A physical map of human Alu repeats cleavage by restriction endonucleases

BMC Genomics

Table 1 Amount of Alu repeats, which contain restriction enzymes recognition site at the certain positions

Restriction enzyme (Recognition site)	Position of site*	Number of Alu repeats with recognition site*	% of Alu repeats with a RE site	% of Alu repeats with RE site in the main subfamilies
				AluJb (129,921 copies)	AluJo (143,179 copies)	AluSq (95,474 copies)	AluSx (342,315 copies)	AluSg (82,849 copies)	AluY (139,479 copies)
AluI (AGCT)	136	284,829	24	22	20	31	28	32	18
	168	751,006	63	53	47	76	72	78	78
	216	134,112	11	6	8	2	3	2	65
	228	261,288	22	20	33	22	23	22	19
AsuHPI (GGTGA)	61	213,081	18	2	1	54	33	1	1
	99/101	453,607	38	18	2	58	51	63	64
	259	243,227	20	23	18	11	27	28	20
Bpu10I (CCTNAGC)	46	229,143	19	18	19	21	22	22	16
	181	633,313	53	41	35	63	59	68	72
BssECI (CCNNGG)	47	480,634	40	27	24	48	47	50	59
	89	190,713	16	47	46	3	6	2	2
	205	639,461	54	44	38	62	59	65	71
	255	607,377	51	42	35	62	59	64	72
BstDEI (CTNAG)	47	273,350	23	23	25	24	26	25	18
	65	281,670	24	16	8	60	41	1	1
	173**	276,082	23	24	23	25	26	36	20
	182**	760,759	64	55	49	75	72	78	79
	230	184,220	15	9	3	22	23	22	14
BstMAI (GTCTC)	79/81	513,948	43	31	29	49	47	52	66
	110/112	461,551	39	27	26	44	42	49	60
	270***	391,589	33	31	23	10	41	44	53
	278***	410,275	34	36	29	31	37	36	50
HinfI (GANTC)	193	344,902	29	6	4	53	46	50	5
	272	422,725	35	7	7	10	53	63	71
Bst2UI (CCWGG)	3	257,322	22	20	19	25	26	25	20
	71	183,209	15	37	43	3	10	2	2
	87/89	658,863	55	49	48	62	66	58	76
	138	270,331	23	23	21	27	28	27	23
	205	494,290	41	41	37	48	48	48	38
	255	640,134	54	42	36	62	60	65	72

Data are given for all analyzed sequences and for six main subfamilies.
* – Positions and numbers of sites which present in more than 30% of Alu repeats are shown in bold.
** – Because of possible overlapping the following regions were considered: 168–177 and 178–187.
*** – Because of possible overlapping the following regions were considered: 265–274 and 275–283.

ISSN: 1471-2164