TargetScan 3.0 information

TargetScanS predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA.

TargetScan Release 3.0 displays predicted regulatory targets of mammalian microRNAs. Targets are predicted using the TargetScanS algorithm and are mostly the same as those published in January 2005 (ref. 1) and presented in previous versions of the TargetScan site (Releases 2.0 and 2.1).

Changes introduced in this version of the website include:

  1. A more user-friendly interface, with mouse-, rat- and human-centric options.
  2. Predictions for additional miRNA families.
  3. Annotation of nonconserved sites, which can often mediate repression when the miRNA and mRNA are both present in the same cell (Farh et al., 2005) (example).
  4. Depiction of the UTRs, showing the positions of each site (example).
  5. Depiction of the local alignment surrounding each site (example).
  6. Depiction of the predicted pairing between each miRNA and each site (example).

The predictions presented in the tables of this website are listed simply based on the number of conserved sites and types of conserved sites. For a more sophisticated ranking based on estimated false-discovery rate (which takes into account other considerations, such as conservation to chicken and the overall conservation of the UTR), please see Release 2.1.

This website considers matches to sites in the UTRs. 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.

Known bug: Some conserved sites are missed due to alignment artifacts. This will be corrected in the next version.