The use of bioinformatics to identify the genomic structure of the gene that encodes neutrophil antigen NB1, CD177

Abstract

The gene encoding neutrophil alloantigen NB1, CD177, is highly homologous to a gene overexpressed in polycythemia vera neutrophils, polycythemia rubra vera-1 (PRV-1). The cDNAs of both genes have been cloned, but their genomic structure is unknown. The purpose of this study was to determine the intron-exon organization of NB1 and PRV-1 and discern if they are separate members of a homologous gene family or alleles of the same gene. GenBank's human genome sequences were probed in silico with PRV-1's 1605-nucleotide coding sequence. Searches identified two adjacent bacterial artificial chromosomes (BACs) on chromosome 19q13.2: BC338531 and BC52850. BC338531 contained sequences 100% homologous to the first 654 nucleotides of PRV-1. Comparison of coding and genomic sequences allowed us to separate this region into exons 1 through 5, interrupted by five introns. BC52850 contained sequences 95% homologous to nucleotides 413 through 1605 of PRV-1, organized into exons 4 through 9. However, the orientation of PRV-1-homologous in the first BAC was plus-plus and of the second was plus-minus, indicating they could not be portions of the same gene. The GenBank sequence of BC338531 was incomplete, creating a sequence gap in chromosome 19q13.2. Evaluation of BC338531's unfinished sequences in Joint Genome Institute public databases allowed us to complete the gap and revealed that BC338531 contained sequences 98% homologous to all nine PRV-1 exons followed by a second gene consisting of exons 9 through 4. Most likely, NB1 and PRV-1 are alleles of the same gene, CD177, and the duplication of exons 4 through 9 is a pseudo gene.