The use of bioinformatics to identify the genomic structure of the gene that encodes neutrophil antigen NB1, CD177.
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.
Bettinotti
Maria P
MP
Department of Transfusion Medicine, Warren G. Magnuson Clinical Center, Bethesda, Maryland 20892-1184, USA.
Olsen
Anne
A
Stroncek
David
D
D000595:Amino Acid Sequence; D000954:Antigens, Surface / Q000235:genetics; D001483:Base Sequence; D002874:Chromosome Mapping; D002888:Chromosomes, Human, Pair 19; D030541:Databases, Genetic; D058851:GPI-Linked Proteins; D015894:Genome, Human; D006801:Humans; D007519:Isoantigens / Q000235:genetics*; D008562:Membrane Glycoproteins / Q000235:genetics*; D008969:Molecular Sequence Data; D009504:Neutrophils; D011956:Receptors, Cell Surface; D016415:Sequence Alignment
D000954:Antigens, Surface; C407242:CD177 protein, human; D058851:GPI-Linked Proteins; D007519:Isoantigens; D008562:Membrane Glycoproteins; D011956:Receptors, Cell Surface