>SEC24D|NM_014822|3'UTR
   1 TTGAAACTTCTCTGTCATTGATGTTGCATTTCCAAGGAGATAATCTCCTTCTTGGTGCCTAATTTTCTAGATGATAATAG
  81 GCTAGTTTTGATTTCTTGCTCATTTTCAGAATAACTTTCCAGGAAGAGATGGCATTTAGAACTTCAGCTTTGGTGCTCAG
 161 GTATAAAGCCAATTAAGGTACAATTGTACCATAAAGGGAACAATCTGTTTCTGATTGCACAGTTTCTAATTTTTAAAACT
 241 GATGTGGTTTGCATTTCATAAAAGGCAAAGTTTACAGAACCATAAACATTCTCAATTTTCTTTATGCTAGACATATAAAT
 321 TATTTTTCAAACTGTATAGATTTGGGGTAAAAAGTTGTCTCAGTTCCTCTCCCAATTGCAATGAGAAAAAAAAGCTTAAT
 401 TTTTACATTATACTTAATTTTCTAAAACCATGTAACTCCATTGAACACATTTTTCAACTTAAGGTCTGCATAGCAGACTT
 481 TTAATAACCTTGGGATTTATCTGGTAGAACAATATGTGTTCTACATTTTTTTCATAATTATATATTGTGTATGTTAAAAC
 561 TATTTTCCAGTTGTTTTGTCTGTAAAACTGTCTTTATCAATATGCTTAATGGTTCTTTGTACAATTTTGAAAGTTTCTAC
 641 CTGTATATAATGGATGTTAACCAGTATCAATAAATCACTTCGTATAATCTTAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uccucuuccgUGGUACCCUAAAu 5' ||| |||||||| Target 5' acttttaataACCTTGGGATTTa 3'	477 - 499	157.00	-14.70
2	miRNA 3' uccUCUUCCGUGGUACCCUAAAu 5' ||:| | : |||| |||| Target 5' tccAGGAAGAG--ATGGCATTTa 3'	118 - 138	124.00	-10.21
3	miRNA 3' uccucuuccgUGG-UACCCUAAAu 5' ||: ||| |:||| Target 5' aatttttaaaACTGATGTGGTTTg 3'	228 - 251	105.00	-5.40

Mutant ID	Mutant Position	Mutant Source
1181948	172	ClinVar
COSN30152377	47	COSMIC
COSN5051480	71	COSMIC
COSN30150847	126	COSMIC
COSN31527335	212	COSMIC
COSN29395316	265	COSMIC
COSN31523924	397	COSMIC
COSN31609148	425	COSMIC
COSN31530561	681	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1486077264	1	dbSNP
rs1186702152	2	dbSNP
rs768293988	3	dbSNP
rs768845637	7	dbSNP
rs747558960	8	dbSNP
rs1425372432	10	dbSNP
rs1165077788	12	dbSNP
rs1193851720	18	dbSNP
rs1407857251	19	dbSNP
rs1399423418	20	dbSNP
rs775824353	25	dbSNP
rs374214917	26	dbSNP
rs1223123144	29	dbSNP
rs745928760	35	dbSNP
rs1311274871	36	dbSNP
rs779170223	37	dbSNP
rs757454816	38	dbSNP
rs749450416	39	dbSNP
rs1279082994	41	dbSNP
rs1489357830	44	dbSNP
rs760263151	45	dbSNP
rs777624625	48	dbSNP
rs755825038	50	dbSNP
rs775267354	50	dbSNP
rs1276753000	51	dbSNP
rs550715370	65	dbSNP
rs1029179283	74	dbSNP
rs1221941902	78	dbSNP
rs1165157135	84	dbSNP
rs1422346828	111	dbSNP
rs1354146658	114	dbSNP
rs187212597	116	dbSNP
rs752205242	118	dbSNP
rs1430839523	119	dbSNP
rs370583638	122	dbSNP
rs1020255967	128	dbSNP
rs1231769944	139	dbSNP
rs563055755	146	dbSNP
rs1186310846	148	dbSNP
rs1488972618	153	dbSNP
rs1010280635	156	dbSNP
rs79586191	172	dbSNP
rs1220604364	183	dbSNP
rs1409429683	184	dbSNP
rs1036041279	190	dbSNP
rs772945797	193	dbSNP
rs1377682455	198	dbSNP
rs905664609	200	dbSNP
rs1435514935	201	dbSNP
rs1328446944	204	dbSNP
rs1048234041	211	dbSNP
rs1056062720	213	dbSNP
rs931028218	215	dbSNP
rs939012823	282	dbSNP
rs1377620436	289	dbSNP
rs886227272	293	dbSNP
rs1277877387	294	dbSNP
rs1358965383	315	dbSNP
rs1271931457	323	dbSNP
rs1275489976	323	dbSNP
rs1229644498	335	dbSNP
rs1309200864	336	dbSNP
rs1239285595	337	dbSNP
rs771838798	342	dbSNP
rs1192328292	345	dbSNP
rs1047454060	357	dbSNP
rs1435729414	359	dbSNP
rs1167555613	375	dbSNP
rs1394682696	378	dbSNP
rs1801879	379	dbSNP
rs1036649593	384	dbSNP
rs930501098	391	dbSNP
rs1329671191	394	dbSNP
rs1393878288	394	dbSNP
rs943733974	408	dbSNP
rs1440017976	412	dbSNP
rs1301176672	422	dbSNP
rs1372825156	428	dbSNP
rs1213916740	430	dbSNP
rs1345976416	436	dbSNP
rs1337083998	441	dbSNP
rs1304710054	445	dbSNP
rs574247912	448	dbSNP
rs145220003	453	dbSNP
rs1212288726	463	dbSNP
rs932264782	466	dbSNP
rs1255514712	469	dbSNP
rs540231026	470	dbSNP
rs974958793	471	dbSNP
rs1476491780	476	dbSNP
rs943270588	478	dbSNP
rs1417183264	500	dbSNP
rs1459945351	504	dbSNP
rs922060918	510	dbSNP
rs978954317	514	dbSNP
rs1317322092	515	dbSNP
rs1324486850	521	dbSNP
rs1229083234	523	dbSNP
rs182872788	525	dbSNP
rs1170438416	532	dbSNP
rs1230990266	534	dbSNP
rs15128	543	dbSNP
rs987506059	545	dbSNP
rs140430151	547	dbSNP
rs1489118290	547	dbSNP
rs956025156	556	dbSNP
rs1260029155	560	dbSNP
rs1032198616	561	dbSNP
rs1481040071	562	dbSNP
rs978857583	566	dbSNP
rs1431960926	576	dbSNP
rs571060983	578	dbSNP
rs1474253791	584	dbSNP
rs1197670102	593	dbSNP
rs764781096	594	dbSNP
rs144149070	596	dbSNP
rs1458301721	596	dbSNP
rs1382424406	600	dbSNP
rs968786826	604	dbSNP
rs1023134408	609	dbSNP
rs191831989	615	dbSNP
rs1354484911	617	dbSNP
rs896103787	618	dbSNP
rs1294552965	619	dbSNP
rs988793641	619	dbSNP
rs1321818002	620	dbSNP
rs1259492836	622	dbSNP
rs146746449	624	dbSNP
rs1452152388	625	dbSNP
rs1217869026	639	dbSNP
rs1203792276	648	dbSNP
rs1257038843	653	dbSNP
rs1035708063	661	dbSNP
rs1324148094	663	dbSNP
rs1190357187	664	dbSNP
rs186928596	670	dbSNP
rs547651736	680	dbSNP
rs149722407	681	dbSNP
rs553245330	682	dbSNP
rs1362047832	687	dbSNP
rs1421269358	692	dbSNP
rs1159075265	693	dbSNP

- Genome research, 2009

MicroRNAs (miRNAs) are known to post-transcriptionally regulate target mRNAs through the 3'-UTR, which interacts mainly with the 5'-end of miRNA in animals. Here we identify many endogenous motifs within human 5'-UTRs specific to the 3'-ends of miRNAs. The 3'-end of conserved miRNAs in particular has significant interaction sites in the human-enriched, less conserved 5'-UTR miRNA motifs, while human-specific miRNAs have significant interaction sites only in the conserved 5'-UTR motifs, implying both miRNA and 5'-UTR are actively evolving in response to each other. Additionally, many miRNAs with their 3'-end interaction sites in the 5'-UTRs turn out to simultaneously contain 5'-end interaction sites in the 3'-UTRs. Based on these findings we demonstrate combinatory interactions between a single miRNA and both end regions of an mRNA using model systems. We further show that genes exhibiting large-scale protein changes due to miRNA overexpression or deletion contain both UTR interaction sites predicted. We provide the predicted targets of this new miRNA target class, miBridge, as an efficient way to screen potential targets, especially for nonconserved miRNAs, since the target search space is reduced by an order of magnitude compared with the 3'-UTR alone. Efficacy is confirmed by showing SEC24D regulation with hsa-miR-605, a miRNA identified only in primate, opening the door to the study of nonconserved miRNAs. Finally, miRNAs (and associated proteins) involved in this new targeting class may prevent 40S ribosome scanning through the 5'-UTR and keep it from reaching the start-codon, preventing 60S association.