Identification of plant promoter constituents by analysis of local distribution of short sequences

BMC Genomics

Table 1 Y Patch and TATA Box identified from Arabidopsis hexamer analysis

Sequence	Peak position¹ (bp)	Peak width² (bp)	#promoter³	Relative Peak Height (RPH)	Relative Peak Area (RPA)
Y Patch
TCTCTC	-13	158	6,741	10.96	0.25
CCTCTC	-13	107	3,106	8.13	0.20
CTTCTC	-13	88	5,916	7.64	0.15
CTCCTC	-13	81	3,180	7.23	0.12
CTCTTC	-13	91	5,393	7.02	0.14
CTCTCC	-13	108	3,153	6.95	0.16
TCCCTC	-13	93	2,140	6.13	0.15
TTCTTC	-13	75	8,829	5.78	0.11
TTCTCT	-13	109	8,314	5.77	0.12
TATA Box
TATAAA	-35	30	10,704	9.0	0.10
TATATA	-36	27	10,315	6.38	0.07
ATATAA	-35	27	10,062	6.14	0.07
ATAAAT	-35	27	10,572	5.14	0.05
TAAATA	-34	25	9,801	4.65	0.04
ATATAT	-35	24	10,412	3.84	0.04
TTATAA	-36	23	9,172	3.36	0.03
TTATAT	-36	23	9,639	3.10	0.03

¹In this analysis, -13 is the position for an average from -20 to -6 that covers a region from -20 to -1, so -13 is the most downstream position.
²Peak width at the bottom of the peak.
³Number of promoters containing the element out of 15,607 Arabidopsis promoters (-1,000 to -1). Number of promoters containing an element within the peak area can be roughly estimated by #promoters × RPA. For example, TATAAA is found in approx. 1,070 promoters within the peak area (10,704 × 0.10).

ISSN: 1471-2164