Sequence analysis

Genomic sequence data for the following species were downloaded from the National Center for Biotechnology Information FTP site (ftp://ftp.ncbi.nlm.nih.gov/genomes): Homo sapiens (human), Mus musculus (house mouse), Dasypus novemcinctus (nine-banded armadillo), Sarcophilus harrisii (Tasmanian devil), Gallus gallus (chicken), Chrysemys picta (western painted turtle), Xenopus tropicalis (tropical clawed frog), Danio rerio (zebrafish), and Callorhinchus milii (elephant shark). The region containing Rag1 and its upstream sequence up to the start of Traf6 (i.e., Rag1 upstream region) and the 100-kb region containing Rag2 and its upstream sequence (i.e., Rag2 upstream region) were extracted from each of the genomic sequences. The dot matrix for the Rag1 and Rag2 upstream regions were generated by an in-house script using BLASTN (62). MEME Suite (63) was used to identify the conserved motifs in the Rag1 and Rag2 upstream regions and to generate sequence logos.