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
| 
US Server