A novel explanation for the existence of open reading frames on latency-associated transcripts of alphaherpesviruses

Recent studies indicate that alphaherpesviruses express latency associated transcripts (LATs) from the antisense strand of immediate early (IE) genes of the viral genome. It has been discussed that LATs containing extended open reading frames (ORFs) might be translated into protein products. We found that a salient feature of some herpesvirus DNAs is a high GC preference at the third codon positions. As a consequence, the probability of a stop codon arising at two of the six frames of the DNA strand is very low. The regions missing stop codons frequently start with ATG, resulting in extended ORFs. Therefore, the presence of a gene-long ORF does not necessarily mean that it is relevant to real translation.