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Table 2 Format of RCARE annotation Results.

From: RCARE: RNA Sequence Comparison and Annotation for RNA Editing

Column
number
Column
name
Definition References
1 Chr Chromosome of the RNA editing site in the reference genome. [5, 11, 14]
2 Pos Coordinate of the RNA editing site in the reference genome.  
3 In DNA Base of the RNA editing site in the DNA reference sequence.  
4 In RNA Base of the RNA editing site in the RNA sequence of sample.  
5 Gene Gene name to which the RNA editing site belongs.  
6 Evidence level The evidence level consists of five levels (A-E), where A is highest level (e.g., if an RNA editing site had level "A," it appeared in all five of the resource databases/papers used).
*Level A: The RNA editing site appeared in five resources (evidence No. 5).
*Level B: The RNA editing site appeared in four resources (evidence No. 4).
*Level C: The RNA editing site appeared in three resources (evidence No. 3).
*Level D: The RNA editing site appeared in two resources (evidence No. 2).
*Level E: The RNA editing site appeared in one resource (evidence No. 1).
[5, 11, 14, 15]
RepeatMasker
7 Strand + for positive strand; - for negative strand. [5, 11, 14]
8 Source This field contains information regarding the tissue source from which the RNA editing instance was obtained.  
9 PubMed ID This field provides the reference article from which the RNA editing data was extracted.  
10 Alu This field provides information of Alu at the RNA editing site. RepeatMasker
11 Data reference Reference database. Each database or reference
12 ENSG Ensembl Gene ID. GTF(Homo sapiens,
13 ENST Ensembl Transcript ID.  
14 ENSE Ensembl Exon ID. GRCH37.17) in Ensembl
15 Genomic feature Genomic feature of the RNA editing site.
*Exonic: the variant overlaps a coding exon.
*Splicing: the variant is within 2 bp of a splicing junction.
*ncRNA: the variant overlaps a transcript without coding annotation in the gene definition.
*5'UTR: the variant overlaps a 5' untranslated region.
*3'UTR: the variant overlaps a 3' untranslated region.
*Intronic: the variant overlaps an intron.
*Upstream: the variant overlaps the 1-kb region upstream of the transcription start site.
*Downstream: the variant overlaps the 1-kb region downstream of the transcription end site.
*Intergenic: a variant is in the intergenic region.
[19]
16 Synonymous or nonsynonymous Synonymous or nonsynonymous substitutions at the RNA editing site. [19]
17 Noncoding RNA This field indicates whether the location of an RNA editing site is in ncRNA. GTF (Homo sapiens, GRCH37.17) in Ensembl