Genes contain sequences called exons that will be transcribed to RNA and then translated to protein. These are separated by segments called introns that will not become RNA. The cell can include or exclude different exons, resulting in multiple versions of the gene in RNA form. These are called splice variants.
Studying gene expression by sequencing RNA provides valuable insights into normal biology as well as disease states. To do this, cell’s RNA is converted into DNA in a process called reverse transcription, which produces ‘complementary DNA’ or cDNA. The presence of cDNA for individual genes is assessed using PCR.
The PCR primers should be designed so that the genetic material to be amplified includes a splicing junction between two exons, which only become adjacent when the introns are removed. In this way we can insure that the DNA we are amplifying is cDNA rather than genomic DNA. Because we may not know which splice variants are most expressed in the cells of interest, we also want our primers to amplify cDNA from as many splice variants as possible.
The new online tool, called TraC (http://labs.pathology.jhu.edu/nauen/trac/), for transcript consensus, uploads mRNA data from public repositories of gene sequences and finds all sequences shared by two or more splice variants. It returns results including where each sequence falls relative to exon-exon boundaries in an intuitive, information-dense, interactive plot. This tool is potentially of value for anyone exploring gene expression by mRNA analysis. The manuscript is located at https://www.ncbi.nlm.nih.gov/pubmed/29763731