Schema for TS miRNA sites - TargetScan miRNA Regulatory Sites
  Database: hg19    Primary Table: targetScanS    Row Count: 54,199   Data last updated: 2010-12-14
Format description: Browser extensible data
fieldexampleSQL type info description
bin 591smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 879822int(10) unsigned range Start position in chromosome
chromEnd 879830int(10) unsigned range End position in chromosome
name SAMD11:miR-504varchar(255) values Name of item
score 90int(10) unsigned range Optional score, nominal range 0-1000
strand +char(1) values + or -

Sample Rows
 
binchromchromStartchromEndnamescorestrand
591chr1879822879830SAMD11:miR-50490+
591chr1900599900606KLHL17:miR-299/299-3p26+
591chr1900605900612KLHL17:miR-124/5067+
591chr1900933900941KLHL17:miR-1982+
591chr1901054901061KLHL17:miR-13714+
592chr1990829990836AGRN:miR-14410+
592chr1990831990838AGRN:miR-27ab47+
592chr1990831990838AGRN:miR-12816+
592chr1990834990841AGRN:miR-22450+
593chr111690731169080B3GALT6:miR-340/340-5p43+

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

TS miRNA sites (targetScanS) 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 5.1.

Method

Putative miRNA binding sites in UTRs were identified using seven-nucleotide seed regions from all known miRNA families conserved across mammals. Using all human RefSeq transcripts and CDS annotation from NCBI, aligned vertebrate 3' UTRs were extracted from multiz alignments and masked for overlap with protein-coding sequences. 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 (0 to 100) based on their context score (Grimson et al., 2007). For further details of the methods used to generate this annotation, see the references and the TargetScan website.

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.

References

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

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

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