miRTarBase - #MIRT593646


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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 Tbc1d5   
Synonyms 1600014N05Rik
Description TBC1 domain family, member 5
Transcript NM_028162   
Expression
Putative miRNA Targets on Tbc1d5
3'UTR of Tbc1d5
(miRNA target sites are highlighted)		 
>Tbc1d5|NM_028162|3'UTR
   1 GCACAGGGCCCCACTGGCGGACACCCTGCTGAACCAGTGTCTTTTTCCCAGCATGCATTTGGCATTGGTTCAACCCACTG
  81 GAACTCTTTACAAAAAGAGGCAACTATGCTTCTTTCAATGCACTATGTTTACCAAAATGCAGATAGAGGTTTCCAGACCC
 161 TTACCTGACCCTGTGACCCTTGTTCCAATTAGGGCCAGGTCAGGTCCCCAGCTCCATACCCACTGTCAGACACAGCAGAC
 241 CACATCAGAGCCACATGTCTTCCGTCCCCTCCTCCCCAGCAGCTCTGCCAGTTTACACTCAGAAGGAAAAGTTGGTTTCA
 321 CAACTTCCCCTTATCAAAGCTTCAGCCACAGGGAACTTGTTGATACTGAGTGAATCTGGCAGGCAGTCTCACTCCTGCCT
 401 TGGAAGCCCAACATGCCACACAGAGGGAGCAGAGCGGGTGGCTCCCAGGGCTGGAGTCAGAGTGAATTGTAGGAGCAGGG
 481 TTTCAGATTAGGAATCAGATTCTTGTTTGACACAAATACAGTTCTGGACCCTGGGCTTCCTAAGCTTCAGCCACCGCTGT
 561 TCCTCCTTGAACAACTGGATTTCTCCTTCCAGAGTCCCCACAGCCGGGAGTGCAGTGGCTCCACGCCAGTCTGCTCTGAG
 641 ATGGTTTTAAGAGTCACAGGGCTAACATCCTTGAATTGGAGAAATGTGTCCAGAGCTCTCCGGTCAGGTCTCTGAGCATG
 721 TTTAGAGCTACAGTGGCCTGTTAAATGAGGAGCACAGAGGAAAACCACATTCGCACAACCCGGAGTCAGACCTCCTGGGA
 801 ATTAGACCTGGAGTTCCTTCTGTGGGAGCAGGTTTCCTGTAGAGCGTTCCAGGTACCACAAGATACAGGGCTCCTATTCA
 881 ACCCCCAACACCCTATTCTTGGAGCTCAGCTGTAAACTCTGCATCCAGACACTCCAAGGATGGGCCTGCCTGCCTCGGGG
 961 CCCCTGCCTGGGCTGGGTATACATGAGACATCTCCCCGTCTATTGGCCGAGTACAGAGCTGTATTGGGCACAAAGCTAGG
1041 GACAGTGGAAATGGTGGATAGATGTAGCATCTGTTAGATGTCACCTCTGCCTTCTGTCCTCCTCAGAGAGCAGCTGGGCC
1121 TCTGGGCAGTGCCCCACCCACTAATAGCATTGTAATTCTCTACAGACAGGAATGCTAATGTCAGGATGCTCTGCAGGCTT
1201 CTTAGCTGTACTGCATAGCAGGGCTGGTGGCTCACTCACATGGTGGCGGGGCTCAGTCATGGCCTCATGAATTCTACCCC
1281 CTGCCTCTGACCAGTCTTCTCAGCATTCTGAGGAGCCTGCTTGCATACATGTCCCATGAAGCTGCTCTGTAAGAATCAGG
1361 GCCACCATCCATCCCTGCTAGAAGGCTTCCAGCAAGCATTCCACTTAAAGCCTTGACATAACCGTGTCAGTACCTTAGAT
1441 CTAGTGTGGGAAGTATTGACTGATCCATCCAGGTCTGGGACAGTGCCGGCCATGTCTGTCACTGCTGAGCCCTGTCCCCA
1521 GCATCTCCTTTGCGTTGAGAATAAGGTCAATAGATAACTATCACTGGCTACCCACCAGGCCAAGAAGATGATAGGCTGAC
1601 CCATTACTGTTTGAATGGACATTTCATAACCCCTCGACCTACCTGCCCTGCCCATGCCCGTGATGTGCCCCGCTCCTGTG
1681 CTTGTGTGGGTGCCACATGAGAACCCCAGGTTCACACTGAGATGTTTCTATGGTCCCTAGGCAGGCCACTCTCTCCTTGG
1761 AAGAACCAAGGATGGAAAGCTCTTCTCTAAGTGACTCTATTCTTCGTTGGTGACCATTGCTTCCCTTGGTTACCTACACT
1841 GCTGGTTTGGGATGCATTCCGTCCCTGTTATTTTATCAGGTACTTCTGTCTAATTGTACATTTTAAAGTCCTGGATATAT
1921 AGAACCTTTTTCTTTAACCACATGGTAATCATCAGTTTTAATCTCTCACATTTTGATTATAGCAGCTAATACAGTTTTAT
2001 ACAAGCCAAGCCTAGATTAAGCCCTACTGTCGTCTGCTTTTTTATACACATTTCTGTGTTTCATGCAGTCCTCTCTGATC
2081 AGATTGGAAGTGTGAAGTAAAACATACCTGTGTGCCACAGAGGGTCGGTTCAGTGCCTCGGTTCAGTTCTCGAGAACTTC
2161 CTGGCTTAGCTTGGCAAGATGACCTTCTGCTCTGCACTAACTGCAACTTGAAGTGACCACACTGCTGCTGAGTGTAACTC
2241 TGGAGGGCAGCTGCCTCCCCGGAGCCCAGTTCTCGTAGGGGTGAATCTCCTCCGCACGGGTTGGCTGTGCTGGACAACCT
2321 TGCCAGCCATGTCTTTAGTGTCAGAAAGGCTGGACAAATGCCAAAACTCTAGTATAACCTGCTGTTCAGTACAGGTTGCT
2401 TTTGCTTGCTAAAAGCTCTCCCAGTGGCCACTAAAGACAAAGCGGGGAGCACCTGTGGCCCTGCACCGGCCAGTGCCATC
2481 TCCCTTCCCCACCCTGGAACTGCTAGGAAATGAGAGCTGGGGAAGAGGCCATGTGCATGGAGAGCTGTGGCGGCAGGCTC
2561 TTCACAGATCACATGGCCTCCTCCATGCTAGGCCCAAAAGCTGCTTCTCTCTTGTTGAAAAGAGGTGTCGTTCCTATAAC
2641 CAGGCTGGTGTGGAAGTTTTCCTTCGGTGCATGAGGCTCGGCTCATCTAGTTGATATCCCAGCAGTGCCAACAATGTCCT
2721 CACGAGCCTTGGTGCCGGAGCTCATACTGATGTAGGAAATGCCTCCTTGGCAGAGCGAGCCCACTTGATGTGTACTAATA
2801 AAGGACTACTGAGAACTG
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' ugUAACG-GAUCCUUAACAAAUGu 5'
            | ||| |||     ||||||| 
Target 5' tcAATGCACTA-----TGTTTACc 3'
 115 - 133 148.00 -8.20
2 
miRNA  3' uguaaCGGAUCCUU-AACAAAUgu 5'
               |:||  ||:  ||||||  
Target 5' gtcagGTCTCTGAGCATGTTTAga 3'
 703 - 726 130.00 -9.20
3 
miRNA  3' ugUAAC------GGAU--CCUUAACAAAUGu 5'
            ||||      || |  |||| | ||||| 
Target 5' gcATTGGTTCAACCCACTGGAACTCTTTACa 3'
 62 - 92 129.00 -10.31
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions CD4+ T cells (C57BL/6)
Disease MIMAT0004745
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 GSM1013598. RNA binding protein: AGO2. Condition:CD4+ T cells ...

- Loeb GB; Khan AA; Canner D; Hiatt JB; et al., 2012, Molecular cell.

Article - Loeb GB; Khan AA; Canner D; Hiatt JB; et al.
- Molecular cell, 2012
MicroRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3' untranslated region (UTR). However, it is unclear to what extent miRNAs target sites without seed matches. Here, we performed a transcriptome-wide identification of the endogenous targets of a single miRNA-miR-155-in a genetically controlled manner. We found that approximately 40% of miR-155-dependent Argonaute binding occurs at sites without perfect seed matches. The majority of these noncanonical sites feature extensive complementarity to the miRNA seed with one mismatch. These noncanonical sites confer regulation of gene expression, albeit less potently than canonical sites. Thus, noncanonical miRNA binding sites are widespread, often contain seed-like motifs, and can regulate gene expression, generating a continuum of targeting and regulation.
LinkOut: [PMID: 23142080]
CLIP-seq Support 1 for dataset GSM1013598
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, WT, biological rep12
Location of target site NM_028162 | 3UTR | GUUUACACUCAGAAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
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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