This resource provides optimized guide RNAs to target transcripts in the human transcriptome, model organisms and viral RNA genomes.
Here are the steps to use the design tool:
Navigate to the desired species. For human transcript gRNA design, users can (optionally) access a list of all associated Ensembl transcript isoforms for a gene along with expression data for each isoform in different human cell lines by typing the desired gene in the table stored under the Lookup human transcript expression tab.
After finding the Ensembl transcript ID of the desired transcript, either click or type it in the search box on the upper left side.
Upon lookup, you can browse individual guide RNAs and download a graphical representation of guide RNAs or a table with all guide RNAs that target the transcript.
This online resource for the prediction Cas13d guide RNAs for target transcripts integrates guide RNA design rules from the following manuscripts:
Hans-Hermann Wessels*, Alejandro Méndez-Mancilla*, Xinyi Guo, Mateusz Legut, Zharko Daniloski, Neville E. Sanjana
Xinyi Guo, Jahan Rahman, Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Daniel Haro, Xinru Chen, Neville E. Sanjana
* These authors contributed equally
This resource currently features:
- Selection of perfect match guides for all human protein coding and non-coding genes, separted by transcript and mRNA sub-annotation categories (5'UTR, CDS, 3'UTR).
- Integration of Cancer Cell Line Encyclopedia (CCLE) gene expression data for the selection by cell type specific expression level.
- Selection of perfect match guides for protein coding and non-coding genes in the main model organism, separted by transcript and mRNA sub-annotation categories (5'UTR, CDS, 3'UTR).
- Perfect match guides for SARS-CoV-2, MERS, H1N1 and HIV1 RNA virus genes
Please retrieve transcript isoform expression information directly from the CCLE repository if you don't find your cell line represented.
- 11.2020: v1.1 more user-friendly layout+search, interactive plots, multi-sequence/fasta custom grna design, off-target metrics
- 07.2020: v1.0.1 addition of RNA viruses.
- 06.2020: v1.0 guide RNA efficacy predictions for mRNA and ncRNA in human and model organisms.
- 05.2020: v0.3.1 addition of custom guide predictor.
- 12.2019: v0.3 model update with improved prediction accuracy. The model is now trained on four tiling screen data sets.
- 09.2019: v0.2 improved data structure to allow real-time start up. Adding improved visualizations and data download.
- 07.2019: v0.1 goes online