miRTarBase - #MIRT592906


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pre-miRNA Information
pre-miRNA mmu-mir-363   
Genomic Coordinates chrX: 52741693 - 52741767
Synonyms Mirn363, mmu-mir-363, Mir363
Description Mus musculus miR-363 stem-loop
Comment The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies . The 5' end of the miRNA may be offset with respect to previous annotations.
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-363-5p
Sequence 7| CAGGUGGAACACGAUGCAAUUU |28
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol Mmachc   
Synonyms 1810037K07Rik, CblC
Description methylmalonic aciduria cblC type, with homocystinuria
Transcript NM_025962   
Expression
Putative miRNA Targets on Mmachc
3'UTR of Mmachc
(miRNA target sites are highlighted)		 
>Mmachc|NM_025962|3'UTR
   1 TAACTTTTCCCCTTCAGGATCCCACTCATAGTAGATTTATTTTAAGTAGGATTTGGGTTTTGAAAAAAACACTTTCTCCT
  81 TTTTTAGTTTTTTTGAGACAAGGTTCCTCTATGTAGCTCAGACCAGGTTGGCCTCAAGCTAAGAGAGATCCATCTGCCTC
 161 TGTCTTCTCCAGAGTGCTGATTTTTTGCACTGTGGAAAAACCATTTTATTTTAGGTAGGATTTCCTGATAATAGTGCTTC
 241 AGACAGTCAAGACTCAATTTACATTGGTCAAGATAAATCATATGCCAAGGCAGACTCAAAAATCAGCAGTTGACTTCAAA
 321 TATTAGACTCATGCCCATTACTATTTTTTTGTTTTTGTTTTTTGTTTTTTCAAGACAGGGTTTCTCTGTGTAGCCCTGGC
 401 TGTCCTGGAACTCACTCTGTTGACCAGGCTGGCCTCAAACTCAGAAATCCACCTGCCTCTGCCTCCCGAGTGCTGGGATT
 481 AAAGGCGTGCACTACCAAGCCCGGCTTTGTGTAGTACTCTTAAGATACTATTTAAGAACCATGGTTCTCACTGTTCGTTC
 561 CTAAAGCTGCTATCATTTAATGCAGTTCCTCATGTTGTAGTGACCGCAACCATAAAATTATTTTTGTTGCTACCTAATAA
 641 TTTTGCTAGTTATGAATCAATTGTCTTAGGGAATCCAGTGAAAGGGTTGTTCAACAACCCCTGGGGGCTGAGAATCACAG
 721 ATTTAGCAGCTCCTAGGGGTACCCACCACATTGAGCTATGCTGAATTAATATTTAAGTAAACTACATTGAAACTGCCCCG
 801 ACCTACAGTGTGCTATTACTAAAGGCTCAGGCAATCTTATACTTATGCTCAAATAGATGTACTTTGAATTCTGGAATGTT
 881 GGAAGGACATGATGTCATAGGATTATTTTGTCAACCCTAACCAAGAATCCAGAAGAAACTTCCTGACTTTACAGGATCAG
 961 AAAGGAATATTCTCTCATCACAGCTAAAATACAAGTAGTTGAATACAATCATATCCAAAGCCAAAAAAAAAAAAAAAAAA
1041 AAA
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
miRNA-target interactions
(Predicted by miRanda)
ID Duplex structure Position Score MFE
1 
miRNA  3' uuuaacguagcacaAGGUGGAc 5'
                        ||||||| 
Target 5' ctcaaactcagaaaTCCACCTg 3'
 434 - 455 140.00 -13.80
2 
miRNA  3' uuuaacguagCACAAGGUGGAc 5'
                    | | ||||:|| 
Target 5' caagctaagaGAGATCCATCTg 3'
 135 - 156 128.00 -12.00
3 
miRNA  3' uuUAACGUAGCACAA-GGUGGAc 5'
            ||| : |: |||| |:|||| 
Target 5' aaATTAT-TTTTGTTGCTACCTa 3'
 615 - 636 115.00 -7.90
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions mESCs
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 GSM622572. RNA binding protein: AGO2. Condition:WT2 HITS-CLIP data was present in GSM622573. RNA binding protein: AGO2. Condition:KO1 ...

- Leung AK; Young AG; Bhutkar A; Zheng GX; et al., 2011, Nature structural & molecular biology.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' uuuaacguagcacaAGGUGGAc 5'
                        ||||||| 
Target 5' ---aaacucagaaaUCCACCUg 3'
 		1 - 19
Article - Leung AK; Young AG; Bhutkar A; Zheng GX; et al.
- Nature structural & molecular biology, 2011
MicroRNAs (miRNAs) are 19-22-nucleotide noncoding RNAs that post-transcriptionally regulate mRNA targets. We have identified endogenous miRNA binding sites in mouse embryonic stem cells (mESCs), by performing photo-cross-linking immunoprecipitation using antibodies to Argonaute (Ago2) followed by deep sequencing of RNAs (CLIP-seq). We also performed CLIP-seq in Dicer(-)/(-) mESCs that lack mature miRNAs, allowing us to define whether the association of Ago2 with the identified sites was miRNA dependent. A significantly enriched motif, GCACUU, was identified only in wild-type mESCs in 3' untranslated and coding regions. This motif matches the seed of a miRNA family that constitutes ~68% of the mESC miRNA population. Unexpectedly, a G-rich motif was enriched in sequences cross-linked to Ago2 in both the presence and absence of miRNAs. Expression analysis and reporter assays confirmed that the seed-related motif confers miRNA-directed regulation on host mRNAs and that the G-rich motif can modulate this regulation.
LinkOut: [PMID: 21258322]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
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 ERR266295. RNA binding protein: AGO2. Condition:B_Liver partial hapatectomy 1h ...

- Schug J; McKenna LB; Walton G; Hand N; et al., 2013, BMC genomics.

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]
CLIP-seq Support 1 for dataset GSM4656408
Method / RBP HITS-CLIP / AGO
Cell line / Condition mouse liver / P7
Location of target site NM_025962 | 3UTR | GCUGGCCUCAAACUCAGAAAUCCACCUGCCUCUGCCUCCCGAGUGCUGGG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE153876
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4751761
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of eWAT 2
Location of target site NM_025962 | 3UTR | GCCCUGGCUGUCCUGGAACUCACUCUGUUGACCAGGCUGGCCUCAAACUCAGAAAUCCACCUGCCUCUGCCUCCCGAGUGCUGGG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4751762
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of eWAT 3
Location of target site NM_025962 | 3UTR | UAGCCCUGGCUGUCCUGGAACUCACUCUGUUGACCAGGCUGGCCUCAAACUCAGAAAUCCACCUGCCUCUGCCUCCCGAGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM622572
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / WT2
Location of target site NM_025962 | 3UTR | AAACUCAGAAAUCCACCUGCCUCUGCCUCCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM622573
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / KO1
Location of target site NM_025962 | 3UTR | AAACUCAGAAAUCCACCUGCCUCUGCCUCCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset ERR266295
Method / RBP HITS-CLIP / AGO2
Cell line / Condition Liver / B_Liver partial hapatectomy 1h
Location of target site NM_025962 | 3UTR | ACCAGGCUGGCCUCAAACUCAGAAAUCCACCUGCCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23597149 / E-MTAB-1612
CLIP-seq Viewer Link
76 mmu-miR-363-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT577239 Zfp933 zinc finger protein 933 2 4
MIRT578026 Pfas phosphoribosylformylglycinamidine synthase (FGAR amidotransferase) 2 2
MIRT578034 Pde4c phosphodiesterase 4C, cAMP specific 2 2
MIRT578102 Nup133 nucleoporin 133 2 2
MIRT578143 Nfatc4 nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 4 2 6
MIRT578431 Nmrk2 nicotinamide riboside kinase 2 1 1
MIRT579036 Cts8 cathepsin 8 2 4
MIRT579251 Car5b carbonic anhydrase 5b, mitochondrial 2 4
MIRT579607 4930519G04Rik RIKEN cDNA 4930519G04 gene 2 4
MIRT581397 Rbms2 RNA binding motif, single stranded interacting protein 2 2 4
MIRT585497 Ttc26 tetratricopeptide repeat domain 26 2 4
MIRT585507 Tspan31 tetraspanin 31 2 4
MIRT585583 Tox4 TOX high mobility group box family member 4 2 4
MIRT585842 Slc3a2 solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2 2 2
MIRT586452 Nploc4 NPL4 homolog, ubiquitin recognition factor 2 4
MIRT587010 Gngt1 guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1 2 4
MIRT588115 Aco1 aconitase 1 2 4
MIRT589171 Rab11b RAB11B, member RAS oncogene family 2 2
MIRT589338 Ostf1 osteoclast stimulating factor 1 2 4
MIRT589488 Mzt1 mitotic spindle organizing protein 1 2 4
MIRT589617 Lrrc58 leucine rich repeat containing 58 2 4
MIRT589816 Hnrnpab heterogeneous nuclear ribonucleoprotein A/B 2 4
MIRT590086 Evi2b ecotropic viral integration site 2b 2 2
MIRT590799 2810474O19Rik RIKEN cDNA 2810474O19 gene 2 2
MIRT590993 Slc28a3 solute carrier family 28 (sodium-coupled nucleoside transporter), member 3 2 4
MIRT592906 Mmachc methylmalonic aciduria cblC type, with homocystinuria 2 4
MIRT593320 Slc25a51 solute carrier family 25, member 51 1 2
MIRT594758 Ttn titin 2 2
MIRT594872 Magt1 magnesium transporter 1 2 2
MIRT595323 Gfap glial fibrillary acidic protein 2 2
MIRT595614 Abce1 ATP-binding cassette, sub-family E (OABP), member 1 2 2
MIRT596863 Ttc23 tetratricopeptide repeat domain 23 2 2
MIRT597329 Senp5 SUMO/sentrin specific peptidase 5 2 2
MIRT597745 Polr1b polymerase (RNA) I polypeptide B 2 2
MIRT597779 Plin3 perilipin 3 2 2
MIRT597900 Paxip1 PAX interacting (with transcription-activation domain) protein 1 2 2
MIRT598014 Nop16 NOP16 nucleolar protein 2 2
MIRT598196 Mrgprb1 MAS-related GPR, member B1 2 2
MIRT598360 Man2a2 mannosidase 2, alpha 2 2 2
MIRT598933 Git2 G protein-coupled receptor kinase-interactor 2 2 2
MIRT599064 Epb4.2 erythrocyte membrane protein band 4.2 2 2
MIRT599072 Eif2b1 eukaryotic translation initiation factor 2B, subunit 1 (alpha) 2 2
MIRT599119 Dynll1 dynein light chain LC8-type 1 2 2
MIRT599271 D14Abb1e family with sequence similarity 208, member A 2 2
MIRT599613 Birc5 baculoviral IAP repeat-containing 5 2 2
MIRT599909 Abcc9 ATP-binding cassette, sub-family C (CFTR/MRP), member 9 2 2
MIRT600060 Smco1 single-pass membrane protein with coiled-coil domains 1 1 1
MIRT600067 Knop1 lysine rich nucleolar protein 1 1 1
MIRT600320 Stxbp5l syntaxin binding protein 5-like 2 2
MIRT600337 Strbp spermatid perinuclear RNA binding protein 2 2
MIRT600524 Ppargc1a peroxisome proliferative activated receptor, gamma, coactivator 1 alpha 2 2
MIRT600646 Med18 mediator complex subunit 18 2 2
MIRT600683 Mapre1 microtubule-associated protein, RP/EB family, member 1 2 2
MIRT600802 C5ar2 complement component 5a receptor 2 1 1
MIRT601265 9930104L06Rik RIKEN cDNA 9930104L06 gene 2 2
MIRT601726 Rfxank regulatory factor X-associated ankyrin-containing protein 2 2
MIRT601751 Rasl12 RAS-like, family 12 2 2
MIRT601888 Pctp phosphatidylcholine transfer protein 2 2
MIRT602148 Irgm2 immunity-related GTPase family M member 2 2 2
MIRT602904 Fam219b family with sequence similarity 219, member B 1 1
MIRT603138 Ufd1l ubiquitin recognition factor in ER-associated degradation 1 2 2
MIRT603213 Tnfrsf26 tumor necrosis factor receptor superfamily, member 26 2 2
MIRT603268 Svopl SV2 related protein homolog (rat)-like 2 2
MIRT603291 Spib Spi-B transcription factor (Spi-1/PU.1 related) 2 2
MIRT603922 Hist1h2br histone cluster 1 H2br 2 2
MIRT603924 Hist1h2bq histone cluster 1, H2bq 2 2
MIRT604014 Fut4 fucosyltransferase 4 2 2
MIRT604105 Dll3 delta-like 3 (Drosophila) 2 2
MIRT604166 Cyb5d2 cytochrome b5 domain containing 2 2 2
MIRT604313 Ccdc127 coiled-coil domain containing 127 2 2
MIRT605041 Efr3b EFR3 homolog B 2 2
MIRT605716 Gpr157 G protein-coupled receptor 157 2 2
MIRT605741 Gipc1 GIPC PDZ domain containing family, member 1 2 2
MIRT605747 Fam96a family with sequence similarity 96, member A 2 2
MIRT606125 Tnfrsf10b tumor necrosis factor receptor superfamily, member 10b 2 2
MIRT606693 Cnnm3 cyclin M3 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-363 Emodin NULL 3220 Microarray K562 cells 23744534 2013 down-regualted
miR-363 Emodin NULL 3220 Quantitative real-time PCR K562 cells 23744534 2013 down-regualted
miR-363 Formaldehyde NULL 712 Microarray Human lung epithelial cells (A549) 21147603 2011 down-regulated
miR-363 Arsenic trioxide approved 14888 Quantitative real-time PCR acute promyelocytic leukemia 22072212 2012 up-regulated
miR-363 Bicalutamide approved 2375 Microarray prostate 22674191 2012 down-regulated
miR-363 17beta-estradiol (E2) approved 5757 Microarray rat breast 17700064 2007 up-regulated
miR-363 Acetaminophen approved 1983 Microarray rat liver 17965554 2007 up-regulated
miR-363 Carbon tetrachloride NULL 5943 Microarray rat liver 17965554 2007 up-regulated
miR-363 Dexamethasone approved 5743 Microarray primary rat thymocytes 20847043 2010 down-regulated

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