Words similar to nonamer
Example sentences for: nonamer
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While 62% (219/356) of these RSS contain a consensus heptamer, just 16% (57/356) contain a consensus nonamer and only 13% (48/356) contain both a consensus heptamer and a consensus nonamer.
Using the ZAS-N- and ZAS-C-selected DNA sequences as input, the MEME program discovered motifs containing sequences similar to the κB or Sb transcriptional enhancer motifs as well as the conserved heptamer or nonamer elements of the RSS.
Because the pentameric motifs derived from the KRC/ZAS-N dataset more closely resemble the canonical RSS nonamer and the motif derived from the KRC/ZAS-C dataset more closely resemble the canonical RSS heptamer and a canonical sequence was derived from the majority of sequences, we propose that the ZAS-N domain of KRC binds RSS nonamers more frequently than the ZAS-C domain, and vice versa for the RSS heptamer in vivo .
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".
Although RSS are evolutionarily conserved, the sequences of individual nonamer and heptamers vary [ 32 40 ] . To further determine the physiological significance of KRC's DNA binding, we compared the datasets with known endogenous RSSs of Ig and TCR loci.
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