CUNE

Contents:

Locus

Genome and Locus

Enter a chromosome and location here to specify the base that you aim to edit. CUNE uses reference genomes from the Genome Reference Consortium (GRC). As such, the "Location" specified here should be 1-based.

Point Mutation

Point Mutation

Enther the nucleotide that you aim to induce at the specified location. This enables CUNE to correctly design the ssODN.
The nucleotide specified here is for the + strand of the reference genome, as depicted below the input form.
This is not used to predict the HDR efficiency of targets.

Region Information

The following three sections display general information about the region specified.

Genomic region

Genomic Region

This figure displays information about features (such as genes) that are around the specified region. Lines represent introns, Boxes represent transcribed regions and the solid areas of the boxes represent translated regions.
This information is retrieved from Ensembl.

Genomic sequence

Genomic Sequence

This displays the forward and reverse strand of the specified nucleotide and the 35 bases surrounding this location.

Amino Acid

Amino Acid

This displays the amino acid (before edit) in any translated regions overlapping the specified location. The codon number (out of the codon count) is also specified.
This information is calculated locally using data retrieved from Ensembl.

Base Editors

Base Editors

These cards display the potentially editable regions using base editing.
These results are based on information in the literature. Click the base editor name to see the relevent publication.

For each base editor:

  • The underlined region indicates the editing window.
  • A green letter indicates that the user-specified location is predicted to be editable.
  • A red letter indicates a potential proximal off-target.

The efficiency depends on factors including the type of base editor and location of the base, relative to the guide.
Please see the relevent publication for further information.

Click "Add new" to add a new type of base editor. CUNE includes:

  • BE4 (C→T)
  • BE3 (C→T)
  • BE (C→T)
  • Target-AID (C→T)
  • ABE (A→G)

Additionally, you can define an unlisted base editor by selecting "Custom".

HDR

HDR

Here you can see all available guides and ssODNs for editing the specified base with CRISPR/Cas9. Listed is the

  • An ID for the target.
  • The distance from the mutation to the PAM (toward the 5' side of the PAM).
  • The reference genome strand that the gRNA and ssODN are homologous to.
  • The guide RNA (gRNA).
  • The ssODN (with symmetric arms of 60 bases. Total length is 121 bases).
  • The predicted efficiency.

If you specified a nucleotide in the Point Mutation card, this nucleotide will be present in the ssODN. Otherwise the center base will be an "N".
Please note that you may observe the complementary nucleotide in the ssODN, if the ssODN is homologous to the "-" reference genome strand.