Words similar to nonamer
Example sentences for: nonamer
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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".
Furthermore, we were able to align the κB motif, the Sb sequence, the RSS nonamer, and part of the RSS heptamer "TGTG" with both PSSMs (Figs.
The patterns of nucleotide diversity at individual positions are similar for both 12- and 23-RSS: the initial CAC of the heptamer is invariant, the remaining four positions of the heptamer are moderately diverse, the spacer is highly diverse, and the A tract of the nonamer (positions 5 through 7) is better conserved than the other nonamer positions (Figure 1a).
A recent bioinformatics analysis of labile mRNAs with AUUUA motifs extended this core motif to the nonamer UAUUUAWW, and a database of mRNAs that have matches to this motif in their 3' untranslated regions was created [ 36].
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 .
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