RESOPS: a database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures.
Transcripts from mitochondrial and chloroplast DNA of land plants often undergo cytidine to uridine conversion-type RNA editing events. RESOPS is a newly built database that specializes in displaying RNA editing sites of land plant organelles on protein three-dimensional (3D) structures to help elucidate the mechanisms of RNA editing for gene expression regulation. RESOPS contains the following information: unedited and edited cDNA sequences with notes for the target nucleotides of RNA editing, conceptual translation from the edited cDNA sequence in pseudo-UniProt format, a list of proteins under the influence of RNA editing, multiple amino acid sequence alignments of edited proteins, the location of amino acid residues coded by codons under the influence of RNA editing in protein 3D structures and the statistics of biased distributions of the edited residues with respect to protein structures. Most of the data processing procedures are automated; hence, it is easy to keep abreast of updated genome and protein 3D structural data. In the RESOPS database, we clarified that the locations of residues switched by RNA editing are significantly biased to protein structural cores. The integration of different types of data in the database also help advance the understanding of RNA editing mechanisms. RESOPS is accessible at http://cib.cf.ocha.ac.jp/RNAEDITING/.
Yura
Kei
K
Computational Biology, Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610 Japan. yura.kei@ocha.ac.jp
Sulaiman
Sintawee
S
Hatta
Yosuke
Y
Shionyu
Masafumi
M
Go
Mitiko
M
D002736:Chloroplasts / Q000235:genetics; D018742:DNA, Chloroplast / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D030562:Databases, Protein; D018745:Genome, Plant; D008928:Mitochondria / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics*; D011487:Protein Conformation; D017510:Protein Folding; D017393:RNA Editing; D018749:RNA, Plant / Q000235:genetics; D016415:Sequence Alignment; D014584:User-Computer Interface
D018742:DNA, Chloroplast; D018076:DNA, Complementary; D004272:DNA, Mitochondrial; D010940:Plant Proteins; D018749:RNA, Plant