BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species

BMC Research Notes

Table 2 Characteristics of 16 SINE families in the B . rapa and B . oleracea genomes

SINE family	No. of SINE members in B. rapa (283 Mb) genome								No. of SINE members in B. oleracea (385 Mb) genome							Copies in A. thaliana (119 Mb)
	Total	Intergenic space^a	Near gene^b	Elements in genic regions				Un mapped^d	Total	Intergenic space^a	Near gene^b	Elements in genic regions
	Total	Intergenic space^a	Near gene^b	5’ UTR^c	CDS	Intron	3’ UTR^c	Un mapped^d	Total	Intergenic space^a	Near gene^b	5’ UTR^c	CDS	Intron	3’ UTR^c
SB-1	3	3	0	0	0	0	0	0	98	49	32	7	0	4	6	0
SB-2	43	2	0	2	0	38	1	0	59	8	4	0	0	45	2	132
SB-3	134	70	36	6	0	12	6	4	278	156	80	20	0	9	13	4
SB-4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	38
SB-5	155	72	54	6	0	11	7	5	375	205	99	23	0	18	30	3
SB-6	248	134	71	12	0	7	14	10	394	213	132	21	0	7	21	28
SB-7	372	202	106	17	0	11	20	16	355	197	119	16	0	2	21	3
SB-8	0	0	0	0	0	0	0	0	80	28	26	14	0	2	10	0
SB-9	141	62	49	7	0	6	12	5	201	102	69	11	0	7	12	0
SB-10	16	5	10	0	0	0	0	1	134	67	48	7	0	6	6	0
SB-11	4	4	0	0	0	0	0	0	56	22	25	3	0	2	4	0
SB-12	10	5	3	0	0	2	0	0	101	46	37	7	0	5	6	0
SB-13	1	0	1	0	0	0	0	0	95	43	30	7	0	7	8	0
SB-14	142	69	43	9	0	12	8	1	137	74	37	10	0	6	10	0
SB-15	1	1	0	0	0	0	0	0	1	0	0	0	1	0	0	0
SB-16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4
Total	1270	629	373	59	0	99	68	42	2364	1210	738	146	1	120	149	212

^aMITE members categorized by their insertion >2 kb from the nearest gene.
^bMITE members categorized by their insertion 500–2000 bp from the nearest gene.
^cMITE members resid in the 500 bp upstream (5’UTR) or downstream (3’UTR) of the start or stop codon, respectively.
^dMITE members found in unanchored scaffolds of the B. rapa genome.

ISSN: 1756-0500