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Table 4 Summary of Novel and Unannotated Viral Genes

From: Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes

  Direct. Proposed Gene Name Temporary Name 5'-ends¥/ORF Start 3'-end/Stop Codon Length Figure & Ref.
KSHV        
Transcript FW K1.5 α¢-vIL6/ORF2 17150 18200 1.0 Kbp 1A/F †‡
   K3.5 α¢-K4s 22125 22964 0.8 Kbp 1A
   K4.5 T6.1 23596 29741 6.1 Kbp 1A §
   K4.7 T1.5 24080 25585 1.5 Kbp 1A §
   K11.5 α¢-ORF58/59 94589 96779 2.2 Kbp 1D
   K12.5 ALT 120570 130546 10.0 Kbp 1E
  RC K1.3 ALE 16969 21 17.0 Kbp 1A
   K7.3 α¢-K7/PAN 29875 28615 1.3 Kbp 1A
   K7.7 α¢-ORF50 74627 71616 3.0 Kbp 1C *
Protein FW K1.5 α¢-vIL6/ORF2 17402 17599 43 or 54 AA 1A/F †‡
   K7.5 ARF-ORF30 50806 50856 16 AA 1B §
  RC K14.5 ARF-ORF75 132195 132452 85 AA 1E
EBV        
Transcript RC BELF3B α¢-EBNA3B 85090 82960 2.1 Kbp 2D
   BELF3C α¢-EBNA3C 88511 87130 1.4 Kbp 2D
Protein FW BURF1 α¢-BPLF1 54414 55160 220 or 236 AA 2C/F
   BKRF1.5 ARF-EBNA1 95708 96889 370 AA 2D £
  RC BALF3.5 ARF-BALF3 159401 159909 169 AA 2E
   BALF0 (same) 164978 165055 25 AA 2E
  1. KSHV and EBV nucleotide positions are based on the sequences NC_009333 and NC_007605, respectively.
  2. Proposed gene names for KSHV and EBV follow viral nomenclature conventions described by Russo et al, 1996 [13], and Baer et al, 1984 [12], respectively. These gene names are indicated in bold.
  3. Temporary gene names are indicated through the text, including previously-published gene names.
  4. Unannotated/novel viral genes are cross-referenced to figures 1 and 2, indicated in bold.
  5. ¥5'-ends are less well detected by tiling array, and are therefore approximate values.
  6. §Taylor et al, 2005 [26]; £Ossevoort et al, 2009 [22]; Chandriani and Ganem, 2010 [27]; Chandriani et al, 2010 [28]; *Xu and Ganem, 2010 [18].
  7. Direct. = direction; Ref. = reference; α¢ = antisense; ARF = alternative reading frame; ORF = open reading frame; AA = length in amino acids; FW = forward strand; RC = reverse complement strand.