update: 30th, Aug., 2009
The curated data of conversion type RNA editing sites on cDNA and amino acid sequence is available at the middle of this page.
The data are converted from GenBank/EMBL/DDBJ and the data format mimics that of UniProt. The conversion is automatically done following rules of CDS in GenBank. Location of edited nucleotide is given in /note of misc_feature in GenBank. In addition to the automatic conversion, the data contains RNA editing sites only found in the literature.
The length of amino acid sequence at "ID" line (PRT; xxx AA.) is the real length plus one, because the data may contain RNA editing at the termination codon.
Accession number (AC) is inherited from Genbank.
"FT EDITING" is one of the unique features in the data. In each line, a number after the colon is amino acid position number, then comes the amino acid type before RNA editing with a codon in parentheses (uppercase is the nucleotide before RNA editing), then an arrow, then the amino acid type after RNA editing with a edited codon in parentheses (uppercase is the nucleotide after RNA editing). Note that nucleotides are shown in DNA, not in RNA.
"CL CDNALEN" shows the length of cDNA, and "CD" shows the cDNA sequence BEFORE RNA editing with unedited target nucleotide in uppercase. After "FT EDITED CDNA" line, "CD" shows the cDNA sequence AFTER RNA editing with edited target nucleotides in uppercase.
"SQ" line and the following lines contain amino acid sequence translated from EDITED cDNA with termination mark (*) at the end.
Each entry ends with "//".
The data can be download from down below. Please refer to our manuscripts when publishing a paper based on the data here.
Quite a number of entries in Genbank have an error in description of RNA editing site location, and we put some energy to rectify the errors. The data linked up above include these manually corrected entries. The following table shows the Genbank entry with possible errors based on the result of our automatic test program. We made contact to the depositor of the data one by one and corrected the entry as much as possible. When we cannot get in touch with the depositor, then we discard the entry. Genbank corrects the entry only with the order from the original depositor and we wish that this effort will make the original depositors update the data and reduce the error in RNA editing site description in Genbank. So far our small effort has corrected errors in some entries, namely AY521591, AF357519, AB254134 and AY820131. The following table is the entry with putative errors automatically detected by the test program. Correction files were basically generated with the discussion with each dipositor. When no contact was made to the depositor, the entry was discarded from the file.
RNA editing sites of RuBisCO Large subunit were determined in the early 90s and the results only appears in the literature. Here is the sequence data with RNA editing sites.
Reference:
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