||||
| 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 GSM1385342. RNA binding protein: 聽AGO2. Condition:C2C12_GM_Ago2_CLIP-Seq_myoblast
... - Zhang X; Zuo X; Yang B; Li Z; Xue Y; Zhou et al., 2014, Cell. |
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| miRNA-target interactions (Provided by authors) |
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| Article |
- Zhang X; Zuo X; Yang B; Li Z; Xue Y; Zhou et al. - Cell, 2014
MicroRNAs are well known to mediate translational repression and mRNA degradation in the cytoplasm. Various microRNAs have also been detected in membrane-compartmentalized organelles, but the functional significance has remained elusive. Here, we report that miR-1, a microRNA specifically induced during myogenesis, efficiently enters the mitochondria where it unexpectedly stimulates, rather than represses, the translation of specific mitochondrial genome-encoded transcripts. We show that this positive effect requires specific miR:mRNA base-pairing and Ago2, but not its functional partner GW182, which is excluded from the mitochondria. We provide evidence for the direct action of Ago2 in mitochondrial translation by crosslinking immunoprecipitation coupled with deep sequencing (CLIP-seq), functional rescue with mitochondria-targeted Ago2, and selective inhibition of the microRNA machinery in the cytoplasm. These findings unveil a positive function of microRNA in mitochondrial translation and suggest a highly coordinated myogenic program via miR-1-mediated translational stimulation in the mitochondria and repression in the cytoplasm.
LinkOut: [PMID: 25083871]
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| CLIP-seq Support 1 for dataset GSM1385342 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO2 |
| Cell line / Condition | C2C12 / C2C12_GM_Ago2_CLIP-Seq_myoblast |
| Location of target site | NM_178606 | 3UTR | CUGUAGGUCAGGCUGGCCUCAAACUCACA |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 25083871 / GSE57596 |
| CLIP-seq Viewer | Link |
5 mmu-miR-1839-3p Target Genes:
Functional analysis:
ID |
Target | Description | Validation methods |
 |
 |
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| Strong evidence | Less strong evidence | |||||||||||
 |
 |
 |
 |
 |
 |
 |
 |
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| MIRT578567 | Hist1h1d | histone cluster 1, H1d |  |
|
2 | 2 | ||||||
| MIRT581504 | Pvrl4 | nectin cell adhesion molecule 4 | |
|
2 | 6 | ||||||
| MIRT583197 | Grb14 | growth factor receptor bound protein 14 | |
|
2 | 2 | ||||||
| MIRT589054 | Reep3 | receptor accessory protein 3 | |
|
2 | 2 | ||||||
| MIRT594623 | Myo9a | myosin IXa | |
|
2 | 2 | ||||||