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AGO7 specifically associates with miR390 and cleaves TRANS-ACTING siRNA3 (TAS3) RNA to set the nucleotide frame for tasiRNA production, but the basis of this specific association is unknown [12].
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Our assay showed that single nucleotide frame-shifts associated to cancer were non-randomly enriched in TP53.
We detected 195 variants within coding regions between the two S. Virchow genomes, including 166 SNPs, 13 single nucleotide frame-shift indels, and 5 three-nucleotide in-frame indels (Additional file 2: Table S2).
This particular sequence variant has a nine nucleotide in frame deletion (nucleotides 1546 to 1554 corresponding to amino acids 516 to 518).
Six-nucleotide in frame deletions at amino acid positions 159 and 160 reported previously [11] were observed in four of the Newcastle HRSV isolates from 1985 , 1986and 2009.
Keeping the nucleotides in frame, there were no ambiguously aligned regions.
The hexamers were calculated in steps of three nucleotides in frame (dicodons).
We have previously reported a novel three consecutive nucleotide in-frame (CGG) insertion in ORF 1 between nucleotide positions 780 and 781 in the VZV genome [ 10].
BLASTn hits with < 4 mismatches were chosen as candidate targets, and then <span class="lh">nucleotide 6-frame translation-protein (blastx) was used to obtain their putative functions.
The alignment was manually checked for errors and then back-translated into nucleotide sequences, removing frame shifts and in-frame stop codons.
The lepr cDNA consisted of a 22-nucleotide 5'-untranslated region (5' UTR), a 402-nucleotide open reading frame (ORF) and a 929-nucleotide 3' UTR.
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