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 TargetScanS.

Method

Putative miRNA binding sites in UTRs were identified using seven-nucleotide seed regions from all known miRNA families conserved among human, mouse, rat, dog and sometimes chicken. 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 Lewis et al. (2005). 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

Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing. Molecular Cell. 2007 Jul 6;27(1):91-105.

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.

Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell. 2003 Dec 26;115(7):787-98.