Modified bases

New Nomenclature Name Short Name RNAMods abbrev. HTML abbrev. Formula Monoisotopic mass Average mass
01A 1,2′-O-dimethyladenosine m1Am œ œ C12O4N5H17 295.128053 295.298867
01G 1,2′-O-dimethylguanosine m1Gm ε ε C12O5N5H17 311.123 311.2977
019A 1,2′-O-dimethylinosine m1Im ξ ξ C12O5N4H16 296.112069 296.283473
1309U 1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine m1acp3Y α α C14O8N3H21 359.132864 359.336617
1A 1-methyladenosine m1A " " C11O4N5H15 281.112403 281.271879
1G 1-methylguanosine m1G K K C11O5N5H15 297.107318 297.271183
19A 1-methylinosine m1I O O C11O5N4H14 282.096419 282.256484
19U 1-methylpseudouridine m1Y ] ] C10O6N2H14 258.085186 258.231306
28A 2,8-dimethyladenosine m2,8A ± ± C12H17N5O4 295.12804 295.29828
21U 2-geranylthiouridine ges2U Γ Γ C19H28N2O5S 396.17187 396.5078
21C 2-lysidine k2C } } C15O6N5H25 371.180483 371.394395
2A 2-methyladenosine m2A / / C11O4N5H15 281.112403 281.271879
2160A 2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine ms2io6A C16O5N5H23S1 397.141989 397.454563
2163A 2-methylthio-N6-hydroxynorvalylcarbamoyladenosine ms2hn6A C17O8N6H24S1 472.137631 472.478213
2161A 2-methylthio-N6-isopentenyladenosine ms2i6A * * C16O4N5H23S1 381.147074 381.455259
621A 2-methylthio-N6-methyladenosine ms2m6A C12O4N5H17S1 327.100124 327.363255
2162A 2-methylthio-N6-threonylcarbamoyladenosine ms2t6A [ [ C16O8N6H22S1 458.121981 458.451225
20U 2-selenouridine se2U ω ω C9O5N2H12Se1 305.9919 306.122097
02U 2-thio-2′-O-methyluridine s2Um C10O5N2H14S1 274.062342 274.296389
2C 2-thiocytidine s2C % % C9O4N3H13S1 259.062676 259.284795
2U 2-thiouridine s2U 2 2 C9O5N2H12S1 260.046692 260.269401
0A 2′-O-methyladenosine Am : : C11O4N5H15 281.112403 281.271879
0C 2′-O-methylcytidine Cm B B C10O5N3H15 257.10117 257.2467
0G 2′-O-methylguanosine Gm # # C11O5N5H15 297.107318 297.271183
09A 2′-O-methylinosine Im C11O5N4H14 282.096419 282.256484
09U 2′-O-methylpseudouridine Ym Z Z C10O6N2H14 258.085186 258.231306
0U 2′-O-methyluridine Um J J C10O6N2H14 258.085186 258.231306
0503U 2′-O-methyluridine 5-oxyacetic acid methyl ester mcmo5Um Ͽ Ͽ C13H18N2O9 346.292 346.101230168
00A 2′-O-ribosyladenosine (phosphate) Ar(p) ^ ˆ C15O11N5H22P1 479.105343 479.340753
00G 2′-O-ribosylguanosine (phosphate) Gr(p) C15O12N5H22P1 495.100257 495.340057
3377N 2′3′-cyclic phosphate end (pN)2′3′>p None None
03U 3,2′-O-dimethyluridine m3Um σ σ C11O6N2H16 272.100836 272.258295
308U 3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine acp3D Ð Ð C13H21N3O8 347.13285 347.32516
309U 3-(3-amino-3-carboxypropyl)pseudouridine acp3Y Þ Þ C13H19N3O8 345.1172 345.30928
30U 3-(3-amino-3-carboxypropyl)uridine acp3U X X C13O8N3H19 345.117214 345.309629
3C 3-methylcytidine m3C ' ' C10O5N3H15 257.10117 257.2467
39U 3-methylpseudouridine m3Y κ κ C10O6N2H14 258.085186 258.231306
3U 3-methyluridine m3U δ δ C10O6N2H14 258.085186 258.231306
4G 4-demethylwyosine imG-14 C13O5N5H15 321.107318 321.293257
74U 4-thiouridine s4U 4 4 C9O5N2H12S1 260.046692 260.269401
05C 5,2′-O-dimethylcytidine m5Cm τ τ C11O5N3H17 271.11682 271.273689
05U 5,2′-O-dimethyluridine m5Um \ \ C11O6N2H16 272.100836 272.258295
0522U 5-(carboxyhydroxymethyl)-2′-O-methyluridine methyl ester mchm5Um b b C13H18N2O9 346.10121 346.294
522U 5-(carboxyhydroxymethyl)uridine methyl ester mchm5U , , C12O9N2H16 332.085579 332.267246
2583U 5-(isopentenylaminomethyl)-2-thiouridine inm5s2U ½ ½ C15H23N3O5S 357.13583 357.43084
0583U 5-(isopentenylaminomethyl)-2′-O-methyluridine inm5Um ¼ ¼ C16H25N3O6 355.17432 355.39112
583U 5-(isopentenylaminomethyl)uridine inm5U ¾ ¾ C15H23N3O6 341.15867 341.36424
21510U 5-aminomethyl-2-geranylthiouridine nm5ges2U Δ Δ C20H31N3O5S 425.19842 425.54936
20510U 5-aminomethyl-2-selenouridine nm5se2U π π C10O5N3H15Se1 335.0185 335.163597
2510U 5-aminomethyl-2-thiouridine nm5s2U C10O5N3H15S1 289.073241 289.311088
510U 5-aminomethyluridine nm5U C10O6N3H15 273.096085 273.246005
531U 5-carbamoylhydroxymethyluridine nchm5U r r C11H15N3O8 317.0859 317.2555
253U 5-carbamoylmethyl-2-thiouridine ncm5s2U l l C11H15N3O6S 317.06814 317.32272
053U 5-carbamoylmethyl-2′-O-methyluridine ncm5Um ~ C12O7N3H17 315.106649 315.283335
53U 5-carbamoylmethyluridine ncm5U & & C11O7N3H15 301.090999 301.256347
520U 5-carboxyhydroxymethyluridine chm5U C11O9N2H14 318.069929 318.240257
2540U 5-carboxymethyl-2-thiouridine cm5s2U C11O7N2H14S1 318.052171 318.306036
2151U 5-carboxymethylaminomethyl-2-geranylthiouridine cmnm5ges2U f f C22H33N3O7S 483.2039 483.58604
2051U 5-carboxymethylaminomethyl-2-selenouridine cmnm5se2U C12O7N3H17Se1 393.0239 393.200297
251U 5-carboxymethylaminomethyl-2-thiouridine cmnm5s2U $ $ C12O7N3H17S1 347.07872 347.347723
051U 5-carboxymethylaminomethyl-2′-O-methyluridine cmnm5Um ) ) C13O8N3H19 345.117214 345.309629
51U 5-carboxymethylaminomethyluridine cmnm5U ! ! C12O8N3H17 331.101564 331.28264
52U 5-carboxymethyluridine cm5U C11O8N2H14 302.075015 302.240952
55U 5-cyanomethyluridine cnm5U Ѷ Ѷ C11H13N3O6 283.08042 283.24083
071C 5-formyl-2′-O-methylcytidine f5Cm ° ° C11O6N3H15 285.096085 285.257042
71C 5-formylcytidine f5C > > C10O6N3H13 271.080435 271.230053
50C 5-hydroxycytidine ho5C Ç Ç C9H13N3O6 259.08042 259.21884
51C 5-hydroxymethylcytidine hm5C C10O6N3H15 273.096085 273.246005
50U 5-hydroxyuridine ho5U C9O7N2H12 260.06445 260.203622
2521U 5-methoxycarbonylmethyl-2-thiouridine mcm5s2U 3 3 C12O7N2H16S1 332.067821 332.333024
0521U 5-methoxycarbonylmethyl-2′-O-methyluridine mcm5Um C13O8N2H18 330.106315 330.29493
521U 5-methoxycarbonylmethyluridine mcm5U 1 1 C12O8N2H16 316.090665 316.267941
501U 5-methoxyuridine mo5U 5 5 C10O7N2H14 274.0801 274.230611
25U 5-methyl-2-thiouridine m5s2U F F C10O5N2H14S1 274.062342 274.296389
21511U 5-methylaminomethyl-2-geranylthiouridine mnm5ges2U h h C21H33N3O5S 439.21407 439.57624
20511U 5-methylaminomethyl-2-selenouridine mnm5se2U C11O5N3H17Se1 349.0341 349.190497
2511U 5-methylaminomethyl-2-thiouridine mnm5s2U S S C11O5N3H17S1 303.088891 303.338077
511U 5-methylaminomethyluridine mnm5U { { C11O6N3H17 287.111735 287.272994
5C 5-methylcytidine m5C ? ? C10O5N3H15 257.10117 257.2467
58U 5-methyldihydrouridine m5D ρ ρ C10O6N2H16 260.100836 260.247258
5U 5-methyluridine m5U T T C10O6N2H14 258.085186 258.231306
254U 5-taurinomethyl-2-thiouridine tm5s2U C12O8N3H19S2 397.061355 397.427368
54U 5-taurinomethyluridine tm5U Ê Ê C12O9N3H19S1 381.084199 381.362285
455N 5′ (3′ -dephospho-CoA) CoA(pN) C21H32N7O13P2S 684.1254 684.538
4155N 5′ (3′ -dephosphoacetyl-CoA) acCoA(pN) C22H40N7O15P2S 736.17781 736.6113
4255N 5′ (3′ -dephosphomalonyl-CoA) malonyl-CoA(pN) C23H40N7O17P2S 780.16764 780.6211
4355N 5′ (3′ -dephosphosuccinyl-CoA) succinyl-CoA(pN) C24H41N7O17P2S 793.17546 793.64004
552N 5′ diphosphate end p(pN) ϒ ϒ PO3 78.9585 78.97196
550N 5′ hydroxyl end 5′-OH-N None None
N 5′ monophosphate end (pN) m m C5H7O10P2 288.95144 289.0521
255N 5′ nicotinamide adenine dinucleotide NAD(pN) Ξ Ξ C21H25N7O14P2 661.0935 661.4158
553N 5′ triphosphate end pp(pN) ϖ ϖ P3O9R 157.91701 157.94392
47G 7-aminocarboxypropyl-demethylwyosine yW-86 ¥ ¥ C17O7N6H22 422.154996 422.398569
347G 7-aminocarboxypropylwyosine yW-72 Ω Ω C18O7N6H24 436.170646 436.425557
348G 7-aminocarboxypropylwyosine methyl ester yW-58 C19O7N6H26 450.186296 450.452546
101G 7-aminomethyl-7-deazaguanosine preQ1tRNA C12O5N5H17 311.122968 311.298172
100G 7-cyano-7-deazaguanosine preQ0tRNA φ φ C12O5N5H13 307.091668 307.266269
7G 7-methylguanosine m7G 7 7 C11O5N5H17 299.12295 299.28668
79553N 7-methylguanosine cap (cap 0) m7Gpp(pN) © © C11H15N5O11P2 455.0243 455.21472
8A 8-methyladenosine m8A â â C11O4N5H15 281.112403 281.271879
02G N2,2′-O-dimethylguanosine m2Gm γ γ C12O5N5H17 311.122968 311.298172
027G N2,7,2′-O-trimethylguanosine m2,7Gm æ æ C13H21N5O5 327.15425 327.34044
27G N2,7-dimethylguanosine m2,7G C12O5N5H19 313.1386 313.31356
279553N N2,7-dimethylguanosine cap (cap DMG) m2,7Gpp(pN) ® ® C12H17N5O11P2 469.04 469.2416
022G N2,N2,2′-O-trimethylguanosine m2,2Gm | | C13O5N5H19 325.138618 325.325161
227G N2,N2,7-trimethylguanosine m2,2,7G C13O5N5H21 327.15425 327.34044
2279553N N2,N2,7-trimethylguanosine cap (cap TMG) m2,2,7Gpp(pN) C13H19N5O11P2 483.05561 483.26848
22G N2,N2-dimethylguanosine m2,2G R R C12O5N5H17 311.122968 311.298172
2G N2-methylguanosine m2G L L C11O5N5H15 297.107318 297.271183
04C N4,2′-O-dimethylcytidine m4Cm λ λ C11O5N3H17 271.11682 271.273689
044C N4,N4,2′-O-trimethylcytidine m4,4Cm β β C12O5N3H19 285.13247 285.300678
44C N4,N4-dimethylcytidine m4,4C μ μ C11O5N3H17 271.11682 271.273689
042C N4-acetyl-2′-O-methylcytidine ac4Cm C12O6N3H17 299.111735 299.284031
42C N4-acetylcytidine ac4C M M C11O6N3H15 285.096085 285.257042
4C N4-methylcytidine m4C ν ν C10O5N3H15 257.10117 257.2467
06A N6,2′-O-dimethyladenosine m6Am χ χ C12O4N5H17 295.128053 295.298867
066A N6,N6,2′-O-trimethyladenosine m6,6Am η η C13O4N5H19 309.143703 309.325856
66A N6,N6-dimethyladenosine m6,6A ζ ζ C12O4N5H17 295.128053 295.298867
60A N6-(cis-hydroxyisopentenyl)adenosine io6A ` ` C15O5N5H21 351.154268 351.363186
64A N6-acetyladenosine ac6A C12O5N5H15 309.107318 309.28222
67A N6-formyladenosine f6A Ϩ Ϩ C11H13N5O5 295.09165 295.25491
65A N6-glycinylcarbamoyladenosine g6A C13O7N6H16 368.108046 368.306566
68A N6-hydroxymethyladenosine hm6A Ϫ Ϫ C11H15N5O5 297.1073 297.2708
63A N6-hydroxynorvalylcarbamoyladenosine hn6A C16O8N6H22 426.149911 426.386836
61A N6-isopentenyladenosine i6A + + C15O4N5H21 335.159353 335.363882
662A N6-methyl-N6-threonylcarbamoyladenosine m6t6A E E C16O8N6H22 426.149911 426.386836
6A N6-methyladenosine m6A = = C11O4N5H15 281.112403 281.271879
62A N6-threonylcarbamoyladenosine t6A 6 6 C15O8N6H20 412.134261 412.359848
10G (base) Qbase Qbase C12O3N5H15 277.117489 277.283611
A adenosine A A A C10O4N5H13 267.096753 267.24489
20C agmatidine C+ ¿ ¿ C14H25N7O4 355.1968 355.3973
2551N alpha-dimethylmonophosphate cap mm(pN) C7H14O10P2 320.00621 320.12968
1551N alpha-methylmonophosphate cap m(pN) C6H12O10P2 305.99056 306.1028
103G archaeosine G+ ( ( C12H16N6O5 324.1182 324.29648
69A cyclic N6-threonylcarbamoyladenosine ct6A e e C15O7N6H18 394.12368 394.34416
C cytidine C C C C9O5N3H13 243.08552 243.219712
8U dihydrouridine D D D C9O6N2H14 246.085186 246.220269
102G epoxyqueuosine oQtRNA ς ς C17O8N5H23 425.154662 425.399126
104G galactosyl-queuosine galQtRNA 9 9 C23O12N5H33 571.21257 571.542325
1553N gamma-methyltriphosphate cap mpp(pN) § § CH3O6P2 172.94048 172.97874
105G glutamyl-queuosine gluQtRNA C22O10N6H30 538.20234 538.515474
G guanosine G G G C10O5N5H13 283.091668 283.244195
GN guanosine added to any nucleotide pG(pN) none none C10H13N5O8P 362.05016 362.21587
9553N guanylylated 5′ end (cap G) Gpp(pN) ϑ ϑ C10H12N5O14P3 440.00084 440.1799
34830G hydroxywybutosine OHyW C21O10N6H28 524.18669 524.488486
9A inosine I I I C10O5N4H12 268.080769 268.229496
42G isowyosine imG2 C14O5N5H17 335.122968 335.320246
106G mannosyl-queuosine manQtRNA 8 8 C23O12N5H33 571.21257 571.542325
3480G methylated undermodified hydroxywybutosine OHyWy y y C19H26N6O8 466.18119 466.45108
342G methylwyosine mimG C15O5N5H19 349.138618 349.347235
34832G peroxywybutosine o2yW W W C21O11N6H28 540.181605 540.48779
100G (base) preQ0base preQ0base ψ ψ C7O1N5H5 175.04941 175.150058
101G (base) preQ1base preQ1base C7O1N5H9 179.08071 179.181962
9U pseudouridine Y P P C9O6N2H12 244.069536 244.204317
10G queuosine QtRNA Q Q C17O7N5H23 409.159747 409.399821
3470G undermodified hydroxywybutosine OHyWx š š C18O8N6H24 452.16554 452.4242
0X unknown methylated base Xm Î Î - 0.0 0.0
X unknown modification xX @ @ - 0.0 0.0
?A unknown modified adenosine xA H H - 0.0 0.0
?C unknown modified cytidine xC < < - 0.0 0.0
?G unknown modified guanosine xG ; ; - 0.0 0.0
?U unknown modified uridine xU N N - 0.0 0.0
unknown nucleotide residue N . . - 0.0 0.0
U uridine U U U C9O6N2H12 244.069536 244.204317
502U uridine 5-oxyacetic acid cmo5U V V C11O9N2H14 318.069929 318.240257
503U uridine 5-oxyacetic acid methyl ester mcmo5U υ υ C12O9N2H16 332.085579 332.267246
3483G wybutosine yW Y Y C21O9N6H28 508.191775 508.489181
34G wyosine imG C14O5N5H17 335.122968 335.320246