Expression pattern analysis of transcribed HERV sequences is complicated by ex vivorecombination

Flockerzi, Aline; Maydt, Jochen; Frank, Oliver; Ruggieri, Alessia; Maldener, Esther; Seifarth, Wolfgang; Medstrand, Patrik; Lengauer, Thomas; Meyerhans, Andreas; Leib-Mösch, Christine; Meese, Eckart; Mayer, Jens

doi:10.1186/1742-4690-4-39

Retrovirology

Table 2 Analysis of HERV-KX sequences with Locus Assigner and RECCO.

From: Expression pattern analysis of transcribed HERV sequences is complicated by ex vivorecombination

1	2	3	4	5	6	7	8	9
HERV-KX sequence	Locus- Assigner	# diff's	# recom's	loci involved	recom region	# diff's to locus	p value	# diff's after recom
*B251 ()**	7_450	56	3	3_610/5_147/7_345	59–67	0	0,059
				7_450	182–191	0	0,001
				10_019 1_504/K115/19_352	385–436	3 1	0,023	4
*B251 ()**	7_450	56	2	7_450	182–191	6	0,001
				10_019	385–436	3	0,023
				1_504/K1_15/19_352		1		10
*B251 ()**	7_450	56	1	7_450	182–191	6	0,001
				10_019		14		20
B100	7_450	54	2	7_450	164–181	0	0,001
				3_385 7_345	510–551	0 0	0,004	0
B260	7_450	53	1	7_450	164–181	0	0,001
				5_544		4		4
B81	7_450	52	1	7_450	192–205	1	0,001
				1_259		6		7
108 ()**	3_610	51	1	21_019	68–181	0	0,001
				7_450		0		0
*B83 ()**	7_450	51	2	7_450	192–209	3	0,001
				10_019	437–466	2	0,201
				1_504/19_352/K115		2		7
*B83 ()**	7_450	51	1	7_450	192–209	3	0,001
				10_019		13		16
B358 ()**	11_424/3_354/1_504/5_544/K115	50	2	5_544	68–181	2	0,001
				7_450	727–752	0	0,004
				3_385		0		2
B269 ()**	3_610	48	1	3_610/7_345/5_147	68–181	0	0,001
				7_450		0		0
B281	7_450	43	1	7_450	238–242	0	0,001
				1_504/1_259		4		4
*B268 ()**	7_450	41	2	7_450	164–181	0	0,001
				1_504/22_012/6_324	583–712	0	0,122
				7_450		0		0
*B268 ()**	7_450	41	1	7_450 1_504/22_012/6_324	164–181	0 6	0,001
B270	7_450	39	2	7_450	267–273	0	0,001
				3_385	502–505	0	0,001
				3_014		0		0
B282	1_504	36	2	3_354/1_504	238–242	1	0,001
				7_450	583–712	0	0,004
				3_385		0		1
*B362 ()**	1_259	31	2	11_424	389–401	2	0,001
				7_450	583–624	0	0,102
				10_019		0		2
*B362 ()**	1_259	31	1	11_424	389–401	2	0,001
				7_450		9		11
94	11_456	26	2	11_456	415–422	0	0,001
				7_450	583–651	0	0,003
				11_456		0		0
B98a	3_496/7_345	20	1	10_019	214–263	2	0,001
				7_345/1_504		8		10
*622 ()**	3_014	19	2	HOM/6_324	316–388	0	0,001
				3_014	676–764	0	0,330
				3_385		0		0
*622 ()**	3_014	19	1	HOM/6_324	316–388	0	0,001
				3_014		5		5
*B276 ()**	1_504	18	2	3_354/1_504	192–306	0	0,021
				3_385	521–553	0	0,001
				7_450		0		0
*B276 ()**	1_504	18	1	3_385	521–553	5	0,001
				7_450		0		5
B188	11_424	18	3	1_259/11_424	256–265	0	0,006
				7_450	404–414	0	0,006
				(***)	583–610	1	0,002
				7_450		0		1
B262	3_496	17	1	4_742	209–226	0	0,001
				5_544		4		4
B12	5_544	14	1	5 544	583–673	7	0,001
				7_450		0		7
93	7_450	13	1	7_450	583–610	1	0,001
				21 019		0		1

Designation of columns is the same as in Table 1.
(*) RECCO provided alternative explanations with different p-values. The lowest p-value did not neccessarily correspond to the explanation with the least nt differences. By visual inspection of sequences, another explanation may be favored despite a higher p-value.
(**) HERV-KX sequences without 96 bp sequence. RECCO predicted recombination with loci having the 96 bp sequence (see text), and predicted a recombination involving the 96 bp sequence. Regions of recombination events may therefore be shorter then the ones given by RECCO.
(***) Among 10 different proviral loci, RECCO does not specify a particular locus because all 10 loci are very similar or identical in sequence to each other in the concerned region. By visual inspection, a more optimal explanation among the 10 loci may be specified.

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ISSN: 1742-4690

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