Skip to main content

Table 1 Datasets used in the study

From: Lineage specific evolution of the VNTR composite retrotransposon central domain and its role in retrotransposition of gibbon LAVA elements

Species VNTR composite family Subfamilies Number of elements analyzed Remarks
Macaca mulatta (MMU) SVA2MMU   30  
Nomascus leucogenys (NLE) SVA2NLE   30  
  SVANLE (SINE-R-VNTR-Alu)   26  
  PVA (PTGR2-VNTR-Alu)   89 Only elements displaying a 5’ complete VNTR (i.e. containing at least the 3’ part of the Alu-like region)
  FVA (FRAM-VNTR-Alu)   7  
  LAVA (L1-Alu-VNTR-Alu) LAVA_A – LAVA_F (22 subfamilies) 5, 10 or 20 per subfamily, representing 5-10% of the subfamily members Only elements displaying a 5’ complete VNTR (i.e. containing at least the 3’ part of the Alu-like region)
Pongo abelii (PA) SVA (SINE-R-VNTR-Alu) SVAPA_1 - SVAPA_11 (11 subfamilies) 5, 10 or 20 per subfamily For the younger subfamilies SVAPA_7 to SVAPA_11 5’ truncated elements and elements with assembly gaps had to be taken into account to obtain consensus VNTR schemes with sufficient support
Pan troglodytes (Pt) SVA (SINE-R-VNTR-Alu) SVA_PtA 83 Only elements with full-length VNTR
Homo sapiens (HSA) SVA (SINE-R-VNTR-Alu) SVA_A – SVA_F (6 subfamilies) 10 per subfamily Only full-length elements