Search for predicted microRNA targets in mammals         [Go to the newest version of TargetScanMouse]
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 TargetScanHuman]
[Go to TargetScanWorm]
[Go to TargetScanFly]
[Go to TargetScanFish]

1. Select a species    


2. Enter a mouse Entrez Gene symbol (e.g. "Lin28a")


3. Do one of the following:

  • Select a broadly conserved* microRNA family

  • Select a conserved* microRNA family

  • Select a poorly conserved microRNA family Note that these families also include small RNAs that have been misclassified as miRNAs.

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

  • * 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. 2). In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using the context+ scores of the sites (ref. 3, 4). As an option, predictions are also ranked by their probability of conserved targeting (PCT, 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 6.2 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, 4.0 - 4.2, 5.0 - 5.2, and 6.0). Compared to previous releases, Release 6 extends context score contributions to include seed-pairing stability and target-site abundance (ref. 4), includes all 3' UTRs from RefSeq (rather than just the longest UTR from each gene), and includes more miRNA families.

    An introduction to microRNAs (iBioseminar)

    Frequently Asked Questions (FAQs)

    More information about Release 6.2

    Download all data or code

    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) 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).
    3) 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).
    4) 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).

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