Cloned human apo-C-II cDNA was used as a hybridization probe to identify the 
human apo-C-II gene in a genomic library constructed in our laboratory. The 
isolated apo-C-II DNA was studied both by electron microscopy and by direct 
sequence analysis. Ultrastructural morphological analysis of RNA-DNA hybrids 
revealed that the apo-C-II gene had complex structures because of regions of 
inverted complementary sequences in and around the gene forming stem-and-loop 
structures which interfere with the formation of stable RNA:DNA hybrids. 
Extensive morphological analysis revealed a minimum of 3 intervening sequences 
(IVS), and their lengths were measured. Direct sequence analysis of the cloned 
gene confirmed the presence of 3 IVS. There are 4 Alu type sequences in IVS-I. 
We sequenced 4340 nucleotides which include 545 nucleotides in the 5' flanking 
region, the entire gene which spans 3320 nucleotides, and 475 nucleotides in the 
3' flanking region which also encompasses an additional Alu sequence. The 5' end 
of the gene was identified by primer extension and sequencing of the primer 
extended cDNA. Apo-C-II mRNA structure was deduced from the cDNA sequence, the 
primer extension experiments, and the genomic sequence. It is 494 nucleotides in 
length. Its sequence differs from previously published sequences in that there 
are 7 additional nucleotides before the polyadenylate tail. In the 5' flanking 
region, nucleotides -234 to -213 encompass a GC-rich region which exhibits high 
homology (greater than 70%) to the 5' flanking regions of the genes of all the 
apolipoproteins published to date, namely, apo-A-II (-497 to -471), apo-A-I 
(approximately -196 to -179), apo-E (-409 to -391), and apo-C-III (approximately 
-116 to -103). This highly conserved region might represent some evolutionarily 
conserved sequences from these related genes and/or might represent a region 
with regulatory function.