A method for aligning RNA secondary structures and its application to RNA motif detection

Liu, Jianghui; Wang, Jason TL; Hu, Jun; Tian, Bin

doi:10.1186/1471-2105-6-89

BMC Bioinformatics

Table 2 HSL3 motifs found by RSmatch and PatSearch^a,b

From: A method for aligning RNA secondary structures and its application to RNA motif detection

RefSeq ID	Location by PatSearch^c	Score of RSmatch	Location by RSmatch	Annotation
NM_002105	551–572	16	549–574	Hs H2A histone family, (H2AFX)
NM_003493	454–475	16	452–478	Hs histone 3, H3 (HIST3H3)
NM_003495	342–363	16	341–366	Hs histone 1, H4i (HIST1H4I)
NM_003509	445–466	16	444–469	Hs histone 1, H2ai (HIST1H2AI)
NM_003512	521–542	16	520–542	Hs histone 1, H2ac (HIST1H2AC)
NM_003517	413–434	16	412–437	Hs histone 2, H2ac (HIST2H2AC)
NM_003518	408–429	16	407–432	Hs histone 1, H2bg (HIST1H2BG)
NM_003519	429–450	16	428–450	Hs histone 1, H2bl (HIST1H2BL)
NM_003520	425–446	16	424–449	Hs histone 1, H2bn (HIST1H2BN)
NM_003522	406–427	16	405–427	Hs histone 1, H2bf (HIST1H2BF)
NM_003525	413–434	16	413–434	Hs histone 1, H2bi (HIST1H2BI)
NM_003526	414–435	16	413–435	Hs histone 1, H2bc (HIST1H2BC)
NM_003527	442–463	16	441–466	Hs histone 1, H2bo (HIST1H2BO)
NM_003528	476–497	16	475–500	Hs histone 2, H2be (HIST2H2BE)
NM_003530	443–464	16	442–467	Hs histone 1, H3d (HIST1H3D)
NM_003535	454–475	16	453–478	Hs histone 1, H3j (HIST1H3J)
NM_003537	445–466	16	444–469	Hs histone 1, H3b (HIST1H3B)
NM_003539	343–364	16	342–367	Hs histone 1, H4d (HIST1H4D)
NM_003546	340–361	16	339–364	Hs histone 1, H4l (HIST1H4L)
NM_005320	753–774	16	752–777	Hs histone 1, H1d (HIST1H1D)
NM_005325	733–754	16	732–757	Hs histone 1, H1a (HIST1H1A)
NM_021052	494–515	16	493–516	Hs histone 1, H2ae (HIST1H2AE)
NM_021059	483–504	16	483–504	Hs histone 2, H3c (HIST2H3C)
NM_021062	407–428	16	406–431	Hs histone 1, H2bb (HIST1H2BB)
NM_021063	463–484	16	462–484	Hs histone 1, H2bd (HIST1H2BD)
NM_021064	470–491	16	469–494	Hs histone 1, H2ag (HIST1H2AG)
NM_021066	414–435	16	413–435	Hs histone 1, H2aj (HIST1H2AJ)
NM_021968	331–352	16	330–355	Hs histone 1, H4j (HIST1H4J)
NM_170610	413–434	16	412–437	Hs histone 1, H2ba (HIST1H2BA)
NM_175055	428–449	16	427–450	Hs histone 3, H2bb (HIST3H2BB)
NM_003542	N/A^c	14	365–390	Hs histone 1, H4c (HIST1H4C)
NM_003548	N/A	14	371–396	Hs histone 2, H4 (HIST2H4)
NM_021058	457–478	14	455–481	Hs histone 1, H2bj (HIST1H2BJ)
NM_003510	436–457	12	435–456	Hs histone 1, H2ak (HIST1H2AK)
NM_003511	446–467	12	445–466	Hs histone 1, H2al (HIST1H2AL)
NM_003514	463–484	12	462–483	Hs histone 1, H2am (HIST1H2AM)
NM_003516	510–531	12	509–530	Hs histone 2, H2aa (HIST2H2AA)
NM_003523	411–432	12	412–435	Hs histone 1, H2be (HIST1H2BE)
NM_003529	439–460	12	440–462	Hs histone 1, H3a (HIST1H3A)
NM_003536	449–470	12	448–469	Hs histone 1, H3h (HIST1H3H)
NM_005319	709–730	12	708–729	Hs histone 1, H1c (HIST1H1C)
NM_005322	766–787	12	767–787	Hs histone 1, H1b (HIST1H1B)
NM_021018	444–465	12	445–466	Hs histone 1, H3f (HIST1H3F)
NM_175054	389–410	12	388–409	Hs histone 4, H4 (HIST4H4)
NM_175065	425–446	12	424–445	Hs histone 2, H2ab (HIST2H2AB)
NM_033445	472–493	10	471–492	Hs histone 3, H2a (HIST3H2A)
NM_003513	452–473	8	454–476	Hs histone 1, H2ab (HIST1H2AB)
NM_003521	N/A	8	421–441	Hs histone 1, H2bm (HIST1H2BM)
NM_003524	401–422	8	400–420	Hs histone 1, H2bh (HIST1H2BH)
NM_003533	453–474	8	452–472	Hs histone 1, H3i (HIST1H3I)
NM_003534	N/A	8	442–462	Hs histone 1, H3g (HIST1H3G)
NM_003540	N/A	8	348–368	Hs histone 1, H4f (HIST1H4F)
NM_003541	331–352	8	330–350	Hs histone 1, H4k (HIST1H4K)
NM_003543	N/A	8	349–369	Hs histone 1, H4h (HIST1H4H)
NM_003545	N/A	8	352–372	Hs histone 1, H4e (HIST1H4E)
NM_170745	441–462	8	440–460	Hs histone 1, H2aa (HIST1H2AA)
NM_003531	435–456	4	438–459	Hs histone 1, H3c (HIST1H3C)
NM_003532	438–459	4	441–459	Hs histone 1, H3e (HIST1H3E)
NM_005323	701–722	-4	705–721	Hs histone 1, H1t (HIST1H1T)
NM_021065	436–457	-10	314–335	Hs histone 1, H2ad (HIST1H2AD)
NM_005321	761–782	-41	85–116	Hs histone 1, H1e (HIST1H1E)
NM_014372	1345–1366	-42	1381–1389	Hs ring finger protein 11 (RNF11)

^aItems listed here include those found by PatSearch and those found by RSmatch using cutoff value of 8 that are related to histone genes.
^bRSmatch gets 33 hits at cutoff value of 14 and gets 184 hits at cutoff value of 8.
^cmRNAs that are not detected to have the HSL3 motif by PatSearch are marked with "N/A".

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ISSN: 1471-2105

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