Selected Regions of Aligned Transcripts, Proteins, and Gene Annotations from KSHV. KSHV genes are displayed in three parts according to strand as indicated in the Legend. 1) Annotations of viral transcripts or ORFs: purple = KSHV class I (constitutive) or KSHV class II (latent and lytic); red = KSHV class III (lytic-only); and yellow = unannotated/novel transcript/ORF. Transcriptional splicing is joined by dashed lines. Tick marks correspond to one kilobase-pair. 2) Viral transcriptome data: purple = BC-1 latent; orange = BC-1 lytic; and blue = BCBL-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, orange = BC-1 lytic, blue = BCBL-1 latent, and dark blue = BCBL-1 lytic. The width of each raised line corresponds to ORF length. The height of each raised line (Log2 scale) is the sum total of all peptide spectra (or counts) per ORF. Panels A-E are arranged by increasing nucleotide position of KSHV (NC_009333), spanning from: A) 0-30.1 kbp; B) 49.9-51.2 kbp; C) 71.4-74.6 kbp; D) 83.9-96.7 kbp; and E) 116.7-134.7 kbp. * One unique peptide is detected corresponding to the short ORF antisense-vIL6/ORF2, or K1.5 (panel A). F) The protein sequence of the full ORF from antisense-vIL6/ORF2 (K1.5) is displayed from one stop codon to the next (hyphens). Putative start methionines are in bold, italicized, and underlined. The peptide detected by LC-MS/MS analysis is highlighted in yellow. ORF = open reading frame; FW = forward direction; RC = reverse complement direction; Kbp = kilobase-pairs; Alt. = alternatively; α¢ = antisense; (ARF) = alternative reading frame.