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How do I use the RealTime Design tool so that I detect either all splice common transcripts or splice specific transcripts?

To detect splice common transcripts

  1. Enter accession numbers of all related transcripts
  2. Click 'design assays'
  3. Within the target Locations page click on transcript and mature transcript view to determine exon/intron structure
  4. Determine which exons are common between all transcripts
  5. Select only those exons that are common to all transcripts
  6. Click 'design assay'

To detect splice specific transcripts:


  1. Enter accession numbers of all related transcripts
  2. Click 'design assays'
  3. Within the target locations page click on transcript and mature transcript view to determine exon/intron structure
  4. Determine which exons are common between all transcripts and determine which exons are unique to your transcript of interest
  5. Select only those exons that are unique to your gene of interest
  6. Click 'design assay'
  7. Blast the primer and probe sequences to ensure that only your specific transcript will be amplified

You can also use the Refseq look up tool to identify accession numbers of all related transcripts. Once you click on the REfSeq look up tab, enter the gene description or gene symbol, select the relevant species. Look through the view transcript view to compare exon/intron structures of transcripts that are related to your gene of interest.

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