Studying transcriptomes by ultra deep sequencing provides an in-depth picture of transcriptional regulation and it facilitates the detection of rare transcriptional events. Using ultra deep sequencing of amplicons we identified known isoforms and also various new low frequency variants. Most of these variants likely involve the splicing machinery except for two events that we named variations affecting multiple exons, which are mainly deletions affecting parts of adjacent exons and intra-exonic deletions. Both events involve short identical sequences of 1 to 8 nucleotides at the junction and canonical splice sites are missing. They were identified in different genes and species at very low frequencies. We excluded that they are an artifact of PCR, sequencing, or reverse transcription. We propose that these variants represent intramolecular slippage events that require short identical sequences for reannealing of dissociated transcripts.