miRTarBase - #MIRT599928


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pre-miRNA Information
pre-miRNA mmu-mir-3084-1   
Genomic Coordinates chr19: 24942235 - 24942303
Description Mus musculus miR-3084-1 stem-loop
Comment None
RNA Secondary Structure
pre-miRNA mmu-mir-3084-2   
Genomic Coordinates chr19: 60774329 - 60774397
Description Mus musculus miR-3084-2 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-3084-3p
Sequence 44| UUCUGCCAGUCUCCUUCAGAC |64
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol Rmi2   
Synonyms A630055G03Rik, Gm537, Gm929
Description RecQ mediated genome instability 2
Transcript NM_001162932   
Expression
Putative miRNA Targets on Rmi2
3'UTR of Rmi2
(miRNA target sites are highlighted)		 
>Rmi2|NM_001162932|3'UTR
   1 CGCTGGGACCCTCTAAGAACAGTTTACCCCCATATGGGTCTCAGGAACATCACAAAAGTTTCTTGAAGAGATTCGCTTTG
  81 GTTGAGCCAGCCGTCTGGACCCTGGGAACTGGATCCTCGGTTGTCTAAGCCACTCCTCCCTGCCTTCCTGCTGCTGCTGC
 161 AAAGCATATGCCCCCCCCCCCCCCCGTCACTTACGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGC
 241 GCGTGCGCGCGCGCGAAAGTGTGCCTTTCTCTTGCTGAAGCTCGTGGAAAGCTCATGTTGTCATTTCCTGGTTCTTCGAA
 321 TGATAACACTTTCTCCTTGACCATACCTCTGAATTTCAGTTTGTTGCCAATGGATTAAAATTACAGATGTGAGGACAGAA
 401 TGGCATAGTGGCCTGCCTCCCATCACCAGCTATTGCCAACTTGTAGGGACAGGTACCAGCCCCTTGCTGACAGCTTGCTC
 481 TCATATGCATTGTGCTCATACTGAAGCTGAGGCCAGCTGTTGAGAATGGTGGGAATTCTCACAATTCTCTGTTGAACTTA
 561 AAAATCCAAGATGGAGACAGACTTTTCAAGCACTTCTGCTTCAAAACTGTTGTGGAGAGACATCCAAGGTGGAACAGCCT
 641 GTAGGCTTAGAGTCCTGGCCTCCTTTCTGTATGAAACGCCTTTCTGTTGGGGTTGTATCAGTGTTGGGTTTGGCTTTCTG
 721 CTGACAACCCAGGCTAGATTCCTATTTGGATGGCAAAGACCCAGCAGGCCATCTTATGTTACAGTCTTGCTGTAGGACTC
 801 TTCCTAGTAACACTTTTTTTGTTTTGTTTTTTGTTGTTTTTCGAGACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGA
 881 ATTCACTTTTTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCCAGTGCTGGGATTAAAGGCGTG
 961 CGCCACCACACCCGGCCCTAGTAACATTTTTTGTGTGGTGTAGTTTTTAAAAGTAAGCCCTACTATCTGTTTGTCTTAAA
1041 GACAGGGTCTTATATAGCTCAGGTAGTCTCCAGCTCATGACTCTCTTCCCTCCCCTCCAGCCCGTTGAGATTACGGGTGT
1121 GCACTACTGTGTCTGCAGTGCTGGGGATGGAACCCAGGGCTTCCTGCAAGCTAAGCAAACACTGTATTACTGAGCCACAT
1201 TTCCAGCCTAAAATGTTGATTTATTAAAACAGTTTTAGGTTTTTGGAAAGAATGAACAGAAAGTGTTTCCATAAGCACAC
1281 TGAAGCTGAGGCTGTGTATGTGTTAAGCAAACACATGAGCTAGAGCCCCAGCTCTTGTGTCTTCAAGGCTAGCCAGATGT
1361 GGCAGGCCTCCTGCTGCAGCCTCCAGAGTGTGGCCCACACCCCACACTCGGCCCCCACACCCAGCCTCACCTGGATTGCC
1441 ATGAGCATCAGGTGGTACTTGTCACCAGAAAAGCTAAGGAGTCACCTGGCAGGAGATGGACATCGAGGGACAAGAGAGGA
1521 TGAGGACTCAGGTGATCTAGACCTGCCTCCTTCCTGCCCTCCACCCCCTAGAAAAAGCATCGAGGCCTTGAGCCCAGTTT
1601 GTAGCTCAGGCCAACCTCAGATTTCCCATCTTCCTGCCTCTGGTTAACTGGGATTGCAGGCCTGCTCCTCCAGCCTGCTT
1681 ACATGGACGCCTTAAAAAAAAGATTTTATCTTTAGTTATGTGTTCGTGGGGTGCTTTGGAGCCCAAGAGAGAGTGTTGAT
1761 AAATAAACTTTACCAGCCCCATGCCAGGTAGCTCACAGCTTCAGTAACTCCCTGTAGTTCCTAGGCATCTGACGCCGCCT
1841 TCTGGCCCCTGGAAAACCCTCACAACCTAGCATATAGACTTCAAATAAATACTTAAAAAAAAATAAGTCCTAAAAAATAA
1921 AGAGAGCCAGGTGGTGGTAGCGCACGCCTTTAATCCCAGGGAGGCAGAAGCAGGCGGATTTCTGAGTTCGAGGCCAGCCT
2001 GGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCGAAAAACAAATAAATAAATAAATAAA
2081 TAAATAGGGTTTAAGAATAGTAGTAATGAGGGCTGGTGAGATGGCTCAGTGGGTAAGAGTACCCGACTGCTCTTCCAAAG
2161 GTCCGGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAAACCATCTGTAACAAGATCTGACGCCCTCTTCTGGTGTGT
2241 CTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATCTTAAAAAAAAAAAAAAAAAAACAGTAGTAATGAATGGCA
2321 CTGGGGTTGGACCACGGGGTCCCCAGGGTCTCACACACGCCAGAGTAGCACTCGACCAGCTAGCCTCCTCTGACCTTTAA
2401 ACTGATGGATGTCTGTTGTGCTGGGAGGATGGTGCCCTACAATCCCACGTAAAGACTACCAGCTGATTCATCTTTCTGCA
2481 TGACTGCCTTCCTGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCAGTAGTCAGTCTCTCTGGCCTTCCCTTCTTCCT
2561 TCCCTCCCCTCCTCACCCTGCCTTCCCCACCCTACCTTTTTAGGCAGTGTCTCTAGTTCAGACTGGCCTTGAACTTGGGC
2641 TTTCCTGGAACTCATTATGTAGAGCAGATGAGTTTCTGCCTCCTGAGTGCTGTGTTAAAGGTGCTAACATTTTCTTTTAA
2721 AGGAAGGCCAAGTTGAAAAGTGATCTGTGTTTGACTGCTGAACCATTCATTTTTTAGGTCTATTTTTATTTGTGTGTGTG
2801 TGAGTCTAAAAGAGGACCTTGGAATCTTGAGCTGGGGTTACAGCAGGTCTGAGCATCCCTGTGTGGGTTCTGGGAACCAA
2881 ACTCAGGTCCTCTGGAAGAGCAGCAAGTGCTCTTAATTGCTGAGCCATCTCTCCAGCTCCAATGTACGTTGTTTGAGCCT
2961 CAGAAAATTTGCCAAAATAGTGCAGCTGTTTATATTTTTATTTGCCTATTTATTTGCATGGTCTCTGTAGCCAAGTTTGT
3041 CCTGGAACTCCTGATCCTCCTGCCTCAGCTTCCTGAGTATTGAGATCACAGGTGTGCGCCATTAAGCTTGGTTTATGCAG
3121 TATTGGGGCTCAAACCCAGGATGTCTTAAATTATAGACATACCAGGTTCCTATCATGAATATCTTACATTAGTATGGCAT
3201 GGATGTTAAAATTAATTAACAAATTAACTAATGAACAAATACTGAAAAGTTAGTAACC
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' caGACUUCCUC--U-GACCGUCUu 5'
            || ||||||  | |||||||: 
Target 5' agCT-AAGGAGTCACCTGGCAGGa 3'
 1472 - 1494 148.00 -22.50
2 
miRNA  3' caGACUUCC------UCUG-ACCGUCUu 5'
            :| ||||      |||: ||||||: 
Target 5' tcTTCAAGGCTAGCCAGATGTGGCAGGc 3'
 1340 - 1367 137.00 -13.60
3 
miRNA  3' cagACUUC-CUCUGACCGUCUu 5'
             |||:|  ||| ||||| | 
Target 5' atgTGAGGACAGAATGGCATAg 3'
 387 - 408 130.00 -11.90
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 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' cagacuUCCUCUGACCGUCUu 5'
                || || | |||:|| 
Target 5' ------AGAAG-CAGGCGGAu 3'
 		1 - 14
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]
15 mmu-miR-3084-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT577468 Trim72 tripartite motif-containing 72 1 1
MIRT581090 Sept9 septin 9 1 2
MIRT583858 Eaf1 ELL associated factor 1 1 1
MIRT584586 Bcl6 B cell leukemia/lymphoma 6 1 1
MIRT584631 Bbx bobby sox HMG box containing 1 1
MIRT588486 Wdr26 WD repeat domain 26 1 1
MIRT589287 Pin1 protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1 1 2
MIRT589555 Mfhas1 malignant fibrous histiocytoma amplified sequence 1 1 1
MIRT596659 Zfp329 zinc finger protein 329 1 1
MIRT597539 Rangap1 RAN GTPase activating protein 1 1 1
MIRT598147 Mtif2 mitochondrial translational initiation factor 2 1 1
MIRT599821 Afmid arylformamidase 1 1
MIRT599928 Rmi2 RecQ mediated genome instability 2 1 1
MIRT601578 Ssr1 signal sequence receptor, alpha 1 1
MIRT603200 Trappc9 trafficking protein particle complex 9 1 1

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