The CRISPR-SKIP webtool identifies which exons can be skipped by editing the flanking G nucleotide of the conserved dinucleotide sequence at the splice acceptor site. The base editors supported in this webtool are BE3, SaKKH-BE3, VRER-BE3, VQR-BE3. The genome assembly and gene annotation used are GRCh38 and GENCODE release 26, respectively. Only primary PAMs are considered.
To query the exons to be targeted, enter the Ensembl transcript ID, followed by a colon and the exon numbers separated by commas. To specify exons from multiple transcripts, add a semi-colon between different transcripts, e.g. ENST00000375114.7: 3, 6; ENST00000525123.5: 16
You can also query exons by their Ensembl exon ID by ticking the "Exon ID" box and entering the exon ID's separated by commas; e.g.,
CRISPR-SKIP excludes exons that have off-target sequences with off-target hit scores above 10, calculated as described by Hsu et al. NBT 2013 . Checking the "High Specificity" box decreases the threshold from 10 to 5. For each qualifying target sequence, CRISPR-SKIP displays potential off-target sequences that differ from the target sequence by up to two mismatches.