Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves

Table 3 Motifs positioned at the transcription start site and shared between the four model organisms.

Element	At1500tss	Ce1500tss	Dm1500tss	Sc1500atg
TATATA	81.6	6.7	10.9	16.3
ATATAA	67.7	6.7	18.0	15.1
CTCTCT	43.3	6.2	8.1	4.2
TAAATA	41.4	6.1	10.8	8.1
GTATAT	25.8	8.0	11.2	7.8
ATTTAA	9.8	8.0	11.6	4.5
CTCTCG	9.4	8.1	6.2	-
GGCTAT	9.2	6.1	10.8	4.3
TAATAA	9.0	6.7	10.9	7.3
TAAAAT	8.8	6.5	13.0	4.5
AAATAT	8.2	6.5	10.5	8.6
TCACAC	7.1	6.3	15.3	5.2
CATTTT	6.5	14.8	6.4	7.6
AATTTT	6.3	16.5	10.7	9.6
TTAATA	6.3	6.8	10.3	6.5
TTATTT	6.3	10.3	10.2	8.4
TTTATT	6.1	8.9	10.4	7.6
ATTAAT	6.1	6.2	7.6	5.7

The standard deviation fold difference for the most significant peak is shown for each shared motif of the transcription start site datasets. Motif distribution curves were conducted and analyzed for all possible hexanucleotide motifs that have frequency disequilibria which exceeded ≥ 6 fold SD from the background average. Background average and SD were calculated as described in the material and methods. The table is sorted according to the fold differences found in the Arabidopsis promoters.

ISSN: 1471-2105