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

Table 4 Summary of Novel and Unannotated 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

KSHV and EBV nucleotide positions are based on the sequences NC_009333 and NC_007605, respectively.
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.
Temporary gene names are indicated through the text, including previously-published gene names.
Unannotated/novel viral genes are cross-referenced to figures 1 and 2, indicated in bold.
^¥5'-ends are less well detected by tiling array, and are therefore approximate values.
^§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].
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.

ISSN: 1471-2164