miRTarBase - #MIRT588281


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pre-miRNA Information
pre-miRNA mmu-mir-493   
Genomic Coordinates chr12: 109580233 - 109580315
Synonyms Mirn493, mmu-mir-493, Mir493
Description Mus musculus miR-493 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-493-3p
Sequence 51| UGAAGGUCCUACUGUGUGCCAGG |73
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol Saysd1   
Synonyms 1810063B07Rik, 4930488P03Rik
Description SAYSVFN motif domain containing 1
Transcript NM_026209   
Expression
Putative miRNA Targets on Saysd1
3'UTR of Saysd1
(miRNA target sites are highlighted)		 
>Saysd1|NM_026209|3'UTR
   1 ACGTGGACTTTAGAGGACAAAGGACAGCTTGCAGGGTGGTCATGTCCTCCACTTTCCCCCTGACCTGCTGCAGTTTCATC
  81 TTTGAACTCCACTTTGATTTAGGTGAATTTCTCTAAAGGACACTCAGGGTGGGGCTGGTGCTGTATATAAAAGCCATAAA
 161 AGAAGGAGGCTGGTTTGTCTCATTATTGGAGTGGTGATGCTGGCATGCTAGAGATACACTGTGAGGTTCTTTGGTTTACT
 241 GAGTGATTTGGTGGAGGAGTAGGCACATTGGGGCTCCTTTTAAATATTTTAATATTTACATAGCTAAGTTCCAGGCCAGG
 321 GAAACTGGTCTGCCCCCACCTTAAATGTGTGAATGTTTTGTCCAAATGTATATAGATATACCATGTGTGTGCCTGGAACC
 401 CTCAGAGCGCCAAAGAGAGCATCAGATCCTCTGGAACTGAGTTATGGATGGTTGTAAGCCACCATGTGCATGCTGGGAAC
 481 TGAACCTCAGTCTTCTGCGAGAGCAACAAATGCTCTCAACCACTGAGCCATCTCTCTAACCTTCAAAAAAATATTTTCAG
 561 AATTATTTTCTCAAAAGGTTTAGGTTGTAAGGTTTAGAAATTTTTGTTTGTTTTTGTCTTGTTTCTCCTCTTTTCCATCA
 641 TCAGTGCTATTGAAATATAAAATGTCTTTAAGATTCTATAAGCAGGTCCCCATATACTACCTGTGACCATCTTTCATTTT
 721 CCCCTTAACCCTGTCCCTACTTAGGCAGGAAACCTAAGAGAAGAGAAAAAGTTTCAATAGGACAAAGTCAATAGTGGAGA
 801 TAAAAAATACTTTATTTGTATGACTGTCTACATATGTATGTGTGTACCATGTGCCTGAGGATGTCAGATCGCCTGGAATT
 881 GGAGTTCTGTATGGTGGTGGGTTCTGGTAACCAGCTCATCTGCAAGAGCAGCCTGCTCTTAACTGCTGAGCCATCTTCCC
 961 AGCCCTGGAAGAAATTTGATAAGAGGTTATTTATGATTGGTACATCAAGAGAAATTCTTGAGTATGTGCAGAGGGAAGGG
1041 CTAGGAGACGGGATTCTAGTTTTACTGCTTGGGTTTTGTCTCTTTCTTTTAGGTATTTTTAAAAAAGATTTATTTATTAT
1121 ATGTAAGTACACTGTAGCTGTCTCAGACACACCAGAAGAGGGCATCAGATCTCATTACCGATGGTTGTGAGCCACCATGT
1201 GGTTGCTGGGATTTGAACTCAGGACCTTCAAGAAGAGCAATCGGTGCTCTTAACCGCTGAGGCATCTCACCAGCCCCCTT
1281 TTAGGTATTTTTGAGAGGGTCTCCTGTAGCTCAGACTGGTCTTAGACTCATTTTGTGGTTCTGGTTTATATATTGGGGAC
1361 CAAACCTGGGATGTTTTATGCTTTGGGTGAGCACTCTGCCAATGGAGTTACTTTCCCGGCCCTTGCTTTTCATGTTTCAA
1441 TTGCCGTAGAACCCTGTATGTTTCTGTCTGTGGGCTCTAGTTAGCAGTTGTATAGGTAGCAGCTGTTGGGCCTGGCTTGG
1521 GTGTTATTTCGTCTTCCAGTACAGCAGTGGAGTTTAGTTTCATTGGAATTGGGCCACACATACTTTTTCTGTGAGTCATT
1601 CTGATGAATAAAAAGATTAATTTTGTTCAAACTTAAGGTTTGAAAAAACTTAAAAAAAAAAA
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' ggACCGU--GUGUCA-UCCUGGAAGu 5'
            ||| |  :: | | ||||||||| 
Target 5' gcTGGGATTTGAACTCAGGACCTTCa 3'
 1205 - 1230 155.00 -22.40
2 
miRNA  3' ggaccGUGUGUCAU---C-CUGGAAGu 5'
               ||:|:| ||   | |||| || 
Target 5' gtcccCATATACTACCTGTGACCATCt 3'
 686 - 712 122.00 -9.30
3 
miRNA  3' ggaccgugugucauccUGGAAGu 5'
                          |||||| 
Target 5' ctgagccatctctctaACCTTCa 3'
 523 - 545 120.00 -12.32
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 GSM622570. RNA binding protein: AGO2. Condition:WT1A HITS-CLIP data was present in GSM622571. RNA binding protein: AGO2. Condition:WT1B 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 HITS-CLIP data was present in GSM622574. RNA binding protein: AGO2. Condition:KO2 ...

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

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 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.

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]
16 mmu-miR-493-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT578138 Noc3l NOC3 like DNA replication regulator 1 1
MIRT585573 Tpmt thiopurine methyltransferase 1 2
MIRT585645 Tmco3 transmembrane and coiled-coil domains 3 1 1
MIRT585997 Sfrp1 secreted frizzled-related protein 1 1 2
MIRT586928 H2-T24 histocompatibility 2, T region locus 24 1 2
MIRT588281 Saysd1 SAYSVFN motif domain containing 1 1 2
MIRT597205 Snhg11 small nucleolar RNA host gene 11 1 1
MIRT597340 Sec23ip Sec23 interacting protein 1 1
MIRT598077 Neu3 neuraminidase 3 1 1
MIRT598944 Ggps1 geranylgeranyl diphosphate synthase 1 1 1
MIRT600663 March5 membrane-associated ring finger (C3HC4) 5 1 1
MIRT600853 Gas2l3 growth arrest-specific 2 like 3 1 1
MIRT601713 Rnf168 ring finger protein 168 1 1
MIRT601980 Nanog Nanog homeobox 1 1
MIRT604236 Chrna1 cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle) 1 1
MIRT606762 Zdhhc3 zinc finger, DHHC domain containing 3 1 1
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-493 1,2,6-Tri-O-galloyl-beta-D-glucopyranose NULL NULL Microarray HepG2 hepatocarcinoma cells. 22506400 2011 up-regulated
miR-493 Dexamethasone approved 5743 Microarray adrenals and granulosa cells 24205079 2014 down-regulated
miR-493 (S)-3,5-dihydroxyphenylglycine (DHPG) NULL 443586 Quantitative real-time PCR mouse brain 22309833 2012 up-regulated
miR-493 (S)-3,5-dihydroxyphenylglycine (DHPG) NULL 443586 Quantitative real-time PCR mouse brain 22309833 2012 up-regulated
miR-493 (S)-3,5-dihydroxyphenylglycine (DHPG) NULL 443586 Quantitative real-time PCR mouse brain 22309833 2012 up-regulated
miR-493-3p Diethylstilbestrol approved 448537 Microarray mammosphere-derived epithelial cells (MDEC) 19549897 2009 up-regulated

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