Figure 2.

Hundreds of putative PASs show a high CDI. Panel A. PhyloP scores for the genomic region spanning the end of an EST cluster that originated a PTE (black arrowhead). The intervals used to calculate the PTE CDI are indicated below. T, transcribed interval encoding for the mature transcript; NT, interval not encoding for the mature transcript. Panel B. A PTE in a wider genomic context. The position of the PTE is indicated with a black arrowhead. The last two exons (and the last intron) of the most proximal RefSeq and Ensembl transcripts are shown above. Their direction of transcription is indicated by the black arrow. The positions of the annotated PASs are indicated with open arrowheads. The PTE was classified as a putative PAS for both RefSeq and Ensembl databases because the proximal reference transcripts are transcribed towards the PTE. Below a TransMap transcript that ends in the same position as the PTE is shown (Trans). In this case, the Trans transcript is supporting the PTE. On the bottom, the genomic region covered by total RNA deep sequencing reads (RNA seq). Panel C. Absolute frequency of PTEs, either putative PASs or putative TSS, according to their CDI. The PTEs were obtained using the RefSeq database as reference. Panel D. As in Panel C but using the Ensembl database as reference. PTEs with CDI in between −0.5 and +0.5 were omitted from the graphs shown in Panels C and D.

Morgan et al. BMC Genomics 2012 13:708   doi:10.1186/1471-2164-13-708
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