High microvariation sequence polymorphism at short tandem repeat loci: human beta-actin related pseudogene as an example.
The human beta-actin related pseudogene (HUMACTBP2) seems to be one of the most informative microsatellite markers known because of the high number of length and sequence variants. A total of 50 alleles found in white Caucasians from the Pomerania-Kujawy region of Poland were analyzed by automated sequencing. In addition to STR length polymorphism, seven different types of sequence variation were observed. Alleles ranging in size between 233 and 273 bp showed regular sequence structure with tetranucleotide repeats AAAG. In the alleles ranging in size from 275 to 323 bp, hexamer units AAAAAG or AGAAAG occurred in the repeat region in addition to AAAG repeats. Two alleles (317 and 321 bp) contained two hexamers in the repeat region. There was considerable polymorphism of the hexamer position leading to allelic variants of the same size but different sequence structures. A large amount of variation in both 5' and 3' flanking regions was also observed. Allelic designation based on the number of all types of units within the repeat region (including the hexamer unit) is proposed. An allelic ladder composed of 21 sequenced alleles was constructed to add precision and accuracy to the identification of alleles at ACTBP2 locus.
Miścicka-Sliwka
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Forensic Medicine Institute, Ludwik Rydygier's University School of Medical Sciences, Bydgoszcz, Poland. tomekg@aci.amb.bydgoszcz.pl
Grzybowski
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D000199:Actins / Q000235:genetics*; D000483:Alleles; D001322:Autoanalysis; D001483:Base Sequence; D004591:Electrophoresis, Polyacrylamide Gel; D005554:Forensic Medicine; D014644:Genetic Variation; D006801:Humans; D018598:Minisatellite Repeats; D008969:Molecular Sequence Data; D011044:Poland; D011110:Polymorphism, Genetic; D011544:Pseudogenes; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D009626:Terminology as Topic
D000199:Actins