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Fig. 5 | Retrovirology

Fig. 5

From: Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats

Fig. 5

Characteristics of ERV-9/LTR12C sequences associated with induction upon infection of primary T cells with HIV89.6. a An alignment of the 3′ end of the U3 region of repeats annotated as ERV-9/LTR12C. Each row is a section of the long terminal repeat sequence and each column a base in that sequence colored by nucleotide identity. For clarity, positions appearing in less than 2 % of sequences are omitted. Two distinct classes are visible with a short form and long forms containing varying numbers of repeated sequence. Mutations away from the consensus can also be seen. b The proportion of LTR12C regions with significant increases in read abundance after infection with HIV and their 95 % confidence intervals separated by the length class of the LTR, presence in a gene, presence of a TATA box and the number of GATA2 motifs in the U3 region. These variables were selected by stepwise regression regression comparing differential expression of LTR12C to the length class of the LTR, the number of mutations away from consensus, the number of NFY, GATA2 and MZF1 motifs and the presence of a TATA box motif within 50 bp of the transcription start site. Variables are labeled with the estimated change in log odds ratio (\(\beta\)) and their Wald test p values

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