>C16orf74|NM_206967|3'UTR
   1 GGAGGTGTCCTGGGTTTGGCTGGCTGGCTCCTGCTCCAGCGGCCCGGCTTCAGGTGTCCGGGGGCGTGGCTGCCTGGAGC
  81 AGGTGTGCTGAATACCCTGGATGGGAACTGAGCGAACCCGGGCCTCCGCTCAGAGAGACGTGGCAGGACCAGCGAGGAAT
 161 CCAGCCTGTCCACTTCCAGAACAGTGTTTCCCAGGCCCCGCTGAGTGGACCGGACCTCTGACACCTCCAGGTTCTTGCTG
 241 ACTCCGGCCTGGTGAAAGGGAGCGCCATGGTCCTGGCTGTTGGGGTCCCAGGGAGAGGCTCTCTTCTGGACAAACACACC
 321 CTCCCAGCCCCCAGGGCTGTGCAAACACATGCCCCTGCCATAAGCACCAACAAGAACTTCTTGCAGGTGGAGTGGCTGTT
 401 TTTTATAAGTTGTTTTACAGATACGGAAACAGTCCAAAATGGGATTTATAATTTCTTTTTTGCATTATAAATAAAGATCC
 481 TCTGTAACAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gucgggAGGACC---ACCGACCGg 5' |||||| |||||||| Target 5' gaggtgTCCTGGGTTTGGCTGGCt 3'	2 - 25	163.00	-28.00
2	miRNA 3' gucgggAGGACCACCG-ACCGg 5' ||| || ||| |||| Target 5' caggtgTCC-GGGGGCGTGGCt 3'	51 - 71	122.00	-22.00
3	miRNA 3' guCGGGAGGACCACCGAC-CGg 5' |||| || | ||||| || Target 5' caGCCC-CCAG--GGCTGTGCa 3'	325 - 343	122.00	-22.70

Mutant ID	Mutant Position	Mutant Source
COSN30538104	65	COSMIC
COSN30127105	172	COSMIC
COSN31492670	205	COSMIC
COSN31483878	284	COSMIC
COSN18000762	318	COSMIC
COSN31612095	398	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1378543405	5	dbSNP
rs1309878729	7	dbSNP
rs1447109501	10	dbSNP
rs1011243349	11	dbSNP
rs1335882279	12	dbSNP
rs1414854193	13	dbSNP
rs1360098695	14	dbSNP
rs758711586	21	dbSNP
rs1035103998	22	dbSNP
rs1346002898	22	dbSNP
rs1441609465	23	dbSNP
rs1381073367	24	dbSNP
rs1181361080	26	dbSNP
rs1472064756	28	dbSNP
rs748505363	30	dbSNP
rs1211217729	36	dbSNP
rs761840901	40	dbSNP
rs755456516	41	dbSNP
rs749961558	42	dbSNP
rs1238768020	44	dbSNP
rs187864191	45	dbSNP
rs375000202	46	dbSNP
rs1227264248	47	dbSNP
rs1165968196	54	dbSNP
rs1375292349	59	dbSNP
rs1399607098	60	dbSNP
rs538590184	65	dbSNP
rs940724953	66	dbSNP
rs1447946216	68	dbSNP
rs763928620	70	dbSNP
rs763126441	76	dbSNP
rs1381822034	85	dbSNP
rs569570855	89	dbSNP
rs1403253410	96	dbSNP
rs549775265	104	dbSNP
rs984880523	109	dbSNP
rs998051663	112	dbSNP
rs948088616	113	dbSNP
rs371280589	114	dbSNP
rs1185358947	116	dbSNP
rs942463701	119	dbSNP
rs1156523114	120	dbSNP
rs991756817	122	dbSNP
rs34170991	123	dbSNP
rs866301667	124	dbSNP
rs1043145449	127	dbSNP
rs567059798	128	dbSNP
rs946973248	129	dbSNP
rs146658214	131	dbSNP
rs1461316137	136	dbSNP
rs977363381	137	dbSNP
rs914196783	139	dbSNP
rs547579700	140	dbSNP
rs1260319750	144	dbSNP
rs1237204681	145	dbSNP
rs960829331	147	dbSNP
rs1343714582	148	dbSNP
rs1307520007	149	dbSNP
rs928153080	151	dbSNP
rs527880364	153	dbSNP
rs565197006	154	dbSNP
rs1476929748	156	dbSNP
rs1196139442	157	dbSNP
rs767792630	159	dbSNP
rs1477762620	162	dbSNP
rs1460480520	164	dbSNP
rs1427935941	166	dbSNP
rs776687320	167	dbSNP
rs1016915277	171	dbSNP
rs888887669	172	dbSNP
rs1359052787	173	dbSNP
rs1028729365	177	dbSNP
rs1318611792	179	dbSNP
rs998126520	184	dbSNP
rs1025532003	190	dbSNP
rs1276546067	191	dbSNP
rs998104147	194	dbSNP
rs1351675839	195	dbSNP
rs551675319	199	dbSNP
rs1207087284	200	dbSNP
rs1489164707	200	dbSNP
rs1037021380	202	dbSNP
rs1262752710	203	dbSNP
rs531703706	204	dbSNP
rs1286726341	208	dbSNP
rs1455075041	210	dbSNP
rs1423715251	211	dbSNP
rs940887715	212	dbSNP
rs1159557513	220	dbSNP
rs887789366	223	dbSNP
rs1444409824	224	dbSNP
rs1049069350	230	dbSNP
rs747487915	234	dbSNP
rs1158609117	235	dbSNP
rs1018538610	236	dbSNP
rs1421961039	237	dbSNP
rs1158776513	242	dbSNP
rs948018432	245	dbSNP
rs1384724248	246	dbSNP
rs1324877462	252	dbSNP
rs1371116634	255	dbSNP
rs1445902103	261	dbSNP
rs904295370	263	dbSNP
rs916697904	264	dbSNP
rs945739404	270	dbSNP
rs992250625	277	dbSNP
rs1254925484	283	dbSNP
rs1052599907	284	dbSNP
rs1178547253	287	dbSNP
rs562719549	291	dbSNP
rs928449193	293	dbSNP
rs543042727	298	dbSNP
rs368010258	303	dbSNP
rs977750647	315	dbSNP
rs1394531315	317	dbSNP
rs988233732	318	dbSNP
rs574043631	319	dbSNP
rs967239679	320	dbSNP
rs1329207782	328	dbSNP
rs1379112610	330	dbSNP
rs1391900469	335	dbSNP
rs1021477618	336	dbSNP
rs989801894	337	dbSNP
rs953041520	339	dbSNP
rs1242844096	349	dbSNP
rs984228718	352	dbSNP
rs1357038364	353	dbSNP
rs1335536726	354	dbSNP
rs7773	357	dbSNP
rs1256245728	362	dbSNP
rs541182310	365	dbSNP
rs572280724	367	dbSNP
rs772439319	368	dbSNP
rs1418193599	373	dbSNP
rs1015062149	377	dbSNP
rs1477206349	378	dbSNP
rs1005154763	380	dbSNP
rs888054756	383	dbSNP
rs1292904119	388	dbSNP
rs1383418641	390	dbSNP
rs1049331143	399	dbSNP
rs142541010	399	dbSNP
rs1385153909	402	dbSNP
rs948072521	404	dbSNP
rs1462398423	419	dbSNP
rs895148424	421	dbSNP
rs1056954138	424	dbSNP
rs1424373909	425	dbSNP
rs1364139707	426	dbSNP
rs1295347616	427	dbSNP
rs939417859	435	dbSNP
rs1165991366	441	dbSNP
rs1458920016	442	dbSNP
rs1018089625	449	dbSNP
rs1218270993	455	dbSNP
rs928471804	464	dbSNP
rs1276336324	468	dbSNP
rs1372576474	478	dbSNP
rs572132944	479	dbSNP
rs1255970869	480	dbSNP
rs1482472086	482	dbSNP
rs1007177903	484	dbSNP
rs1430399657	491	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.