ID	Duplex structure	Position	Score	MFE
1	miRNA 3' guCUGGACUCAUCG-CGUUCCac 5' | :|| | ||| ||| || Target 5' agGCTCTTA--AGCAGCATGGaa 3'	14 - 34	100.00	-9.20
2	miRNA 3' gucUGGACUCAUCGCGUuccac 5' |||||:| | :||| Target 5' aatACCTGGG-ATTGCAtatca 3'	108 - 128	86.00	-11.63
3	miRNA 3' guCUGGACUCAUCGCGUuccac 5' ||| ||||| :|:| Target 5' tcGACATGAGT--TGTActtct 3'	152 - 171	72.00	-7.23

Mutant ID	Mutant Position	Mutant Source
COSN29462101	15	COSMIC
COSN26665559	28	COSMIC
COSN31586582	28	COSMIC
COSN30152834	66	COSMIC
COSN31579926	87	COSMIC
COSN20069130	164	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs745630638	5	dbSNP
rs775402341	6	dbSNP
rs746957644	7	dbSNP
rs769811769	8	dbSNP
rs545703827	10	dbSNP
rs766485272	12	dbSNP
rs774689053	13	dbSNP
rs759970132	17	dbSNP
rs1291599698	20	dbSNP
rs767994374	22	dbSNP
rs1041347114	24	dbSNP
rs1355088146	25	dbSNP
rs887019850	28	dbSNP
rs753196270	36	dbSNP
rs1308728570	37	dbSNP
rs1465093148	38	dbSNP
rs1375536498	39	dbSNP
rs756710364	53	dbSNP
rs1328084762	58	dbSNP
rs1313373578	62	dbSNP
rs1429264471	64	dbSNP
rs1335053880	66	dbSNP
rs1175534583	78	dbSNP
rs1238424522	80	dbSNP
rs565402392	91	dbSNP
rs772441203	107	dbSNP
rs559288026	114	dbSNP
rs531161498	129	dbSNP
rs1471349635	134	dbSNP
rs577649232	148	dbSNP
rs751231360	151	dbSNP
rs74680958	154	dbSNP
rs746601718	162	dbSNP
rs1463301250	165	dbSNP
rs1210926610	169	dbSNP
rs1298706184	170	dbSNP
rs1202495503	171	dbSNP
rs1257525184	173	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.