During the late stage of adenovirus 2 infection, RNA chains are initiated at a 
site near coordinate 16 (Evans et al., 1977) and transcribed approximately 
30,000 nucleotides to the far end of the genome at coordinate 100. Late mRNAs 
processed from these transcripts contain a common spliced tripartite leader 
(Berget, Moore and Sharp, 1977; Chow et al., 1977a) encoded at approximately 16, 
20 and 27, and protein coding sequences which map downstream. This report maps 
the late promoter and the capped 5' end of nuclear and cytoplasmic RNAs from 
this transciption unit, and analyzes their structures. We show that nascent RNA 
chains pulse-labeled in vivo are initiated at coordinate 16.5 +/- 0.5 and 
contain the sequences intervening between the leader segments. We map the capped 
5' terminus of late nuclear transcripts at a site between 16.4 and 16.6 by 
aligning T1 RNAase oligonucleotides from nuclear RNA with the DNA sequence of 
the promoter region. The structure of the first eleven residues of the capped 5' 
terminus of late mRNA was determined by direct RNA sequencing. This structure 
corresponds exactly to a DNA sequence at coordinate 16.4 and precisely positions 
the mRNA cap template within the promoter region. These results suggest that the 
promoter and the cap template sites are coincident, and that the initiating 
residues of the primary transcript are precursors of the capped 5' end of mRNA. 
Residues removed from transcripts by splicing were identified. These plus caps 
were detected in large polyadenylated nuclear RNA, indicating that capping and 
polyadenylation can occur on unspliced molecules. Residues retained in the mRNA 
first leader contain a nine residue sequence adjacent to the cap which is 
complementary to the 3' end of 18S rRNA, suggesting that the first leader 
functions in ribosome binding. Nucleotide sequences from the promoter region are 
compared with cellular counterparts. Strong homologies at cap sites and splice 
points suggest that for the noted cases, the virus and cell share closely 
related mechanisms for mRNA 5' end synthesis and splicing.