ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ugacuccccggagucuggCUCGa 5' |||| Target 5' attaaaacttgaaacaaaGAGCc 3'	24 - 46	80.00	-10.90
2	miRNA 3' ugacUCCCCGGAGUCUG-GCUCGa 5' || :||:| |: | ||| Target 5' ----AGTAATCTTATATACAAGCt 3'	1 - 20	75.00	-9.70

Mutant ID	Mutant Position	Mutant Source
COSN30103875	36	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1379476482	3	dbSNP
rs1332230862	7	dbSNP
rs757141344	9	dbSNP
rs141543173	11	dbSNP
rs112624153	13	dbSNP
rs753047259	14	dbSNP
rs756142285	18	dbSNP
rs752225036	19	dbSNP
rs990422675	23	dbSNP
rs1488763889	37	dbSNP
rs781569196	42	dbSNP
rs767105056	43	dbSNP
rs1176197306	45	dbSNP
rs1376052310	46	dbSNP
rs754575332	48	dbSNP

- Cell, 2013

MicroRNAs (miRNAs) play key roles in gene regulation, but reliable bioinformatic or experimental identification of their targets remains difficult. To provide an unbiased view of human miRNA targets, we developed a technique for ligation and sequencing of miRNA-target RNA duplexes associated with human AGO1. Here, we report data sets of more than 18,000 high-confidence miRNA-mRNA interactions. The binding of most miRNAs includes the 5' seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. Moreover, seed interactions are generally accompanied by specific, nonseed base pairing. 18% of miRNA-mRNA interactions involve the miRNA 3' end, with little evidence for 5' contacts, and some of these were functionally validated. Analyses of miRNA:mRNA base pairing showed that miRNA species systematically differ in their target RNA interactions, and strongly overrepresented motifs were found in the interaction sites of several miRNAs. We speculate that these affect the response of RISC to miRNA-target binding.