Words similar to heptamer
Example sentences for: heptamer
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We had previously shown by methylation interference analysis that KRC/ZAS-C bound specifically to the sequence TGTGG within the context of the canonical RSS heptamer plus the immediately flanking guanine [ 14 ] . Because the pentamer motif for KRC/ZAS-C predicted by MEME completely matched with the empirical results, we conclude that the two pentameric motifs discovered by MEME are likely authentic binding sites for KRC/ZAS-N as well.
After cloning and DNA sequencing, the KRC-selected sequence datasets were analyzed by the computer program Multiple Expectation Maximum for Motif Elicitation (MEME version 3.0) to generate sets of position specific scoring matrices (PSSMs) or motifs [ 30 ] . When the program was set to identify wider sequences (= 9 nucleotides) the PSSMs were homologous to Sb [ 29 ] , the κB motif [ 31 ] , and the canonical heptamer and nonamer elements of the RSS [ 32 ] . However, shortening the width of the motifs to 5 nucleotides, the target length for the C 2 H 2 zinc finger pairs of the tramtrack [ 33 ] , the ZAS-N dataset yielded two motifs, "GGTAT" and "T(T/C)TT(T/G)G" and the ZAS-C dataset yielded a single motif, "TGTGG".
For both 12- and 23-RSS, the positions exhibiting the strongest cooperative influence lie in the nonamer-proximal half of the spacer and in the heptamer and nonamer positions adjacent to the spacer (Figure 2).
Potentially, the DNA binding domains of KRC might interact with the range of heptamer and nonamer sequences found in endogenous antigen receptor loci.
These are the spacer, especially the nonamer-proximal half, and the positions of the heptamer and nonamer that are adjacent to the spacer (Figure 1b).
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