Agarwal 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 a microRNA family with other miRBase annotations
    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

    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 an option, predictions with only poorly conserved sites are also provided. Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing (Friedman et al., 2009) and centered sites (Shin et al., 2010). In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using cumulative weighted context++ scores of the sites (Agarwal et al., 2015). As an option, predictions are also 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 7.1 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 - 6.2 (Lewis et al., 2005; Grimson et al., 2007; Friedman et al., 2009; García et al., 2011). Compared to previous releases, Release 7 uses an improved method to predict targeting efficacy (the context++ model, Agarwal et al., 2015), uses 3' UTR profiles that indicate the fraction of mRNA containing each site (Nam et al., 2014), and uses updated miRNA families curated from Chiang et al., 2010 and Fromm et al., 2015.

    An introduction to microRNAs (iBioseminar)

    Frequently Asked Questions (FAQs)

    More information about Release 7.1

    Download data or code


    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
  • miRBase
  • Bioinformatics and Research Computing (Whitehead Institute)