Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility

Hoeppner, Marc P; Poole, Anthony M

doi:10.1186/1471-2148-12-183

Table 1 Conserved modification sites ^a

From: Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility

	BLAST^b			Arabidopsis thaliana				Homo sapiens				Saccharomyces cerevisiae
rRNA	At	Hs	Sc	snoRNA	Rfam acc	Rfam clan	Target site^c	snoRNA	Rfam acc	Rfam clan	Target site^c	snoRNA	Rfam acc	Rfam clan	Target site^c
LSU	X	X	X	AtU15	RF00067	CL00045	Am2271	U15a	RF00067	CL00045	Am3764	SnR13	RF01223	CL00045	Am2279
LSU	X		X	AtU15	RF00067	CL00045	Gm2278					SnR75	RF01185	CL00045	Gm2286
LSU	X	X	X	AtU18	RF01159	CL00047	Am660	U18	RF00093	CL00047	Am1313	U18	RF00093	CL00047	Am647
LSU	X	X	X	AtU24	RF00069		Am1451	U76	N/A		Am2350	U24	RF00069		Am1447
LSU	X	X	X	AtU24	RF00069		Cm1439	U24	RF00069		Cm2338	U24	RF00069		Cm1435
LSU				AtU29	RF00070	CL00051	Am2936	U29	RF00070	CL00051	Am4493	SnR71	RF00479	CL00051	Am2943
LSU	X	X		AtU30	RF01283	CL00052	Am2311	U30	RF00088	CL00052	Am3804
LSU		X		AtU31	~RF00089		Gm2610	U31	RF00089	CL00053	Gm4166	SnR67	RF01177	CL00053	Gm2616
LSU	X	X	X	AtU34	~RF00147		Um1882	U34	RF00147	CL00055	Um2824	SnR62	RF01205	CL00055	Um1886
LSU	X	X	X	AtU35	RF00328	CL00056	Cm2949	U35	RF00211	CL00056	Cm4506	SnR73	RF01207	CL00056	Cm2956
LSU	X	X	X	AtU36a	RF01302	CL00051	Am2210	U36	RF00049	CL00051	Am3703	SnR47	RF01203	CL00051	Am2218
LSU	X	X		AtU37	~RF00440		Am2204	U37	RF00440		Am3697
LSU	X	X		AtU38	RF00135	CL00051	Am1140	U38a	RF00212	CL00051	Am1858	SnR61	RF00476	CL00051	Am1131
LSU	X	X		AtU49	RF00337	CL00062	Cm1510	U49	RF00277	CL00062	Cm2409
LSU	X			AtU49	RF00337	CL00062	Cm2869	U49	RF00277	CL00062	Cm4426
LSU	X	X	X	AtU51			Am814	U51/U32a	RF00133	CL00054	Am1511	SnR39/59	RF01197	CL00054	Am805
LSU	X			AtU53,AtsnoR37			Cm2355	U53	RF00325	CL00063	Am3848
LSU	X	X		AtU55	RF00358	CL00057	Cm1850	U55 / U39	RF00157	CL00057	Cm2791
LSU	X	X	X	AtU80	RF00309	CL00070	Am824	U80/U77	RF00591	CL00070	Am1521	SnR60	RF00309	CL00070	Am815
LSU	X	X	X	AtU80	RF00309	CL00070	Um915	U80	N/A		Gm1612	SnR60	RF00309	CL00070	Gm906
LSU	X		X	AtsnoR1	~RF00471		Gm2781					SnR48	RF00471	CL00066	Gm2788
LSU	X	X		AtsnoR10	RF00353		Um2641	Nd	RF00151	CL00064	Um4197
LSU	X	X		AtsnoR15	RF00358	CL00057	Cm1850	U55 / U39	RF00157	CL00057	Cm2791
LSU	X	X		AtsnoR33	~RF00189		Am1861	Nd	RF00189		Am2802
LSU	X	X		AtsnoR34	RF00133	CL00054	Gm2907	HB-210	RF00574		Gm4464
LSU	X	X	X	AtsnoR35	RF01281	CL00053	Gm2610	U31	RF00089	CL00053	Gm4166	SnR67	RF01177	CL00053	Gm2616
LSU	X	X	X	AtsnoR37	RF00333	CL00063	Um2411	U52	RF00276	CL00063	Um3904	SnR78	RF01176	CL00063	Um2414
LSU	X	X	X	AtsnoR38Y	RF00213		Gm2805	snR38A	RF00213		Gm4362	SnR38	RF00213		Gm2812
LSU	X	X	X	AtsnoR39BY	~RF00055		Gm812	snR38b	RF01299	CL00072	Gm1509	SnR39B	RF01299	CL00072	Gm803
LSU	X	X		AtsnoR44	RF00357	CL00069	Am2316	U79	RF00152	CL00069	Am3809
LSU	X	X	X	AtsnoR44	RF00357	CL00069	Cm2327	U74	RF00284	CL00069	Cm3820	SnR64	RF00509	CL00069	Cm2235
LSU	X	X	X	AtsnoR58Y	~RF01199		Cm674	U104	RF00289	CL00077	Cm1327	SnR58	RF01199	CL00077	Cm661
LSU	X		X	AtsnoR68Y	RF01287	CL00079	Am2631					SnR68	RF01235	CL00079	Am2637
LSU	X		X	AtsnoR69Y	RF01198	CL00051	Cm2938					SnR69	RF00475	CL00051	Cm2945
LSU	X		X	AtsnoR72Y			Am883					SnR72	N/A		Am874
LSU		X	X								Um4468	snR52			Um2921
SSU	X	X	X	AtU14			Cm416	U14	RF00016		Cm462	U14	RF00016		Cm414
SSU	X	X		AtU16	RF00358	CL00057	Am438	HBII-429	RF00609	CL00073	Am484
SSU	X	X	X	AtU27	~RF00086		Am28	U27	RF00086		Am27	SnR74	RF00086		Am28
SSU	X	X	X	AtU36			Am621	U36a	RF00049	CL00051	Am668	SnR47	RF01203	CL00051	Am619
SSU	X	X	X	AtU43	RF00221	CL00059	Cm1641	U43	RF00221	CL00059	Cm1705	SnR70	RF01238	CL00059	Cm1638
SSU	X	X		AtU54	RF00206	CL00008	Gm597	U54	RF00206	CL00008	Gm644
SSU	X	X		AtU56			Cm471	U56	RF00275		Cm517
SSU	X	X		AtU61	RF01170	CL00067	Um1381	U61	RF00270	CL00067	Um1442
SSU	X	X		AtsnoR14	RF01280	CL00076	Um1232	HBII-55	RF00610	CL00076	Um1288
SSU	X	X		AtsnoR15	RF00358	CL00057	Am438	HBII-429	RF00609	CL00073	Am484
SSU	X	X		AtsnoR17	RF01289		Am466	U45a			Am512
SSU	X	X		AtsnoR18			Am162	U44	RF00279		Am166
SSU	X	X	X	AtsnoR19	RF00054	CL00049	Gm1431	U25	RF00054	CL00049	Gm1490	SnR56	RF01188	CL00049	Gm1427
SSU	X	X	X	AtsnoR21			Gm1272	U32	RF00133	CL00054	Gm1328	SnR40	RF01201	CL00054	Gm1269
SSU	X	X	X	AtsnoR23	RF00350		Am1754	Nd			Am1850	Nd			Am1779
SSU	X	X		AtsnoR30	RF00046	CL00073	Gm390	HBII-429	RF00609	CL00073	Gm436
SSU	X	X		AtsnoR32	RF00330		Am1327	snR53	RF00338	CL00080	Am1383
SSU	X	X	X	AtsnoR34	RF00133	CL00054	Um1270	U33	RF00133	CL00054	Um1326	SnR55	RF00472	CL00054	Um1267
SSU	X	X	X	AtsnoR41Y	~RF00153		Am543	U62a	RF00153	CL00068	Am590	SnR41	RF01218	CL00068	Am541
SSU	X	X	X	AtsnoR53Y	RF01279	CL00080	Am799	HBII-429	RF00609	CL00073		SnR53	RF00338	CL00080	Am796
SSU	X	X		AtsnoR58			Gm391	SNORD100	RF00609		Gm436
SSU	X	X	X	AtsnoR59	~RF00273		Am975	U59	RF00273	CL00065	Am1031	SnR54	RF00473	CL00065	Am975
SSU	X	X	X	AtsnoR77Y			Um580	HBII-135	RF00571	CL00057	Um627	SnR77	RF01181	CL00057	Um578
SSU	X	X	X	U33			Um1270	U33	RF00133	CL00054	Um1326	SnR55	RF00472	CL00054

^aFamilies/clans traceable to LECA based on distribution and parsimony (bold).
^bBlast-mapped hits (X) show agreements with analysis presented in Figures 4 and 5.
^cTarget site data derived from '3D ribosomal RNA modification database' [37].

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ISSN: 2730-7182

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