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.
The track items are colored based on the four classes of target sites identified in
Agarwal et al., 2015.
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
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
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
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
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
Data is also freely available on the Target Scan website
TargetScanHuman V7.2 Data Download.
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
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
Cell. 2005 Jan 14;120(1):15-20.