Search for predicted fly microRNA targets         [Go to the newest version of TargetScanFly]
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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 microRNA family

  • Enter an miRNA gene name (e.g. "dme-miR-4")

    Go to TargetScanFly ORFs to see target predictions in Open Reading Frames.

    Go to TargetScanFly Custom if your RNA is not included in the microRNA families listed above.

  • * conserved = conserved beyond the Sophophora subgenus

    TargetScanS predicts biological targets of microRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each microRNA (ref. 1, 2). As an option, nonconserved sites are also predicted.

    TargetScanFly Release 6.2 displays predicted regulatory targets of 148 D. melanogaster microRNAs (as refined and expanded in ref. 2), including mirtronic microRNAs (ref. 3). Targets are predicted using the TargetScanS algorithm (ref.1) and conservation cutoffs calculated using branch length scores (ref. 4).

    This website considers matches to sites in the 3' UTRs.

    An introduction to microRNAs (iBiology talk)

    Frequently Asked Questions (FAQs) (new)

    More information about TargetScanFly Release 6.2

    Download all data

    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).

  • Bartel lab
  • Whitehead Institute
  • MiRscan Web Server
  • Burge lab
  • MIT Department of Biology
  • miRBase
  • Bioinformatics and Research Computing (Whitehead Institute)