Effect prediction of the A-to-I variants identified by RNA-seq
This protocol is extracted from research article:
Analysis and minimization of cellular RNA editing by DNA adenine base editors
Sci Adv, May 8, 2019; DOI: 10.1126/sciadv.aax5717

The Variant Effect Predictor (Ensembl) was used to determine the location within a transcript of each A-to-I edit found in the sample treated with ABEmax, Cas9(D10A), or ABEmaxAW and whether the mutation was synonymous or nonsynonymous. The category “downstream gene variant” includes mutations found within a region 5-kb downstream of the start of a gene, and the category “upstream gene variant” includes mutations found in the region 5-kb upstream of a protein-coding region. “Intergenic regions” includes A-to-I mutations occurring in noncoding regions more than 5 kb away from the beginning or end of a coding region. SIFT (https://sift.bii.a-star.edu.sg/) was used to predict the outcome of nonsynonymous mutations on protein function. High- and low-confidence calls were made using standard SIFT parameters.

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