RNA modification database

This RNA modification databases are a compilation of databases and web portals and servers used for RNA modification. RNA modification occurs in all living organisms, and is one of the most evolutionarily conserved properties of RNAs.[1][2][3] More than 100 different types of RNA modifications have been characterized across all living organisms. It can affect the activity, localization as well as stability of RNAs, and has been linked with human cancer and diseases.[1][2][3][4]

RNA Modification Databases
Name DescriptiontypeLinkReferences
RMBase RMBase is designed for decoding the landscape of RNA modifications identified from high-throughput sequencing data (Pseudo-seq, Ψ-seq, CeU-seq, Aza-IP, MeRIP-seq, m6A-seq, miCLIP, m6A-CLIP, RiboMeth-seq). It demonstrated thousands of RNA modifications located within mRNAs, regulatory ncRNAs (e.g. lncRNAs, miRNAs), miRNA target sites, RNA-Binding Proteins (RBPs) Binding sites and disease-related SNPs.databasewebsite[5]
MODOMICS MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location of modified residues in RNA sequences.databasewebsite[6]
RNAMDB RNAMDB has served as a focal point for information pertaining to naturally occurring RNA modificationsdatabasewebsite[7]
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References
  1. 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.
  2. 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.
  3. 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.
  4. 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: rna.063503.117. doi:10.1261/rna.063503.117. PMC 5688997.
  5. 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: gkv1036. doi:10.1093/nar/gkv1036. PMC 4702777. PMID 26464443.
  6. 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.
  7. 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.
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