Methods for estimating human endogenous retrovirus activities from EST databases

BMC Bioinformatics

Table 1 Selected highly active HERVs.

rank	chr	start	end	subgenes	group	ESTs	hit area
1	5	52510446	52525065	LTRgagpropolLTR	HERV-48	2981	(short) pol
2	2	98059068	98067632	LTRgagpropolenvLTR	ERV-9	1182	pol, env
3	5	180072600	180059089	LTRgagLTR	UNCL.	373	gag
4	2	62302244	62290382	LTRpropolLTR	UNCL.	310	pol
5	21	37885010	37876409	LTRgagpol	HERV-H	176	(short) pol
6	1	152846189	152836852	LTRgagpolenvLTR	MER-41	148	5' LTR
7	16	25125181	25118816	gagpropolenv	HERV-E	125	overall
8	3	8690554	8695505	gagpropol	HERV-E	113	pol
9	6	123050520	123043680	gagpropolenv	HERV-E	109	(short) pol
10	14	23890064	23879831	LTRgagpol	HERV-H	109	pol
31	7	91719541	91709354	LTRgagpropolenvLTR	ERV-9	40	all genes
62	6	11220436	11211151	LTRgagpropolenvLTR	HERV-FRD	20	env

Details about the 10 most active HERVs and the two HERVs that code for the syncytin proteins. The HERVs are sorted in a decreasing activity order, rank is the position in this ordering. "Chr", "start" and "end" tell the chromosome and sequence start and end positions of the HERV in this chromosome (in the July 2003 version (hg16) of the human genome). "Subgenes" describes the structure and "group" the HERV group of the HERV. "ESTs" is the count of EST matches to the HERV. "Hit area" briefly describes where the ESTs match the HERV. The HERV with rank 31 is syncytin and the HERV with rank 62 is syncytin-2.

ISSN: 1471-2105