miRTarBase - #MIRT597268


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pre-miRNA Information
pre-miRNA mmu-mir-509   
Genomic Coordinates chrX: 68010105 - 68010179
Synonyms Mirn509, mmu-mir-509, Mir509
Description Mus musculus miR-509 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-509-5p
Sequence 10| UACUCCAGAAUGUGGCAAUCAU |31
Evidence Not_experimental
Experiments
Putative Targets

Gene Information
Gene Symbol Slc25a34   
Synonyms Gm1369
Description solute carrier family 25, member 34
Transcript NM_001013780   
Expression
Putative miRNA Targets on Slc25a34
3'UTR of Slc25a34
(miRNA target sites are highlighted)		 
>Slc25a34|NM_001013780|3'UTR
   1 ACTCAACCCTCATCCCACCACCAAGCCTGCCATCTGGTAGAGGTGATGGCCTGTCAGTGTAAGACTGGCTGCCCAGAGCT
  81 AGCTTGAGTCAGGCCCTGCCACAAGCCAGGAGGAGAAGGCAAGGAACAATGGACAACTGGGATCCATTGAGCCCCAGGAC
 161 CAGTGTGCCCCATGTCACCACCTCTTTATTTCCCTTCTCTCCCCTGGGTTACCATGCCTTAGCTCATGGCCACAGCAATG
 241 CCTACATTTAAAGATTCCCATTAGGGGAGCCACTCAGCTGCACTGGCTCCTCAGTCCTCCACCCACTGTGTGACCACATG
 321 AGCCTCTCTCAGCATGGGGAAACTGAGGCTGAGGGGAGCCATGTCTCTGGCTGGAGCCACATATGTTTGCCATGACAGAG
 401 CCAGGACTGGAGTTCAACTCTGCCTACCCCCATACCATGCTCTCAACGAAGACAAGGCTACATCAGGACTACTGGGCTTC
 481 GTGTCCCTCAGAGGCCACTGCATGTGAGACCCTTGTGCCACCAGGGAGTCCTTGGTGTCCCCAGAGTCTGGTTGGCCAAA
 561 GCTAGTTATCAAACCAAGTTCTGAAGCTGCCTCAATGGCTTAGCAAAACAAACAACCCTGTTTTCCTACCTTCTGAAGCT
 641 GGAAGCGCAGGAAGGTATTGGCGGTGTTGGCGTCTCTCTTTTATTTCAGTTATCTGTGGTGCTGTGGTAGAGCCAGGGCC
 721 TGGGCATGCTGGTCACGTGATCTGCCCGTGGTCCACACCACAGCCCAAGGCTGACTTCTCCTGAGACCTCTTTCCTTGAC
 801 TTTAAAATGAGCAGCTTCCTTTGGTCTTCTCTGAATCTGAGTAAAATCAGCTTTCCTCAGGCTGGGGACATAGATCAGTC
 881 GGCAGACTGCCCACCTGATGCCCACGAGGCCCCCCAGGATCCAAATGAACTGGGCATGATGGCCCCTGCCTGTATTCTCA
 961 GCCCTGGGGAGGCAGAGGCAGGAGGATCTGGAGTTCGGAGTCATCCTCGGCTCCATAGCAAGTCTGAGGTCAGCCTGGAT
1041 TCCATGAGAGCCAGAGAGGAGAGAGAGGGAGAGGAGGGGAGAAGGGGGTTGGGGAGGGAGGAAAGGGAGGAAGAGGAGGA
1121 GGAGGAAGAGGAGGAGGAGGAGGACAGGGAGATGGAGACCCAGTTCTGTTGAATAGGACCCACACAGGGACTGCATATTA
1201 CCGAGGGAGCTACCACGGCCTCCCTCTACAGTCCCTGAGGGGCTGGATTAGGGCGTCAGCAGCAGTCTTAGAGCGCTTGA
1281 GTCCAGGCTTCCTGTTTGTGTACGTCCGGGGGAGCTCAGGCCTAGGAAAGAGGGTGCCTGTCCATGTGGGTCACGGAGCA
1361 GAGCCACTGCAGGGCCAACGACACACTCCGAGCCCTCTCTCCAGACTGCAGGCACGCTCCACCACAGGGACAGGTGTGTA
1441 AGGCACCCAGTGGCCTTTCTCCTATGAAAGTGGACACTCGCTCTTGGCCAGGTAGCCTCAACCACCTTCCCCAACCACTT
1521 CCCAAGTGAGAAAAATTACTCCAGATGAACACTCCTGAACACTCCAATAAAGTTTTATATTTTGTAAA
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' uacuaaCGGUGUAAGACCUCAu 5'
                |||| :  ||||||| 
Target 5' gacagaGCCA-GGACTGGAGTt 3'
 394 - 414 147.00 -15.90
2 
miRNA  3' uacuaacgguguaAGACCUCAu 5'
                       |||||||| 
Target 5' agaggcaggaggaTCTGGAGTt 3'
 974 - 995 145.00 -12.20
3 
miRNA  3' uacuaaCGGUGUA---A--GACCUCau 5'
                ||||::|   |  ||||||  
Target 5' aggggaGCCATGTCTCTGGCTGGAGcc 3'
 352 - 378 130.00 -14.40
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 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' uacuaacgguguaAGACCUCAu 5'
                       |||||||| 
Target 5' agaggcaggaggaUCUGGAGUu 3'
 		14 - 35
2 
miRNA  3' uacuaacgguguaaGACCUCau 5'
                        ||||:|  
Target 5' -----------gccCUGGGGag 3'
 		1 - 11
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]
CLIP-seq Support 1 for dataset GSM4751760
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of eWAT 1
Location of target site NM_001013780 | 3UTR | GGAGGCAGAGGCAGGAGGAUCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM622574
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / KO2
Location of target site NM_001013780 | 3UTR | GCCCUGGGGAGGCAGAGGCAGGAGGAUCUGGAGUUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
41 mmu-miR-509-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT578959 Dusp26 dual specificity phosphatase 26 (putative) 2 2
MIRT580254 Trim44 tripartite motif-containing 44 2 10
MIRT580870 Slc7a2 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 2 10
MIRT581746 Plxnc1 plexin C1 2 2
MIRT587519 Cyp2e1 cytochrome P450, family 2, subfamily e, polypeptide 1 2 2
MIRT589364 Ogdh oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) 2 4
MIRT593147 Man1b1 mannosidase, alpha, class 1B, member 1 2 2
MIRT593242 Arpc4 actin related protein 2/3 complex, subunit 4 2 2
MIRT596605 Zfp459 zinc finger protein 459 2 2
MIRT596837 Ttf1 transcription termination factor, RNA polymerase I 2 2
MIRT596841 Ttc9c tetratricopeptide repeat domain 9C 2 2
MIRT597087 Tapbpl TAP binding protein-like 2 2
MIRT597268 Slc25a34 solute carrier family 25, member 34 2 2
MIRT597356 Sap18 Sin3-associated polypeptide 18 2 2
MIRT597676 Pramef8 PRAME family member 8 2 2
MIRT598060 Nip7 NIP7, nucleolar pre-rRNA processing protein 2 2
MIRT598168 Mrpl9 mitochondrial ribosomal protein L9 2 2
MIRT598216 Mpv17 MpV17 mitochondrial inner membrane protein 2 2
MIRT598455 Lcmt2 leucine carboxyl methyltransferase 2 2 2
MIRT598572 Irak1 interleukin-1 receptor-associated kinase 1 2 2
MIRT598680 Hist2h3c1 histone cluster 2, H3c1 2 2
MIRT599285 Cxcr2 chemokine (C-X-C motif) receptor 2 2 2
MIRT599395 Churc1 churchill domain containing 1 2 2
MIRT599401 Chrnb4 cholinergic receptor, nicotinic, beta polypeptide 4 2 2
MIRT599422 Cflar CASP8 and FADD-like apoptosis regulator 2 2
MIRT599581 Brip1 BRCA1 interacting protein C-terminal helicase 1 2 2
MIRT599644 Bbs1 Bardet-Biedl syndrome 1 (human) 2 2
MIRT600276 Tmem69 transmembrane protein 69 2 2
MIRT600608 Mylk2 myosin, light polypeptide kinase 2, skeletal muscle 2 2
MIRT601254 Abcb7 ATP-binding cassette, sub-family B (MDR/TAP), member 7 2 2
MIRT601257 A230046K03Rik WASH complex subunit 4 2 2
MIRT602233 H2-T23 histocompatibility 2, T region locus 23 2 2
MIRT603621 Pdzd8 PDZ domain containing 8 2 2
MIRT603806 Klhl7 kelch-like 7 2 2
MIRT604050 Exosc2 exosome component 2 2 2
MIRT604344 Bcas2 breast carcinoma amplified sequence 2 2 2
MIRT604550 Wdr89 WD repeat domain 89 2 2
MIRT604729 Rs1 retinoschisis (X-linked, juvenile) 1 (human) 2 2
MIRT605172 Bri3bp Bri3 binding protein 2 2
MIRT606241 Rab33b RAB33B, member RAS oncogene family 2 2
MIRT606652 Mrpl11 mitochondrial ribosomal protein L11 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-509 Formaldehyde NULL 712 Microarray Human lung epithelial cells (A549) 21147603 2011 down-regulated
miR-509-5p Glucose NULL 5793 Quantitative real-time PCR endothelial cells 24394957 2014 down-regulated

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