miRTarBase - #MIRT592642


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pre-miRNA Information
pre-miRNA mmu-mir-384   
Genomic Coordinates chrX: 105344282 - 105344369
Synonyms Mirn384, mmu-mir-384, Mir384
Description Mus musculus miR-384 stem-loop
Comment The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies .
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-384-5p
Sequence 16| UGUAAACAAUUCCUAGGCAAUGU |38
Evidence Experimental
Experiments Cloned
Putative Targets

Biomarker Information
Biomarker ID Name Type Discovered From Mode Level Source Testing Methods
BZV7T3 miR-384-5p Safety Biomarker (SAF) Clinical/Experimental Data Expression Increase Serum Real-time reverse transcription PCR
Gene Information
Gene Symbol Lpar3   
Synonyms Edg7, lpA3
Description lysophosphatidic acid receptor 3
Transcript NM_022983   
Expression
Putative miRNA Targets on Lpar3
3'UTR of Lpar3
(miRNA target sites are highlighted)		 
>Lpar3|NM_022983|3'UTR
   1 GCCACGGACGCCTCCGCCCTCTTCCCCTGGGGAAAGAGCTGTTAAGCGTCCTCACCTGTCTCACAAAGCACGTGGACAGG
  81 GTTGTTTGAGGGCTCCATGCATCACTTCTGGGGCTTTTAAGTTTTCATGGTCAAGGAAAATAGATTTACGGCGTTTAGTA
 161 AAAGCGCACAGGAAAGGGAGAGATGAGCAGTGGGTTCCGGCTTGTCTGTGATCCGCTCCCAACATCCTCCAGCTCTTGCG
 241 AGAGCCATGCTGGGCTCTGTCACCATCTTGCCACCATTGTCTGTGTGTTTTCAATGATGGTGTTGAAAGTCCTAGGTCAA
 321 AAGAAAGTAGTAAATAATGGTACCTGAGCCCCCCATTGTGTGGCTACTAGATTCTGTAGTTGTTTCCGCATGGGTTTAAA
 401 ATGTTCAGAAAAATATTTTAGCAGTGAACTTTGATTTCCTCAGAGAAGCCATGGCCAGGAGCTAGGTGGGCAACTGTATA
 481 GTAGAGTAAGTGATGATATTGACCGGTAGGTTGAACTTCTTCCAAATAGCGTCAAATATGAGCACGATTAGATCTTCAGT
 561 CTTGGTTATCAGGATACCGCTGAGGGGCTTGCTGGATCCCAAGTGCAAAGTAATTGCACATCGAGTATTTTAACCAAAGC
 641 TGCCAGCGTATTCTATCTTGTGGACTGCATTTTGATCTTGTATTTTTCTCCTTCAAAGACCTCTGAAAGGTAGATCAGTT
 721 AAAAACAAAAATAGTGTTCATACACATAGGCTACTGACCAGTGTTTTCGGTGTAAGACGTTTAGAGTGTATTCTGACAAA
 801 GTAAGAATAACTTCAAGGCAGGCACTATGGTATTTATGTAGCTTGCAAACGTTTACATGTTCTCTCTCTCTCTCTCTCTC
 881 TCTCTCTCTCTCTCTCTCTCTCCCCTCTGCTGTTGTGATGTAACATTTATGTGCACAAACTACTTGTAATAAAATATTTT
 961 AAGAAGCTATGCTTTGAGATATAATGGCCTAAAATATAGAGCGTTATGATTTGAAGTCTTAGATTTTTACATGCTTGATG
1041 CAGTAGGTAGGTGTACGCAAAGCTTATGTGAAAGCTACCTATAAAATAATAATTTGCGAGGACCTGTTATCCCTTGATGA
1121 GGGCCATTATTGCTCTGTATATTATCTAAGCAAAAATACAGCATGTGGTAACTGTGACTCACACTTGTATTGTAGAAGAA
1201 AAAAAAATCAAATTTGCCATG
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' ugUAACGGAUCCUUAACAAAUGu 5'
            ||||:||: |   ||||| | 
Target 5' ccATTGTCTGTG---TGTTTTCa 3'
 274 - 293 130.00 -12.70
2 
miRNA  3' ugUAACGGAUCCUUAACAAAUGu 5'
            |||  || | |:|||||| | 
Target 5' agATT--CT-GTAGTTGTTTCCg 3'
 369 - 388 128.00 -7.20
3 
miRNA  3' ugUAACGGAUCCUUAACAAAUGu 5'
            :| ||:| | ||  |||||| 
Target 5' atGTAGCTT-GCAAACGTTTACa 3'
 836 - 857 128.00 -8.50
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 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]
Experimental Support 2 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 ERR266298. RNA binding protein: AGO2. Condition:A_Untreated ...

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

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 GSM622572
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / WT2
Location of target site NM_022983 | 3UTR | AUGUUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCCCCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM622573
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / KO1
Location of target site NM_022983 | 3UTR | AUGUUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCCCCUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM622574
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / KO2
Location of target site NM_022983 | 3UTR | CAUGUUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCCCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset ERR266298
Method / RBP HITS-CLIP / AGO2
Cell line / Condition Liver / A_Untreated
Location of target site NM_022983 | 3UTR | ACAUGUUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23597149 / E-MTAB-1612
CLIP-seq Viewer Link
37 mmu-miR-384-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT577998 Pgr progesterone receptor 2 2
MIRT578191 Narg2 interactor of little elongation complex ELL subunit 2 2 2
MIRT578276 Mesdc2 mesoderm development LRP chaperone 2 2
MIRT578464 Ints12 integrator complex subunit 12 2 2
MIRT578486 Il18r1 interleukin 18 receptor 1 2 4
MIRT580032 Wdr89 WD repeat domain 89 2 6
MIRT580041 Wdr44 WD repeat domain 44 2 2
MIRT580302 Tomm70a translocase of outer mitochondrial membrane 70 homolog A (yeast) 2 2
MIRT581000 Six4 sine oculis-related homeobox 4 2 2
MIRT581273 Rrad Ras-related associated with diabetes 2 2
MIRT582217 Nfatc3 nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3 2 2
MIRT582447 Mgea5 meningioma expressed antigen 5 (hyaluronidase) 2 2
MIRT583055 Hoxb3 homeobox B3 2 2
MIRT583626 Strip1 striatin interacting protein 1 1 1
MIRT583683 Amer1 APC membrane recruitment 1 1 1
MIRT583923 Dpy19l1 dpy-19-like 1 (C. elegans) 2 2
MIRT584696 Cep170b centrosomal protein 170B 1 3
MIRT585027 Gskip GSK3B interacting protein 1 1
MIRT585242 Zfp446 zinc finger protein 446 2 2
MIRT586100 Reep4 receptor accessory protein 4 2 4
MIRT587716 Cd300a CD300A molecule 2 4
MIRT588342 Zfp711 zinc finger protein 711 2 2
MIRT588629 Tnrc6b trinucleotide repeat containing 6b 2 6
MIRT589300 Pigh phosphatidylinositol glycan anchor biosynthesis, class H 2 2
MIRT590164 Eno2 enolase 2, gamma neuronal 2 2
MIRT592642 Lpar3 lysophosphatidic acid receptor 3 2 4
MIRT593646 Tbc1d5 TBC1 domain family, member 5 2 2
MIRT595037 Camk4 calcium/calmodulin-dependent protein kinase IV 2 2
MIRT595222 Slc16a1 solute carrier family 16 (monocarboxylic acid transporters), member 1 2 2
MIRT595455 Ptrhd1 peptidyl-tRNA hydrolase domain containing 1 1 1
MIRT595822 Fam227a family with sequence similarity 227, member A 1 1
MIRT596023 Cdk13 cyclin-dependent kinase 13 2 2
MIRT596361 Serpine1 serine (or cysteine) peptidase inhibitor, clade E, member 1 2 2
MIRT596421 Ing1 inhibitor of growth family, member 1 2 2
MIRT596514 Zfp9 zinc finger protein 9 2 2
MIRT599311 Csf1 colony stimulating factor 1 (macrophage) 2 2
MIRT603174 Trp53rk transformation related protein 53 regulating kinase B 2 2

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