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Figure 1 | Retrovirology

Figure 1

From: Identification of endogenous retroviral reading frames in the human genome

Figure 1

A: Genomic organization of simple retroviruses when present as a provirus (DNA) integrated in the host genome. The regulatory long terminal repeats (LTRs) flank the internal three major genes gag, pol and env. A fourth gene pro is present between gag and pol for some retroviruses, while part of either gag or pol in others. B: Individual BLAST hits (white and yellow boxes) on either strand of the human genome were clustered into HERV regions (blue boxes) or discarded by using a score function. Finally, only HERV regions with at least one retroviral ORF were kept (see Materials and Methods). In the example illustrated HERV ID 5715 was presumably inserted into an existing HERV locus with the opposite orientation. HERV ID 5715 is located in the first intron of the CD48 gene (antisense direction) and is also known as HERV-K18 or IDDMK1,222. C: HERV ID 5715 with graphical vORF annotation. Putative LTR structures are indicated and all ORFs (stop-codon to stop-codon fragments above 62 aa) are mapped and annotated by homology criteria

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