Characterization of the 5′ and 3′ ends of the Fugu Surf-3/rpL7a gene. (A) Alignment of the Fugu and mouse Surf-3/rpL7a promoter regions. The Fugu and mouse Surf-3/rpL7a gene promoter region sequences were aligned using the GAP program of the GCG software package. Identical nucleotides are indicated by a vertical line. Gaps in the sequence have been inserted to improve the alignment. The codon for the initiator methionine (Met) is boxed and shaded. A polypyrimidine tract in which the mouse gene initiates transcription (Huxley and Fried 1990a) and theFugu gene is suspected to (see text) is boxed as is an upstream element denoted Box B that is known to be conserved in the promoters of the characterized mammalian and avianSurf-3/rpL7a genes. An alignment of the human, mouse, chicken, and Fugu Box B elements generated using the Pileup program of the GCG software package and shown below shows the conservation of this element in more detail with identical bases being boxed and shaded. The position of the Box A element that is conserved between the promoters of the mammalian and avian Surf-3/rpL7a genes is indicated on the mouse sequence by a broken line box. (B) Sequence of the region between the Fugu Surf-3/rpL7a and Surf-1 gene homologs. The sequence is double-stranded, reading 5′ to 3′ on the top strand in the direction of transcription of the Fugu Surf-3/rpL7a gene. The coding sequence contained in the last exon of each gene is boxed. Arrows indicate the direction of transcription of the two genes. Conceptual translation of the coding sequences is shown above the DNA for the Surf-3/rpL7a gene and below the DNA for the Surf-1 gene. Shaded boxes indicate a consensus polyadenylation signal on the top strand used by the Fugu Surf-3/rpL7a gene and two overlapping near consensus polyadenylation sites (5 out of 6 bp) on the bottom strand within the coding region of the Fugu Surf-1 gene, one of which is used by this gene. Bold dots above (Surf-3/rpL7a) and below (Surf-1) the sequence mark known positions of poly(A) tails in cDNA clones isolated to date. The Fugu Surf-3/rpL7a/Surf-1intergenic distance is therefore a minimum of 184 bp compared with 70 bp in mouse.
