| 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 | Itgav | ||||||||||||||||||||
| Synonyms | 1110004F14Rik, 2610028E01Rik, CD51, D430040G12Rik | ||||||||||||||||||||
| Description | integrin alpha V | ||||||||||||||||||||
| Transcript | NM_008402 | ||||||||||||||||||||
| Expression | |||||||||||||||||||||
| Putative miRNA Targets on Itgav | |||||||||||||||||||||
| 3'UTR of Itgav (miRNA target sites are highlighted) |
>Itgav|NM_008402|3'UTR
1 GGTGCTTCTTAAGTGGCGCCACTTCTGTCCGCTCCAAGTTCACCACCGTGGTGGTGGATTTCAACATCTCTCGTGAACAG
81 TGAAATCCCAGGACTGTATTGCTGAGAGCACCCAGCAGTCTCAGTTTATCCACAAAATTGAAATGGATATTTGTCGACTT
161 CTCTTTATGAATAAGTTCAGATTACATTTACTTCGCCTACACTAACGTGTGTTCTTAGGGACTTAAGTGATGGAATTTCA
241 AGTGATTATCTTTGTTCAGTGTACATAAGACAGACAGCACTGAGTCAGCACGTTACATAGCATAGTACCTCTTCAGTTAC
321 TGTTCCTAATTGACTGTGTGGGGTTTCTCTCTTCGACGTTACGTTAGGGCAATTAGGATTGTAAAGCAGTTCAAATTTAG
401 ACCATCAGTAAGTTTGCACAGGCACTTAGAACAGGTACACATTACACTACAGTTGACTTCATAAGCTACTGAAGACTTTG
481 CAATTGCATGGACTTAGATTTTAATATCATTTACACAGTAGAACTTTTAAATAACACGATACCATCAAAATTCTTTCCTG
561 GGACTATAGCTCACTTCGAAGCGTGTGCAACTCCCTGGGTTCAATCCTGCACACTGGGAGGAAAACCAGCAGTTTCCTGT
641 ATTAACAATGGTACAGTATTTTTATATGAAAGTTAGGTTTTTATTTATGTGTAGTCTGCATTGTGTCTTATTGTATTTTA
721 ACTTTTGTAATTTAAATTCTACATCAAATCCTTTAAGTCGTTTCCTGCAGAAAATTTTATAATTAAAAATACCCGTTAAG
801 TAATAGTGTGGTCTCAGCTGCTGCTGCTGCTGCTGCTGCTGCTGACTGAAGCCCGTGGAGTTGGAAGGGGTTTTTGAAGT
881 ACATCTATTCCCTTTGTTTGGCTGCCTGCAATGTGGAAAAGCCCTGGAGACTCTCCATGGGTCTCTACTCTAACTGCTCA
961 TCAAAAAGACATTCTTTAATTGGACCAGAGCGTTTAATTATTAGTAATTTATTTTCCTCCTGTCCTCATATTTTCCTTCC
1041 ACTTCCAAAACTGAGAATGGCTCAAGACCTTCTTCATAACCTATAGGAACCTGGATCTCGCGCCCTTACCCCACGAGAGA
1121 TGCCTGGGACCCACATTCCAAAGGTGGCTCATGGGATGGTTTCTAGCAATAGCATGGTAGAACCTCAGGTTAAGCAAGGT
1201 GATCTATAAAACCTGCCTCCACTGTCAGAAAGAATGCTACAAAGGTGTTTTTGTAAGCAGTTCTTGTTCCTTAAACCTTC
1281 TAACTCTGTCTTACATTTTTTAATTTAAATTACCTTTCTGGGACTTTAATAGAGGCAGCAGAGGAAGCACGGGACCGTCT
1361 TAAGTGGTGGTGATTTATTCACAGTTCCTCAAGGCCCCGGGATAACTATCAATTATAGCTCTATTTTTGTGCAATTACAT
1441 CATGTTATGCATTGGAAGTTGAGAATTTTAATAGCTTTTTAAAATGCTGTCCTCATTAAGCAATGAAAAATATTTCTCTT
1521 AAATAATTGAATATTTTTCTACATTTTAAAAGTAATTGAAGTTTGTCTCACCGTATCTTAGGCTAATTCCATGTGCATAT
1601 GGATGAGCTAATTTGGAGAATATATTTTCATAACATGAAGCACATTTATGTGAGTTGTACGAATTAGAATATAGACAGGA
1681 CCCTATATTTAGCTTTAATAAAATTTTAAATTAATGAGTTCTGGCTTGAAAGATCATAATCATATATGCAATAATTATTT
1761 TTTTAAACCAATACATTTAAATTCTTTTAAGAAACATTTTGGTCTTAGGGACAAGTGTCTCTAAGCTACTTAGGACTACC
1841 ACACAGGTCACTAAGTTGGCCTATACAAACTTTTACCTTCTTTGTCTGTCAACATAATAGTTGTCATTCCTGAAAATCAA
1921 TGAAATTCATTCTTTGTAAAAATCAATATTGATTTTTACAGTTATTCCTATTATGGCTTCTATGCCAAGGAATAACTTTC
2001 TGTTAGAGATTGAAAGATATTTGTAATTGGAAATTAACATGATGTAGTTTTCAACAATAGCATGGATTTTCTTTTAAAAA
2081 ATATAAATTTGTATCTCTGTAAACTTAGGAACTGTAATTTGAGAGTTAACACTCTGAAAAAAATGTTGAGATACTCTTTA
2161 TCCCATAACAGCATAGGCATGTAGTCAACAAAATAGCAAGAGATTATTTTAGATTCATATTTGTAATTTACCAATAATTA
2241 ACATTTATTTCTAAGCATAAAATTTTCATAATATAGGTTAATTAAAGAAATTGATTGATCCAGAGGACATTTGACACATG
2321 TGAGGAATATTAACGTGGATACTGATTTCTTATAGAGATATTTATTTTAGAGTTGGTACTTTAAAACATCTGTGTGAGGG
2401 TTACTTTCCTCCCTTATGTTTAATTATCATCATAATTCTGATTGTGTTCTGAATGACTACGGAAGGTGAAACAGTCAAAA
2481 TATTGTCTTAAATCTACCTGTATTACAATATTACTTATTAATAGTAAATCCTCATGAATACATTATTTATATAATGAGGA
2561 AAATCACTAAGAGCAGACAAGAGTTTGTTGCCGCCTTACGAGAACAGTGTGAGTTTCTGTAGTGAGTCTAACCCCGAGGA
2641 GGGAATTTAGTGGCAAAGTATATATTGGTAGAGCAACTGGTTCTTGTAGGGCAACAGAAGGCCAAGGTGGCATCCATCCC
2721 CATTTGAGAGAATTCTGGGGAGAGCCTCAAGGAGAAGGAAAGGAAGTTGTTCTAGAGTCTCTGTGTGTGGCCATTGCCTA
2801 TCTCTGTGTCACCTTGTTCTTACTCGTGGCTAGCTTGTACATTTAATTTGATGAGTAAGGGGAGATGACCAAAATGTATT
2881 ATGGGATCTAAAAAGACAAATACAATTGCTTGATGTCTAGTAATTTGTAAAGGTTTCTTTGGACTTGGTCCTTTTATTTG
2961 AACCATGAACCTGTGGCTATGCCATCTGCAGTATACACTGGCATTCATTATAATTTCTGATATGTCATGGACTTCCTGTG
3041 AGGTACTGAATCTTTGAATTTTGTTGTCATTGTTCTTAAGTGCAATATAACAATGTAACGAAACTTAAATATAAGTCACT
3121 ATTTAGTAATCTTAATCCGAAATTTATTAGTATTTTTTTGTTAGCAGAAAAGAACAACTCTGCTGTAGTTGTAGATATAT
3201 AGGTGAAATTTTTTGTTTTTTGCTTTTTCTTTGCTTTTTTTTTTTTGTTTGTTTGTTTTTTTTACCTCTAAACCATCCAA
3281 TCTGCATTTTATTTTAGGTGGAAGATGAACTATTCCTTACCAGTTTTAAAACACTTTCAGTATATTAAGGTAACTTGGAA
3361 GCTGTGTGTATCAAATTCTTTTGCTCGCTAAGTAACCTGGAAGATAATTTTTTTTGGCTTCTCTCGTGATCACCCACATT
3441 GGGTGAGACATAAGATGAGTCTCTCCTGAAATCTGTCATTTGCTAACTTGTTTTGAGTTAGTAAAAGCAGGTACCATGTT
3521 CTGCTTTGTTTCCAGTGTGTAACTTGTGACTGTACAATAAACTTGAACGTGTGGTGCCAGCT
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 GSM4751756 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | adipose tissue / RNA sequencing of iBAT 1 |
| Location of target site | NM_008402 | 3UTR | GCUGCUGCUGCUGCUGCUGCUGCUGAC |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Accession Series | GSE142677 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 2 for dataset GSM4751757 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | adipose tissue / RNA sequencing of iBAT 2 |
| Location of target site | NM_008402 | 3UTR | CUGCUGCUGCUGCUGCUGAC |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Accession Series | GSE142677 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 3 for dataset GSM4751758 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | adipose tissue / RNA sequencing of iBAT 3 |
| Location of target site | NM_008402 | 3UTR | GCUGCUGCUGCUGCUG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Accession Series | GSE142677 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 4 for dataset GSM4751759 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | adipose tissue / RNA sequencing of iBAT 4 |
| Location of target site | NM_008402 | 3UTR | GCUGCUGCUGCUGCUGCUGCUG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Accession Series | GSE142677 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 5 for dataset GSM4751760 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | adipose tissue / RNA sequencing of eWAT 1 |
| Location of target site | NM_008402 | 3UTR | CUGCUGCUGCUGCUGCUGAC |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Accession Series | GSE142677 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 6 for dataset GSM4751761 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | adipose tissue / RNA sequencing of eWAT 2 |
| Location of target site | NM_008402 | 3UTR | CUGCUGCUGCUGCUGCUGCUGCUGCUGAC |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Accession Series | GSE142677 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 7 for dataset GSM4751762 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO |
| Cell line / Condition | adipose tissue / RNA sequencing of eWAT 3 |
| Location of target site | NM_008402 | 3UTR | GCUGCUGCUGCUGCUG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Accession Series | GSE142677 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 8 for dataset ERR266298 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO2 |
| Cell line / Condition | Liver / A_Untreated |
| Location of target site | NM_008402 | 3UTR | CUCAGCUGCUGCUGCUGCUGCUGCUGCUGCUGAC |
| 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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