A new subfamily of recently retroposed human Alu repeats.

The Alu family of repetitive elements from primates contains at least six major subfamilies (1 -5 ) of which the youngest is AluSb (3, 5) — also reported as 'Conserved' (1), 'Class IV' (2) or 'A' subfamily (4). Furthermore, a subset of the human Alu-Sb, called 'HS' or 'PV subfamily (6-9) was determined to be even younger. In this paper a second subset of the Sb subfamily, called 'Alu Sb2' is reported. The subset consists of three human Alu sequences aligned in Figure 1 against Alu Sb and HS/PV (Sbl) consensus sequences. The first sequence comes from lecithin—cholesterol transferase gene (10),the second from a cosmid clone HDAB (1S149), (ref. 11), and the third one interrupts the cholinesterase gene in a patient with acholinesterasemia (12). The three Alu-Sb2 repeats are simultaneously different from the Sb consensus sequence in eight positions which define diagnostic features of the Sb2 subfamily. The major feature is the 8 bp insertion at position 252. The sequences are 98% identical to each other, 96% to the Sb consensus and only 94% to the HS/PV(Sbl) consensus. As can be seen in Figure 1, no diagnostic positions are identical between Sbl and Sb2 sequences which indicates that they shared no common history after they diverged from the Sb subfamily. The first sequence (HUMLCATG) contains 24, second 22 and third 23 CpG doublets. This indicates that the first two Sb2 repeats might have been inserted as recently as the third one involved in acholinesterasemia. The three Sb2 sequences are flanked by direct repeats (not shown).