>SLC39A7|NM_001077516|3'UTR
   1 GGGGTGGATAAACTACCCCTGCCCCAAACCTCTACCCCTAACTCCAGGTCAGGGGTGCGTAGAGGTTGGGGGCCCTGGCC
  81 AGGGACATCTGCCAAAGGAAGGAACTGTAGCCTGGGAGAATGGTTACTTTGGCATTAGGGCCTTCAAGGGCTGGCAGTCT
 161 TACAGAGGCTGGAGCGGTGAGAATGAGAGGCCAGAGGGACCATAGTGTTGGGCACTGTCTGACCATGTTGCATTTGGAAG
 241 GCTAAATGGGGCCATGAAGAAGGCTGGAAGGGACAGGGGGTGATGGCAGCCTACCTGGTGTCCCCTACCCCACCTGTTCT
 321 CGGAGAACCAAGTTGCTACACAGGAAGTTCTCCAAGGTCCAGTTTCCTTTCTCCCACCAGTTGGTGGAGGCTTCAGGGAA
 401 GACCAGAGTCCTGGACAGAGAGGGTAACAGGAGGAGTCGGGGATAAACATCAAACATCAATCGTGTGTCCTGATTTGGGA
 481 GTGATTGGGGGGATGGGGTGGGAGAGGGTTAGTTGGTATTCTCATGGCCTGATTTTTTTTGTTTCTATTCCTTTTATATC
 561 ACTGTGTTTGAATCGAGGGGGAGGGGTGGTAACCGGAAATAAAGACCTCCGATCTTCCGCCCCAAAAAAAAAAAAAAAAA
 641 AAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' aggguccuuGGUACUAUAGUGu 5' |: | ||||||| Target 5' tttctattcCTTTTATATCACt 3'	542 - 563	145.00	-8.00
2	miRNA 3' agGGUCCUUGGUACUAUAGUgu 5' :|:||:|: | | |||| Target 5' agTCGGGGATAA--ACATCAaa 3'	435 - 454	104.00	-10.30
3	miRNA 3' agGGUCCUUGGU--AC---UAUAGUGu 5' :::|| ||:: || ||:|::| Target 5' tgTTGGGCACTGTCTGACCATGTTGCa 3'	206 - 232	102.00	-8.10

Mutant ID	Mutant Position	Mutant Source
COSN30104904	3	COSMIC
COSN31523970	16	COSMIC
COSN30101556	59	COSMIC
COSN31563938	76	COSMIC
COSN30540122	123	COSMIC
COSN16127621	320	COSMIC
COSN31593006	493	COSMIC
COSN31557591	566	COSMIC
COSN30172437	571	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1436950703	1	dbSNP
rs1276465485	3	dbSNP
rs369573351	5	dbSNP
rs1223480188	6	dbSNP
rs1268798865	7	dbSNP
rs1394184391	17	dbSNP
rs907750113	18	dbSNP
rs1212288673	20	dbSNP
rs1310271841	23	dbSNP
rs1252932818	24	dbSNP
rs1469350493	32	dbSNP
rs780518091	33	dbSNP
rs373995549	42	dbSNP
rs377655534	43	dbSNP
rs747721150	45	dbSNP
rs369084525	47	dbSNP
rs1458364811	48	dbSNP
rs372930762	49	dbSNP
rs1393627219	51	dbSNP
rs957742635	56	dbSNP
rs755206565	59	dbSNP
rs374131623	60	dbSNP
rs927259802	67	dbSNP
rs1184099081	85	dbSNP
rs552235200	91	dbSNP
rs987303910	92	dbSNP
rs1430818328	99	dbSNP
rs1219261151	103	dbSNP
rs1323628772	106	dbSNP
rs1290637619	109	dbSNP
rs937355260	110	dbSNP
rs1171669584	111	dbSNP
rs537690621	127	dbSNP
rs907702182	131	dbSNP
rs570964534	134	dbSNP
rs1037634307	135	dbSNP
rs1345260770	149	dbSNP
rs920484617	151	dbSNP
rs1334085172	155	dbSNP
rs1407910707	162	dbSNP
rs1439186059	171	dbSNP
rs1392833480	174	dbSNP
rs1350935924	175	dbSNP
rs895941476	176	dbSNP
rs534707605	177	dbSNP
rs1055115858	182	dbSNP
rs1428306956	195	dbSNP
rs1472827680	195	dbSNP
rs1041900391	198	dbSNP
rs1489439069	199	dbSNP
rs1247163674	207	dbSNP
rs112025510	208	dbSNP
rs1215171622	212	dbSNP
rs553288118	217	dbSNP
rs1270318047	218	dbSNP
rs904746834	219	dbSNP
rs1359525513	233	dbSNP
rs1000424042	247	dbSNP
rs949447145	260	dbSNP
rs116902687	265	dbSNP
rs559176132	266	dbSNP
rs1270061868	271	dbSNP
rs1311707644	272	dbSNP
rs1433804761	275	dbSNP
rs1000076425	278	dbSNP
rs1322189723	280	dbSNP
rs536519441	281	dbSNP
rs995836764	283	dbSNP
rs1265053624	304	dbSNP
rs1425790693	308	dbSNP
rs1032616484	310	dbSNP
rs894045360	311	dbSNP
rs1249944475	312	dbSNP
rs1209394989	314	dbSNP
rs1461056079	317	dbSNP
rs1254430721	322	dbSNP
rs1212694559	323	dbSNP
rs181867061	324	dbSNP
rs1313148552	326	dbSNP
rs1007115600	329	dbSNP
rs187083688	341	dbSNP
rs1226806149	342	dbSNP
rs535090862	363	dbSNP
rs1435125650	368	dbSNP
rs192363712	375	dbSNP
rs1300646143	385	dbSNP
rs558361478	399	dbSNP
rs1359504080	404	dbSNP
rs1167930181	405	dbSNP
rs963566834	408	dbSNP
rs368294462	410	dbSNP
rs1425134830	411	dbSNP
rs1431924813	424	dbSNP
rs1173708581	434	dbSNP
rs1189314359	438	dbSNP
rs1363627352	439	dbSNP
rs1444017870	439	dbSNP
rs1430781567	440	dbSNP
rs973302325	442	dbSNP
rs973625508	449	dbSNP
rs1232631497	450	dbSNP
rs144584311	461	dbSNP
rs1344959829	463	dbSNP
rs937322555	469	dbSNP
rs147878855	480	dbSNP
rs992830841	486	dbSNP
rs916588591	487	dbSNP
rs949331613	489	dbSNP
rs182388247	490	dbSNP
rs902575405	491	dbSNP
rs1403008699	493	dbSNP
rs946168237	497	dbSNP
rs765562999	503	dbSNP
rs529663035	508	dbSNP
rs376596225	509	dbSNP
rs1048782	513	dbSNP
rs1228044323	517	dbSNP
rs1372339511	526	dbSNP
rs369419148	529	dbSNP
rs1029164459	533	dbSNP
rs890131901	533	dbSNP
rs1217018732	534	dbSNP
rs1424644687	540	dbSNP
rs1246476964	551	dbSNP
rs1008954258	552	dbSNP
rs749744272	559	dbSNP
rs1270427397	561	dbSNP
rs1480450249	563	dbSNP
rs1222378211	565	dbSNP
rs1487897328	568	dbSNP
rs962087406	571	dbSNP
rs1405389115	585	dbSNP
rs1402060799	587	dbSNP
rs1159633915	589	dbSNP
rs186100646	595	dbSNP
rs1027488145	596	dbSNP
rs958488817	608	dbSNP
rs991413150	612	dbSNP
rs553333148	622	dbSNP
rs917142867	623	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.