Alignments of sequences outside the PrP coding regions conserved between the human, mouse, and sheep. The most conserved regions are blocked. (A) Two conserved sections of intron 1 that may be involved in transcriptional regulation. Both sites are within an old LINE1 element (Fig. 2). This L1 element is probably ancient, because a notoriously old element (MIR) has been inserted in it. Potential AP-1 and Oct-1 binding sites were identified with the program TFSEARCH (http://pdap1.trc.rwcp.or.jp/research/db/TFSEARCH.html). However, in the sheep gene they all diverge from the consensus binding sites. Using a cat assay in neuroblastoma cells, Baybutt and Manson (1997)identified transcriptional suppressor activity between bases 9744 and 9932 and promoter activity between bases 10,114 and 10,307 of the mouse sequence, suggesting that the second, highly conserved block (bases 10,200–10,233 in mouse) may be involved in transcriptional activation. (B) Alignment of the human, sheep, and mouse PrP gene exon 2 regions. Two sites that are conserved between mouse and sheep but have diverged in the human genome are highlighted in gray. Comparison of the scores given by GeneFinder (C. Wilson and P. Green, unpubl.) for the exon 2 splice sites shows that the donor site is quite distinct in sheep and mouse but has become indistinct in the human genome because of the presence of a C and A at positions 4 and 5. The donor site consensus and that of the other species (including cow, rat, and hamster; data not shown) contain a purine and G. (C) A 40-bp block ∼100 bp before the polyadenylation site in thePrP gene is highly conserved between four mammalian orders. (D) In the 3′ flanking region of the PrP gene are two small blocks of conserved sequences lying within a MER5a DNA transposon fossil. Selective conservation of these blocks is further suggested by their almost complete similarity to the MER5a consensus sequence; MER5 elements are ancient components of the mammalian genome, and sequences are, on average, 25% diverged from the consensus (Smit and Riggs 1996).