An analysis of the human chemokine CXC receptor 4 gene

In this article we analyze some of the structural characteristics of the coding section and the intron of the human chemokine CXC receptor 4 (a 7-transmembrane receptor) pre-mRNA. In the coding sequence the frequencies of the individual nucleotides do not depart significantly from 0.25, while in the intron the frequencies of the As and Gs are significantly lower and higher, respectively, than expected from a random distribution. Analysis of the pattern of association of nucleotides into triplets or couples shows that some triplets or couples occur with frequencies significantly higher or lower than expected when assuming a random association of nucleotides. In particular, in the intron combinations of the same nucleotide are over-represented. 7-or-more nucleotide repeats occur in both the coding section and the intron with frequencies which exceed the confidence limits for a random distribution. For the coding sequence this is possibly explained by the alternans of relatively similar hydrophobic-coding sections and relatively similar intervening intracellular and extracellular hydrophilic-coding sections. 7-or-more nucleotide repeats in reverse order and in reverse/complemented order occur in the intron, but not in the coding section, with frequencies which significantly exceed a random distribution. The numerous intronic repeats in reverse/complemented order may be of relevance for the secondary structure of the intron and might be one important element of the integrated splicing code.