BMC Genomics

Table 2 Comparison of major classes of repeat sequences in chicken and zebra finch BACs mapped on the Siamese cobra W chromosome

From: Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent “a hypothetical ancestral super-sex chromosome” or random distribution?

	NE	LO	%	NE	LO	%	NE	LO	%	NE	LO	%
	1 CH261-89C18			1 TGMCBA-167P13			4 CH261-71L6			9 CH261-95N3
%GC			47.61			59.52			44.85			42.81
Satellites	2	580	0.34	1	19	0.02	0	0	0	0	0	0
Simple repeats	30	988	0.58	23	2011	1.91	36	1910	1.02	70	2777	1.43
Retroelement	94	16874	9.85	37	11027	10.47	21	3668	1.95	17	3847	1.99
1) SINEs	1	49	0.03	0	0	0	2	207	0.11	2	353	0.18
2) LINEs	92	16749	9.77	33	9768	9.28	19	3461	1.84	13	2849	1.47
3) LTR elements	1	76	0.04	4	1259	1.20	0	0	0	2	645	0.33
DNA transposons	4	203	0.12	0	0	0	5	137	0.07	8	1014	0.52
Unclassified	0	0	0	0	0	0	0	0	0	2	330	0.17
Total interspersed repeats		17077	9.97		5191	2.68		3805	2.02		5191	2.68
	9 TGMCBA-217A3			13 TGMCBA-136I12			17 TGMCBA-375I5			17 TGMCBA-67H23
%GC			48.72			51.96			44.44			51.09
Satellites	1	260	0.12	0	0	0	0	0	0	2	1074	0.64
Simple repeats	65	3487	1.63	87	6437	3.8	41	1769	1.24	45	2772	1.66
Retroelement	24	5688	2.66	51	11247	6.64	62	19590	13.73	44	11042	6.6
1) SINEs	0	0	0	1	90	0.05	2	183	0.13	0	0	0
2) LINEs	13	2373	1.11	34	5458	3.22	42	11979	8.4	32	6943	4.15
3) LTR elements	11	3315	1.55	16	5699	3.37	18	7428	5.21	12	4099	2.45
DNA transposons	8	815	0.24	16	911	0.54	6	446	0.31	7	709	0.42
Unclassified	0	0	0	3	316	0.19	1	97	0.07	0	0	0
Total interspersed repeats		6206	2.9		12474	7.37		20133	14.11		11751	7.03
	23 TGMCBA-227A15			27 TGMCBA-23C5			Z CH261-129A16			Z TGMCBA-200J22
%GC			49.38			48.70			41.03			34.62
Satellites	0	0	0	0	0	0	1	98	0.04	0	0	0
Simple repeats	18	909	1.59	40	2247	1.11	68	2973	1.32	47	2450	1.45
Retroelement	28	7991	14	161	47194	23.26	53	26179	11.59	46	16566	9.84
1) SINEs	0	0	0	2	139	0.07	1	95	0.04	1	137	0.08
2) LINEs	15	3180	5.57	117	25323	12.48	50	25215	11.16	32	11149	6.62
3) LTR elements	13	4811	8.43	42	21732	10.71	2	869	0.38	13	5280	3.14
DNA transposons	1	85	0.15	6	979	0.48	12	2842	1.26	11	714	0.42
Unclassified	0	0	0	0	0	0	0	0	0	0	0	0
Total interspersed repeats		8076	14.15		48173	23.74		29021	12.85		17280	10.26

NE; number of elements
LO; length occupied
%; sequence percentage

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ISSN: 1471-2164

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