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Structural and functional analyses were carried out to compare transcription termination and intergenic spacer organization between the two heterogeneous ribosomal DNA size classes of Ascaris lumbricoides. By performing mung bean nuclease mapping in vivo, we localized the 3' end of the mature 26S rRNA to the same position in both forms. This site coincides with the in vivo and in vitro transcription termination site of the 40S-precursor rRNA from both rDNA size classes. We demonstrate that the 3' boundary of sequences necessary for faithful transcription termination extends 35 bp beyond the end of the 26S rRNA gene and that these sequences are perfectly conserved within the two size classes. The intergenic spacers of both rDNA size classes have been completely sequenced; they are 2410 bp and 1937 bp long and show a sequence homology of 92.8%. There is no evidence for the presence of reiterated termination sites or promoters within the relatively short intergenic spacers of the two rRNA gene classes.
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