Table 1. Complex transcripts.
| A | Full-length complex transcripts |
| UL51-50-49.5–49 | |
| UL50-49.5–49 | |
| B | Putative complex transcripts with detected PA |
| ORF-1-UL54-53-52-51 | |
| Ul27-46-47-48-49-49.5–50 | |
| UL30-31-32-33-34-35 | |
| UL36.5-35-34-33-32-31 | |
| UL41-40-39-38-37 | |
| UL35-36.5-36-37-38 | |
| UL40-41-42 | |
| UL26.5-44-43-42-41 | |
| UL44-26.5-26-25-24-23 | |
| UL15-16-17-18-19-20-21 | |
| UL17-16-15-14-13-12-11 | |
| UL11-10-9-8 | |
| UL7-8-9-10 | |
| EP0-LLT-UL1-2-3-3.5 | |
| IE180-LLT-EP0 | |
| C | Putative complex transcripts with non-detected PA |
| UL18-15E2-17-16 | |
| UL31-30-29 | |
| AZURE-US1-PTO-NOIR2 | |
| US2-US1-PTO-NOIR2 | |
| NOIR1-NOIR2-PTO-US1 | |
| D | Putative complex transcripts with no PacBio detection |
| UL3.5-4-5-6 | |
| UL10-11-12-13-14-15E2-16-17-15E1 | |
| UL22-CTO-UL21-20 | |
| UL21-CTO-UL22-23-24-25-26 | |
| UL46-27-28-29-30 |
The complex transcripts harbor genes with at least two different orientations. The presence of antisense sequences allows the detection of these transcripts by RT2-PCR and DNA sequencing, using strand-specific primers for the reverse transcription. We gave ad hoc names to these transcripts because their missing sequences were only predicted. We also analyzed those parts of the genome for antisense RNA expression which were undetected as parts of complex transcripts. The complex transcripts are categorized in terms of their identified region as follows: full-length complex transcripts (a); putative complex transcripts with identified PA sequences (b); putative complex transcripts with non-identified PA sequences (c); putative complex transcripts not detected with PacBio sequencing at all (d). The ratios of antisense to mRNAs obtained with RT2-PCR and Illumina sequencing were calculated. MOI stands for ‘multiplicity of infection’ of PRV used for the infection experiment (high MOI: 10 pfu; low MOI: 0.1 pfu; pfu: plaque-forming units). The antisense parts of the complex transcripts are underlined in Table 1a–d.