miRTarBase - #MIRT577176


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pre-miRNA Information
pre-miRNA mmu-mir-350   
Genomic Coordinates chr1: 176772325 - 176772423
Synonyms Mirn350, mmu-mir-350, Mir350
Description Mus musculus miR-350 stem-loop
Comment Kim et al. cloned 40 new miRNAs from rat E18 primary cortical neurons .
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-350-3p
Sequence 61| UUCACAAAGCCCAUACACUUUC |82
Evidence Experimental
Experiments Cloned
Putative Targets

Gene Information
Gene Symbol Tet1   
Synonyms 2510010B09Rik, AA517754, BB001228, Cxxc6, D10Ertd17e, LCX, mKIAA1676
Description tet methylcytosine dioxygenase 1
Transcript NM_027384   
Expression
Putative miRNA Targets on Tet1
3'UTR of Tet1
(miRNA target sites are highlighted)		 
>Tet1|NM_027384|3'UTR
   1 AGGCTTCTCTCATGTAATGCCTTTGCTAATGTGGTGTAGTGGGTATTTTTGTTTGTTTGTTTGTTTTCTTTTGTTTTTTT
  81 GTTTTTTCCGGTGCTGTTAAAAAGAAAGTCATTCTGTTGTTTACTGTAGCTTTGTTTCGCCCATTTCAACTCCGACGTAA
 161 ATATTAAAAAAAAAAAAAGGGTGAATACTTAACTGTGATTACATTTTGAGAATTGGTAGAAGGTGAACATTTTCAGCAAA
 241 AATAAACTTTTTATAGTTTTAAATACTTAAAGGAACATCTTGGTTAGGTGTTGGCCATGCTAGAACCATAGAGTCTGGTG
 321 CTTTCCCCCGGGTTTGTTTACTATTCAGAGGGTTTATAACAGGTTCCTGCAATAAGAAGTAAAGACCAAGATGTAGTGTT
 401 AACTCTACACAGTTCCTGGTGCTTTAACCACATCAACACACGGAGTGATGAGCTGAGTGATTGTTTTCTGGTGCCATTGC
 481 TCAAGCCTCTTCCAATCATTGCCATCGTGTCTGCACATTTCTTTGAAGTAAACCAATGAAATGCTTTTTCTCTTAAAACA
 561 TTTCTCCTATATAAAGTAGTTCTCTATTCTCATGATGGTTGGAAGCTGTTCGCTAACTATAAATGTATATATTTTAAAAA
 641 GCACTTTCTACTTTTAAGAGTAACTTGAAATAGTATAGTAGCAGAATCCTATTGTCTATTATGTGTGCATATTTGAATAC
 721 CAGAGAAGTCATTTGTTCTTGCTCTGTAGAGTCCCATCCCGTTAACCTCAGCCTGTACTCAAATAACACACGGCTTCTGT
 801 TCTTTACTTATAGAATAGAGGGTCTCTAAAAAAAAAAATTTAAATACAAGATGCTACCAATATCAATTTTCCCTCTTTAA
 881 CTAGAAAAAATATTGTCTTCTGAAGTCACCTCGTCAATTAACTATATGACCCAATTACAGGTGTTTTCAAAGGAAAAGGA
 961 GGCAAATTGGGATCAGTCAAAAGTTCCCAGTGTTTCAAGATTAGAAAATACATAATTAAGAGACATGTCCTTCCCAAATG
1041 AGAAGGAAATATTCTATAGAGATAATTGAGGGGACATGCTTGCGTTAGCATTGTCACCCTTACCCTGGAGTTCCATGGTA
1121 ATATTGAGAGCCAAACTATTCATTAATAGTGCCCTATCAGGTTTAGGAAAATGGGAACCCAAACTTGCTTAGTAATCCTC
1201 TATTGAAGGTCACAACTGAAATCAGCATCCTGATTACTTTGTGTTCCAGTGTTCTGCCCATTGTTTAATTGACTTCTTTA
1281 TATACCAAGAATGATTTCCCCAAACAAAAAAGCCTAGAACCAAGCGACCTTTCTGAGAGATCCAAATGCACAGGTGCTAT
1361 TGCCATTGCTTGGGTTGAAGTCTTTGGATCTGGATTAGGATTCCTGTCCTTCAGGGACCCTGATGGTGCTTCTCAGAGAT
1441 GCCACAAGAAGCCCACAACTACCACAATCTTGGTGCAAATGTAAGCCGTTGCAGTAAACTCCTTAGGGAATAACTTATTA
1521 AACACAATACATGGTGCAAAGTGTCAGCCTCTGACTGAGGCACGTTCAGGAAGAGGAAGGGACTGTAAATAAGAACGTGT
1601 CCACTGACTTTCATCCCATCCTGCACAGGGAGCTGGATGCTCTTGGGATCCATACACATGTGGATCTGAGTTAGTGTTCT
1681 GTGTGCCTTAGAGTTCTGTTTATAAACCTTTTTTTAAGTTTCTTATGTCGGTATGTGAATGTGGTCCTTTCTTGCTGTGT
1761 CTGCTTCAGTTAGGTATTTATTTGTTAGTGTAGACCATCAGAAATCCTCCCTCATGAGTTAACCTTTGAGGTTTCAGACC
1841 TTATCTAGAAATCATTTTCTTGCCATTATGGGATAGAATCGCCTCTTCCTGCCTTTATTTGTCCATTCATCTGTCCGCTC
1921 GATTAGTTTGTTTTCCCTTGAATTACCCCTTATCACACAAACTTATAACGAATGCTTGGAACTGCTTTCTAAGAACATAA
2001 CAAACTACCTATAAATGAAGAGCTACAGTAATATATATTCAAGCTGATGTGTTTTTAATGATAAGGCCACATTCTTGGTG
2081 CTTAATCAGTTGAATACACCAATGTTGATGAATGGGACTGTTGGTGTTTATGAATCTAGTTGCAGTTTGACAAAATAAGT
2161 ACATGAAACTAACCACTTTCAACAAAAATGTTGTCATTCCATCGCTAGAGTTAGCATCAGAGATGGAGTGCCTCAGCCAA
2241 CAGCCCTCTGTGGGGACTTCATTATATTACTTTCATGGTCTCTGATGTGCTTTGTAGGCATCCTCTACTTGGTTGGTGTT
2321 CTACTGCACCATCTGCTGGCTATACACGGCTTTAAGAATGGACTTTCTTAAAAACAAAATACAACCGGACAGTGGTAGAG
2401 CATGCCTTTAATCCCAGTACTTGGGAGGCAGAGGCAGGTGGATTTCTGAGCTCGAGGACAGCCAGGGCTACACAGAGAAA
2481 CCCTGTCTCAAAAAGACAAAAAGTAAAATACATTGGTTTGAGATGACAGTCACTTATCTGACAATCTTTCTACACCTCTA
2561 CTGTTTTAATTAGATTGCGTTCCTCTGACCTCGTTTGTGGAGCTCTGACTAAGACTGTTCTCGCTGTGAACATTGGATAC
2641 ATTGTTATATGACTTCCACAGTAGCCCTGGTGATGCTACAATTCATTCCTGCCTGCTTTAGAATTAGACATCACCTGCCC
2721 TCTTAAAACCATTTTTGGTGGGTTTTGGTTTTATGAGACTGGATCTCTATGTAGTTCCGGCTGTCCTGGAACTCATGTAG
2801 CAGACCAGGCTATCCTAGAATTCACAGAACTATCTTCCTGCTCCTACCTATGTGCTGGGATTAAAGTTGTCCTCCTCCAC
2881 TCTCCTAGTTCTTTTGTTCTTGTGCTTGTCAGCCTCGTGTATATCCTGTTTCCAGTTCTCTACAAAGTACCAAATAAGAC
2961 CAGGTACTAAAGAGACTGTTATCACTGTCATTGAAATATAGTGTTTGGACTTGAGGATAATAGAGGCAAATTTTTGGGAA
3041 CAAGTCCACATCTTAAGTGATTTCCCAAGCATAACGTTGCATTTGTGAGACACAGAACTTCATTAGGTGAAAACCGTAAG
3121 CCATTCACTTCCATTCACCCCGTTAAACAGTTAACTGAGTGGCTATTATTCTGTAAATGATGTACTGGCTTGATTCACAT
3201 GAGGTAACCTACTACTTCTGATTATCATTTCACAAGAACATGTACAAAACTAACCCCAAATTATTCATTCATATATATAA
3281 AATGAGACTTCTGTGTGGGGTGGAGCTATCAAGCTATCATGTCATCACATGACCTCTTCTATCGATTGTGGGTGCATTTA
3361 CCTTTGTGCCAAACAAGTAAGTGTATGCAACCTTAACACAAAGCTACCCTGAGTTTCACCCCCTCAATGCATGGGAATCT
3441 TTTTGAGTCTAGATTTAATACAACTGAGTTTCATCTATACTAGAAATGTATAACAAGAATTATGACAAAGGATAGTGTGG
3521 TGGCTGTTGCTGCACCAATAGTCTCCTTAGAAGGCAGAGCTCAATCCCTGAGTTCTCGGGACAGACAGCGCCTAATTGCT
3601 TGAGGGCCATTCTGCTCTTAGAGCTGTTCAAGACAAACTACTTTTCTCACTCAGAGAGGATTATATTACTAAGAACTTAT
3681 CTTGATTTTTGTCCAAGTCAAAAATAAAACAACTTTCTGTCCTCTGGTGAGGTTCAGGACAAGAAAGACATTGGTGAGAT
3761 TAGGTCAAGATTGCCTTTACTGTCTATCCTAGGCTTTGCCAGGAGAACCTATGACATTAACCTACTAACTCTTCCCGATG
3841 CAGAAGGCAATCCTTGTCTCTGCCATTCCCTCTGGAACCTAGTATTAGGAATAAATACCCAAGGAGTTCTTGAGGACTGG
3921 CTGTGGGAACCATTGAGGGAAGCATGCCTTCACTGTATATACTCTGTAGCCGCGGTTGCACAGTCCCTACTGCCCCTCCC
4001 CTACTTCAGTGCTGGCAGCTCACTGTGATGTGGCCGTCACCATAAACAGGCGCGCTGCTTCACTTCTCTGTGCTGGTCAC
4081 GTTGGCATATTTAGCCATGTGGTGTGGTCATTGCTTAGTGGTTTGAGATGACTAAGTTTTTTTTTTTTTTTCAAATGAAA
4161 TGGGTGTTTCATATTGTATTTCATCAGAAAACAGTGGCAATTGTGAAGACCATTTAGATAGTCACTGTATCCTCCCACAA
4241 AACCTAATTCTGTATATTTTCTTCAAAATTGTTAAAATTCCTAAGCATGGTTTTTTAAGTTTTGTTTTGTTTTTTTGGTT
4321 GGTTGGTTGATTTGTCTTTGTGTAATAGAAGTTGGGCTTTTATTAAATTGTGAGCCTGGACTTCCTTAAGAATCTCATGG
4401 TGGCGTATAGCACAGTTTTGAACTATGGCTAAGGATGTTGAGAACGTCTTTTTCCCTTTCTTTGCTTCTGGAACTGGGTC
4481 TCACTATACAGACCTGGCCAGGACAAAGATCAAGTTGCTCTTGAACCTGCAAGGGTTCTTTCTGACCTCTGGCTGTGCCA
4561 CTCTTAGTTTCTCTGGTGCTGGGATTGAACCAGGCCTTTTTGTGTGTCTGGTAAACACCATCAACATTCCCTCCCATCCT
4641 AGACCTTGGGGTTTTTTCCGTAGGGAATCATCATTTGTGTTTGTTTTCAGCTCTACAAAATCTTAGCATGCTGCCAAATC
4721 CTTTTCTGAACCTTCTGGTTCAGGTGATCTCTTATTGATTGCTAGGGTATAGACACAGGGCTCCCTGCCCAGCTAATGTA
4801 CATTTGTATTAGCCCAGCTCTTTTCTCAGATAATCAGTTTGTTCAAAATATGTGTTACTCATAAATCTCACATTGACCCT
4881 GAGACCCCAGTGATCAAAATTACCTTGTGGCAGTCTGTAATGTTTCCAGCTTCAAAATTACAAGGTTAATAATTTATTTA
4961 TTCCTTTTCTACATTCAGATTTCCTTATGATTAAAAATCTTCTGTACTCCTGTATGTACACCCTGGCTCCACCACCCAGA
5041 TCATCCCATATGCAAATATATCTGATTAGTTCCAGTTTTCCATTTCTCTGCCTTCCTTTTGCCTCAGCACCTTGGCTTAT
5121 CTTTTTCAACCATGTGTCATAAAGTCTAACACCATGCTTGGCTCAAGTGTGTGTGATCCCAACTGCTTGAGGGACTGAGA
5201 CAGGATGATAGAAAGAAAAGGAACACCAGCAGGGCGCAGAGCTGCCTGCCATAGAGTTCATGAAAGAGTGGTGCTTGCCA
5281 ACCTTGCTGGAAGCAATCCCTAGTACTGCAGAAAGGACCAAGGATGTGTATGCAGAACTTTTCAATTAGGAGTAAGTACA
5361 ACTTAAGTTTCATATTCCCATTCTTTTGGCCTTTTCCATCTCCAGCTGCTAAAATTGAAACCTGCAAGGCAGTTTTAGTC
5441 ACTGGATCTTATATGCAGACAGAGTTTCTTTTCCTTCTCCTCATTTTCAACAATCTCATTCTGTTGATGGGAGCCTGTTT
5521 CCTAAGGTAAATTAACTCTAGAAGTTCTTCAGCTGTACTCGTCCCTTAATAATGGCCCTGATGTACTGCAAGTAGGATCC
5601 TGTCTCCAACCCCAGCTCAGACAGTACAGCCCCACATCCTTACACATAATCTAGTTTCAAACATAAGTCCTTGGTGATGA
5681 GCTACCAGAATCCCTGGTGAGGAAGTCATGGGGATTAATAGTTCTTGTCTGCCCTCTTCTAATTTTAACTGAAAATAGGT
5761 GATCTTTTGACAATAAATAGGACATGAACAAAAAACAAAAAACAAAAAAGCTTAGCATCTCTCCCTAGGTGTGATGTGCC
5841 CATCTATAATTCAGCTCCCGGGGAGGCAGAAGAAATGGGATGGGATCATGTCTTCAGAGCTCTTTGTGGGATTTCTCACC
5921 AGTACTGAACTCAGAAAGCAGTTCAGCCGCCAGCGAGAATAGCCAGGAGCTTACTCCATGTCACACAGCAAGTCAAGTAA
6001 TACGAGTGAAATGTAGTTGCCTGCATGTATGTGTGTGCCTTGTGTGTTGTCTAAGTAGAGCTGATAGGAGAAAAACAGAA
6081 AACTTATAAGCCTGTTTCATTTCCGTTGTTTAGCCAGCTGTTGCACATATGAAAGATCTCAAATCCTTATTTATGCATCA
6161 AAGCTTAGGTTTATGGTTTTGTGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTAAAACAGGTTCACAATGTTGCTCTAG
6241 CTGGCCTGGAAGATGCTGTTCTGTCCTCAGGTTGCTTTGGTCCTACGTCAGGGACTGCAGGTGTAAACCTCTCCATTCAG
6321 TGATAATAAGCAGAGAGAGAGAGAGAGAGAGCGTGCGCATCCTGTTGCCATTAATAGGAAGACACTTTCACCAAGTAATT
6401 TTCTAAATAGGAATTTTAAAGCCCCTCATAATCAAAGTTTAATATATTTAAGTATGCTGAAATGAAGGTTTCTTGAAGGA
6481 GATGGTGCTAGCTGAACAATTTTAGTTCCTAGCCCTTCATTATAAATATGCAAAATTGTTGATAACAGGTTTTATTAACT
6561 CTGGATTATATCTTTTGTCTTGTTGGGTGTTTGGCTTTTTGTTCGTCCTGGTGTGTGAGTGTTCCCTCTGCTTTGCTGGT
6641 AGCCATATCAATCTTTGGAGCAAGTATCCTAGAGTTAAGAGTGCTGAGATGTATTTGTAAAGTTCCTAGTGATTTGTCTA
6721 TAGGTTATTTTAACAACCTCTCTATATAGAGGTATATTTTGACTATAGTGATACATTCTTTGGCACAAATATAAGGGAAG
6801 AGGCCAAAGAACCGTGAATATTCAGTATGGCCTCCTCTTACGTTGGTGAGTCGTCTTGCCAACATCAGTTTGTGCTGTGA
6881 TAAAACGGCTGACTGACTATATTTGACTTTACAAACACAGCTCATAGGAAAGATTAAATATTTTTATTGCGATGTATGGT
6961 CATATTTTTTTTAGCTTTATGGAGTTAACATTGTGATAGGTGCTTTAAGAGAAATATTTTTCCAGAAATGGTTTTATAGC
7041 TAAACTATGGGCAGCTTTTGCATTGTGATGTGTGGGTCGATGGCTCTATTTGGGTTACTAGGAAATCATGAAGTGTTCCC
7121 TATGGAGATACCTGTCCGCATCCATGGCAGAGAGATCAGCATGAAGTCTCAGTTGACTCCCTTTTCTCTCATAGAGTGAG
7201 CTAGCACGTAAATGACCATGTGTGGCATTACTTGGTTTACAGGACTCAGCGGGCTGGTTAGCGGTGGTGGGAATAAGGCA
7281 TCAATTCACATTCCTCACCACATACAGTGGGGCTGAGTCCGTTTCCAGTCTCTTATGTGAAGGCCTCCCCAGCAGTCCCT
7361 GGAAGAGGCTCGCTGTTCATTTTGATGGTTACAATTCTACCGTTGCATCTCAGTAATTGAAGGCTTTTATCTTTGGAAAT
7441 GCTGTTAAAATTCCAAAAACCAGTTTAGTTCTTCACCTATGAGGAAAATAGTTAAAGCACTTCATGACATTAAAGGGAAA
7521 GAGAATCCTATACCCATGATAGTTTCAATACCTAATCAATATTGAGTCCTCTGCACAGAATGGGACGCTTCGTAGCAGTA
7601 CTTGAATACCTGTGAGTTGGAATTGCATGTTACTTGAAAGATCTAATTAAGCTAAATTTTGGTGCACAGCAGTTGTACAT
7681 GATTTCATGTTTATGTAGCAAAATACATTGAAATGTACTAGGATTGAAACATAAATGTAAAAATAGTTGTGGAAATTGTC
7761 TTATTTTCCTTATGTCTCATTTGTTTAAAGCATAAATTTTCTTTTAAAAAATTCTAACTAAGGATAAAGGAATACTGTAA
7841 TTGAAGATATATTTTAAATCTTTGTCATGTTTTTTTTTTTAAAGCTATTGCAAATTGTATCATTCCTGACTATATAGAAC
7921 TTTGTGGGTGGTATAAAATAAATTTTATACTTCTATTTTGCA
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' cuUUCACAUACCCGAAACACUu 5'
            |:|| ||| ||:||||||| 
Target 5' ttAGGTTTAT-GGTTTTGTGAg 3'
 6165 - 6185 171.00 -16.40
2 
miRNA  3' cuUUCACAUACC--CG-AAACACUu 5'
            |||  ||  |  || ||||||| 
Target 5' ccAAGCATAACGTTGCATTTGTGAg 3'
 3065 - 3089 150.00 -8.00
3 
miRNA  3' cuUUCACAUA-CCCGAAACACUu 5'
            :| | ||| |  |||||||: 
Target 5' ctGACTATATAGAACTTTGTGGg 3'
 7906 - 7928 140.00 -9.70
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Brain (Mouse neocortex)
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 Chi_BrainB_130_50. RNA binding protein: AGO. Condition:Brain B 2A8 P13 130 KD ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' cuUUCACAUACCCG-AAACACuu 5'
            :|||||:|| |: | ||||  
Target 5' -uGAGUGUGUGUGUGUGUGUGug 3'
 		1 - 22
Article - Chi SW; Zang JB; Mele A; Darnell RB
- Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
Experimental Support 2 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 GSM622570. RNA binding protein: AGO2. Condition:WT1A 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 3 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions CD4+ T cells (C57BL/6)
Disease MIMAT0000605
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 GSM1013595. 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]
Experimental Support 4 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 ERR266287. RNA binding protein: AGO2. Condition:B_Liver partial hapatectomy 36h HITS-CLIP data was present in ERR266292. RNA binding protein: AGO2. Condition:B_Liver partial hapatectomy 48h HITS-CLIP data was present in ERR266293. RNA binding protein: AGO2. Condition:A_Liver partial hapatectomy 36h HITS-CLIP data was present in ERR266298. RNA binding protein: AGO2. Condition:A_Untreated HITS-CLIP data was present in ERR266300. RNA binding protein: AGO2. Condition:B_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]
Experimental Support 5 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Primary Keratinocytes
Disease 52463.0
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 GSM1613679. RNA binding protein: AGO2. Condition:Ago2-HITS-CLIP ...

- Riemondy K; Wang XJ; Torchia EC; Roop DR; Yi R, 2015, eLife.

Article - Riemondy K; Wang XJ; Torchia EC; Roop DR; Yi R
- eLife, 2015
In many mouse models of skin cancer, only a few tumors typically form even though many cells competent for tumorigenesis receive the same oncogenic stimuli. These observations suggest an active selection process for tumor-initiating cells. Here, we use quantitative mRNA- and miR-Seq to determine the impact of Hras(G12V) on the transcriptome of keratinocytes. We discover that microRNA-203 is downregulated by Hras(G12V). Using a knockout mouse model, we demonstrate that loss of microRNA-203 promotes selection and expansion of tumor-initiating cells. Conversely, restoration of microRNA-203 using an inducible model potently inhibits proliferation of these cells. We comprehensively identify microRNA-203 targets required for Hras-initiated tumorigenesis. These targets include critical regulators of the Ras pathway and essential genes required for cell division. This study establishes a role for the loss of microRNA-203 in promoting selection and expansion of Hras mutated cells and identifies a mechanism through which microRNA-203 antagonizes Hras-mediated tumorigenesis.
LinkOut: [PMID: 26203562]
27 mmu-miR-350-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT435011 Lars2 leucyl-tRNA synthetase, mitochondrial 1 2
MIRT577176 Tet1 tet methylcytosine dioxygenase 1 1 5
MIRT577951 Pole4 polymerase (DNA-directed), epsilon 4 (p12 subunit) 1 1
MIRT579173 Cd70 CD70 antigen 1 1
MIRT580234 Tsga10 testis specific 10 1 1
MIRT581630 Prkaa1 protein kinase, AMP-activated, alpha 1 catalytic subunit 1 1
MIRT584029 D230025D16Rik RIKEN cDNA D230025D16 gene 1 1
MIRT588424 Zbtb6 zinc finger and BTB domain containing 6 1 1
MIRT588528 Usp45 ubiquitin specific petidase 45 1 2
MIRT588917 Skor1 SKI family transcriptional corepressor 1 1 1
MIRT589679 Larp1 La ribonucleoprotein domain family, member 1 1 2
MIRT590168 Elp4 elongator acetyltransferase complex subunit 4 1 1
MIRT593065 Ehf ets homologous factor 1 1
MIRT593183 BC068281 WD repeat and coiled coil containing 1 4
MIRT595160 Cbfa2t3 core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human) 1 1
MIRT596758 Utp23 UTP23 small subunit processome component 1 1
MIRT596783 Ubxn2a UBX domain protein 2A 1 1
MIRT597289 Slc1a7 solute carrier family 1 (glutamate transporter), member 7 1 1
MIRT597494 Rbm41 RNA binding motif protein 41 1 1
MIRT600204 Ube2j2 ubiquitin-conjugating enzyme E2J 2 1 1
MIRT603448 Ric3 RIC3 acetylcholine receptor chaperone 1 1
MIRT604253 Cercam cerebral endothelial cell adhesion molecule 1 1
MIRT604915 Iqcj IQ motif containing J 1 1
MIRT605131 Cnnm3 cyclin M3 1 1
MIRT605214 Arnt aryl hydrocarbon receptor nuclear translocator 1 1
MIRT605697 Ifnar1 interferon (alpha and beta) receptor 1 1 1
MIRT606256 Polr1e polymerase (RNA) I polypeptide E 1 1
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-350 Hesperidin NULL 10621 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-350 5-aminoimidazole-4-carboxamide-1-β-d-ribofuranoside (AICAR) NULL 16078949 Microarray hepatocytes 23107762 2013 down-regulated
miR-350 Tamoxifen approved 2733526 Microarray rat liver 17343880 2007 down-regulated
miR-350 Ursodeoxycholic acid (UDCA) approved 31401 Microarray rat Liver 20689055 2010 down-regulated

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