Reverse transcriptase template switching and false alternative transcripts

Genomics. 2006 Jul;88(1):127-31. doi: 10.1016/j.ygeno.2005.12.013. Epub 2006 Feb 2.


Reverse transcriptase (RT) can switch from one template to another in a homology-dependent manner. In the study of eukaryotic transcripts, this propensity of RT can produce an artificially deleted cDNA, which can be wrongly interpreted as an alternative transcript. Here, we have investigated the presence of such template-switching artifacts in cDNA databases, by scanning a collection of human splice sites (Information for the Coordinates of Exons, ICE database). We have confirmed several cases at the experimental level. Artifacts represent a significant portion of apparently spliced sequences using noncanonical splice signals but are rare in the context of the whole database. However, care should be taken in the annotation of alternative transcripts, especially when the RT used is poorly thermostable and when the putative intron is flanked by direct repeats, which are the substrate for template switching.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing
  • Base Sequence
  • Forkhead Box Protein L2
  • Forkhead Transcription Factors / genetics
  • Gene Library
  • Humans
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • RNA-Directed DNA Polymerase / metabolism*
  • Reverse Transcriptase Polymerase Chain Reaction / methods*
  • Reverse Transcriptase Polymerase Chain Reaction / standards
  • Templates, Genetic


  • FOXL2 protein, human
  • Forkhead Box Protein L2
  • Forkhead Transcription Factors
  • RNA-Directed DNA Polymerase