miRTarBase - #MIRT597494


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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 Rbm41   
Synonyms BB131279, D330023I21Rik
Description RNA binding motif protein 41
Transcript NM_001172147   
Other Transcripts NM_001172148 , NM_153586   
Expression
Putative miRNA Targets on Rbm41
3'UTR of Rbm41
(miRNA target sites are highlighted)		 
>Rbm41|NM_001172147|3'UTR
   1 GAATTCGTATCTACACACATGTACATGCACATTTGGATATATGTATGTAAATGAATATTCAGATGATTTTTCTTTTCTCA
  81 TTTCTTAGATCAAGAATATGTAAATTCATAAAAATTTGTTGAAAATTGAAGAGGAAATATAAGAAAGAAATTAGGACAGT
 161 TGCTCTCAGCATTTGGAGAGAATTGATAAAAGTATTTTCTTTTTTTAAGATATATTTATTTATTTTATGTATGTGAGTAC
 241 AGTGTAGCTGTCTTCAGACACACCAGAAGAGGGCATTTGATCCCAGTATAGATGGTTGTGAACCACCATGTGATTGCTGG
 321 GAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCTCTGAGTCATCTCTCCACCCTAAAAAGTATTTTCT
 401 ATAATTAAATACTGTATAGTATTGAAAAAGATTGTATAAAATTGACAATATCCTGGGTGTTAAAGATAATAATGAAACAC
 481 TATATATGGCAGAAAATACCCTGAGGGGTAAGACCATGTGAAAACCTTTAATTCTCAGGATACATTACATAGGACTGTTC
 561 CTAAAGATCCCAAAAATCCTTTAATAATTTTGTAGTCTTCAGTGTTTAGTCCTAGAGATAAGACTTTTTCTAGGAGTGTT
 641 TCCTGTATACGAAGTTTTAAAACTAACCCAGTGTTAAAATATTTCTTTACTGAACTCAAACTGTGTTTTGTCAGAACCTT
 721 CAACAGTTTCAGTAGGTAGATTCATAAGTTTATTAACTTAATGATTGCTTCCACACTAAGTTTTCAGAGTCCTCAAAAGC
 801 ATATTTATTATTATGACATCTTTTAAACCAAAATATTGGTAGTCTATGATACTATTGCATTCAAAACAATATCCATTAAA
 881 CATGGAGTATCTGTCTAATGTATGAACTTTCAAGACAAATGAACTAGCATCTATATTAAAGGGACAGGAAAGAAAGTTCT
 961 TTAGAGGAAAGGCAGCCTGCCTCAAATTCCCTAGTGATTCGTTTATAGTTGTTGAAGAAGAAGAAGAACCTAAATGGTTT
1041 AGACGGTAGAACCAGCTTTGGAGTCAGACCTGTGACCCTCAAAGTCACCCATGTTTACCATCCTGAGCTTAGAAAGTCAC
1121 TCACTCTGAGCCTCATTTATCTCATCTATAAAAAGTAACATTGCTTCTGACCTCCCTGAGTAAGGGTTAAATGAGATTAT
1201 AATATCCAAGGTATTATATTATATTATATTATATTATAACAAGGGGAAAAATGAACTTTAGGGTACTCCACTAAGTACAT
1281 CAAACAACATATAATAAGAATTTCATTCAAAAGCGAGAAAGAAGCATAAAATACTACAAAAGGTCGAGTGAAATGGCTCA
1361 GTGAGTAAAGGCATTTGCCACCAAACAGGAAGACCTGAGTTCAAACCCTCAGACCTGCCAATAATAGGACAAAAAGGCTG
1441 GGAAATAATGCTATAGTTTCTTTAAAAATCCTGTAAATCCATAGGAACAAATAAAACAAAAGGGAAATAAGGTGGCTAAA
1521 TTTTACTAGGCTGTAAACCTAATTCTGCTTCCTAGAAGTAACAGAATTATATTGGTAGTTGTACTGTTCTGTTAGCCCTA
1601 CAGTGTGTTGAAAGAGTTCGCATGGCTGAGGAAAGGGAAACAAAAATGCTAGAGATAAAGATCCACTTTGTGTTTAAAAG
1681 GTTGGTGTTTTAAGATGTGAGAATTTTAATCACATATTTTCATAACTACAGAGCCCTCAAATAACCTGAAACAAGGTAGC
1761 AAACAAAGTAAAGAATGAAAGGAGAAACAGGCACATCTCCAAACTGGTGGGTACTCAGTGTCTCCTTCCTAATACAAGTA
1841 CTGCTGCACAGTTGATAAACAAGGAAGTAGCCAGTTTCAGCACTGGATGCTGGATAGATCTGAAAGACAGCTCTAGAATA
1921 TAGCTCTACTAGAATATATATATTTTATCCCATGTATATGAAACATCTTTAGGCTAGATCATGAACTGAACCACAAAACA
2001 GGCCTTAATAAATACAAATGGACTAAAGTCTTGTCAAACATGTTCTCTTCCACATGGAAGAAGGTTACACATCAGTACCA
2081 ATAAATCGGGAAACTCACAGATAAGTGAAAATTAGTGATAACTTAAAGACCAAGTCGGTCAATAAAGAAGCGGGAGAGAT
2161 GGCTCAGTGCATAAGAGTACTTACTGCTCTTGCAGAGGACCTGAGTTTGATCCTCAGCATCCACACTGATGGTTCCCAGC
2241 TACCTTTGTCTATATATGGGATATGCTTAGAGATAAGCCTATTCAATGAGAAGAAAGACCGTGTAACAGTAATTCACTTC
2321 ATATCTTAAGCCATAGGAAAATAATAGCAAACTACACCTAGAACAAACAAAAAGGGGAAAACATGCAAAATGCCTGAGAA
2401 TAGAGTACAAGAGAGAAAATGCAAGGAATCCAAGCGAGAAACTGGCAAGCCTTTTGCTACATACAGCAGGAAGAGGTAGA
2481 ATGTAATCATTAGTTTGAGAAATAAAGGAGGGAATGTTGCTACTGACCTTTGAAAAATAGAAGGTGTGTGAGGGAGTACT
2561 GTTGTACTCATGTGTCAATAGATTAACCTACTAAAAATGAACAAATCCCTAAAAAGATAAAGTACCAAGAACCAAATATA
2641 GGAAGCCAGAATCGACCTACTAACAAATAGGTTAAAGAAGTCACAAGACAGATAAGCCACAACAATACCTATACTTAAGT
2721 TGCTTTAGATTTGAAATCTAGAGTTCTACTAAATGTTTAATAAAACAGTAATCCAGTTTCTTCACATGCTGTTTATTAAG
2801 AAAATAAGGAATACTTCTGAGATATACCACCACATGGGAGAACCCTGAGAGTATGTTCAGGGAAAGAAGCCAGTCACTGG
2881 TGAGGACAAAATGTGCAATTCCATATATATGTCAAGTACAGAGTTGGTTTAAAAAGTGCATATATATGTAGTAATAAATG
2961 GTAGGCAAGAAAAGCTAGAGTGTTCATAAATTACATCAGTGGTTGTATAACAATGAACATACCAAGTGGGTGAATGTTGT
3041 GGTATGTGAATTAAATCTCAGTGAAACTCAAAAACATAGGAACTTGGACATTATCCAAATGTCCACCTGTCAACATGAGT
3121 GACTTTTAACTGATGGCACATCCATTTAGTTGGGTATTATGAAGCCATTAAAACAGTAGACTAGATCTATGAATATATTG
3201 TGACCTCTACTCATATCCAAGATTTTATATTAAGTTATAAGCTAAGATACATGTATGTATGTATTTATGTATGTTTGTAT
3281 GTATGTATGTAACACATTTTTAAGCAAATAGTTCATGTGTATAGTTTGTAGAGATAATTTCAAAACAAATATAGGAATAA
3361 AATAGGAAATGTATATAACGGGCTGTAAACCTTCTGCAAGTGACTCCGTACAAGCTAAAAACAAAACACCTCCACCTTGG
3441 AAACATTTTTAGGTGGTATGATTTGGAGCGATTTTTACCTTTTTCACTACTTTTTAATTAAAGTAATTTTTAAATATTCT
3521 TACAAACACTTGGCTTCCAAAATATTAGTCAGACCTACTCTGAGGGTTTCTGACTTTACTCAGGACAAACTTGTATTCAT
3601 TTGCTATATTGCTCACGCGATTAACACTTCAATTTCTCCTAGAGTTTAAGGGGTGGGACGTGAAGGAGCCACCCTGGTTA
3681 CAGCCTCTTGCACATGTTACCCTGGGCTACACTTCTCAGCCAGGTTTCCCGGAAGGGACTGCTTCCTCTCAGGTGGGCAG
3761 CCTTACCTCCTCCTTGCTAGACCTGCAGACCACTTAAAAATGGAGACAATCTAATCGAGGGTACCTTTCAACTGGTGCAG
3841 AGATAGAGAAATTGGTGTATCCCGACAGCAAGATTCTACTCAGCAATAACAAACTAAGGAACCATATATGCAACAACTTG
3921 GATACATCTGAAATGTATTTTGCTAAGTAGAAGAAGCCAGACTCAAACGGCTGCTTACTGTTATATTTCATTTGTGTTGT
4001 TTTCTGGAAAGGATGAAGCAATAAGGCAGAAAAAGCAGTAGACACCAAGTATCGGCACAAGGGATTTCTTTTTAATAATA
4081 GGAACTTTCTCTGTGTTATTTATAGTTACAATGTGTATGTGTTTGTTAAAACTCAGAGAATTATGCAACAAAAGAATGGA
4161 TTTTAATGTGTGAATTTTTTAACAATAAAAGTAATTTTTGATGAAATAG
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' caATGTGTATGTG-TTTGTTAa 3'
 4109 - 4129 139.00 -9.60
2 
miRNA  3' cuUUCACAUACCCGAAACA-CUu 5'
            | |||||| |  ||||| || 
Target 5' tcATGTGTATAG--TTTGTAGAg 3'
 3313 - 3333 132.00 -7.60
3 
miRNA  3' cuUUCACAUACCCGAAACACuu 5'
            |||   ||   |||||||  
Target 5' taAAG---ATCCACTTTGTGtt 3'
 1656 - 1674 129.00 -8.10
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 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]
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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