Insertionally polymorphic sites of human endogenous retrovirus-K (HML-2) with long target site duplications

BMC Genomics

Table 1 Candidates for novel HML-2 pre sites

Chr	Position	Region	Structure	ID	Genomes of other primates^a	Frequency^b			Total alleles	Age^c (MYA)	Reference^d
Chr	Position	Region	Structure	ID	Genomes of other primates^a	pre	pro	solo	Total alleles	Age^c (MYA)	Reference^d
chr3	195654396–195655363	3q29	solo LTR	esv2668264	ins	0.152	0	0.848	46	2.27	[3]
chr4	120263689–120264654	4q26	solo LTR	esv2661724	ins	0.708	0	0.292	48	2.11	[3]
chr7	16237347–16238314	7p21.2	solo LTR	esv2662783	ins	0.5	0	0.5	48	2.42	this study
chr8	37050886–37051853	8p11.23	solo LTR	esv2677273	ins	0.813	0	0.187	48	2.15	this study
chr11	71875418–71876385	11q13.4	solo LTR	esv2675196	ins	n.d.	n.d.	n.d.	n.d.	2.35	[3]
chr6	3055034–3055749	6p25.2	LTR+ ORF + 7bp^e	esv2731485	ins panTro4 /ponAbe2	0.435	0.565	0	46	n.d.	this study

^aReference genomes for chimpanzee (PanTro4), gorilla (gorGor3), orangutan (PonAbe2), and rhesus macaque (rheMac8). ins: Retroviral insertion
^bTested in this study; pre: preintegration, pro: provirus, solo: solo LTR, n.d. not determined
^cThe previous study by Subramanian et al. was used to obtain the ages of solo LTRs [12]. MYA million years ago, n.d. not determined
^dInsertional polymorphisms were inferred from the previous study by Wildschutte et al. [3].
^eThe ORF was partially deleted and the flanking 7-bp sequence was assigned as part of the ORF

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