Search for predicted microRNA targets in mammals         [Go to the newest version of TargetScanMouse]
  [Go to TargetScanHuman]
The 3' UTRs of many genes are annotated less well in mouse than in human. For these genes, mouse predictions should be obtained from within TargetScanHuman, which can predict mouse targets using the mouse orthologs of the human annotations. [Go to TargetScanWorm]
[Go to TargetScanFly]

1. Select a species    

AND

2. Enter a human Entrez Gene symbol (e.g. "LIN28")

AND/OR

3. Do one of the following:

  • Select a broadly conserved* microRNA family

  • Select a conserved* microRNA family

  • Select a poorly conserved microRNA family

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

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

    • * broadly conserved = conserved across most vertebrates, usually to zebrafish
      conserved = conserved across most mammals, but usually not beyond placental mammals

    TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA (ref. 1). As an option, nonconserved sites are also predicted. Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing (ref. 3). In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using the context scores of the sites (ref. 2). TargetScanMouse considers matches to annotated mouse UTRs and their orthologs, as defined by UCSC whole-genome alignments. Conserved targeting has also been detected within open reading frames (ORFs). A listing of these ORF sites can be found at the bottom of Supplemental Table 2 of reference 1.

    This search page of TargetScan Release 5.2 retrieves predicted regulatory targets of mammalian microRNAs. Many targets are the same as those presented in previous versions of the TargetScan site (Releases 2.0, 2.1, 3.0, 3.1, and 4.0 - 4.2). Compared to previous releases, Release 5.2 considers site conservation in many more genomes, uses more sensitive methods to detect conservation, and reports when appropriate the probability of preferentially conserved targeting (ref. 3).

    Frequently Asked Questions (FAQs) (new)

    More information about Release 5.2

    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) Most Mammalian mRNAs Are Conserved Targets of MicroRNAs
    Robin C Friedman, Kyle Kai-How Farh, Christopher B Burge, David P Bartel.     Genome Research, 19:92-105 (2009).
    Links
  • Bartel lab
  • Whitehead Institute
  • MiRscan Web Server
  • Burge lab
  • MIT Department of Biology
  • miRBase
  • Bioinformatics and Research Computing (Whitehead Institute)

    • TargetScan 5.2 has been developed and tested with the following browsers: Firefox (Windows/Mac/Linux), Internet Explorer (Windows), Safari (Mac)