Table 1.

Position, type, and stoichiometry of modified nucleotides found in human rRNAs

rRNA	Modified nucleotide	Typea	Percent modification	rRNA	Modified nucleotide	Typea	Percent modification	rRNA	Modified nucleotide	Typea	Percent modification	rRNA	Modified nucleotide	Typea	Percent modification
5.8S	14	Um	5	18S	1004	Ψ	97	28S	1768	Ψ	100	28S	3866	Cm	99
5.8S	55	Ψ	60	18S	1031	Am	97	28S	1769	Ψ	100	28S	3878	Gm	98
5.8S	69	Ψ	61	18S	1045	Ψ	92	28S	1779	Ψ	100	28S	3899	Ψ	100
5.8S	75	Gm	87	18S	1046	Ψ	100	28S	1847	Ψ	95	28S	3904	Um	96
				18S	1056	Ψ	93	28S	1849	Ψ	95	28S	3923	Gm	80
18S	27	Am	100	18S	1081	Ψ	94	28S	1858	Am	96	28S	3938	Ψ	93
18S	34	Ψ	100	18S	1136	Ψ	7	28S	1868	Cm	35	28S	4020	Gm	83
18S	36	Ψ	82	18S	1174	Ψ	100	28S	2338	Cm	99	28S	4032	Cm	100
18S	93	Ψ	87	18S	1177	Ψ	100	28S	2350	Am	100	28S	4166	Gm	98
18S	99	Am	99	18S	1232	Ψ	98	28S	2351	Gm	100	28S	4190	m6A	100
18S	105	Ψ	99	18S	1238	Ψ	97	28S	2352	Cm	90	28S	4197	Um	97
18S	109	Ψ	99	18S	1244	Ψ	100	28S	2388	Am	73	28S	4198	Gm	92
18S	116	Um	98	18S	1248	m1acp3Ψ	100	28S	2402	Um	87	28S	4263	Ψ	98
18S	119	Ψ	94	18S	1272	Cm	47	28S	2409	Cm	98	28S	4266	Ψ	90
18S	121	Um	98	18S	1288	Um	98	28S	2411	Gm	90	28S	4269	Ψ	93
18S	159	Am	96	18S	1326	Um	100	28S	2495	Ψ	92	28S	4276	Um	88
18S	166	Am	100	18S	1328	Gm	100	28S	2619	Ψ	90	28S	4282	Ψ	83
18S	172	Um	96	18S	1337	ac4C	79	28S	2774	Am	84	28S	4323	Ψ	95
18S	174	Cm	92	18S	1347	Ψ	98	28S	2791	Cm	93	28S	4331	Ψ	93
18S	210	Ψ	83	18S	1367	Ψ	98	28S	2802	Am	92	28S	4340	Gm	99
18S	218	Ψ	100	18S	1383	Am	98	28S	2811	Cm	87	28S	4362	Gm	97
18S	296	Ψ	25	18S	1391	Cm	95	28S	2824	Um	99	28S	4373	Ψ	96
18S	354	Um	20	18S	1442	Um	78	28S	2826	Ψ	20	28S	4390	Ψ	99
18S	406	Ψ	87	18S	1445	Ψ	90	28S	2830	Ψ	9	28S	4393	Ψ	97
18S	428	Um	76	18S	1447	Gm	34	28S	2848	Cm	72	28S	4401	Ψ	89
18S	436	Gm	76	18S	1490	Gm	100	28S	2863	Gm	49	28S	4412	Ψ	100
18S	462	Cm	100	18S	1625	Ψ	79	28S	3606	Gm	96	28S	4417	m5C	100
18S	468	Am	99	18S	1639	m7G	100	28S	3616	Ψ	89	28S	4426	Cm	98
18S	484	Am	97	18S	1643	Ψ	96	28S	3618	Ψ	95	28S	4427	Ψ	98
18S	509	Gm	98	18S	1668	Um	8	28S	3674	Ψ	99	28S	4441	Ψ	87
18S	512	Am	83	18S	1678	Am	94	28S	3680	Cm	100	28S	4463	Ψ	17
18S	517	Cm	100	18S	1692	Ψ	98	28S	3694	Ψ	100	28S	4464	Gm	91
18S	572	Ψ	97	18S	1703	Cm	92	28S	3697	Am	88	28S	4468	Um	100
18S	576	Am	96	18S	1804	Um	86	28S	3703	Am	100	28S	4469	Gm	100
18S	590	Am	72	18S	1832	m6A	99	28S	3709	Ψ	72	28S	4470	Ψ	100
18S	601	Gm	89	18S	1842	ac4C	99	28S	3713	Ψ	98	28S	4491	Ψ	91
18S	609	Ψ	90	18S	1850	m62A	94	28S	3723	Gm	83	28S	4493	Am	87
18S	621	Cm	62	18S	1851	m62A	94	28S	3737	Ψ	85	28S	4500	m3U	120
18S	627	Um	99					28S	3739	Am	90	28S	4502	Ψ	100
18S	644	Gm	98	28S	389	Am	98	28S	3741	Ψ	100	28S	4506	Cm	100
18S	649	Ψ	93	28S	391	Am	98	28S	3743	Ψ	100	28S	4522	Ψ	98
18S	651	Ψ	93	28S	1303	Gm	71	28S	3747	Ψ	100	28S	4541	Am	43
18S	668	Am	99	28S	1309	m1A	100	28S	3749	Ψ	100	28S	4546	Ψ	100
18S	681	Ψ	67	28S	1310	Am	44	28S	3761	m5C	100	28S	4549	Ψ	100
18S	683	Gm	99	28S	1313	Am	100	28S	3764	Am	96	28S	4560	Am	37
18S	686	Ψ	95	28S	1327	Cm	92	28S	3771	Gm	100	28S	4588	Gm	75
18S	797	Cm	68	28S	1509	Gm	99	28S	3787	Cm	80	28S	4590	Um	82
18S	799	Um	98	28S	1511	Am	99	28S	3797	Ψm	100	28S	4593	Gm	100
18S	801	Ψ	100	28S	1521	Am	109	28S	3801	Ψ	50	28S	4598	Ψ	92
18S	814	Ψ	100	28S	1523	Ψ	88	28S	3804	Am	92	28S	4606	Ψ	42
18S	815	Ψ	100	28S	1569	Ψ	68	28S	3809	Am	100	28S	4607	Gm	100
18S	822	Ψ	99	28S	1612	Gm	100	28S	3820	Cm	100	28S	4643	Ψ	39
18S	863	Ψ	95	28S	1664	Ψ	97	28S	3823	Ψ	66	28S	4659	Ψ	87
18S	866	Ψ	88	28S	1670	Ψ	96	28S	3830	Ψ	92	28S	4937	Ψ	81
18S	867	Gm	28	28S	1731	Ψ	100	28S	3832	Ψ	100	28S	4966	Ψ	86
18S	897	Ψ	23	28S	1747	Gm	89	28S	3846	Am	43	28S	4975	Ψ	72
18S	918	Ψ	42	28S	1760	Um	70	28S	3848	Cm	67
18S	966	Ψ	89	28S	1766	Ψ	40	28S	3863	Ψ	33

^aThe abbreviations for nucleotides are as follows: Ψ, pseudouridine; Am, 2′-O-methyladenosine; Cm, 2′-O-methylcytidine; Gm, 2′-O-methylguanosine; Um, 2′-O-methyluridine; Ψm, 2′-O-methylpseudouridine; m¹A, 1-methyladenosine; m⁶₂A, N6, N6-dimethyladenosine; m⁵C, 5-methylcytidine; m⁷G, 7-methylguanosine; m³U, 3-methyluridine; m⁶A, N6-methyladenosine; ac⁴C, N4-acetylcytidine; m¹acp³Ψ, 1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine.

Underline denotes the modified nucleotides newly identified in this study. The standard deviation of the values described here is expected to be around 2%, deduced from the average value of the standard deviation in previous SILNAS-based PTM quantitation (Taoka M, Nucleic Acids Res. 2015; 43: e115).