CRISPinatoR Tutorial

Searching for a Target Gene


Gene Search Panel
Hover over instructions to highlight information in the image.
  1. Go to the Finder tab using navigation bar.
  2. Enter your targer gene symbol in the Gene textbox.
  3. You can also select one of the following parameters from the Source field:
    • Gene Symbol
    • Ensembl Gene ID
    • Ensembl Transcript ID
  4. Click the Search! button to activate your query.

Once your query is completed, your results will be displayed as follows:

Results Panel
Hover over descriptions to highlight information in the image.
  1. The current gene's symbol and ensemble id are displayed at the top of the gene card.
  2. Click the collapse button to hide the DNA sequence.
    Click the expand button to a show DNA sequence.
  3. The gene's longest coding transcript is displayed by default. Select a different transcript from the dropdown menu to display it.
  4. Exons are displayed in their order within the selected transcript. The first number is an exon's overall position.
  5. Each displayed exon is titled by its Ensembl exon id.
  6. The ordinal number in an exon's title corresponds to its coding position within the selected transcript
  7. If an exon is noncoding, NC will be displayed instead of an ordinal number.
  8. The exon's symmetry is displayed in parentheses at the end of the exon's title.
  9. Asymmetric exons do not have a length that is a multiple of 3bp.
  10. Symmetric exons have a length that is a multiple of 3bp.
  11. The exon's coding sequence is displayed in UPPERCASE letters
  12. Exon sequences are flanked by 23bp of the adjacent introns. These sequences are displayed in ...lowercase... letters.
  13. Exon Splicing Enhancer (ESE) sequences are displayed with a dotted underline that will turn wavy when hovered over.
  14. The transcript's Start Codon sequences are displayed with in green: ATG.

sgRNA Panel
Hover over descriptions to highlight information in the image.
  1. Candidate guide RNA (sgRNA) sequences that match the sense strand are displayed in red and show a solid underline when hovered over.
  2. Candidate guide RNA (sgRNA) sequences that match the antisense strand are displayed in blue and show a solid underline when hovered over.
  3. The best rated guide RNA (sgRNA) sequences for the current transcript are displayed with a dark shade.
  4. Candidate guide RNA (sgRNA) sequences that have been saved to favorites are displayed with a yellow shade.