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In total, WRKY33 binding was found at 133 TF gene loci.
PU.1 binding was found at different Sfpi1/PU.1 enhancer regions (–15.7, –13.7, –12.6, and –10.3 kb; Fig. 4C), in line with the positive autoregulation described for PU.1.
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Furthermore, ORC binding was not detected at 23% of known ARSs, while nimACSs, which predict ORC binding, are found at 103 of 178 of the MCM2-only sites.
Instead, LSD1 binding was found to be enriched at certain enhancer regions DNA sequences remote from the transcription start site that bind proteins that upregulate transcription.
Differential AR binding sites were clearly enriched for specific chromosomes, and a strong enrichment of resistance-associated AR binding sites was found at chromosome 8.
The average surface binding energy was found at the same value of 3.1 eV irrespective to the used density of Ag (Fig. 6 a, b).
An SP1 binding site was found at postion −188 to −203.
A putative MrpC binding site was found at +40 relative to the predicted TSC of nsd (MXAN_7402) (Additional files 3 and 6).
A putative MrpC binding site was found at -335 relative to the predicted prw (MXAN_2491) TSC (+200 relative to that of MXAN_2490; Additional file 3).
The socE gene (MXAN_0731) was on our list of potentially interesting genes (Additional file 6) and a putative MrpC binding site was found at -231 relative to the predicted TSC (Additional file 3).
Although the GT[CT]CGN 6 CG[GA]AC putative binding site was found at 49 locations on the Rhizobium sp. NT-26 chromosome, it is only in the upstream region of the aioBA operon that this motif was associated with the -12/-24 σ-depromoterpromoter sequence needed for the RpoN-dependent transcription initiation of arsenite oxidase genes (Koechler et al. 2010).
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