Designations. On an axes abscissas - sequence DNA mobile element in bp; on an ordinate axis - ascribed numbers of the regulatory sites (their titles are reduced in tab.1); 1 group - the sites of replication and transcription initiation and termination; 2 group - enhancers and silencers of chromosomal, viral, etc., genes; 3 group - the sites recognized by cellular protein transcription and translation factors; and 4 group - the sites recognized by protein receptors for inductive signals; the arrows mark the discovered location of regulatory sites on the left-directed (leftward arrows) and right-directed (rightward arrows) DNA strands.
(b) Schematic structure of the DNA sequence of retrotransposon 1731.
Designations. LTR, long terminal repeats; GAG and POL, big open reading frame; P is the motif of amino acid sequence of protease domain; RT, of reverse transcriptase domain; RH, of RNase H domain; and I, of integrase domain.
(c) Consolidated distribution of the revealed motifs of functional sites along the 1731 DNA sequence.
Designations. On an axes abscissas - number of segments of genome each size 1/15 length given MGE; on an ordinate axis - total number of nucleotides contained in the motifs of functional sites and falling within the scanning window by a size 75 bp. The upper direct line - 95%th level of the nonrandomness of the condensations of the motifs of functional sites; the lower direct line - average for 50 of casual sequences the same lengths and same nucleotide's of structure as DNA 1731 distribution of motives functional saites.
Jamming of the motifs correlates with the potential regulatory regions in the LTR and in the vicinity of the ends (start and beginning) of the ORFs and domains of the ORF2 (POL-gene).