Nucleic acid modification databases This page compiles a list of databases, web portals and servers containing information on nucleic acid modification . RNA modification occurs in all living organisms, and is one of the most evolutionarily conserved properties of RNAs.[ 1] [ 2] [ 3] [ 1] [ 2] [ 3] [ 4]
Name
Scope
Notes
Type
Link
Ref
Molecules
Cause of modification
Data origin
Addition Info?
RMBase
mRNA, regulatory ncRNAs (e.g. lncRNAs, miRNAs)
Natural
high-throughput sequencing (pseudo-seq, Ψ-seq, CeU-seq, Aza-IP, MeRIP-seq, m6A-seq, miCLIP, m6A-CLIP, RiboMeth-seq)
miRNA target sites, RNA-Binding Proteins (RBPs) Binding sites and disease-related SNPs
database
rna.sysu.edu.cn/rmbase/ [ 5]
MODOMICS
Any RNA
Natural and synthetic
Curation
modified ribonucleosides (symbols, chemical structures, biosynthetic pathways), RNA-modifying enzymes, location of modified residues in RNA sequences
database
modomics.genesilico.pl [ 6]
RNAmods
Any RNA
Natural
?
modified ribonucleosides (symbols, chemical structures), distribution (type of molecule, phylogenetic domain)
database
rna.rega.kuleuven.be/rnamods [ 7]
DNAmod
Any DNA
Natural and synthetic
Curation from ChEBI
symbols, chemical structures
database
dnamod.hoffmanlab.org [ 8]
NAMDB
DNA and RNA
?
?
symbols, chemical structures; for some entries: location and frequency, enzymes and reactions
database
www.namdb.cn/index.php
References
^ a b Li, S; Mason, CE (2013). "The pivotal regulatory landscape of RNA modifications" . Annual Review of Genomics and Human Genetics . 15 : 127– 50. doi :10.1146/annurev-genom-090413-025405 PMID 24898039 . ^ a b Song, CX; Yi, C; He, C (October 2012). "Mapping recently identified nucleotide variants in the genome and transcriptome" . Nature Biotechnology . 30 (11): 1107– 16. doi :10.1038/nbt.2398 . PMC 3537840 PMID 23138310 . ^ a b Meyer, KD; Jaffrey, SR (April 2014). "The dynamic epitranscriptome: N6-methyladenosine and gene expression control" . Nature Reviews Molecular Cell Biology . 15 (5): 313– 26. doi :10.1038/nrm3785 . PMC 4393108 PMID 24713629 . ^ Jonkhout, Nicky; Tran, Julia; Smith, Martin Alexander; Schonrock, Nicole; Mattick, John S; Novoa, Eva Maria (30 August 2017). "The RNA modification landscape in human disease" . RNA . 23 (12): 1754– 1769. doi :10.1261/rna.063503.117 . PMC 5688997 PMID 28855326 . ^ Sun, WJ; Li, JH; Liu, S; Wu, J; Zhou, H; Qu, LH; Yang, JH (11 October 2015). "RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data" . Nucleic Acids Research . 44 (D1): D259 – D265 . doi :10.1093/nar/gkv1036 . PMC 4702777 PMID 26464443 . ^ Machnicka, MA; Milanowska, K; Osman Oglou, O; Purta, E; Kurkowska, M; Olchowik, A; Januszewski, W; Kalinowski, S; Dunin-Horkawicz, S; Rother, KM; Helm, M; Bujnicki, JM; Grosjean, H (December 2012). "MODOMICS: a database of RNA modification pathways--2013 update" . Nucleic Acids Research . 41 (Database issue): D262-7. doi :10.1093/nar/gks1007 . PMC 3531130 PMID 23118484 . ^ Cantara, WA; Crain, PF; Rozenski, J; McCloskey, JA; Harris, KA; Zhang, X; Vendeix, FA; Fabris, D; Agris, PF (December 2010). "The RNA Modification Database, RNAMDB: 2011 update" . Nucleic Acids Research . 39 (Database issue): D195-201. doi :10.1093/nar/gkq1028 . PMC 3013656 PMID 21071406 . ^ Sood, Ankur Jai; Viner, Coby; Hoffman, Michael M. (December 2019). "DNAmod: the DNA modification database" . Journal of Cheminformatics . 11 (1): 30. doi :10.1186/s13321-019-0349-4 PMC 6478773 PMID 31016417 .
