CK2alpha loci in the human genome: structure and transcriptional activity

Two CK2alpha loci are present in the human genome. First, locus 20p13, that contains the CK2alpha coding gene. It spans around 70 kb, is composed of 13 exons and shows homology to the respective gene in the nematode Caenorhabditis elegans. The translation start site is located in the second exon, the stop codon in exon 13. Two transcription start sites were identified, the further 5' located site defines position 1 of the gene, the second site is located at position 50, respectively. The promoter region shows characteristics of a so-called house keeping gene: A high GC content, lack of a TATA-box and presence of several GC-boxes. By reporter gene assays, the promoter region of the CK2alpha gene could be located between position -256 and 144 relative to the first transcription start site. In the 3' noncoding region of the CK2alpha gene, six polyadenylation signals were identified. As indicated by Northern blot analysis and by comparison with expressed sequence tags from the EMBL databank, the most 3' located, active polyadenylation signal seems to be the fourth defining the end of the CK2alpha gene. The second CK2alpha locus is at 11p15. It contains a processed pseudogene, which shows all typical features of a processed sequence, such as absence of introns, short poly-A tail and direct flanking repeats. Interestingly, it contains a complete open reading frame and has potential promoter elements in its 5' region. Nevertheless, no promoter activity could be detected in reporter gene assays.