miRTarBase - #MIRT603448


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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 Ric3   
Synonyms E130307J04Rik
Description RIC3 acetylcholine receptor chaperone
Transcript NM_001038624   
Other Transcripts NM_178780   
Expression
Putative miRNA Targets on Ric3
3'UTR of Ric3
(miRNA target sites are highlighted)		 
>Ric3|NM_001038624|3'UTR
   1 AAGCAGCCTGCTTGGGAAAGTATCCATTACTCTGTTCCCATGGCACCTTTCCTCAGTTTCATCCATGGCCTTGTGCCCTC
  81 TGCATCCTCTGTGTTCAATACCATAGCTCTTGGGCCACTACCATGGATACAGCTAATCCTTCCCGGTGCTTGCACACCTG
 161 TCACTTTGTAAAGTAGCCAGTAGTGTGAACACGGGACAGAATCACCTTCCTAGTCATGCGCTTCCCTATCAGAGTGTGAA
 241 CACAGCACAGAATCACCTTCCTATTCATGAGTTTCCCTATCAGAGACACTAATCCACTCGGTAATTGTATTTGGTTGTTT
 321 GTGCTTGCAGGTGGTACCACCTAGGCAAATGTCTGACCCCTCCTCATAGGAGCAACAGATGATTTACCTGTGAATGATTT
 401 ATTGAATGGATTTGTTAGGATAGGATGACCGTGAAAGAGAACTGGGTTAGCTGATATTGAGGACTTAAGTTTTAAGAATG
 481 AAGATTTTAGATTCCCAAATGCCTTATTCTTTGGGCCTTCAGCTGGTTAGTGGTCCCTGAGAAGAGCATGCTCAATTCTG
 561 AGCCTAGGGGCCCAGAGCACAGCAAGATATCTGATTGAGCTGCAGTCTCTCCTCACAGCCTTCTAAGATGCCCTGACTCC
 641 TCCAGAGCAGCAGGCCATGAACTCACGGGCCTATTTGGAGACCATTTTGCTTGTATATTCCCTCGATCCCTGCTTCCTTT
 721 GTCTTTATTCTGTTGAACAGAACTGCCAAATCTAGAGGCAACTCTGAATGTCTTCTGTGGCTAGAGGGATTTGGAGGCAT
 801 TAATCTGTGTCCCACAGAGCTGAAGTTTGAGGCTGTTGAAGCTACAGGACTGCTTAAGTATGGTGGTCCTTCCATGAGGA
 881 GCTCAAGTAGCCAGGAAACCCTGAGAATTCTAACAAGGGTGTGTCAGTTCAGTTACATGAATTGAAAGCTGAAAGGCTGT
 961 GCATCTCCAACAACATTCCGAGTCATGAAATGGGAGACTCAAAATTTAAGGAATTCTGTGAAGCTGGATAGTCTTTAGAG
1041 TTCTATTGTGCCTGGCATGCCTATGATGCCAGAAGATAGTTTGGACCACTCAGGAGCGTACTGCCCTGGCTGTCATCAGG
1121 TCTGAGACCACACTAAGACACTGTCAGCTACTAGAAAGCTTTACATGTTAACGGGACTAGAGAAACACAAACGCTGCACT
1201 GTACCAATCCCTGTGTAGAATGTTTGATTGAAATTGTGCAGAATGCAGTTGAACATGTACTGAAGATGGTCTTGACATAA
1281 CTAAGTGTAAAAAGCAACGCAGATACTCTTGTTTGAGCAGATTGTTTTCTGGATGGTTCTGGCATCCACCATGAGAAGTT
1361 GATTTAAGATAGCCCCGTATCACTGGTTCTAATTTTTGTTCATAGGATATAATTCTGTTATTAGATAAGAACTTGTTTCC
1441 TTCTCATTCATTTGTTGGACAACGGCCCTGTGCTAAGTACTGAGTGTCTGTGCATAGTCCAATGCCCCAACTAAGAAGAC
1521 TGAATTTGTACGAATTTCAGTTTAATGTGCTAATCTAACAGATGCACTATGGACCATAGGAAGGCTAGAGATTGTGAATT
1601 CTTCAGACAGATTTCCCTGCAATTCAGGCTGTGGAATTCTGGATTGGCTCCTTAAGCATCCCAAGCCTGGTTGGGCATCT
1681 ATAAAGTGTGAGGGTAGTAAAAACACAGGTCTTACAGGGCTGTAAGCTGCAAATGAGGTAGTCAGTGCACATAGGGCAGC
1761 ATGCTTATGTTGTTAGCTCATGCAAAACAACATATCATGTGGTAGCTGTTTTATTCATTATAGTGTGGACCCTAAACTGT
1841 AGGAGCACAGAAGAACAAGAATGTTCTTGCCAAGTACCAAAAAAATCTCAGAGACACCTTGTGGAAAGCTAAAACATGGC
1921 AAGAGGAGGAAGGACATTTGGGCAAAAAAAGTAGGTTAGCAAGAACAGTGTGGTTGGTGTATAGATGGGTAATCAGGTGA
2001 AAAGGGTTTAGCACCAACTCTATCATTGGGGATTAGCTATGGAAACAATTCCTGCCAAAAGGACCAGTCCTTCATGGTTC
2081 TTGCCACTCTACATGTTAGTCTGCATATAGGAATATATTTGTTTGTATATACCAGAAACTTTGAAGAACCTATTAGTAAT
2161 TTGGAATATAGGCATTTTTTCCCAGAATTTTATCTTTTAGATATGATTTTTACAGGTTGACCAAAATCAAGGGGCTTGGT
2241 TTCATTGTATGATCTTCATTTCTCAATATTAAGGGTTTCATCAAGGCCTTACCATTAGGTCTCCAGTGACCTATGGGGCA
2321 CCATAGCAGTAGTTGGCCTAAGAAGCCACTGTACATCACCTAGGAGTGTGCTTGGTAAGTCAGGTGGGTGATCAGCCAGA
2401 AGACCCCTTAACACAGCTATGGAACAAGACTGTGTGCCTCCTTATCTCAAGGCCTGGGCCTGGGAGGTATGCTGAAGAGT
2481 GGAGATGGACTCAGCCTCTAGAAATAATGGCTTGAGAGAATTATGTTCTTTGTATTTAGACTTAAGCAATAATGGTCTTC
2561 ACTCAGACACTCTGGAAAGAAGAACCTAAACTCACGGCATAATTAAACGTTCTCATTGTATGGAAGGTAACAATGCAGGA
2641 GGAGCATGTAGTTGAGGGCAGTCCTTCAGGGCAGCAGGAGCCAGCGGGCAGGCTCACAGGGAGCTGAGGTGAATGATGAT
2721 ACACAGCACTTGGCTTGTTTTGCCCCTCTTATCAGTCTGGGACCCCAGCCAAAGGGATGATACTGTCCATAGTAAGGATG
2801 GGTCTTCCTCCTCAACTAACTTTCTTGTAAACACCTTCATAGACAAGTATGTTTTCATGGTGATTCTAAGCCCCTTAAGT
2881 TGGCAATCAAGAGCAAACCAGAGGTAATAGGTATAAATAAAGATTTTCCTCTGCATGTGTTCTACACAATTGAGGATTTT
2961 TTCTTAAACTTGATGACTAAACAAACAAAACCTCTTCCCTTTGTCGAACACCCTGTATATGGTCTTCACAAATGCAATCA
3041 CTACAGGAACCAGGCCATGTTCAGGTAGGGAATGCTTTTGACTCACATCAAAAACACTTAGCTGAGTAGATAAATGAACC
3121 CTAATTATAGACCTGCTCTTAAATTCTTTTTATTTAGACAATTTGTATCTGCAAAGAACATTTCATATGTCACCTATTGG
3201 GCAGTGATCAGGAAGGATACTAATCAACTATTCTGTAATCTCCTTAACCATTAGCATGTCTAAAACACTTTGTAGTATCA
3281 AAAAACCAGGCCATTCCTTCACTTCAAAGGGTACCACTTTCCTTATGGATGGACCAGGAATCACGTCCACCTTACAGGAC
3361 TGTTTCTGAAAGCTGCCCAGTGTGAAGTGTGCAATGGTAGGTGCTTATTAGCACATCACTGTCTTGAATCTCATGCTTCT
3441 GGACTACCCAACTTGATACTCTATGGCCACTCTGCATGCCAAGAATGGTCCAGAGTCACTCTGAGGAGTTCTTGTGACTT
3521 TGTGATGACTCCTTTTAGAACAACTATAGGCTTTCATCATGTTGGCCTCAAATCCACCACAGACTGAAAAAGGGTTCCCA
3601 CTATGTAAGAGTCCTGTTTAAATAGACCCACCTCCAAGCAAGGCCTGCAGTCATGTGGCTGGGCCTTTCCCACTCTTGAG
3681 TACTACAGCCCAGTTCTGTCCACAAGGGCCATGTCCACCAAGCATACTTAAGAACTGTCAGCCAGTTCCTTAAGTGACCA
3761 GATGACCTGAAGTATCCTCTAACCCTTTTTTCCCCATGCTATAGATGTGGTTTCACAGGAGAAGGCAGTGCTGATCTGTA
3841 TGCCACTCACTGGTTCTAAACGTGCTCTGGGCCCTCAGTTGCTCTTACGCACCTGACCCTTTGAAGCGCCTAGAAAGGAC
3921 TGGGATGGAGAACATTTTAGGAGAGACATGTTCTCTTCTCTATGAAAACCAAGGACACAGCCGTCAAACAGTTCAAGTTT
4001 AATGTGTTGATACATGTCTGTACTTAGACAAACACTAAATTCTACAACATACATAATGTCATTATGGGAAAATACCAAGT
4081 TTGTCATTGCACATACCAATAAATAAATACATTTGCTTCAGAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4161 A
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' cuUUCACAUAC-CCGAAACACUu 5'
            :|||   || | |||||||| 
Target 5' agGAGTTCTTGTGACTTTGTGAt 3'
 3504 - 3526 156.00 -12.00
2 
miRNA  3' cuUUCACAU--ACCCG-AAACACuu 5'
            || ||||  ||| : ||||||  
Target 5' gtAATTGTATTTGGTTGTTTGTGct 3'
 301 - 325 142.00 -8.00
3 
miRNA  3' cuUUCACAUACCCGAA-ACACUu 5'
            || | || ||  || ||||| 
Target 5' caAAATTTAAGGAATTCTGTGAa 3'
 1000 - 1022 128.00 -6.30
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 ...

- 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' gaGAGAGAGAAGGUUUUGUGAu 3'
 		15 - 36
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]
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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