Nucleic acid modification databases
From Wikipedia, the free encyclopedia
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] 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]
| 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 | [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 | [6] | |
| RNAmods | Any RNA | Natural | ? | modified ribonucleosides (symbols, chemical structures), distribution (type of molecule, phylogenetic domain) | database | rna | [7] | |
| DNAmod | Any DNA | Natural and synthetic | Curation from ChEBI | symbols, chemical structures | database | dnamod | [8] | |
| NAMDB | DNA and RNA | ? | ? | symbols, chemical structures; for some entries: location and frequency, enzymes and reactions | database | www | ||