Ancient viral remnants in the humangenome are active in normal tissues plos PLOSBiology
genes without a fully intact Gag polyprotein. Two proviruses, 7p22.1a and 12q14.1, express an intact env ORF, yet 7p22.1a is the only one with a fusogenic]. This provirus is expressed in 12 different tissues from numerous different organ systems. Despite there being only 2 intact Env ORFs expressed in the GTEx cohort, 6 different proviruses with an intact Rec ORF are expressed.
When analyzing the RNA-seq data from GTEx, it was important to use bioinformatics software that correctly aligns and counts the reads coming from HML-2 proviruses. Correct read assignment has long been an issue in the field due to the sequence similarity among many of the proviruses, especially the younger insertions. This similarity can create many multimapping reads that are difficult to assign to an individual provirus [].
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