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Fig. 5 | BMC Genomics

Fig. 5

From: Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq

Fig. 5

Novel and updated features within P. falciparum genes. a Splice sites detected in the 3D7 time course using DAFT-seq data. A total of 8206 splice sites were supported by at least 5 reads; of these, 7386 were in online databases. There are 1377 splice sites not described in online databases (17% of the total), including 659 in UTRs. b Length of introns found in this study, using the DAFT-seq data for the 3D7 time course. c Schematic diagram of “exitrons” (protein-coding introns) modified from Marquez et al. [54]. An exitron may be retained in an mRNA, generating a fully coding mRNA sequence (left). If the excised sequence is a multiple of 3 nt the open reading frame is maintained and a full-length protein may be produced (top right). If the excised sequence is not a multiple of 3 nt this may generate a change to the C-terminus (middle left) or cause the transcript to be degraded through the nonsense-mediated decay pathway (bottom right). d Exitrons are present in the 3D7 transcriptome. There are examples of mRNAs where a multiple of 3 nt are excised, such as Pf3D7_0420300 (which encodes an ApiAP2 protein). Here ~ 90% of the reads support the “exitron-out” form, with ~ 10% of the reads supporting the “exitron-in” form. e Exitrons are present in the 3D7 transcriptome. There are examples of mRNAs where even numbers of nt are excised, such as Pf3D7_1417200 (which includes a putative NOT family protein). For this gene ~ 80% of the reads support the exitron-out form, with ~ 20% of the reads supporting the “exitron-in” form

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