miRetina enables queries by miRNA gene name (e.g. MIR182 or miR-182) or genomic coordinates and provides graphical information on the genomic location by presenting an alignment of the reference miRNA in a Genome Browser window along with the respective isomiRs.
Browser
Only sequence variants that were identified in all 16 individuals are depicted.
The relative expression level of each miRNA variant in the retina is shown as relative frequency (RF, %) out of the total miRNA reads.
A colour code discriminates between the miRNA sequence variants (red: reference miRNA; green: isomiRs with a canonical seed; blue: isomiRs with a modified seed). For all categories, a darker shade indicates variants that contribute with more than 10% to the total reads of a given miRNA.
Nucleotide substitutions are indicated by the actual nucleotide within the isomiR field.
isomiR Predicted Targets
The predicted targets of the isomiRs (for the 100 top-ranked miRNAs) that bear a modified seed sequence and have a relative frequency >1% have been compared with the predicted targets of their respective canonical miRNA using Targetscan. For each isomiR analysed, the following three lists of genes are provided:
(a) a list of isomiR-specific targets (predicted to be targeted by the isomiR and not the canonical miRNA)
(b) a list of shared targets (predicted to be targeted by both the isomiR and the canonical miRNA) and
(c) a list of canonical miRNA-specific targets (predicted to be targeted only by the canonical miRNA and not the isomiR)
NOVEL miRNAs
Putative novel miRNAs that were predicted independently in at least half of the samples analysed are shown by enabling the track “Novel” in the Genome Browser window. Only miRNAs with an expression level higher than 1/100 of the small nucleolar RNA (snoRNA) SNORD44 are listed. For each novel miRNA, the predicted hairpin structure and associated score (miRDeep2 output; .pdf file) can be downloaded. A list of predicted gene targets (according to Targetscan Custom; http://www.targetscan.org/; .xlsx file) can be retrieved as a table with active hyperlinks to the NCBI database.
How to cite
Marianthi Karali, Maria Persico, Margherita Mutarelli, Annamaria Carissimo, Mariateresa Pizzo, Veer Singh Marwah, Concetta Ambrosio, Michele Pinelli, Diego Carrella, Stefano Ferrari, Diego Ponzin, Vincenzo Nigro, Diego di Bernardo, and Sandro Banfi. High-resolution analysis of the human retina miRNome reveals isomiR variations and novel microRNAs. Nucleic Acids Res. 2016 : gkw039. Abstract