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Background  The genome of herpes simplex virus 1 encodes at least 84 transcripts from which proteins are translated and several additional RNAs whose status as mRNAs is unknown. These RNAs include latency-associated transcript, Ori S 1 and Ori S 2 RNAs and in case of α4 null mutant additional transcript that spans the junction between L and S component of the HSV-1 genome. Current data do not suggest that a peptide is translated from these RNAs.    Results  We describe here a novel RNA designated U S 5-1 that spans 4.5 kb of the unique-short (U S ) region. The RNA initiates in U S 5 and terminates in the α22 open reading frame. It is expressed antisense to U S 5, U S 4, U S 3 and ICP22 mRNAs. This transcript is expressed with γ 2  kinetics and has a half-life of 80 minutes.    Conclusion  These results identify a novel transcript encoded within HSV-1 genome. Since no major hypothetical open-reading frames are present in this transcript it is feasible that this RNA exerts its function as a non-coding RNA.

The novel HSV-1 US5-1 RNA is transcribed off a domain encoding US 5, US 4, US 3, US 2 and α22