Figure 4

Sequencing analysis of the truncated PCR product. A) Multiple sequence alignment of the full-length and the truncated PCR products from 70.15-transduced CEMx174 cells with the PCR product from plasmid template. The sequence of the full-length clones match the 654 bps predicted sequence from the plasmid template. The truncated product aligns with the predicted sequence except for a 139 bp deletion. The colored boxes indicate the transcription factor binding sequences: TATA box (red), the PSE (plum), and the sequences related to the octamer consensus (ATTTGCAT, blue), the protected SPH domain (light blue), while the grey boxes are non-functional octamer-related sequences [19, 20, 28]. The grey shading is the sequence of the HIV-1-specific RT aptamer 70.15 and the black box is the pol III termination signal. The bold sequences are the proposed splice donor and splice acceptor sequences. B) Schematic map of the predicted amplicon in forward orientation as described in Figure 1. The black arrows indicate the amplification primers. The boxes represent from left to right the 3' end of GFP, the Pol III termination sequence, a self-splicing ribozyme, the HIV-1-specific RT aptamer 70.15 (grey box), a self-splicing ribozyme, the human U6+1 promoter, and MMP 3' UTR sequences. The line represents linker sequences between the functional sequences. The spotted ovals represent the TATA box (red) and PSE (plum) in proximal promoter; the non-function octamer sequences (grey), the Staf-binding domain (light blue) and the two octamer-related sequences (blue) in the distal promoter all within the U6 promoter. A curved arrow represents the position and direction of the transcriptional start site. The black X represents the splicing deletion.