Cas13 Guide Design Resource

This resource provides optimized guide RNAs to target protein-coding transcripts in the human transcriptome. To use the tool, you will first need to find the Ensembl transcript ID for the transcript isoform to target and then paste this transcript ID into the Cas13 guide designer. These two steps are performed using the tabs in the navigation bar.

Here are the steps to use the design tool:

  1. Click on the Lookup transcript 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.
  2. Copy the Ensembl transcript ID of the desired transcript.
  3. Click on the Design guide RNAs button in the navigation bar.
  4. Paste the Ensembl transcript ID into search box in the upper left side and click the submit button.
  5. 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.
Questions, comments or feedback? Please do not hesitate to get in touch with us here. feedback




This online resource for the prediction Cas13d guides for protein coding transcripts integrates guide RNA design rules from this manuscript:

Principles for rational Cas13d guide design

Hans-Hermann Wessels*, Alejandro Méndez-Mancilla*, Xinyi Guo, Mateusz Legut, Zharko Daniloski, Neville E. Sanjana
* These authors contributed equally

This resource currently features:
  • Selection of perfect matching guides for all protein 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.

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.
Release notes:
  • 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

Sanjana Lab
Please use the Search fields to type in a gene symbol or Ensembl gene ID to retrieve its transcript isoforms and their expression in different human cell lines. Transcript expression data is given as transcripts per million (TPM)
Copy the transcript ID and paste it in the submission field in the next Design guide RNAs tab.
Find your transcript isoform of interest based on CCLE data in the previous tab Lookup transcript.

Download plot

Download table

Cas13 guide RNA predictions along the target transcript

Cas13 guide RNA scores and quartiles are assigned according to the tiling screens used to predict guide efficiency.

Cas13 guide RNA predictions

Please use the search field for searching or rank the guide RNA predictions column-wise.