miRTarBase - #MIRT588528


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pre-miRNA Information
pre-miRNA mmu-mir-350   
Genomic Coordinates chr1: 176772325 - 176772423
Synonyms Mirn350, mmu-mir-350, Mir350
Description Mus musculus miR-350 stem-loop
Comment Kim et al. cloned 40 new miRNAs from rat E18 primary cortical neurons .
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-350-3p
Sequence 61| UUCACAAAGCCCAUACACUUUC |82
Evidence Experimental
Experiments Cloned
Putative Targets

Gene Information
Gene Symbol Usp45   
Synonyms 3110003C05Rik, 4930550B20Rik, AI843191, Gcap7
Description ubiquitin specific petidase 45
Transcript NM_152825   
Expression
Putative miRNA Targets on Usp45
3'UTR of Usp45
(miRNA target sites are highlighted)		 
>Usp45|NM_152825|3'UTR
   1 TATCTGTTCATTGTTATTTAGTTCATTTTTATTTTAATGCTGAAGTCGTAACCATAATATGTAATGTGCCTTCTTAGTCT
  81 TTAGGAATAGTGCATCCTTCCAGCGTTATTTAACTCTTTCAACATGTGGTGAATCCTTTAAAAAAAAATTAATTAATTTG
 161 ACAGGCAGTTGTGCATGCCTTTAATTCCAGCACTTGGGAGGCAGAGGCAGACAGATCTCTGTTTGAGGCCAACTAGGGCT
 241 ATTCAATAAAACCTTGTCTTGAAATATTAAACAAAAAGTTAATTAATGCTTTCAAATCTATATTCTTTTTTTTTCTTTTT
 321 TTTTGCTTTTGTGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTTTGTATCACTTTGTAGACCAGGC
 401 TGGCCTCGAACTCAGAAATCCACCTACCTCTGCCTCCCAAGTGCTGGCATTAAAGGCGTGCGCCACCACTGCCTGGCTCA
 481 AATCTATATTTTTAAATGTAAAAACATGTTTTATGTTAATTTTCATGTCCATGGAAATTGCCCCTACACACACACACACA
 561 GAGTTGATAGTAAAGCAACCCCCTCTATGATATGACTCATCCTTACATGCATTCAAAGATGATGCTAAATTGGATCTTTA
 641 GTATACTATTTCCTAATGTAATACAACCTTCCTGAGTGGATCCAATATATCTTATGCTACAATTTGCTTACTTTTTGTTG
 721 AAGCCTTTTTTAAGCTTGGCTGTTTTGAATCATACTTCACATTTTTATGTGCTAGTTATTTTTCTAGTAAACATTGATGT
 801 GAGTTTATAACTATGAAAGGAAAATCATACATCCTTGCACCACCCCACTTTAAATCATCTCAGGGCTCTGCAGTGGTGTG
 881 TGTGTTAGTCTATAGGAAAAGTTTCTAGAACAGTCTGAACTAGTGCCTAATGTAACATAATTAATTTTTCATATTTTATG
 961 TGAGTCAGTAGTATAAAAAGGAGCCATTGTAATTTTGGTAGTGTGAGTTTACAAGTAATGAATTGATTCGCTTATTGCTT
1041 TGAATATTTGAAGGTATTGAAACATTTCATAAACTAATCATTTGCAGTCTTTGAAAGATAATTTACAACACATAAAACTG
1121 GTAAATAGAAGTTATAGTCTATATAGGAATATAGAATACTTTAAAGTTTAAGGATATCTTTGAACTGTAAACCACCAAAT
1201 TATATTTATAAATGGTAGAGATCATATTCTTATAACCAACAATGAATATATAATACTTTTTTACTTCTATACATTAATAC
1281 ATGTTAAGCATAGTTTTGTCTTCATAAGCATTTATTTAAAACTTCAGGTGGATAGTTAGGGTTGTAGTTCAATGGCAAAG
1361 CACTTGCCTGGTTCCATCCCTAGCAAAACAAAGAAAATATTCAGGTGGGCTTGGCTACTTTCATGGGACACAGACTTGCC
1441 ACTTCTGTTCCCCTTAAATAAGCAGTAACACAGAATAGTTTCTTCTAGCATTCAAAGGATTGAACTGTGAAAACTTAGCA
1521 TGAAAAATATTACTACCAAGATTTTCAATAATCAATGAAGTGGCTCACTGATACATAGTATTGAATCAAGATGTAAGGGA
1601 ACAGGTTCAATGTCTTAGTCATCAGTGCCTGTGTTTGATTCTATGGGCAAATGTGAGGGAGAGAGGCTGTAAACTGTCCA
1681 GACCTTTAGCCAGGATGGAACCTTCTTAACATGTGTAACATAAAGTCCCCAGTGTTGCCTCTTGATATGTGGCTGGGTGA
1761 AACTGATTGTCTAATGGAGACATTTTAAGATTGTGGAGAAATTTTCAATGGTATTTGAATTTTTTTAATTGAAGGTGAAG
1841 AAATATATTTTATCTGTAGAGCCCAGTTGTGTCCTCTAAAAAGAACTTTCCAGTGTCTTCTGTTTCATCAGACATTCAGT
1921 GTTATTAATCTATTGACACGGAAGAGTCTAGCACCAGAGCAATGAATGAGAAAAATAATTTATTTGTTCAAGCTAGCCTG
2001 TCATAGCAGTTGCACCCACACCCCCAAACAAATGCAAGCGGTCAGCCTTTTTCCCCCCTCTCTCCTGGAAAAGATACTAT
2081 TAAGACATGTACAATCTAAGCAGGTTCCAATACCGGGCATATGATAGTATTTTATGAGCCTTTAAAACAGAAAAACCTGC
2161 TGAGTGATGGTGGCCCATGCCTTTAGATTCAGCACTTGGGAGGCAGAGGCAGGTGGATTTGAGTTCAAGGACACCCTGGT
2241 CCACAGAGCAGGTTCCAGGAAAGCCAAGACAACACAGAGAAACCTTGCCTGAAAAACCTTGGGGAAAAAAAAAACACCCT
2321 AAAATCTATATGATTTTATACATTATTCTAGTAGTGATGTACAAATAAAATGTTCATTTATTACCTAGTTCTGAGGAGAT
2401 TCTGGAATGTATTTTTTTTTAATGACCTAAAGTTTGAGTGTTTTTCTTGTCACCTGAAAATGTAGGAAAATGGTTTGATT
2481 TGATATCTAGGAATTTCTTATCAAGCTTATGTAATATAGAAAAATCACCCAGATCTACACTTAAATTTTTGTTCTTACTT
2561 TGAAGTTTTCCAAAGCACATTTGTAGAAATTTTAAATTGTGAGGCCACTGTACTAACAGATTACCTCAGGAAACCGTGCA
2641 AACAAACAAGAATGTTTACAGATCCGCACAACTAGTCAGTGCTTTGGCACCGTGAATTTGAAAGGTAAAAGAGAGAAGTT
2721 TTTATCTAGAAACTGGTTTACAGGGTACCTCTAGCCCCAGTTCTCCCCTGACTTTCCCATATTTAAAATAATAAAATTCT
2801 GATGATGTGCCAATTATGTGAATGCTTGTGACATAAACAAATATACATCTGTATTTAAGATTTGTTGTTTAATGTTTTAA
2881 AAAATAATATGAAGACTGCTTATGTAGGTGGTCAAGGGGATGATCATATATCAACAGAGCTATTTTACCATAGTTCTTAG
2961 CTTGCATGTGTGATTAATTAGTGATTTTTATGTAATACTTGAATAAGATATCCTGAAGATATGAAATGTCTTCGTGAAAT
3041 GTAGCTGTGAAATGTCACCGCACATCAAATTTTTATAGTACAAAATAACATCCTGCCTACTTTCATGAACTTTATACTCA
3121 GCTTATTTTTCTGCATGACATCTGGTCATATAAACCTAAACCAAATATGTGCGATAAAATCAAGCTTTCAGCTAGCATCC
3201 ATTGCAGTATTAGAGAAATGATTTCTGCATTAAAATGTTTTTGTTCATGCAGAAATCATCAATTGAAATGTGTTTAAAAG
3281 ATGATTATTTTTAGGTATCAGTAATACATTCATGGTATCATTCCTTCTCTTTCATCCAGTTTTACAGTATTTTAAAAATA
3361 TCTGTGTAACTTATTGAGCATTATTTGATCATTGCTGTATGTAAAAGATCACAATAAATATTAGATTCTTATGTTAATTG
3441 ATTAGGCCTAGAGTTTTTGCATTATACATTGTTAGCAGAATGTTAATAAACATTGTGTCATTGCCTAAAAAAAAAAAA
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' cuuucACAUACCCGAAACACUu 5'
               | | | | :||||||| 
Target 5' tctttTTTTTTGCTTTTGTGAg 3'
 314 - 335 149.00 -8.00
2 
miRNA  3' cuUUCACAUACCCGAAACACUu 5'
            | ||| |||    |||||| 
Target 5' ttATGTGAATGC---TTGTGAc 3'
 2814 - 2832 128.00 -7.70
3 
miRNA  3' cuUUCACAUAC----CCGAAACACUu 5'
            |||  ||||    | ||| |||| 
Target 5' tgAAG-ATATGAAATGTCTTCGTGAa 3'
 3014 - 3038 125.00 -8.20
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 GSM622574. RNA binding protein: AGO2. Condition:KO2 ...

- 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' cuuucacauacccGAAACACUu 5'
                       :||||||| 
Target 5' -------------UUUUGUGAg 3'
 		1 - 9
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]
27 mmu-miR-350-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT435011 Lars2 leucyl-tRNA synthetase, mitochondrial 1 2
MIRT577176 Tet1 tet methylcytosine dioxygenase 1 1 5
MIRT577951 Pole4 polymerase (DNA-directed), epsilon 4 (p12 subunit) 1 1
MIRT579173 Cd70 CD70 antigen 1 1
MIRT580234 Tsga10 testis specific 10 1 1
MIRT581630 Prkaa1 protein kinase, AMP-activated, alpha 1 catalytic subunit 1 1
MIRT584029 D230025D16Rik RIKEN cDNA D230025D16 gene 1 1
MIRT588424 Zbtb6 zinc finger and BTB domain containing 6 1 1
MIRT588528 Usp45 ubiquitin specific petidase 45 1 2
MIRT588917 Skor1 SKI family transcriptional corepressor 1 1 1
MIRT589679 Larp1 La ribonucleoprotein domain family, member 1 1 2
MIRT590168 Elp4 elongator acetyltransferase complex subunit 4 1 1
MIRT593065 Ehf ets homologous factor 1 1
MIRT593183 BC068281 WD repeat and coiled coil containing 1 4
MIRT595160 Cbfa2t3 core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human) 1 1
MIRT596758 Utp23 UTP23 small subunit processome component 1 1
MIRT596783 Ubxn2a UBX domain protein 2A 1 1
MIRT597289 Slc1a7 solute carrier family 1 (glutamate transporter), member 7 1 1
MIRT597494 Rbm41 RNA binding motif protein 41 1 1
MIRT600204 Ube2j2 ubiquitin-conjugating enzyme E2J 2 1 1
MIRT603448 Ric3 RIC3 acetylcholine receptor chaperone 1 1
MIRT604253 Cercam cerebral endothelial cell adhesion molecule 1 1
MIRT604915 Iqcj IQ motif containing J 1 1
MIRT605131 Cnnm3 cyclin M3 1 1
MIRT605214 Arnt aryl hydrocarbon receptor nuclear translocator 1 1
MIRT605697 Ifnar1 interferon (alpha and beta) receptor 1 1 1
MIRT606256 Polr1e polymerase (RNA) I polypeptide E 1 1
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-350 Hesperidin NULL 10621 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-350 5-aminoimidazole-4-carboxamide-1-β-d-ribofuranoside (AICAR) NULL 16078949 Microarray hepatocytes 23107762 2013 down-regulated
miR-350 Tamoxifen approved 2733526 Microarray rat liver 17343880 2007 down-regulated
miR-350 Ursodeoxycholic acid (UDCA) approved 31401 Microarray rat Liver 20689055 2010 down-regulated

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