The orientation of transcription factor binding site motifs in gene promoter regions: does it matter?

BMC Genomics

Table 1 Base compositions

Upstream sequence interval [nt] / composition [%]	A	C	G	T
−500 to −1	33.9	16.8	15.8	33.4
−250 to −1	33.9	17.4	15.5	33.1
−500 to −401	33.6	16.3	16.5	33.6
−400 to −301	34.0	16.0	16.0	34.0
−300 to −201	34.3	16.1	15.6	34.0
−200 to −101	34.4	16.8	15.7	33.1
−100 to −1	33.3	18.7	15.4	32.5
−50 to −1	33.0	19.4	15.1	32.5
−500 to −51	34.0	16.5	15.9	33.6
TFBS motifs	29.4	24.9	20.9	24.8

Base composition of the intervals of upstream regions of Arabidopsis genes (coding strand) and of the TFBS motifs used in this study. As motifs are frequently reported in both the forward and reverse-complement orientation, the directionality reported as “forward” was chosen. Composition of the reverse-complement sequence version can be imputed from the given percentages based on canonical base-pairings A-T and G-C. In case of ambiguous bases as part of the sequence, correspondingly allowed individual bases A, C, G, or T, were counted fractionally

ISSN: 1471-2164