Genomic sequence and organization of the family of CNR/Pcdhα genes in rat☆
Section snippets
BAC clones
Rat (Long Evans) BAC clones were isolated using two specific probes made by Incyte Genomics. Three clones, 229/F1, 186/M24, and 208/B15, were isolated with a 700-bp SpeI/PvuII mouse constant region probe. Three other clones, 227/J23, 118/K06, and 237/N17, were isolated with a 800-bp BglII/NotI plasmid B1 probe, which was composed of the mouse CNR1 EC1 region inserted into pBluescript II. We assembled the BAC clones using the terminal sequences as PCR primers.
Sequencing and assembly
Three BAC clones covering the 240-kb
Genomic organization of the rat CNR gene clusters on the 18c chromosomal region
Three overlapping BAC clones, 227/J23, 237/N17, and 229/F1, containing sequences that were homologous to the mouse CNR genes (from v1 to c3) were selected for DNA sequencing (Fig. 1). Analysis of the rat genomic DNA sequences revealed 15 CNR genes that were very similar to the mouse CNR genes. The 13 variable exons of the rat CNRs were organized in a tandem array, as with the mouse and human gene clusters. The constant region was divided into 3 small exons that were located downstream of the
Discussion
Here we report the complete DNA sequence, genomic organization, and expression profiles of the rat CNR genes. A detailed comparative sequence analysis of mouse and human CNR/Pcdhα has already been reported [17], [20]. Although many studies have compared genomic sequences in human and mouse, relatively few have compared rat and mouse or rat and human genomic sequences, especially for cluster genes spanning over 200 kb.
We found that the rat CNR genes have an organization similar to those of the
Acknowledgements
We thank members of the Yagi labs (Graduate School of Frontier Biosciences, Osaka University, and NIPS, Japan) for useful comments and help. This work was supported in part by a grant from CREST, Japan Science and Technology Corp., the Ministry of Education and Science of Japan, and the Uehara Memorial Foundation.
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