Table 4.

Splice junction sites of the VZV transcriptome

Intron Start	Intron End	Strand	Intron Length	Donor Site	Acceptor Site	Accepted as novel	Intron depth	Transcript name	References
585	714	+	129	GT	AG		45,62%	ORF0–1-C-SP	[25]
5004	4155	–	849	GT	AG	✓	2,90%	ORF5–4-SP
16,712	16,886	+	174	GT	AG	✓	5,04%	ORF12–13-SP
43,826	43,505	–	321	GT	AG	✓	4,11%	ORF24-SP
43,950	43,863	–	87	GT	AG	✓	1,40%	ORF24-SP-2
61,790	63,564	+	1774	GT	AG	✓	2,40%	–
77,870	78,148	+	278	GT	AG	✓	11,29%	ORF42–43-AS
78,938	78,039	–	899	GT	AG	✓	38,88%	ORF42/ORF45-SP-2
81,537	78,039	–	3498	GT	AG		100,00%	ORF42/45-SP-1	[6]
81,537	79,053	–	2484	GT	AG	✓	12,72%	ORF42/ORF45-SP-2
87,759	86,782	–	977	GT	AG		4,15%	ORF50B	[24]
87,759	86,982	–	777	GT	AG		2,33%	ORF50A	[24]
87,436	86,782	–	654	GT	AG		0,62%	ORF50C	[24]
86,982	87,436	–	454	GT	AG		0,33%	ORF50D
101,728	102,420	+	692	GT	AG		87,50%	VLTly	[9]
102,484	102,853	+	369	GT	AG		100,00%	VLTly	[9]
102,983	103,827	+	844	GT	AG		2,42%	VLTly	[9]
103,924	104,293	+	369	GT	AG		3,99%	VLTly	[9]
104,433	104,768	+	335	GT	AG		5,22%	VLTly	[9]
104,824	110,509	+	5685	GT	AG	✓	2,18%	ORF63-SP2-C
108,830	110,509	+	1679	GC	AG	✓	11,12%	NTO1v1 (ORF63-SP-1)
114,920	115,050	+	130	GT	AG	✓	1,04%	ORF67-SP
121,067	119,388	–	1679	GC	AG	✓	10,65%	NTO1v1 (ORF63-SP-1)

The splice junctions listed in this table passed our criteria of intron detection, with the exception of ORF50C, which is listed as a confirmation, and ORF50D, which is a novel combination of previously known splice sites. Other rare splice variants below the 1% spliced read limit are listed in Additional file 2: Table S6. The TSS and TES belonging to the transcript with splice sites in row 7 could not be determined with certainty