Locus ACTBP2 (SE33). Sequencing data reveal considerable polymorphism.

A total of 50 different ACTBP2 (human beta-actin related pseudogene) alleles and the cell line K562 were sequenced and analysed. Sequence data revealed not only length polymorphism but also a highly variable sequence polymorphism. 2 different sequence structures were characterised. Type I (223-259bp) contained the known regular 4bp repeat AAAG. Type II (265-309bp) revealed a further hexanucleotide unit AAAAAG in addition to the common AAAG which only occurs once in the repeat region. The position of this insertion showed considerable variation. To obtain a regular spaced allelic ladder 20 of the sequenced alleles were selected. Denaturing gels and high resolution/non-denaturing gels were compared and striking differences could be seen between the 2 gel systems. Separation of the alleles on a 6% denaturing gel and analysis on the ABI 373A Sequencer revealed fragment sizes which corresponded to the sequencing data but were in general 6-10bp longer. In contrast, in non-denaturing gels some alleles showed different electrophoretic mobilities compared to the sequenced allelic ladder which could indicate different fragment length and/or different sequence structure.