An endogenous lentivirus in the germline of a rodent

Table 3 Springhare endogenous lentivirus loci

ERV locus^a	Structure	Age (Mya) ^b	Contig	Orientation	Start	End
SpELV.1-PedCap	LTR-Gag-Pol	8,750,000	VMDO01011022.1	+	63,971	68,252
SpELV.2-PedCap	LTR-Gag	12,500,000	VMDO01050306.1	+	2112	3978
SpELV.3-PedCap	Gag	ND	VMDO01082106.1	−	284	997
SpELV.4-PedCap	Gag	ND	VMDO01088624.1	−	445	1155
SpELV.6-PedCap	LTR	10,084,925	VMDO01001729.1	−	65,134	65,652
SpELV.14-PedCap	LTR	11,194,029	VMDO01006229.1	+	41,369	41,857
SpELV.15-PedCap	LTR	11,460,554	VMDO01001857.1	+	174,371	174,854
SpELV.16-PedCap	LTR	11,460,554	VMDO01001488.1	+	108,014	108,496
SpELV.17-PedCap	LTR	8,528,784	VMDO01000902.1	+	172,296	172,776
SpELV.18-PedCap	LTR	11,143,410	VMDO01003412.1	+	3534	4013
SpELV.21-PedCap	LTR	9,594,882	VMDO01035581.1	−	11,304	11,783
SpELV.24-PedCap	LTR	11,388,286	VMDO01046849.1	+	1434	1906
SpELV.25-PedCap	LTR	13,592,750	VMDO01015080.1	+	21,755	22,226
SpELV.28-PedCap	LTR	17,665,952	VMDO01001033.1	−	148,080	148,542
SpELV.32-PedCap	LTR	ND	VMDO01012895.1	+	13,691	14,124
SpELV.34-PedCap	LTR	ND	VMDO01003146.1	−	134,124	134,544
SpELV.35-PedCap	LTR	ND	VMDO01018267.1	+	34,458	34,865

^aLoci were assigned unique identifiers (IDs) following a standard nomenclature system [42]. PedCap = Pedetes capensis. The ages of LTR-encoding elements was estimated by measuring divergence from an LTR consensus sequence and applying a neutral rate calibration, as described by Subramanian et al. [33]. ND = not done. SpELV = Springhare endogenous lentivirus