miRTarBase - #MIRT598064


—
pre-miRNA Information
pre-miRNA mmu-mir-3058   
Genomic Coordinates chr10: 95559231 - 95559321
Description Mus musculus miR-3058 stem-loop
Comment This sequence was identified as a miRNA candidate by Berezikov et al .
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-3058-5p
Sequence 14| UCAGCCACGGCUUACCUGGAAGA |36
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol Nif3l1   
Synonyms 1110030G24Rik
Description Ngg1 interacting factor 3-like 1 (S. pombe)
Transcript NM_022988   
Expression
Putative miRNA Targets on Nif3l1
3'UTR of Nif3l1
(miRNA target sites are highlighted)		 
>Nif3l1|NM_022988|3'UTR
   1 ATGCAAGGACGTCAAGGACACCATGATGACAGAAGCCACAGATCACCTGGATTGAAACGGCTGTGCAGGAGTTGGTGTTC
  81 CACCCTCTGCAGAGCTGTATTGGACTTCTCATTTCAGTTCACGACTCTGGCTCAACAAAAGCCATAGCTCATTCGGTAAA
 161 ACTGTCTGTAAAGAGTACATTAAAGGCAAACCTTCTCTAATTTTTGTTTTGTTTCTTGGTGGTGCAGGGATCAAACTGGA
 241 CACTGTTTACCACTCTAGTTGGCAGCATGGACTTGAGAGTAGGGCCTAAAAATGAGGTGAGCTGATGTCTCACGCAATAG
 321 CCAAGTTTATTCAGAGCCATCGGACAATTTACACTCTGAGGGCTAAGAGTCAACTGAATAAAGGCACAATCACAAGGACA
 401 AGCCTCATGTAGCAAAACCATGGTTTCCATGGAGGTGTATGAACAATAAGAATAGCCAGCCAACTGTAAGGAATGATCTA
 481 AAGTCACCTCACTCCTATCTGCTTGCTCCACTGGGGAAGGGCACAGAAGCACATCCCAAGAACAATTTTGTGTTTTTGAA
 561 GAAACTGTTTTCTCACAAACACTCAGAAGTCCCTCACAGGACTGGACTATTCTTGGACTATGTTCTAGCTCTATGAATGG
 641 AAGGCAAGTGTTCTACCACTGAACTCCAAACTCCTCCTAATTAATGGTGTTAAGTGTTCAAAATATGACTGATTACTACC
 721 CAGCATTTTCTGCAGTCACTGTACAAGCCAGACCCAGAAAGAAACTGGGGTGCCCGGGGGGAAGGGGTGGCTGGAGAGAT
 801 GGCTCAGCAGTTAAGGGCACTGACTGCTCTTCCATAGGTCCTGAGTTCAATTCCCAGCAACCACATGTAATGGGATCCAA
 881 TGCCCTCTTCTAGTGTGTGTAAAGACAGTTACAATGTATTCACATACATTAAATAAACCTTAAAAAAAGGAAAAAAAAAA
 961 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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' agaaggUCCAUUCGGCACCGACu 5'
                :|| |||  ||||||| 
Target 5' gcccggGGGGAAGGGGTGGCTGg 3'
 772 - 794 157.00 -24.00
2 
miRNA  3' agaagguccAUUCGGCAC-CGACu 5'
                   |:||  ||| |||| 
Target 5' gcctaaaaaTGAG--GTGAGCTGa 3'
 284 - 305 114.00 -14.06
3 
miRNA  3' agAAGGUCCA-UUC-GGCACCGAcu 5'
            ||:||| | | | |: |||||  
Target 5' caTTTCAGTTCACGACTCTGGCTca 3'
 110 - 134 113.00 -9.60
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' agaaggUCCAUUCGGCACCGACu 5'
                :|| |||  ||||||| 
Target 5' -----gGGGGAAGGGGUGGCUGg 3'
 		1 - 18
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]
14 mmu-miR-3058-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT582584 Lsm6 LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated 1 2
MIRT596389 Ulk1 unc-51 like kinase 1 1 2
MIRT597024 Thap2 THAP domain containing, apoptosis associated protein 2 1 1
MIRT598064 Nif3l1 Ngg1 interacting factor 3-like 1 (S. pombe) 1 1
MIRT598727 H2-D1 histocompatibility 2, D region locus 1 1 1
MIRT598925 Gjc3 gap junction protein, gamma 3 1 1
MIRT600197 Vsig10 V-set and immunoglobulin domain containing 10 1 1
MIRT601407 Uba1y ubiquitin-activating enzyme, Chr Y 1 1
MIRT603601 Pigv phosphatidylinositol glycan anchor biosynthesis, class V 1 1
MIRT604125 Ddx58 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 1 1
MIRT604495 2510049J12Rik makorin, ring finger protein 2, opposite strand 1 1
MIRT605081 Dennd5b DENN/MADD domain containing 5B 1 1
MIRT605584 Ncl nucleolin 1 1
MIRT606040 Zmynd12 zinc finger, MYND domain containing 12 1 1

Error report submission