Selected Regions of Aligned Transcripts, Proteins, and Gene Annotations from EBV. EBV genes are displayed in three parts according to strand as indicated in the Legend. 1) Annotations of viral transcripts or ORFs: light blue = type I EBV-latency; purple = type II EBV-latency; dark blue = type III EBV-latency; red = lytic-only; and yellow = unannotated/novel transcript/ORF. Transcriptional splicing is joined by dashed lines and split with star marks. Tick marks correspond to one kilobase-pair. 2) Viral transcriptome data: green = MutuIII; purple = BC-1 latent; orange = BC-1 lytic; and red = JSC-1. Normalized transcriptional data (Log10 scale) is based on the ratio of Cy3 and Cy5 fluorescent signals (experimental and reference samples, respectively). Tick marks correspond to tens of kilobase-pairs. 3) Viral proteome data: purple = BC-1 latent, and orange = BC-1 lytic. The width of each raised line corresponds to ORF length. The height of each raised line (Log2 scale) is indicated as the sum total of all peptide spectra (or counts) per ORF. Panels A-E are arranged by increasing nucleotide position of EBV (NC_007605), spanning from: A) 0-10.5 kbp; B) 32.7-44.8 kbp; C) 52.7-56.3 kbp; D) 79.3-97.7 kbp; and E) 152.6-170.1 kbp. * Two unique peptides are detected corresponding to the ORF antisense-BPLF1, or BURF1 (panel C). F) The protein sequence of the full ORF from antisense-BPLF1 (BURF1) is displayed from one stop codon to the next (hyphens). Putative start methionines are in bold, italicized, and underlined. The peptide sequences detected by LC-MS/MS analysis are highlighted in yellow and blue, and their overlap is highlighted in green. ORF = open reading frame; FW = forward direction; RC = reverse complement direction; oriP = latent origin of replication; Kbp = kilobase-pairs; Alt. = alternatively; α¢ = antisense; (ARF) = alternative reading frame.