Search fly ORFs for predicted microRNA targets           [Go to TargetScanFly]

1. Enter an Flybase gene symbol, ID, or transcript ID
        (e.g. "Khc-73", "FBgn0019968", "FBtr0087356")

AND/OR

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")

    • * conserved = conserved beyond the Sophophora subgenus

    TargetScanFly ORFs Release 6.2 predicts biological targets of D. melanogaster microRNAs (refs 2-3) by searching ORFs for the presence of conserved 8mer and 7mer sites that match the seed region of each microRNA (ref. 1). Conserved seed sites are those conserved beyond the level expected from conservation of amino-acid coding (ref. 4).

    Frequently Asked Questions (FAQs)

    More information about TargetScanFly ORFs Release 6.2

    Download all data

    References:
    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) Conserved microRNA Targeting in Drosophila is as Widespread in Coding Regions as in 3'UTRs
    Michael Schnall-Levin, Yong Zhao, Norbert Perrimon, Bonnie Berger    PNAS, 107(36):15751-15756 (2010).
    Links
  • Bartel lab
  • Whitehead Institute
  • MiRscan Web Server
  • Burge lab
  • MIT Department of Biology
  • miRBase
  • Bioinformatics and Research Computing (Whitehead Institute)

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