miRTarBase - #MIRT593242


—
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 Arpc4   
Synonyms 20kDa, 5330419I20Rik, AI327076, p20-Arc
Description actin related protein 2/3 complex, subunit 4
Transcript NM_001170485   
Other Transcripts NM_001170486 , NM_026552   
Expression
Putative miRNA Targets on Arpc4
3'UTR of Arpc4
(miRNA target sites are highlighted)		 
>Arpc4|NM_001170485|3'UTR
   1 AACATCTAGCTGGATCTCGCAGCCTTCCCCTCGGCCTCCCTGTGTCTCTGCGTCTGCAAAGGTGTCCTGGAGTCACTCCC
  81 CGGAGCAGCGGTGCAGCAGCAGCAGCCGGAAGCTGGGTTGGGTGGGCATTGGATGTGGGAGGTGGGTGTGGTGTGCTTGC
 161 TAGCTGTGCAGAAAGGCAGCAGTGGGCCTGCCCCATAGCCACATGTGTCTGCTCTGGCTAGTTTCTGATGCTCAGTCCCC
 241 TGGACCGGGACAGACTTTTTTTTTAAACGTCTTGAAACCTAAACTCTGTGCTTGTAGAAGACTGTAACCTTTTTGTCTTT
 321 TTTTTTTTTTTTTTAAACAAACAAAAAAACCAACCTCCAGCTCCAGTGGCTGTGACTGGCCCCAGTGATTGTACCTTATT
 401 GGTCGCTGTGGTCTGGGCGGGCCTGGAGCCAGAAGGCGACTATTTTTCCCGAGCCACCCCCGGTGGGGAAAGAGGGAAAT
 481 TTCAGACTACAGTTTTTTTCCCTTGCTGTCTTACAAGCCTCCTTAGGCCTAGTAGAGAGGCGGTATGGACCCTCTACTAG
 561 CCTCCTGAGTCCTGCCTGAAGATGCCCACTGCACTGGTTGGGAACAAGGGCTGAATCTATGATTGCCGGGCAGGCCTAGG
 641 AGCGGGGGCCCAGAAGCCAGGCAAACTTCTGGCCGTAGGGGCCACCCGGTGTCCATCCGACCCCTTCCAGCTGAGAGGCC
 721 CAAGGTTTGCCCGTCTGGGTGCAGGGCCTGTGCTGCAGGTCCAGAGGTGAGTCCTGCCTGCTCGGGCTCCTCTGCTCCCA
 801 TGCTCGCTGTCTCGGATTCTGATGAACTCCCCTCCCCCCTAATTAAAGTCTCTTCCTGCCCCTTCGGGGCTGCATGAGGT
 881 CTGTGCTCTGTGTGGGTGTGTGAAAGGATGCGTGTTTTGATGCCTTGGAGCCTTGTGGCTGGCATTTGGGTCTGGAGCAG
 961 CCCACCAGACAATTTTGTCATCGATCCCGGCCAAGGGCCCCAACTCGGAGCACTTCACTACAGCCAAGCACCGTCATTCT
1041 GAAGGCGGTTTCTGCCCAGACAGAGATGCGGTGCTTCCACAGCCTGCTTCCATTCTAGCTTTCGGGGACCCCAGGAACCA
1121 TGATCCTACTTTGTGGATAAGAAGAGTCATTTCCCACGCTACCTAACCTTGTTAGTCTGACTGGTGCCTCAGCAGGTGTT
1201 GGGGGTAACTCGGTATTGAACATGCTGGGAACTTCCGTTGGATAGTGCTCACTCCTCAAGTAAGCAGTCCTTTCTCTCGC
1281 TGTGTCCTGATACTTGGAGACCTGTGAACTCTATGCCATTATCCCTGTCACACAGGGGCTAGGTGAAGTAGTTGATCTCT
1361 CTACCTTCTGTTTAACTTGTGTATGCTGGCCATCTGTACTGACATCCAGTCCTACTTTGACAAAACTCAGTTCCAGGAAA
1441 AATGAGGTCTGTCTGCAGACAGGCCGATGAGAGTGGTGTACCTAGTTGGAAGAGGGGGGTATGGGGCTTACAGGAGAGGT
1521 TGTCAGGGAAAGCTTAGAAAATATTTGGCCTTGAGCCAGGTATGGTGGCTCACACTTGTAATTCTAGCTCTTGGAAATTG
1601 GAGACAGGAGGACTTTTGAGTTCTAGGCCATACTGGAAGTACACTGTCTCAAAATAAAGAGTATATGTGAG
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' uacuaACGGU---GUAAGACCUCAu 5'
               ||| |   ::| ||||||| 
Target 5' gcgtcTGCAAAGGTGTCCTGGAGTc 3'
 50 - 74 149.00 -12.60
2 
miRNA  3' uaCUAACGGUGUA---AGACCUCau 5'
            |: || ||: |   |||||||  
Target 5' gtGGCTGGCATTTGGGTCTGGAGca 3'
 935 - 959 136.00 -16.70
3 
miRNA  3' uaCUAACGGU---GUAAGACC-UCAu 5'
            || | |:|   ||| |||| ||| 
Target 5' ttGAGTTCTAGGCCATACTGGAAGTa 3'
 1616 - 1641 128.00 -15.40
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Liver
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 ERR266292. RNA binding protein: AGO2. Condition:B_Liver partial hapatectomy 48h ...

- Schug J; McKenna LB; Walton G; Hand N; et al., 2013, BMC genomics.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' uacuaacggUGUAAGACCUCAu 5'
                   :::| ||||||| 
Target 5' --------gGUGUCCUGGAGUc 3'
 		1 - 14
Article - Schug J; McKenna LB; Walton G; Hand N; et al.
- BMC genomics, 2013
BACKGROUND: Validation of physiologic miRNA targets has been met with significant challenges. We employed HITS-CLIP to identify which miRNAs participate in liver regeneration, and to identify their target mRNAs. RESULTS: miRNA recruitment to the RISC is highly dynamic, changing more than five-fold for several miRNAs. miRNA recruitment to the RISC did not correlate with changes in overall miRNA expression for these dynamically recruited miRNAs, emphasizing the necessity to determine miRNA recruitment to the RISC in order to fully assess the impact of miRNA regulation. We incorporated RNA-seq quantification of total mRNA to identify expression-weighted Ago footprints, and developed a microRNA regulatory element (MRE) prediction algorithm that represents a greater than 20-fold refinement over computational methods alone. These high confidence MREs were used to generate candidate 'competing endogenous RNA' (ceRNA) networks. CONCLUSION: HITS-CLIP analysis provide novel insights into global miRNA:mRNA relationships in the regenerating liver.
LinkOut: [PMID: 23597149]
CLIP-seq Support 1 for dataset ERR266292
Method / RBP HITS-CLIP / AGO2
Cell line / Condition Liver / B_Liver partial hapatectomy 48h
Location of target site NM_001170486 | 3UTR | GGUGUCCUGGAGUCACUCCCCGGAGCAGCGGUGCAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23597149 / E-MTAB-1612
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

Error report submission