Genome-wide amplification of proviral sequences reveals new polymorphic HERV-K(HML-2) proviruses in humans and chimpanzees that are absent from genome assemblies

Table 1 Characteristics of new HERV-K(HML-2) proviral loci

Locus ^a	Location	Type	Direct repeat	Allele frequency			Inter-LTR divergence	Estimate of proviral integration (mya)
				PI	Provirus	sLTR
19p12c	19p12	I	NA^b	0.57	0.43	0.0	NA^b	NA^b
Pan8q	8q	I	AGGAGA	0.0	1	0.0	0.008	2.42 (1.57-3.27)
Pan2Ap	2Ap	U^c	GCTG(G\A)TGGGCGAGAA(AAA/---)	0.0	1	0.0	0.006	1.81 (1.17-2.45)
1p31.1a	1p31.1	I	CATGT	0.0	0.965	0.035	(HSA)^d 0.004	1.205 (0.78-1.63)
1p31.1a	1p31.1	I	CATGT	0.0	0.965	0.035	(PTR) 0.026	7.87 (5.09-10.65)

^aNewly identified HERV-K loci were named according to their chromosome band location in humans or chromosome arm in chimpanzee. PI = Pre-Insertion site allele. ^bNA = Not applicable as one of the proviral LTRs is absent. ^cU = Undetermined as the reference genome assembly contains a solo LTR. ^dHSA = Human sequence. PTR = Chimpanzee sequence.

ISSN: 1742-4690