MIRT590828 [miRNA, mmu-miR-486b-5p :: Zcchc9, target gene]

miRTarBase - #MIRT590828

—

pre-miRNA Information
pre-miRNA	mmu-mir-486b
Genomic Coordinates	chr8: 23142573 - 23142662
Description	Mus musculus miR-486b stem-loop
Comment	None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA	mmu-miR-486b-5p
Sequence	15\| UCCUGUACUGAGCUGCCCCGAG \|36
Evidence	Experimental
Experiments	Illumina
Putative Targets

Gene Information

Gene Symbol

Zcchc9

Synonyms

1810019C21Rik

Description

zinc finger, CCHC domain containing 9

Transcript

NM_145453

Expression

Putative miRNA Targets on Zcchc9

3'UTR of Zcchc9
(miRNA target sites are highlighted)

>Zcchc9|NM_145453|3'UTR
   1 TACTAATTGGTACAATTGTTAATTACCACCTCAAGGTTACTTTCCAAACTCAGCCTTTAGCGATTGAAGCTGGGCAACTG
  81 TGGAGGCAAAGCTGTGTTATAGACACCACTCTGACCTTGGTAGCTTGCCTACAATCAATCTATCAAGGCGTACAGGTTGA
 161 TTAATTACACTCTCTAGAAATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGTCT
 241 ATCTATCTCTCTGTGCCTGTGTGTCTGTCTGTATTTGAAGCAGATTCTATGTAGCCCAGGTTGGCTTCACACTAATAACC
 321 GTGCTCCAGCATCCAGAGTACTGTGCCTAAGAGCATATTTTACAGATGGAACTTAGAAATGACTAAATGCCTCTATACCT
 401 GATTATAGCAGTCATCACTATAAATGTAAATTATGAATCAAAATTGACCCCTAAACAAAGCACATGCCTTTCAGCTTGTG
 481 AATCAAAAAATATTTTGTTATATGCTCTTAATTCAGAGTATCAATTTTTTGTAATAGAAATTTATTTATATGTTGTCACA
 561 AAATCTGTAATTCTTAGTACTGAATAAAATTATATCAGCTGTTAAAAAAAAAAAA

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' gagccccgucgAGU----CAUGUCCu 5' \|\|\| \|\|\|\|\|\|\| Target 5' caatcaatctaTCAAGGCGTACAGGt 3'	132 - 157	141.00	-11.90
2	miRNA 3' gaGCCCCGUCGAGUCAUGUCCu 5' \| \|\|\|\|\| \|\| \|\|: \|\|\| Target 5' agCTGGGCAACT--GTGGAGGc 3'	68 - 87	116.00	-15.30
3	miRNA 3' gagccccgucGAGUCAUGUCcu 5' \|\|:\|\|\|\|\| \| Target 5' atctgtaattCTTAGTACTGaa 3'	563 - 584	104.00	-9.80

Experimental Support 1 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 ERR266300. RNA binding protein: AGO2. Condition:B_Untreated ... - Schug J; McKenna LB; Walton G; Hand N; et al., 2013, BMC genomics.
Article	Dynamic recruitment of microRNAs to their mRNA targets in the regenerating liver. - 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]