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

BMC Research Notes

Table 1 Characteristics of five TRIM families in the B . rapa and B . oleracea genomes

TRIM family	No. of TRIM members in B. rapa (283 Mb) genome								No. of TRIM 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
TB-1	206	71	54	12	1	39	17	12	273	164	61	17	0	19	12	65
TB-2	319	147	92	15	2	35	18	10	321	162	110	11	0	29	9	16
TB-3	52	22	7	4	3	8	4	4	51	25	15	3	1	3	4	0
TB-4	351	157	78	14	7	37	14	44	392	235	106	19	2	16	14	0
TB-5	465	233	96	8	1	40	13	74	602	397	150	21	0	13	21	96
Total	1393	630	327	53	14	159	66	144	1639	983	442	71	3	80	60	177

^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 residing 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