The mRNA species for S-HDAg contains little more than the open reading frame. It is 5'-capped and 3'-polyadenylated, just as for a typical host mRNA. Recent studies indicate that S-HDAg mRNA can be bound with an antibody that can recognize 5'-cap structures (Nie et al. 2004). It is also bound by the poly(A) binding protein, PABP, a host protein that binds to the poly(A) sequences of host mRNAs (X. Nie, J. Chang, C. Tarn, C.-M. Chiang, J. Keene, L. Penalva and J. Taylor, unpublished results).

For the mRNA there is evidence that the 5'-end has a preferred location at nucleotide 1630 (Gudima et al. 1999). At least for the majority of this mRNA the 5'-end has been modified to have a cap structure (Gudima et al. 2000; Nie et al. 2004). Therefore it is plausible but not directly proven, that this 5'-end corresponds to a preferred site for the initiation of RNA-directed transcription from a genomic RNA templates (Sect. 3.3).

At the 3'-end of the mRNA is a poly(A) tail of about 150 adenosines, typical of cellular mRNA species. Consistent with this, the nascent RNA that is processed to become this mRNA, has a poly(A) signal, AAUAAA, and other features expected for an RNA transcript that undergoes polyadenylation. Mutation of this signal inhibits polyadenylation (Nie et al. 2004).

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