cDNA cloning and genomic structure of a novel gene (C11orf9) localized to chromosome 11q12-->q13.1 which encodes a highly conserved, potential membrane-associated protein.

We have cloned and characterized a novel gene (C11orf9) mapping to chromosome 11q12-->q13.1. The transcript was initially identified as a partial cDNA sequence in the course of constructing a transcript map of the region between markers D11S1765 and uteroglobin known to encompass the gene causing Best disease. Using a combination of EST mapping, computational exon prediction, RT-PCR, and 5'-RACE its 5. 7-kb full-length cDNA sequence was subsequently obtained. The C11orf9 gene consists of 26 exons spanning 33.1 kb of genomic DNA and is located about 4.3 kb centromeric to FEN1. Biocomputational analysis predicts that its conceptual translation product of 1,111 amino acids contains two transmembrane helices as well as two proline-rich regions. Alignment reveals significant homology to hypothetical peptides from several other species including C. elegans and D. melanogaster, indicating a high degree of conservation throughout evolution. Northern Blot and RT-PCR analyses demonstrate widespread expression of a single transcript but varying degrees of abundance among the individual tissues tested. Mutation analysis of the entire coding sequence excluded C11orf9 as the Best disease gene.