Search for predicted microRNA targets in zebrafish         [Go to TargetScanHuman]
  [Go to TargetScanMouse]
  [Go to TargetScanWorm]
  [Go to TargetScanFly]

1. Enter a zebrafish gene symbol or Ensembl gene ID (e.g. "bmp4", "ENSDARG00000019995")

AND/OR

2. Do one of the following:

  • Select a broadly conserved* microRNA family

  • Select a poorly conserved microRNA family

  • Enter a microRNA name (e.g. "dre-miR-7a")

  • * broadly conserved = conserved across most vertebrates to zebrafish


    TargetScan predicts biological targets of miRNAs by searching for the presence of 8mer and 7mer sites that match the seed region of each miRNA (ref. 1). In vertebrates, predictions are ranked based on the predicted efficacy of targeting as calculated using the context+ scores of the sites (ref. 2,3). TargetScanFish considers matches to annotated zebrafish UTRs as defined by Ulitsky et. al., 2012 (ref. 4).

    This search page of TargetScanFish Release 6.2 retrieves predicted regulatory targets of zebrafish microRNAs.

    An introduction to microRNAs (iBioseminar)

    Frequently Asked Questions (FAQs)

    More information about Release 6.2

    Download all data or code


    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) MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing
    Andrew Grimson, Kyle Kai-How Farh, Wendy K Johnston, Philip Garrett-Engele, Lee P Lim, David P Bartel.     Molecular Cell, 27:91-105 (2007).
     
    3) Weak Seed-Pairing Stability and High Target-Site Abundance Decrease the Proficiency of lsy-6 and Other miRNAs
    David M García, Daehyun Baek, Chanseok Shin, George W Bell, Andrew Grimson, David P Bartel.     Nat Struct Mol Biol., 18:1139-1146 (2011).
     
    4) Extensive alternative polyadenylation during zebrafish development
    Igor Ulitsky, Alena Shkumatava, Calvin H Jan, George W Bell, Hazel Sive, David P Bartel.     Genome Research, Sep 5. [Epub ahead of print] (2012).


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