FIG 3.

The sgg1 locus encodes a novel spliced transcript. (A) Annotation of the sgg1 locus showing the locations of the ORFs from the previous MCMV genome annotation, i.e., m132.1 and sgg1, as well as the extension of the m133 ORF due to a correction to the original sequence of MCMV strain Smith. The red vertical bar denotes the mutation present in G4209 that introduces a premature stop codon into novel sgg1.1, defined by the results of Northern blotting, RNA-Seq, and RACE analysis, as described below in this legend. (B) Northern blot analysis of the sgg1 locus. Total RNA isolated at 6 hpi or 48 hpi from MEFs infected with the indicated viruses was probed with a strand-specific Northern blot probe (designated by a black bar in panel A and described in Materials and Methods). (C) RNA-Seq profile showing read coverage and splice junctions within the sgg1 region at a late stage of MCMV infection. The raw number of spliced reads spanning each splice junction is shown in the arc connecting the corresponding donor and acceptor splice sites. Total read coverage (Cov.) is shown on the y axis. (D) Sequences of the 5′ RACE and 3′ RACE PCR products were aligned to the G4 genome; the 5′ RACE sequences are shown in light blue, 3′ RACE sequences are in tan, and disagreements over the G4 genomic sequence are designated with a thin black rectangle within each RACE amplicon. The putative coding sequence in the newly identified sgg1.1 transcript is shown in light red, and the presumed poly(A) sequence is shown in yellow. An overview of the genomic region containing the sgg1.1 transcript, together with the genomic coordinates of the relevant features in the G4 genome, is shown at the bottom.