The Structure of RNA modifications

♥ Click on the image to jump to the RNA searching page

♥ Detailed notes are provided for each RNA modification site:
  • Genome annotations include genome coordinates, gene biotypes, gene features, sequence;
  • PWM Score is employed to assess the accuracy of m6A sites and ranges from 0 to 5, where a higher value indicates a more precise site. In RMBase, m6A modification sites are filtered using the criteria of support experimental number >= 2 and PWM score >= 3;
  • Cell lines or tissues;
  • Evolutionary conservation of mammalian m6A modifications is determined by liftOver or phyloP;
  • snoRNA is used to annotate the snoRNA-guided 2'-O-Me (Nm) and Pseudo (Ψ), which can form a snoRNA-target pairing interactions;
  • Writer is applied to annotate RNA modification sites catalyzed by enzymes. e.g. METTL3 regulates the installation of m6A.

The Statistics of high accuracy RNA Modification sites

Species Assembly m6A m1A m5C pseudo Nm m7G RNA editing ac4C Other Total
Homo sapiens hg38 234464 1162 46025 15078 8490 919 144122 1861 1484 453605
Mus musculus mm10 220022 91 47839 22518 1193 55 8864 0 950 301532
Macaca Mulatta rheMac8 16699 0 0 0 0 0 0 0 0 16699
Pan Troglodytes panTro5 27828 0 0 0 0 0 0 0 0 27828
Rattus rn6 43880 75 118 1317 3418 46 10 24 977 49865
Sus Scrofa susScr11 62116 0 0 0 0 0 0 0 0 62116
Danio Rerio danRer11 5071 0 0 5 40 0 0 0 0 5116
Arabidopsis thaliana TAIR10 35373 0 0 76 286 0 0 0 0 35735
Saccharomyces cerevisiae sacCer3 24486 151 231 2147 263 75 66 120 1767 29306
Drosophila melanogaster BDGP6 56 78 46 614 559 47 5049 13 494 6956
Pseudomonas aeruginosa ASM676v1 1560 0 0 0 0 0 0 0 0 1560
Escherichia coli ASM584v2 243 0 21 206 55 66 4 2 508 1105
Schizosaccharomyces pombe ASM294v2 1 8 8 41 18 9 0 0 87 172
Bacillus subtilis ASM69118v1 15 6 0 99 3 39 0 0 185 347
Bombyx mori ASM15162v1 0 82 178 185 95 33 0 0 453 1026
Bos taurus bosTau9 0 127 94 381 105 29 0 16 770 1522
Brassica napus AST_PRJEB5043v1 0 49 0 175 128 59 0 0 425 836
Caenorhabditis elegans WBcel235 (ce11) 0 0 0 296 151 0 18 0 106 571
Candida albicans Cand_albi12Cv2 0 1 1 3 1 0 0 1 6 13
Chlamydomonas reinhardtii CHLRE3 0 0 2 30 34 0 0 0 9 75
Clostridium acetobutylicum ASM78585v1 0 0 0 0 1 1 0 0 0 2
Cucumis sativus ASM407v2 0 12 14 34 0 0 0 0 105 165
Enterobacteria phage T4 ViralProj14044 0 0 0 14 6 3 0 0 39 62
Enterobacteria phage T5 ASM292140v1 1 0 0 9 1 2 0 0 10 23
Fusarium graminearum ASM24013v3 0 0 0 0 0 0 48493 0 0 48493
Fusarium verticillioides ASM14955v1 0 0 0 0 0 0 5227 0 0 5227
Gallus gallus GRCg6a 0 4 0 36 55 2 0 0 37 134
Geobacillus stearothermophilus ASM74998v1 1 3 0 11 5 3 0 0 25 48
Glycine max glyMax2 0 0 0 4 1 1 0 0 7 13
Halobacterium salinarum ASM680v1 0 0 10 17 10 0 0 0 31 68
Halococcus morrhuae ASM33669v1 0 0 0 1 0 0 0 0 1 2
Haloferax volcanii ASM2568v1 0 0 51 79 51 0 0 5 167 353
Lactococcus lactis ASM76111v1 11 2 0 0 0 30 0 1 64 108
Mesocricetus auratus MesAur1 0 2 0 5 0 0 0 0 9 16
Mycobacterium smegmatis ASM76770v1 0 1 0 1 0 1 0 0 1 4
Mycoplasma capricolum ASM83033v1 12 10 0 38 2 17 0 0 78 157
Mycoplasma mycoides ASM25307v1 4 1 0 4 0 3 0 0 14 26
Neurospora crassa NC12 0 22 14 36 0 10 47345 0 134 47561
Nicotiana tabacum Ntab_TN90 0 25 0 134 123 0 0 0 296 578
Oryctolagus cuniculus OryCun2 0 88 98 225 46 70 0 0 493 1020
Ovis aries Oarv3 0 24 35 35 0 15 0 0 132 241
Phaseolus vulgaris PhaVulg1 0 35 19 78 42 15 0 12 256 457
Pichia jadinii Cybja1 0 40 43 108 31 17 0 7 311 557
Pyrococcus abyssi ASM19593v2 0 0 0 0 0 0 0 0 1 1
Rhodospirillum rubrum ASM1308v1 0 0 0 2 0 1 0 0 4 7
Salmonella typhimurium ASM553737v1 0 0 0 19 7 3 0 0 42 71
Solanum tuberosum SolTub3 0 18 14 46 17 0 0 16 117 228
Spinacia oleracea ASM200726v1 0 11 0 89 81 17 0 0 251 449
Spiroplasma citri ASM188685v1 0 0 0 3 0 1 0 0 3 7
Streptomyces coelicolor A3(2) ASM20383v1 0 0 0 1 0 0 0 0 1 2
Streptomyces griseus ASM93222v1 0 26 0 4 25 18 0 0 48 121
Sulfolobus acidocaldarius ASM1228v1 0 1 1 0 4 0 0 0 1 7
Sulfolobus solfataricus ASM96839v1 0 0 0 0 0 0 0 0 24 24
Synechococcus elongatus PCC 6301 ASM1006v1 0 0 0 8 1 1 0 0 11 21
Synechococcus sp. PCC 7002 ASM1948v1 0 0 0 2 1 1 0 0 5 9
Synechocystis sp. ASM34078v1 0 0 0 1 0 0 0 0 3 4
Tetrahymena thermophila JCVI_TTA1_2 0 50 49 165 81 0 0 0 205 550
Thermoplasma acidophilum ASM19591v1 0 4 0 10 4 2 0 0 15 35
Thermotoga maritima ASM97857v1 0 0 1 0 1 1 0 0 5 8
Thermus thermophilus ASM812v1 0 4 12 19 17 6 0 0 28 86
Xenopus laevis Xenopus_laevisv2 0 55 86 104 46 35 0 0 270 596
Zea mays RefGenv4 0 0 0 15 9 0 0 0 33 57

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