TE insertions terminate transcription in a cell type-specific manner. Clusters of linked paired-end ditag (PET) sequences that indicate the locations of the 5 (green) and 3 (red) ends of full-length transcripts expressed in different cell types are shown above gene models indicating the locations of exons, introns and TEs that terminate transcription. For each example, the cell type-specific fractions of TTS usage for TE-TTS and non-TE-TTS are shown. (a) An ERVL insertion within the first intron of the GALNT2 gene terminates the majority of transcripts in the GM12878 cell type, with a small number terminating in the two canonical TTS. No transcripts terminate within the ERVL in the NHEK cell type. (b) An AluJb insertion within the seventh intron of the EPHX2 gene terminates the majority of transcripts in the K562 cell type, while the majority of transcripts read through this sequence in the GM12878 cell type. (c) Termination of transcription within a FLAM_C insertion in the BSDC1 gene results in a shortened 3′UTR and altered C-terminal coding region. The FLAM_C-derived TTS is utilized extensively in the K562 cell type, while the majority of transcripts read through this sequence in the NHEK cell type.