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:

  1. 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.
  2. Copy the Ensembl transcript ID of the desired transcript.
  3. Click on the Human 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.

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. feedback




This online resource for the prediction Cas13d guide RNAs for target transcripts integrates guide RNA design rules from this manuscript:

Massively parallel Cas13 screens reveal principles for guide RNA 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 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

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.
Release notes:
  • 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

Sanjana Lab

To accurately predict local target site accesibility use sequences of > 80 nt length.
To limit run time please use target sequneces of < 500 nt length.
Please be patient while the gRNAs are being scored. (100nt ~10sec; 500nt ~ 30sec)


Download predictions

Cas13 guide RNA predictions

Please use the search field for searching or rank the guide RNA predictions column-wise.
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.
GENCODE v19 (hg19)

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.
GENCODE M24 (mm10)


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.
Ensembl v99 (GRCz11)


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.
Ensembl v99 (BDGP6)


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.
Ensembl v99 (WBcel235)


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.
Ensembl Plants v46 (TAIR10)


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.


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.


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.


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.


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.