Contents

The alphabets for the modifications used in this package are based on the compilation of RNA modifications by the Bujnicki lab (Boccaletto et al. 2018). The alphabet was modified to remove some incompatible characters.

If modifications are missing, let us know.


Table 1: List of RNA modifications supported by ModRNAString objects.
modification short name nomenclature orig. base abbreviation
1,2’-O-dimethyladenosine m1Am 01A A œ
1,2’-O-dimethylguanosine m1Gm 01G G ε
1,2’-O-dimethylinosine m1Im 019A A ξ
1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine m1acp3Y 1309U U α
1-methyladenosine m1A 1A A "
1-methylguanosine m1G 1G G K
1-methylinosine m1I 19A A O
1-methylpseudouridine m1Y 19U U ]
2,8-dimethyladenosine m2,8A 28A A ±
2-geranylthiouridine ges2U 21U U Γ
2-lysidine k2C 21C C }
2-methyladenosine m2A 2A A /
2-methylthiomethylenethio-N6-isopentenyl-adenosine msms2i6A 2361A A £
2-methylthio-cyclic-N6-threonylcarbamoyladenosine ms2ct6A 2164A A ÿ
2-methylthio-N6-(cis-hydroxyisopentenyl)-adenosine ms2io6A 2160A A ≠
2-methylthio-N6-hydroxynorvalylcarbamoyladenosine ms2hn6A 2163A A ≈
2-methylthio-N6-isopentenyladenosine ms2i6A 2161A A *
2-methylthio-N6-methyladenosine ms2m6A 621A A ∞
2-methylthio-N6-threonylcarbamoyladenosine ms2t6A 2162A A [
2-selenouridine se2U 20U U ω
2-thio-2’-O-methyluridine s2Um 02U U ∏
2-thiocytidine s2C 2C C %
2-thiouridine s2U 2U U 2
2’-O-methyladenosine Am 0A A :
2’-O-methylcytidine Cm 0C C B
2’-O-methylguanosine Gm 0G G #
2’-O-methylinosine Im 09A A ≤
2’-O-methylpseudouridine Ym 09U U Z
2’-O-methyluridine Um 0U U J
2’-O-methyluridine 5-oxyacetic acid methyl ester mcmo5Um 0503U U Ä
2’-O-ribosyladenosine (phosphate) Ar(p) 00A A ^
2’-O-ribosylguanosine (phosphate) Gr(p) 00G G ℑ
3,2’-O-dimethyluridine m3Um 03U U σ
3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine acp3D 308U U Ð
3-(3-amino-3-carboxypropyl)pseudouridine acp3Y 309U U Þ
3-(3-amino-3-carboxypropyl)uridine acp3U 30U U X
3-methylcytidine m3C 3C C ’
3-methylpseudouridine m3Y 39U U κ
3-methyluridine m3U 3U U δ
4-demethylwyosine imG-14 4G G †
4-thiouridine s4U 74U U 4
5,2’-O-dimethylcytidine m5Cm 05C C τ
5,2’-O-dimethyluridine m5Um 05U U ¤
5-(carboxyhydroxymethyl)-2’-O-methyluridine methyl ester mchm5Um 0522U U b
5-(carboxyhydroxymethyl)uridine methyl ester mchm5U 522U U ,
5-(isopentenylaminomethyl)-2-thiouridine inm5s2U 2583U U ½
5-(isopentenylaminomethyl)-2’-O-methyluridine inm5Um 0583U U ¼
5-(isopentenylaminomethyl)uridine inm5U 583U U ¾
5-aminomethyl-2-geranylthiouridine nm5ges2U 21510U U Δ
5-aminomethyl-2-selenouridine nm5se2U 20510U U π
5-aminomethyl-2-thiouridine nm5s2U 2510U U ∫
5-aminomethyluridine nm5U 510U U ∪
5-carbamoylhydroxymethyluridine nchm5U 531U U r
5-carbamoylmethyl-2-thiouridine ncm5s2U 253U U l
5-carbamoylmethyl-2’-O-methyluridine ncm5Um 053U U ~
5-carbamoylmethyluridine ncm5U 53U U &
5-carboxyhydroxymethyluridine chm5U 520U U ≥
5-carboxymethyl-2-thiouridine cm5s2U 2540U U ℘
5-carboxymethylaminomethyl-2-geranylthiouridine cmnm5ges2U 2151U U f
5-carboxymethylaminomethyl-2-selenouridine cmnm5se2U 2051U U ⊥
5-carboxymethylaminomethyl-2-thiouridine cmnm5s2U 251U U $
5-carboxymethylaminomethyl-2’-O-methyluridine cmnm5Um 051U U )
5-carboxymethylaminomethyluridine cmnm5U 51U U !
5-carboxymethyluridine cm5U 52U U ◊
5-cyanomethyluridine cnm5U 55U U Ѷ
5-formyl-2’-O-methylcytidine f5Cm 071C C °
5-formylcytidine f5C 71C C ×
5-hydroxycytidine ho5C 50C C Ç
5-hydroxymethylcytidine hm5C 51C C ∅
5-hydroxyuridine ho5U 50U U ∝
5-methoxycarbonylmethyl-2-thiouridine mcm5s2U 2521U U 3
5-methoxycarbonylmethyl-2’-O-methyluridine mcm5Um 0521U U ∩
5-methoxycarbonylmethyluridine mcm5U 521U U 1
5-methoxyuridine mo5U 501U U 5
5-methyl-2-thiouridine m5s2U 25U U F
5-methylaminomethyl-2-geranylthiouridine mnm5ges2U 21511U U h
5-methylaminomethyl-2-selenouridine mnm5se2U 20511U U ≅
5-methylaminomethyl-2-thiouridine mnm5s2U 2511U U S
5-methylaminomethyluridine mnm5U 511U U {
5-methylcytidine m5C 5C C ?
5-methyldihydrouridine m5D 58U U ρ
5-methyluridine m5U 5U U T
5-taurinomethyl-2-thiouridine tm5s2U 254U U ∃
5-taurinomethyluridine tm5U 54U U Ê
7-aminocarboxypropyl-demethylwyosine yW-86 47G G ¥
7-aminocarboxypropylwyosine yW-72 347G G Ω
7-aminocarboxypropylwyosine methyl ester yW-58 348G G ⇑
7-aminomethyl-7-deazaguanosine preQ1tRNA 101G G ∉
7-cyano-7-deazaguanosine preQ0tRNA 100G G φ
7-methylguanosine m7G 7G G 7
8-methyladenosine m8A 8A A â
N2,2’-O-dimethylguanosine m2Gm 02G G γ
N2,7,2’-O-trimethylguanosine m2,7Gm 027G G æ
N2,7-dimethylguanosine m2,7G 27G G ∨
N2,N2,2’-O-trimethylguanosine m2,2Gm 022G G |
N2,N2,7-trimethylguanosine m2,2,7G 227G G ∠
N2,N2-dimethylguanosine m2,2G 22G G R
N2-methylguanosine m2G 2G G L
N4,2’-O-dimethylcytidine m4Cm 04C C λ
N4,N4,2’-O-trimethylcytidine m4,4Cm 044C C β
N4,N4-dimethylcytidine m4,4C 44C C μ
N4-acetyl-2’-O-methylcytidine ac4Cm 042C C ℵ
N4-acetylcytidine ac4C 42C C M
N4-methylcytidine m4C 4C C ν
N6,2’-O-dimethyladenosine m6Am 06A A χ
N6,N6,2’-O-trimethyladenosine m6,6Am 066A A η
N6,N6-dimethyladenosine m6,6A 66A A ζ
N6-(cis-hydroxyisopentenyl)adenosine io6A 60A A `
N6-acetyladenosine ac6A 64A A ⇓
N6-formyladenosine f6A 67A A Ϩ
N6-glycinylcarbamoyladenosine g6A 65A A ≡
N6-hydroxymethyladenosine hm6A 68A A Ϫ
N6-hydroxynorvalylcarbamoyladenosine hn6A 63A A √
N6-isopentenyladenosine i6A 61A A Θ
N6-methyl-N6-threonylcarbamoyladenosine m6t6A 662A A E
N6-methyladenosine m6A 6A A =
N6-threonylcarbamoyladenosine t6A 62A A 6
agmatidine C+ 20C C ¿
archaeosine G+ 103G G (
cyclic N6-threonylcarbamoyladenosine ct6A 69A A e
dihydrouridine D 8U U D
epoxyqueuosine oQtRNA 102G G ς
galactosyl-queuosine galQtRNA 104G G 9
glutamyl-queuosine gluQtRNA 105G G ⊄
hydroxy-N6-threonylcarbamoyladenosine ht6A 2165A A «
hydroxywybutosine OHyW 34830G G ⊆
inosine I 9A A I
isowyosine imG2 42G G ⊇
mannosyl-queuosine manQtRNA 106G G 8
methylated undermodified hydroxywybutosine OHyWy 3480G G y
methylwyosine mimG 342G G ∑
peroxywybutosine o2yW 34832G G W
pseudouridine Y 9U U P
queuosine QtRNA 10G G Q
undermodified hydroxywybutosine OHyWx 3470G G š
unknown methylated base Xm 0X N Î
unknown modification xX X N ÷
unknown modified adenosine xA ?A A H
unknown modified cytidine xC ?C C <
unknown modified guanosine xG ?G G ;
unknown modified uridine xU ?U U Ü
uridine 5-oxyacetic acid cmo5U 502U U V
uridine 5-oxyacetic acid methyl ester mcmo5U 503U U υ
wybutosine yW 3483G G Y
wyosine imG 34G G € 
sessionInfo()
## R version 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.13-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
## [1] Modstrings_1.8.0    Biostrings_2.60.0   GenomeInfoDb_1.28.0
## [4] XVector_0.32.0      IRanges_2.26.0      S4Vectors_0.30.0   
## [7] BiocGenerics_0.38.0 BiocStyle_2.20.0   
## 
## loaded via a namespace (and not attached):
##  [1] knitr_1.33             magrittr_2.0.1         GenomicRanges_1.44.0  
##  [4] zlibbioc_1.38.0        R6_2.5.0               rlang_0.4.11          
##  [7] highr_0.9              stringr_1.4.0          tools_4.1.0           
## [10] xfun_0.23              jquerylib_0.1.4        htmltools_0.5.1.1     
## [13] yaml_2.2.1             digest_0.6.27          crayon_1.4.1          
## [16] bookdown_0.22          GenomeInfoDbData_1.2.6 BiocManager_1.30.15   
## [19] bitops_1.0-7           sass_0.4.0             RCurl_1.98-1.3        
## [22] evaluate_0.14          rmarkdown_2.8          stringi_1.6.2         
## [25] compiler_4.1.0         bslib_0.2.5.1          jsonlite_1.7.2

References

Boccaletto, Pietro, Magdalena A. Machnicka, Elzbieta Purta, Pawel Piatkowski, Blazej Baginski, Tomasz K. Wirecki, Valérie de Crécy-Lagard, et al. 2018. “MODOMICS: A Database of Rna Modification Pathways. 2017 Update.” Nucleic Acids Research 46 (D1): D303–D307. https://doi.org/10.1093/nar/gkx1030.