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Figure 8 | BMC Genomics

Figure 8

From: Comparative analysis of neural transcriptomes and functional implication of unannotated intronic expression

Figure 8

Detection of unannotated transcriptionally active regions (TARs). A. Percentage of TAR data of each dataset. Column in red color represents intronic TAR, and column in blue color represents intergenic TAR. X-axis represents different datasets, while Y-axis represents the percentage. B to E: An intronic TAR found located inside mouse PCBP2. B: RNA-seq reads mapped by TopHat to this location. Each black bar represents a RNA-seq read. Because the coverage on the 3' end (right side) of the gene is too high, only part of the reads mapped at this region is shown. Each blue horizontal line connecting two bars indicates a splice-junction-spanning read (read split by splicing activity). Red lines highlighted such reads spanning the intronic TAR and the exon on its left. C: conservation score from 30-Way multi-species genome alignment. Notice the region with high conservation score co-localized with the intronic TAR. D: current PCBP2 gene model, with green box representing known exons. E: amino acid alignment of the ORF of intronic TAR and its human and dog homologues. Gray column plot below: each column represents the similarity of the amino acids in that column. F: RT-PCR validation for intronic TARs. For each intronic TAR inferred from RNA-seq mapping result, primers were picked to validate the connection between the intronic TAR and the flanking exon (upstream/downstream), between the flanking exons, as well as the expression of the intronic TAR.

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