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. | |
2 | Pos | Coordinate of the RNA editing site in the reference genome. | Â |
3 | In DNA | Base of the RNA editing site in the DNA reference sequence. | Â |
4 | In RNA | Base of the RNA editing site in the RNA sequence of sample. | Â |
5 | Gene | Gene name to which the RNA editing site belongs. | Â |
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). | RepeatMasker |
7 | Strand | + for positive strand; - for negative strand. | |
8 | Source | This field contains information regarding the tissue source from which the RNA editing instance was obtained. | Â |
9 | PubMed ID | This field provides the reference article from which the RNA editing data was extracted. | Â |
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. | Â |
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 |