TAG-IN Design

Example Input

Users may input Ensembl Transcript IDs or Custom sequences of choice

  • Ensembl Transcript ID for GRCh38 or GRCm38 Ensembl builds - for example ENST00000229307
  • Batch processing of Ensembl Transcript IDs - for example: ENST00000229307, ENST00000330949
  • Custom sequence with strand orientation and stop codon position - for example AGCTAGAGCTAGCGACTAG...

For optimal use please utilise well annotated transcripts only.

Example Output

TAG-IN results are displayed in the following manner:

Transcript information and Dowloads

Transcript info:

Basic transcript info supplied for each query:

  • Transcript start/stop, CDS orientation, stop position, and chromosome as per Ensembl database


Output for each job submission is in the form of two CSV files.

  • Download: sgRNA and ssDNA list - sgRNA and ssDNA details for a given transcript submission including scoring and metrics.
  • Download: Verbose Off-target Details- verbose details for all off-targets found.

Interactive sgRNA layout


Each sgRNA around the stop codon is drawn and colour coded based on summation of efficiency, specificity and distance from stop.

  • Query transcript is detailed in blue with the CDS and 3UTR separated by the stop codon.
  • SgRNA are positioned along the transcript with either + or - direction.
  • Only the top 20 sgRNA are displayed.


  • On mouse over the summation score and position of each sgRNA is given.
  • On click the following sgRNA/Offtarget/ssDNA tables are filtered.

sgRNA/Off-target/ssDNA data tables

  • Where an sgRNA acts within the intron/exon it will be prefixed with a *.
  • Data tables are displayed for each group of sequences: sgRNA/Off targets/ssDNA
  • Upon select of a chosen sgRNA the subsequent off target and ssDNA table will filter accordingly
  • Filters can be cleared using the clear button.

Please contact us with any queries or concerns:

Pollard Lab - Email: s1578687@sms.ed.ac.uk.