ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cgagcgcGAGUGCGCAGGGGGUc 5' ||| :|| ||||||| Target 5' cagcatcCTC-TGCTTCCCCCAc 3'	58 - 79	155.00	-18.30
2	miRNA 3' cgagcGCGAGUGCGCAGGGGGuc 5' :|| | | | |||||| Target 5' ggagaTGCCCCCACCTCCCCCcc 3'	322 - 344	134.00	-19.80
3	miRNA 3' cgAGCGCG-AGUGCGCAGGGGGuc 5' |:|:|: | | | |||||| Target 5' ccTTGTGTGTGTCTCTTCCCCCca 3'	210 - 233	133.00	-21.00

Mutant ID	Mutant Position	Mutant Source
rs782048019	2	dbSNP
rs782763010	11	dbSNP
rs55736938	19	dbSNP
rs782516329	26	dbSNP
rs975427398	28	dbSNP
rs782632974	30	dbSNP
rs782813979	44	dbSNP
rs955433519	45	dbSNP
rs190219027	47	dbSNP
rs7059013	49	dbSNP
rs782473573	50	dbSNP
rs1380695549	65	dbSNP
rs1336574825	83	dbSNP
rs782706979	84	dbSNP
rs1401828749	87	dbSNP
rs1387536998	102	dbSNP
rs781811623	107	dbSNP
rs1157170676	108	dbSNP
rs990330063	116	dbSNP
rs1453546653	120	dbSNP
rs1362847380	122	dbSNP
rs1183836992	128	dbSNP
rs1240756763	134	dbSNP
rs914709819	136	dbSNP
rs1447485694	142	dbSNP
rs1203160231	148	dbSNP
rs1286304286	148	dbSNP
rs1349765057	156	dbSNP
rs1292704356	160	dbSNP
rs1248454703	166	dbSNP
rs1380626682	166	dbSNP
rs1314489217	168	dbSNP
rs1431637035	169	dbSNP
rs1328676634	183	dbSNP
rs946452926	184	dbSNP
rs1316912657	186	dbSNP
rs1381951049	189	dbSNP
rs782152934	192	dbSNP
rs1163780240	207	dbSNP
rs782815711	209	dbSNP
rs1426184096	213	dbSNP
rs1383050888	216	dbSNP
rs879970914	223	dbSNP
rs904934005	225	dbSNP
rs939061155	228	dbSNP
rs183216290	233	dbSNP
rs1243765716	234	dbSNP
rs1190959110	237	dbSNP
rs1446147143	245	dbSNP
rs1269376359	252	dbSNP
rs1224947662	257	dbSNP
rs1056517840	259	dbSNP
rs887051731	260	dbSNP
rs1357526551	265	dbSNP
rs1291369341	266	dbSNP
rs1215237074	269	dbSNP
rs1341576109	273	dbSNP
rs1004059788	275	dbSNP
rs1227382553	279	dbSNP
rs1016723483	285	dbSNP
rs898371809	287	dbSNP
rs1403528451	290	dbSNP
rs1363321859	293	dbSNP
rs781867947	295	dbSNP
rs1028435098	297	dbSNP
rs1409987257	299	dbSNP
rs1421034377	302	dbSNP
rs955623575	303	dbSNP
rs1477468641	307	dbSNP
rs1429967671	310	dbSNP
rs1201279865	320	dbSNP
rs1489818271	327	dbSNP
rs1268376681	335	dbSNP
rs1205492096	338	dbSNP
rs1439593865	338	dbSNP
rs986836950	341	dbSNP
rs782470523	343	dbSNP
rs1285821840	345	dbSNP
rs1222049796	346	dbSNP
rs868982656	355	dbSNP
rs1442532251	356	dbSNP
rs782608366	357	dbSNP
rs1464684803	358	dbSNP
rs990361323	371	dbSNP
rs914825698	373	dbSNP
rs1479294637	405	dbSNP
rs781789172	406	dbSNP
rs1063371	416	dbSNP
rs1424239716	423	dbSNP
rs970248782	424	dbSNP
rs1177948797	431	dbSNP
rs1471267500	435	dbSNP
rs980254752	436	dbSNP
rs1231430270	439	dbSNP
rs782603998	443	dbSNP
rs11549303	444	dbSNP
rs1461873245	461	dbSNP
rs939077085	462	dbSNP
rs782715555	463	dbSNP
rs1323232659	468	dbSNP
rs782440002	478	dbSNP
rs1225883044	479	dbSNP
rs782668861	481	dbSNP
rs1277481800	482	dbSNP
rs1382890767	490	dbSNP
rs782290807	492	dbSNP
rs1468188961	494	dbSNP
rs1358554429	496	dbSNP
rs1159520544	506	dbSNP
rs11549302	508	dbSNP
rs113193055	513	dbSNP
rs1038292161	525	dbSNP
rs1406042736	527	dbSNP
rs1178267627	536	dbSNP
rs1445246012	545	dbSNP
rs898401330	552	dbSNP
rs1182237955	553	dbSNP
rs1243241406	556	dbSNP
rs1218379462	575	dbSNP
rs1315566152	582	dbSNP
rs1281631081	583	dbSNP
rs1239014933	589	dbSNP
rs1359471762	602	dbSNP
rs782369773	603	dbSNP
rs1449882425	606	dbSNP
rs1289428995	607	dbSNP
rs996665101	614	dbSNP
rs1049998994	617	dbSNP
rs1343224419	635	dbSNP
rs1425562926	638	dbSNP
rs1387372106	639	dbSNP
rs782656600	642	dbSNP
rs1423387239	643	dbSNP
rs1008689429	662	dbSNP
rs1263031109	665	dbSNP
rs1031679622	677	dbSNP
rs1188815839	685	dbSNP
rs1485073693	686	dbSNP
rs1262947100	688	dbSNP
rs1223752135	691	dbSNP
rs1490402320	693	dbSNP
rs1293572343	704	dbSNP
rs1241963434	705	dbSNP
rs782219682	705	dbSNP
rs782386174	715	dbSNP
rs782370077	719	dbSNP
rs1216292267	729	dbSNP
rs1359548997	731	dbSNP
rs1297335803	732	dbSNP
rs111431799	740	dbSNP
rs1011581229	741	dbSNP
rs1049729	747	dbSNP
rs781927333	748	dbSNP
rs1301587197	758	dbSNP
rs1457422389	761	dbSNP
rs782672995	763	dbSNP
rs970283115	767	dbSNP
rs980277679	774	dbSNP
rs1173103013	775	dbSNP
rs928770307	776	dbSNP
rs1423595778	778	dbSNP
rs1200595109	782	dbSNP
rs1481654738	783	dbSNP
rs1270513731	794	dbSNP

- Cell, 2010

RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.

- Nature, 2013

Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.