TS miRNA Targets TS miRNA v7.2 Track Settings
 
Predicted microRNA Target Sites from TargetScanHuman 7.2 (March 2018)

Track collection: TargetScan predicted microRNA target sites

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Minimum Context++ score percentile: (-1 to 99)


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Assembly: Human Feb. 2009 (GRCh37/hg19)
Data last updated at UCSC: 2021-01-28 08:33:40

Description

This track shows conserved mammalian microRNA regulatory target sites for conserved microRNA families in the 3' UTR regions of Refseq Genes, as predicted by TargetScanHuman 7.2.

Display Conventions

The track items are colored based on the four classes of target sites identified in Agarwal et al., 2015.

Purple 8mer
Red 7mer-m8
Blue 7mer-A1
Green Non-canonical

Method

Putative miRNA binding sites in UTRs were found by searching for conserved 8mer, 7mer, and 6mer sites that match the seed regions from all known miRNA families in mammals. Using protein-coding human transcripts from GENCODE v19 and RefSeq, aligned vertebrate 3' UTRs were extracted from Multiz alignments to create 3' UTR profiles. These 3' UTRs were scanned to identify conserved matches to the miRNA seed region, as in Friedman et al., 2009. These sites were then assigned a percentile rank based on their context++ score (Agarwal et al., 2015). This field is set to -1 for some noncanonical sites where the context++ score model isn't applicable. For further details of the methods used to generate this annotation, see the references and the TargetScan website.

Release Notes

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. The previous version released by UCSC was 5.1. For further information on previous releases refer to TargetScan Releases.

Credit

Thanks to George Bell of Bioinformatics and Research Computing at the Whitehead Institute for providing this annotation, which was generated in collaboration with the labs of David Bartel and Chris Burge. Additional information on microRNA target prediction is available on the TargetScan website.

Data Access

The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Data is also freely available on the Target Scan website TargetScanHuman V7.2 Data Download.

References

Agarwal V, Bell GW, Nam JW, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015 Aug 12;4. PMID: 26267216; PMC: PMC4532895

Garcia 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 microRNAs. Nat Struct Mol Biol. 2011 Sep 11;18(10):1139-46. PMID: 21909094; PMC: PMC3190056

Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009 Jan;19(1):92-105. PMID: 18955434; PMC: PMC2612969

Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell. 2007 Jul 6;27(1):91-105. PMID: 17612493; PMC: PMC3800283

Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005 Jan 14;120(1):15-20. PMID: 15652477