Agarwal et al., 2018

Search for predicted fly microRNA targets         [Go to TargetScanHuman]
  [Go to TargetScanMouse]
  [Go to TargetScanWorm]
  [Go to TargetScanFish]

1. Enter an Flybase symbol or ID (e.g. "Khc-73", "FBgn0019968")


2. Do one of the following:

  • Select a conserved* microRNA family

  • Select a poorly conserved but confidently annotated microRNA family

  • Select another miRBase annotation
    Note that most of these families are star miRNAs or RNA fragments misannotated as miRNAs.

  • Enter a microRNA name (e.g. "miR-1-3p")

  •   *conserved = conserved at least among most Drosophilids in the Melanogaster group

    TargetScan predicts biological targets of microRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each microRNA (Lewis et al., 2005). As an option, predictions with only poorly conserved sites are also provided. In flies, predictions are ranked based on the predicted efficacy of targeting as calculated using cumulative weighted context scores of the sites (Agarwal et al., 2018). As an option, predictions are also ranked by their probability of conserved targeting (PCT, Friedman et al., 2009, Agarwal et al., 2018). TargetScanFly considers matches to fly 3' UTRs and their orthologs, as defined by UCSC whole-genome alignments. Conserved targeting has also been detected within fly open reading frames (ORFs), and predictions for sites in fly ORFs are provided at TargetScanFly ORFs.

    This search page of TargetScanFly Release 7.2 retrieves predicted regulatory targets of fly microRNAs. Many targets are the same as those presented in previous versions of the TargetScan site (Releases 4.0 - 4.1, 6.0 - 6.2) (Ruby et al., 2007; Jan et al., 2011). Compared to previous releases, Release 7 uses an improved method to predict targeting efficacy (the context model, Agarwal et al., 2018), uses 3' UTR profiles that indicate the fraction of mRNA containing each site (Nam et al., 2014), and uses updated miRNA families.

    An introduction to microRNAs (iBioseminar)

    Frequently Asked Questions (FAQs)

    More information about TargetScanFly Release 7.2

    Download data, code, or analysis tools


    1) Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets
    Benjamin P Lewis, Christopher B Burge, David P Bartel.     Cell, 120:15-20 (2005).
    2) Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
    J Graham Ruby, Alexander Stark, Wendy K Johnston, Manolis Kellis, David P Bartel, Eric C Lai.    Genome Res., 17:1850-1864 (2007).
    3) Intronic microRNA precursors that bypass Drosha processing
    J Graham Ruby, Calvin H Jan, David P Bartel.     Nature, 448:83-86 (2007).
    4) Reliable prediction of regulator targets using 12 Drosophila genomes
    Pouya Kheradpour, Alexander Stark, Sushmita Roy, and Manolis Kellis    Genome Res., 17:1919-1931 (2007).
    5) Most Mammalian mRNAs Are Conserved Targets of MicroRNAs
    Friedman RC, Farh KK, Burge CB, Bartel DP.    Genome Res., 19:92-105 (2009).
    6) Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs.
    Jan CH, Friedman RC, Ruby JG, Bartel DP.    Nature, 469:97-102 (2011).
    7) Global analyses of the effect of different cellular contexts on microRNA targeting
    Nam J, Rissland OS, Koppstein D, Abreu-Goodger C, Jan CH, Agarwal V, Yildirim MA, Rodriguez A, Bartel DP.    Molecular Cell, 153:1031-43 (2014).
    8) Predicting microRNA targeting efficacy in Drosophila
    Agarwal V, Subtelny AO, Thiru P, Ulitsky I, Bartel DP.    Genome Biology, 19:152. 1-23 (2018).

  • Bartel lab
  • miRBase
  • Bioinformatics and Research Computing (Whitehead Institute)