Schema for TS miRNA v7.2 - Predicted microRNA Target Sites from TargetScanHuman 7.2 (March 2018)
  Database: hg19    Primary Table: targetScanMiRnaSitesV72 Data last updated: 2021-01-28
Big Bed File: /gbdb/hg19/targetScan/targetScanSitesV72.bb
Item Count: 122,607
Format description: Target Scan miRNA site. BED12+1 with V7.2 context++ score.
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart166822284Start position in chromosome
chromEnd166822292End position in chromosome
namePOGK:miR-491-5pmiRNA Target Identifier (Gene name, microRNA name, position)
score0Always zero. See context++ score percentile.
strand++ or - strand
thickStart166822284Start of where display should be thick
thickEnd166822292End of where display should be thick
color128,0,128Colors specify classified miRNA target sites: 8-mer (purple), 7mer-m8 (red), 7mer-A1 (blue), non-canonical (green)
blockCount1Number of blocks
blockSizes8Comma separated list of block sizes
chromStarts0Start positions relative to chromStart
targetScanScore86Context++ score percentile

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndcolorblockCountblockSizeschromStartstargetScanScore
chr1166822284166822292POGK:miR-491-5p0+166822284166822292128,0,12818086
chr1166822515166822523POGK:miR-22-3p0+166822515166822523128,0,12818099
chr1166822836166822844POGK:miR-299-3p0+166822836166822844128,0,12818098
chr1166822862166822869POGK:miR-1-3p/2060+166822862166822869255,0,017096
chr1166822916166822923POGK:miR-135-5p0+166822916166822923255,0,017088
chr1166822935166822942POGK:miR-1-3p/2060+16682293516682294230,144,25517092
chr1166822970166822977POGK:miR-140-5p0+166822970166822977255,0,017091
chr1166823201166823209POGK:miR-143-3p0+166823201166823209128,0,12818088
chr1166823235166823242POGK:miR-1-3p/2060+16682323516682324230,144,25517090
chr1166823321166823328POGK:miR-330-3p0+166823321166823328255,0,017039

TS miRNA v7.2 (targetScanMiRnaSitesV72) Track Description
 

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