Immediate-early (IE) mRNAs-4 and -5 of herpes simplex virus type 2 (HSV-2) are transcribed from the IR/TR genome regions towards the U region. Each of these spliced mRNAs has an untranslated leader sequence of 249 bases and a single intron of approximately 540 bases which are contained entirely within TR/IR sequences. The DNA sequence of the intron largely comprises tandem reiterations of three distinct short sequences. Upstream of the common 5′ mRNA termini the DNA sequence contains regions of homology with the equivalent region of HSV-1. Comparison of the polypeptides encoded by these HSV-2 mRNAs with those of HSV-1 shows blocks of conserved amino acids. The locations of the first initiator ATG triplets of these two HSV-2 mRNAs suggest that the IR/TR regions of HSV expand, by gene conversion or by equal though non-homologous crossover, to an extent determined by the functions of the DNA sequences which are duplicated or deleted as a result of the crossover. This mechanism for expansion of repeats may apply to other herpesviruses which have a genome structure similar to that of HSV.


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