The Use of Bioinformatics to Identify the Genomic Structure of the Gene That Encodes Neutrophil Antigen NB1, CD177

• Published in: Clinical immunology (Orlando, Fla.) Fla.), 2002-02, Vol.102 (2), p.138-144
• Main Authors: Bettinotti, Maria P., Olsen, Anne, Stroncek, David
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Antigens, Surface - genetics; Base Sequence; Biological and medical sciences; CD177; Chromosome Mapping; Chromosomes, Human, Pair 19; Databases, Genetic; Fundamental and applied biological sciences. Psychology; Fundamental immunology; Genome, Human; GPI-Linked Proteins; Hematologic and hematopoietic diseases; human neutrophil antigen-2a (HNA-2a); Humans; Immunobiology; Isoantigens - genetics; Leukemias. Malignant lymphomas. Malignant reticulosis. Myelofibrosis; Medical sciences; Membrane Glycoproteins - genetics; Molecular Sequence Data; Myeloid cells: ontogeny, maturation, markers, receptors; neutrophil-specific antigen NB1; Neutrophils; polycythemia rubra vera-1 (PRV-1); Polynuclears; Receptors, Cell Surface; Sequence Alignment
• ISSN: 1521-6616; 1521-7035
• DOI: 10.1006/clim.2001.5154

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.