TargetScanMouse 8 TargetScan 8 information Agarwal et al. McGeary, Lin et al.

Search for predicted microRNA targets in mammals         [Go to TargetScanHuman]
  [Go to TargetScanWorm]
  [Go to TargetScanFly]
  [Go to TargetScanFish]

1. Select a species    


2. Enter a mouse gene symbol (e.g. "Hmga2")
    or an Ensembl gene (ENSMUSG00000056758) or transcript (ENSMUST00000159699) ID


3. Do one of the following:

  • Select a broadly conserved* microRNA family

  • Select a conserved* microRNA family

  • Select a poorly conserved but confidently annotated microRNA family

  • Select another miRBase annotation
    Note that most of these families are star miRNAs or RNA fragments misannotated as miRNAs.

  • Enter a microRNA name (e.g. "miR-9-5p")

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

    When using default settings, TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer, 7mer, and 6mer sites that match the seed region of each miRNA (Lewis et al., 2005). As options, predictions with only poorly conserved sites and predictions with nonconserved miRNAs are also provided. Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing (Friedman et al., 2009). In mammals, predictions are ranked on the basis of targeting efficacy estimated using cumulative weighted context++ scores of the sites (Agarwal et al., 2015). As an option, mouse predictions are also ranked on the basis of the predicted efficacy of targeting as calculated using a biochemical model of miRNA-mediated repression, which was extended to all miRNA sequences using a convolutional neural network (McGeary, Lin, et al., 2019). As another option, predictions are ranked by their probability of conserved targeting (PCT, Friedman et al., 2009). TargetScanMouse considers matches to mouse 3' 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 Lewis et al., 2005.

    This search page of TargetScan Release 8.0 retrieves predicted regulatory targets of mammalian microRNAs. The predicted targets are essentially the same as those presented in Releases 7.0, 7.1, and 7.2 of the TargetScan site (Agarwal et al., 2015), which had substantial overlap with predictions of previous versions of the site (Releases 2.0, 2.1, 3.0, 3.1, 4.0 - 4.2, 5.0 - 5.2, and 6.0 - 6.2 (Lewis et al., 2005; Grimson et al., 2007; Friedman et al., 2009; García et al., 2011). Thus Release 8 uses the same 3' UTR profiles as Release 7 and the same miRNA families, which were curated from Chiang et al., 2010 and Fromm et al., 2015. Compared to previous releases, Release 8 provides a new option for ranking mammalian predictions using the new biochemical model (McGeary, Lin, et al., 2019).

    An introduction to microRNAs (iBiology talk)

    Frequently Asked Questions (FAQs)

    More information about Release 8.0

    Download data, code, or analysis tools

    To reference information from this database, please cite one of the following papers:

    McGeary SE, Lin KS, Shi CY, Pham T, Bisaria N, Kelley GM, Bartel DP. The biochemical basis of microRNA targeting efficacy. Science 366, eaav1741 (2019).

    Agarwal V, Bell GW, Nam J, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. eLife, 4:e05005 (2015). eLife Lens view.

    Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel DP. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes and Development, 24:992-1009 (2010).

    Friedman RC, Farh KK, Burge CB, Bartel DP. Most Mammalian mRNAs Are Conserved Targets of MicroRNAs. Genome Research, 19:92-105 (2009).

    Fromm B, Billipp T, Peck LE, Johansen M, Tarver JE, King BL, Newcomb JM, Sempere LF, Flatmark K, Hovig E, Peterson KJ. A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. Annual Review of Genetics, 49:213-42 (2015).

    García DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP. Weak Seed-Pairing Stability and High Target-Site Abundance Decrease the Proficiency of lsy-6 and Other miRNAs. Nat Struct Mol Biol., 18:1139-1146 (2011).

    Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing. Molecular Cell, 27:91-105 (2007).

    Lewis BP, Burge CB, Bartel DP. Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets. Cell, 120:15-20 (2005).

    Nam J, Rissland OS, Koppstein D, Abreu-Goodger C, Jan CH, Agarwal V, Yildirim MA, Rodriguez A, Bartel DP.Global analyses of the effect of different cellular contexts on microRNA targeting.Molecular Cell, 53:1031-43 (2014).

    Shin C, Nam J, Farh KK, Chiang HR, Shkumatava A, Bartel DP. Expanding the microRNA targeting code: functional sites with centered pairing. Molecular Cell, 38:789-802 (2010).

  • Bartel lab
  • miRGeneDB
  • miRBase
  • Bioinformatics and Research Computing (Whitehead Institute)