Cas13 Guide Design Resource
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 for human transcripts:
Click on the Lookup human transcript expression button in the navigator bar. Typing in a gene name will retrieve a list of all associated Ensembl transcript isoforms for that gene along with expression data for each isoform in different human cell lines.
Copy the Ensembl transcript ID of the desired transcript.
Click on the Human button in the navigation bar.
Paste the Ensembl transcript ID into search box in the upper left side and click the submit button.
After 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.
To predict guide RNA scores for custom target RNA from command line, please use our
Cas13 guide design software.
Questions, comments or feedback? Please do not hesitate to get in touch with us here.
This online resource for the prediction Cas13d guide RNAs for target transcripts integrates guide RNA design rules from this manuscript:
Hans-Hermann Wessels*, Alejandro Méndez-Mancilla*, Xinyi Guo, Mateusz Legut, Zharko Daniloski, Neville E. Sanjana
* These authors contributed equally
This resource currently features:
For human genes we used
GENCODE v19 (GRCh37)
annotation allowing us to integrate gene expression information from the
Cancer Cell Line Encyclopedia (CCLE).
Please retrieve transcript isoform expression information directly from the CCLE repository if you don't find your cell line represented.
- 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
- 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