>ARHGAP21|NM_020824|3'UTR
   1 ACTGGGGGTATGTCCACTCTAGCAAGTAAAAAAACTACTGTTACACGTTCCAGTAACTCTGTCAATATTTTCTTGTATCA
  81 GAATTGTTATTATGCAGCCTTCATTTGGGCTGGTTTCATCATTTTGCACTGTGAAATAGCTTTACAGTGCATTACTACAG
 161 CCAGAAGAACATATATATATATATATATATTTAAAAATATATCGGATAGTTGTATACAAATGAGCAAGGTATTTGTTGCA
 241 ACTTACTACATAGCATATACCCAAAATCACTGAAGAAAATCGCTGGCATCAGTGTGCAGCAAATTTGTTCTTTTGGTTTC
 321 ATCACTAACAAAAGTGCCTCATCATAAAAATACAGTTGGTTTTTAGGGTGCCATATTGTTAAAATTAGATAACTTACTTA
 401 CATTGAATAAACGAATGCGTTTTATTGGTAACAGATATCATTACATTTACCAGTTTTAACACAGGTGGATACAGAACTTC
 481 CATTCTTTAGTCATTCCAGGTGGATCTGAGTTTTATATTCAAACTTTTAATACAGTTTTTGAGTTTTGTGTGACTTGAAT
 561 TTTTAATCTTTCTGTAAAATACGTAACTTAAATGAACATATTAAATGTGTATCTTTTCTTCAGATACCAGATTTGATATA
 641 ATGTTGTAACATAGGTGTGTAGATAGTGGATCCTGGATGGAACTGGCTTCTTTATCGAGAAGAATATAATTCTGCATGAG
 721 GACTTAATGAATCCAAACCTGTGTCATGCCTGTGTGCATACCCAATTAAACACTGGAAATAAAAATTGTTTTGGTGAATT
 801 TTGAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' accGACUUUCUGGUUUCUUGUu 5' || | || | :||||||| Target 5' ttaCT-ACAGCCAGAAGAACAt 3'	152 - 172	154.00	-9.50
2	miRNA 3' accGACUUUCUGGUUUCUUGUu 5' :| | || :|||||:| Target 5' ttcTTTATCGA--GAAGAATAt 3'	688 - 707	127.00	-5.10
3	miRNA 3' accgacUUUCUGGUUUCUUGUu 5' || ||::||||| | Target 5' acccaaAATCACTGAAGAAAAt 3'	259 - 280	124.00	-5.22

Mutant ID	Mutant Position	Mutant Source
COSN30501557	27	COSMIC
COSN26966579	28	COSMIC
COSN32053084	46	COSMIC
COSN30465780	59	COSMIC
COSN30146812	67	COSMIC
COSN31558615	72	COSMIC
COSN31515589	413	COSMIC
COSN31537303	496	COSMIC
COSN31569915	568	COSMIC
COSN31515690	696	COSMIC
COSN26667788	761	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs555604510	1	dbSNP
rs1474643900	2	dbSNP
rs759190537	6	dbSNP
rs1390579035	7	dbSNP
rs1437830059	10	dbSNP
rs773758295	12	dbSNP
rs770454856	15	dbSNP
rs762350789	16	dbSNP
rs1348733567	17	dbSNP
rs1326024176	18	dbSNP
rs1419478822	25	dbSNP
rs769063034	26	dbSNP
rs747383206	28	dbSNP
rs780396549	29	dbSNP
rs1418852639	32	dbSNP
rs1409265109	34	dbSNP
rs1394912434	35	dbSNP
rs762576373	35	dbSNP
rs772212081	37	dbSNP
rs746051802	38	dbSNP
rs1329892075	39	dbSNP
rs752312348	40	dbSNP
rs778906785	42	dbSNP
rs1413238342	43	dbSNP
rs1266458879	44	dbSNP
rs757379824	46	dbSNP
rs369422926	47	dbSNP
rs536066385	62	dbSNP
rs1004760196	65	dbSNP
rs1418987833	75	dbSNP
rs1197354380	89	dbSNP
rs888724290	90	dbSNP
rs1049104637	91	dbSNP
rs1180219471	93	dbSNP
rs570100677	102	dbSNP
rs550258313	103	dbSNP
rs930359311	117	dbSNP
rs1259155608	146	dbSNP
rs1423916592	149	dbSNP
rs1191760682	152	dbSNP
rs1371858043	157	dbSNP
rs905533232	159	dbSNP
rs1168990898	165	dbSNP
rs201621233	171	dbSNP
rs1491272202	172	dbSNP
rs201287969	172	dbSNP
rs1433220068	174	dbSNP
rs949811600	179	dbSNP
rs1283263076	181	dbSNP
rs199982443	189	dbSNP
rs1316240921	191	dbSNP
rs143956322	191	dbSNP
rs35918968	191	dbSNP
rs397847527	191	dbSNP
rs570975382	191	dbSNP
rs796458314	191	dbSNP
rs796831643	191	dbSNP
rs916966871	191	dbSNP
rs1215315973	201	dbSNP
rs890817363	203	dbSNP
rs570953202	204	dbSNP
rs925923266	208	dbSNP
rs1127899	212	dbSNP
rs1259134492	215	dbSNP
rs1448189498	224	dbSNP
rs1189832043	225	dbSNP
rs1127900	226	dbSNP
rs1241574140	227	dbSNP
rs1127901	230	dbSNP
rs547841916	231	dbSNP
rs954112845	244	dbSNP
rs1387560580	245	dbSNP
rs745733044	247	dbSNP
rs1157043739	257	dbSNP
rs1453393114	257	dbSNP
rs1387289452	259	dbSNP
rs17173421	263	dbSNP
rs1399497675	281	dbSNP
rs965466764	282	dbSNP
rs1361041468	284	dbSNP
rs1015664738	285	dbSNP
rs1160227395	286	dbSNP
rs1464307924	303	dbSNP
rs1237925359	312	dbSNP
rs3184307	326	dbSNP
rs1258557815	327	dbSNP
rs3184308	331	dbSNP
rs1352244962	333	dbSNP
rs1376845759	334	dbSNP
rs1176613503	337	dbSNP
rs1004409968	341	dbSNP
rs1467483012	344	dbSNP
rs1196039282	346	dbSNP
rs1268579533	347	dbSNP
rs952984167	350	dbSNP
rs10327	351	dbSNP
rs1002871978	353	dbSNP
rs1366450369	354	dbSNP
rs3184309	355	dbSNP
rs905418985	355	dbSNP
rs192704606	356	dbSNP
rs548978153	359	dbSNP
rs3184310	364	dbSNP
rs3184312	366	dbSNP
rs1459869504	372	dbSNP
rs3184313	373	dbSNP
rs529091107	376	dbSNP
rs188146861	381	dbSNP
rs1343572274	388	dbSNP
rs1304455911	389	dbSNP
rs753295763	390	dbSNP
rs1053265475	395	dbSNP
rs1234482055	395	dbSNP
rs1272055194	400	dbSNP
rs1216143276	402	dbSNP
rs1325862316	402	dbSNP
rs1276574261	403	dbSNP
rs543596193	410	dbSNP
rs3184321	412	dbSNP
rs765159491	413	dbSNP
rs3184324	418	dbSNP
rs117654517	419	dbSNP
rs921154245	422	dbSNP
rs3184330	426	dbSNP
rs1415817253	434	dbSNP
rs1476213980	435	dbSNP
rs1166855291	436	dbSNP
rs3184337	437	dbSNP
rs976767776	438	dbSNP
rs965354368	439	dbSNP
rs1401462876	442	dbSNP
rs1372163352	449	dbSNP
rs1303193751	451	dbSNP
rs908656996	452	dbSNP
rs1420973833	463	dbSNP
rs1169527130	471	dbSNP
rs1477975798	473	dbSNP
rs1374287318	480	dbSNP
rs3210916	481	dbSNP
rs1234539592	488	dbSNP
rs1314109407	489	dbSNP
rs983268577	489	dbSNP
rs952786869	492	dbSNP
rs1203014968	501	dbSNP
rs1253514728	506	dbSNP
rs1483566995	509	dbSNP
rs1184831002	516	dbSNP
rs1027574171	520	dbSNP
rs1441168623	522	dbSNP
rs1486711909	527	dbSNP
rs3184348	529	dbSNP
rs1182452436	533	dbSNP
rs1002347407	535	dbSNP
rs575732951	535	dbSNP
rs1168228682	548	dbSNP
rs1201345317	549	dbSNP
rs3184353	549	dbSNP
rs969628885	550	dbSNP
rs1430143397	551	dbSNP
rs1025161356	553	dbSNP
rs1013903205	564	dbSNP
rs1256329781	568	dbSNP
rs1302864007	570	dbSNP
rs1218235903	571	dbSNP
rs1318952996	579	dbSNP
rs112035075	582	dbSNP
rs3184359	583	dbSNP
rs557299864	587	dbSNP
rs1339754942	592	dbSNP
rs999016319	608	dbSNP
rs1211070641	615	dbSNP
rs1313390379	630	dbSNP
rs1454317872	631	dbSNP
rs1397867318	643	dbSNP
rs555641259	646	dbSNP
rs749561442	652	dbSNP
rs1249763646	654	dbSNP
rs368935276	655	dbSNP
rs1449884973	658	dbSNP
rs1172712981	661	dbSNP
rs1392899448	662	dbSNP
rs1415865217	667	dbSNP
rs1043295265	670	dbSNP
rs932450494	675	dbSNP
rs145297844	696	dbSNP
rs1040970930	697	dbSNP
rs1127930	712	dbSNP
rs1323145994	714	dbSNP
rs1398242549	716	dbSNP
rs751933390	720	dbSNP
rs1440659260	737	dbSNP
rs944058982	738	dbSNP
rs1347538941	747	dbSNP
rs1487802460	749	dbSNP
rs908539517	754	dbSNP
rs1315209757	755	dbSNP
rs535055328	756	dbSNP
rs931402558	765	dbSNP
rs576664400	769	dbSNP
rs1465250462	771	dbSNP
rs878924808	772	dbSNP
rs1368328671	784	dbSNP
rs1250984727	787	dbSNP
rs1184762242	793	dbSNP
rs763413090	796	dbSNP

- Nature methods, 2011

Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.

- 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.