CRISPinatoR Tutorial

Inspecting sgRNA Candidates


Explore sgRNA Panel
Hover over descriptions to highlight information in the image.
  1. Click on your target guide to display a window with its details.
  2. The sgRNA sequence will be displayed in the window title surrounded by a portion of its adjacent exon sequence.
  3. Tier - This sgRNA's CRISPinatoR tier.
  4. ESE distance - Number of upstream or downstream base pairs from the N in the PAM sequence to an ESE.
  5. Off‑Target Score - Score indicating propensity for off-target effects. Calculated by CRISPinatoR in a 0-100 scale. The higher, the better.
  6. On‑Target Score - Score indicating the affinity to target sequence. Calculated by Azimuth in a 0-100 scale. The higher, the better.
  7. Strand - Strand direction in which the sgRNA matches the sequence:
    • Sense- (5'- 3') guide followed by an NGG PAM sequence.
    • Antisense- (3'- 5') guide preceded by a CCN PAM sequence.
  8. Location - Chromosome and position of the N in the PAM sequence.
  9. Gene - Ensembl gene ID and gene symbol of the gene affected by this sgRNA.
  10. Exon - Ensembl exon ID and symmetry of the exon affected by this sgRNA.
  11. PAM/CDS Ratio - Relative position of the sgRNA's cut site compared to coding sequence length (0.05-0.65 is best).
  12. PPTC‑LEEJ Distance - Distance from the predicted PTC generated when the exon in question is skipped to the last Exon-Exon junction in the transcript (>55bp is best). Note: this feature is only calculated for the gene’s longest coding transcript.
  13. Click the expand button to show the Transcripts or Off-Target Effects tabes.
    Click the collapse button to hide the Transcripts or Off-Target Effects tabes.
  14. Click the Cart icon to add or remove the current sgRNA from your list of Favorite Guides.
  15. Your newly favorited sgRNA will be shaded in yellow and the My Guides indicator will be incremented.

Inspecting the sgRNA Transcripts Table

sgRNA Transcripts Table
Hover over descriptions to highlight information in the image.
  1. The Transcripts table will display all transcripts for the selected gene.
  2. Transcript ID - Displays the Ensembl transcript ID for its corresponding row.
  3. Overall Exon Position - Displays the position of the sgRNAs target exon relative to all exons in that transcript (overall exon position/total transcript count).
  4. Coding Exon Position - Displays the position of the sgRNAs target exon relative to all coding exons in that transcript (coding exon position/total coding exon count).
  5. The current transcript is shaded in yellow.
  6. All transcripts NOT affected by the current sgRNA are greyed out.

Inspecting the sgRNA Off-Target Effects Table

sgRNA Transcripts Table
Hover over descriptions to highlight information in the image.
  1. The Off-Target Effects table will display all identified off-target effects for the selected sgRNA (up to 3 mismatches).
    The tabel title displays the total off-target effect count in parenteses.
  2. Mismatch Count - Number of mismatches found in this off-target region.
  3. Location (Chr) - Chromosome and position where off-target region matches the N in the PAM sequence.
  4. Gene - Gene symbol corresponding to the off-target location. Displays NA for intergenic regions.