LOCUS ACTBP2 (SE33) - SEQUENCING DATA REVEAL CONSIDERABLE POLYMORPHISM

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