Figure 2.

The TIRs in the Transib transposon family are structurally similar to the RSSs in the Ig family. (A) RSS variation in human Ig loci. The conserved nucleotides in the RSSs in the heptamer (underlined in red) and the nonamer sequences (underlined in blue) are necessary for efficient and precise V(D)J recombination. The key feature of the heptamer is the conserved CAC consensus sequence, and the most common heptamer sequence in Ig loci is CACAAAG. The key feature of the nonamer is the core A-rich region, and the most common sequence is ACAAAAAG. Sequences were obtained from the IMGT database (http://www.imgt.org). (B) Transib TIRs compared to RSSs. Alignment 1. The heptamer and nonamer-like sequences are shown for the Transib transposon TIRs with symmetric 20-22 bp spacers (indicated as Ns). Alignment 2. The 5ʹ and 3ʹ TIR sequences of Transib family members with 12/23 asymmetries include Transib 5 from Drosophila melanogaster and Transibs 2, N1, N2 and N3 from the malaria mosquito, Anopheles gambiae. Alignment 3. The most common human RSS sequences are shown that surround Ig family gene segments. TIR sequences in (B) were obtained from (8). (C) RAGL TIRs in invertebrates. Asymmetric TIRs are associated with the RAGL sequences from the eastern oyster, Crassostrea virginica. Symmetric TIRs surround RAGL sequences from the pearl oyster, Pinctada imbricata, and the robber fly, Neomochtherus geniculatus. Asymmetric 27/31 TIRs are present in the protoRAGL from amphioxus, Branchiostoma belcheri. All sequences include a 5ʹ RSS-L heptamer sequence and a partially conserved A-rich transposon region 2 (TR2) located towards the 3ʹ half of the heptamer. No RSS-L distinctive nonamers have been identified in B belcheri. TIR sequences in (C) were obtained from (9).