| pre-miRNA Information | |
|---|---|
| pre-miRNA | mmu-mir-1906-1 |
| Genomic Coordinates | chr12: 109544541 - 109544620 |
| Description | Mus musculus miR-1906-1 stem-loop |
| Comment | None |
| RNA Secondary Structure |  |
| pre-miRNA | mmu-mir-1906-2 |
| Genomic Coordinates | chrX: 88759474 - 88759553 |
| Synonyms | mmu-mir-1906, Mir1906 |
| Description | Mus musculus miR-1906-2 stem-loop |
| Comment | None |
| RNA Secondary Structure | |
| Mature miRNA Information | |
|---|---|
| Mature miRNA | mmu-miR-1906 |
| Sequence | 48| UGCAGCAGCCUGAGGCAGGGCU |69 |
| Evidence | Experimental |
| Experiments | Microarray |
| Putative Targets | |
| Gene Information | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene Symbol | Spsb4 | ||||||||||||||||||||
| Synonyms | D030068E18Rik, SSB-4, Ssb4 | ||||||||||||||||||||
| Description | splA/ryanodine receptor domain and SOCS box containing 4 | ||||||||||||||||||||
| Transcript | NM_145134 | ||||||||||||||||||||
| Expression | |||||||||||||||||||||
| Putative miRNA Targets on Spsb4 | |||||||||||||||||||||
| 3'UTR of Spsb4 (miRNA target sites are highlighted) |
>Spsb4|NM_145134|3'UTR 1 GCGGCGCTGAGGATCGGCTGTCATCTGTGGTCACACAGCTCCAGAGCGTCAGGACACATCAGTGACTTGGAAAAGGAATG 81 CCTGTTGCCATTGCTGCCACCGACCAGGACCAGGAGGCCACCTCGTGAACCAGAGTGTAGAGACCATTATCTTCCTCAAG 161 AGAATGAATAAAACATTGGGCAGGAGACGGCATCCAGTTAGTTCCCCACTGCAGACAGACCCAGGAAAATTGGCCAGTGG 241 AGAGAAAATGGGTTCTGAATAATGAATGACAGAAGCCAGCCCTTGATGGTCTCCTCCACGCCTGCCCCTGGCCAGGGCAG 321 AGAGACTGTCCTCCATTTTAAGACTTGGTACCACTTTGAGAGATGAGTCCAGGGTCCCACAGCAGGGCAAAAGCACCTGG 401 CCTTACCTCTCTGAGCCGGTTTCCTCATCCCCTCCTGCCCTCTTCCGTCATGGATAAAGTTCTTTGGCCATTCCCCTCCC 481 CACTTTATTCAGGGACATGAATCTGATGACTTGCCCTGGGGACAGAGTTTCTTCTTGGGTATGATCATTGTAAGTAGTGT 561 TTGCATTTTTTTTTTTTGAAAGAGGAGTGTGGTGAAGGTGGCTTTCTCCCAAAGGTGCTAAGGAAGATGGGGCCCTCGTG 641 ACACCAAGTCTGAGACACCCTGAGTATCCAGGGCTCTGGCAGCCATCATTCAGGGTGAAGCCTGGCTGTCACAAAGCTTT 721 CTTTGAGCAAATTATTTTTTCACTGTAGGAGACTTCCAGTTTGTTTCTCGTTTCCAATATGTGTGTGATGCACCGTTTAT 801 TTATCAGCTGGGGCCCCGCGGTGTGGCCTTGGGACTGCAAAGGTGGGTATAACAGTCTCTGCAGGACCTGAGACCTATCC 881 TCTCACAGAATGTTGCTGCTGCTGCTGCTGCTGCCGCCAGCGCCACCATTTGGCATCTTTTGTGTGTTCCAAGATACCCT 961 CCACCCAGACTCAGTTTTAACTGGAAATCATCACAGAGTAGGATACAGAGCCAGACAGTGCAGCCTACACTGTAATGTGA 1041 ATGTGACCTACAAGCAAGGAACATTTCTAATAAAAGTTTGTCATTCTGTCCTTCA 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 | Liver | ||||||
| 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 ERR266298. RNA binding protein: AGO2. Condition:A_Untreated
... - Schug J; McKenna LB; Walton G; Hand N; et al., 2013, BMC genomics. |
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| miRNA-target interactions (Provided by authors) |
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| Article |
- Schug J; McKenna LB; Walton G; Hand N; et al. - BMC genomics, 2013
BACKGROUND: Validation of physiologic miRNA targets has been met with significant challenges. We employed HITS-CLIP to identify which miRNAs participate in liver regeneration, and to identify their target mRNAs. RESULTS: miRNA recruitment to the RISC is highly dynamic, changing more than five-fold for several miRNAs. miRNA recruitment to the RISC did not correlate with changes in overall miRNA expression for these dynamically recruited miRNAs, emphasizing the necessity to determine miRNA recruitment to the RISC in order to fully assess the impact of miRNA regulation. We incorporated RNA-seq quantification of total mRNA to identify expression-weighted Ago footprints, and developed a microRNA regulatory element (MRE) prediction algorithm that represents a greater than 20-fold refinement over computational methods alone. These high confidence MREs were used to generate candidate 'competing endogenous RNA' (ceRNA) networks. CONCLUSION: HITS-CLIP analysis provide novel insights into global miRNA:mRNA relationships in the regenerating liver.
LinkOut: [PMID: 23597149]
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| CLIP-seq Support 1 for dataset ERR266298 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO2 |
| Cell line / Condition | Liver / A_Untreated |
| Location of target site | NM_145134 | 3UTR | AUGUUGCUGCUGCUGCUGCUG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 23597149 / E-MTAB-1612 |
| CLIP-seq Viewer | Link |
27 mmu-miR-1906 Target Genes:
Functional analysis:
ID |
Target | Description | Validation methods |
 |
 |
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| Strong evidence | Less strong evidence | |||||||||||
 |
 |
 |
 |
 |
 |
 |
 |
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| MIRT578439 | Irgq | immunity-related GTPase family, Q |  |
|
2 | 10 | ||||||
| MIRT578971 | Dhdh | dihydrodiol dehydrogenase (dimeric) | |
|
2 | 4 | ||||||
| MIRT580446 | Tln2 | talin 2 | |
|
2 | 2 | ||||||
| MIRT582494 | Mbtps2 | membrane-bound transcription factor peptidase, site 2 | |
|
2 | 2 | ||||||
| MIRT587588 | Cox15 | cytochrome c oxidase assembly protein 15 | |
|
2 | 2 | ||||||
| MIRT589524 | Mtf1 | metal response element binding transcription factor 1 | |
|
2 | 2 | ||||||
| MIRT591281 | Klc1 | kinesin light chain 1 | |
|
2 | 4 | ||||||
| MIRT591935 | Ddx19b | DEAD (Asp-Glu-Ala-Asp) box polypeptide 19b | |
|
2 | 2 | ||||||
| MIRT592084 | Sorcs2 | sortilin-related VPS10 domain containing receptor 2 | |
|
2 | 2 | ||||||
| MIRT592206 | Mapkap1 | mitogen-activated protein kinase associated protein 1 | |
|
2 | 4 | ||||||
| MIRT592349 | Armcx6 | armadillo repeat containing, X-linked 6 | |
|
2 | 4 | ||||||
| MIRT592351 | Angel1 | angel homolog 1 | |
|
2 | 2 | ||||||
| MIRT592365 | 4930444A02Rik | protein-O-mannose kinase | |
|
2 | 2 | ||||||
| MIRT592427 | Spsb4 | splA/ryanodine receptor domain and SOCS box containing 4 | |
|
2 | 2 | ||||||
| MIRT592671 | Itgav | integrin alpha V | |
|
2 | 2 | ||||||
| MIRT592712 | Fbxo21 | F-box protein 21 | |
|
2 | 4 | ||||||
| MIRT593155 | Itsn1 | intersectin 1 (SH3 domain protein 1A) | |
|
2 | 2 | ||||||
| MIRT593662 | Spen | SPEN homolog, transcriptional regulator (Drosophila) | |
|
2 | 2 | ||||||
| MIRT593976 | Cdc14b | CDC14 cell division cycle 14B | |
|
2 | 2 | ||||||
| MIRT597931 | Pacsin2 | protein kinase C and casein kinase substrate in neurons 2 | |
|
2 | 2 | ||||||
| MIRT597949 | Opa1 | OPA1, mitochondrial dynamin like GTPase | |
|
2 | 2 | ||||||
| MIRT598550 | Isoc1 | isochorismatase domain containing 1 | |
|
2 | 2 | ||||||
| MIRT599017 | Fgd4 | FYVE, RhoGEF and PH domain containing 4 | |
|
2 | 2 | ||||||
| MIRT600307 | Tacc1 | transforming, acidic coiled-coil containing protein 1 | |
|
2 | 2 | ||||||
| MIRT603647 | Otop1 | otopetrin 1 | |
|
2 | 2 | ||||||
| MIRT605000 | Fam168b | family with sequence similarity 168, member B | |
|
2 | 2 | ||||||
| MIRT606275 | Oxsm | 3-oxoacyl-ACP synthase, mitochondrial | |
|
2 | 2 | ||||||
| miRNA-Drug Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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