Complete nucleotide sequences of the gene for human factor IX (antihemophilic factor B)

Abstract

Two different human genomic DNA libraries were screened for the gene for blood coagulation factor IX by employing a cDNA for the human protein as a hybridization probe. Five overlapping .lambda. phages were identified that contained the gene for factor IX. The complete DNA sequence of .apprx. 38 kilobases for the gene and the adjacent 5'' and 3'' flanking regions was established by the dideoxy chain termination and chemical degradation methods. The gene contained .apprx. 33.5 kilobases of DNA, including 7 introns and 8 exons within the coding and 3'' noncoding regions of the gene. The 8 exons code for a prepro leader sequence and 415 amino acids that make up the mature protein circulating in plasma. The intervening sequences range in size from 188 to 9473 nucleotides and contain 4 Alu repetitive sequences, including 1 in intron A and 3 in intron F. A 5th Alu repetitive sequence was found immediately flanking the 3'' end of the gene. A 50 base pair insert in intron A was found in a clone from 1 of the genomic libraries but was absent in clones from the other library. Intron A as well as the 3'' noncoding region of the gene also contained alternating purine-pyrimidine sequences that provide potential left-handed helical DNA or Z-DNA structures for the gene. KpnI repetitive sequences were identified in intron D and the region flanking the 5'' end of the gene. The 5'' flanking region also contained a 1.9-kb HindIII subfamily repeat. The 7 introns in the gene for factor IX were located in essentially the same position as the 7 introns in the gene for human protein C, while the first 3 were found in positions identical with those in the gene for human prothrombin.