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Table 2 Information on Gamma -like lineages represented in Figure 3

From: Identification and characterization of diverse groups of endogenous retroviruses in felids

  Nonsense/frameshift mutations a Within group p -distance b (SE) Description of lineage and time c Sequence ID d Contig length (bp) Presumed ERV (positions within contig) Avg .LTR length (bp) LTR dist e /No. of differences f Time since integration g Time reported in the literature
I 4 [1-10] 0.105 (0.005) Felis, Pco, Py, Lco, Lgu, Lp, Lg, OC, tiger [10 MY] AANG02165009.1AANG02150893.1 ATCQ01141921.1 12666 19424 35074 3998-12096 983-9298 24631-32736 166 294 298 0.28/27 0.131/32 0.084/22 60.8/28/11.7 28.5/13.1/5.5 18.26/8.4/3.5 gamma1 (30MY/8.2 MY/-) [14]
II 5 [4-6] 0.040 Felis, Lg, tiger [10 MY] - - - - - ND -
III 11 [3- 14] 0.144 (0.006) Felis, Lg, tiger [10 MY] AANG02100182.1 AANG02102504.1 ATCQ01007049.1 91034 54996 22449 82322-90764 41175-50607 291-8884 343 260 314 0.20/53 0.22/43 0.20/49 43.7/20.1/8.4 49.1-22.6-9.4 45.2/20.8/8.7  
IV 2 [1-5] 0.093 (0.007) Felis, Py, Lwi, tiger [10 MY] AANG02131012.1 ATCQ01021699.1 6326 12087 280-6325 2033-9148 341 398 0.024/08 0.043/16 5.2/2.4/1 9.35/4.3/1.8  
V 0 [0] 0.113 Felis [3.36 MY] enFeLV-AGTT (AY364318.1) 9895 9895 568 0/0 Recent [45]  
VI 0 [0-3] 0.037 Felis [3.36 MY] ERV-DC10 (AB674444.1) 9363 9363 551 0/0 Recent [13] The oldest ERV-DC integration (2.8 MY) [13]
VII 3 [0-6] 0.054 (0.004) Felis, Py, Pco, Lwi, tiger [10 MY] AANG02094865.1AANG02162912.1 23420 80539 4845-11356 2477-9063 336 375 0.064/19 0.028/10 13.9/6.4/2.7 6.1/2.8/1.2 gamma 6 (16 to 3.8 MY) [14]
VIII 2 [0-4] 0.046 (0.005) Felis, Pco, Py, tiger [10 MY] ACBE01419578.1 AANG02080262.1ATCQ01044240.1 12392 23123 16168 2915-9700 2586-11074 5551-14181 542 538 501 0.069/34 0.042/21 0.029/14 15/6.9/2.9 9.3/4.2/1.75 6.3-2.9-1.21  
IX 1 [0-5] 0.058 (0.005) Felis, tiger [10 MY] AANG02049862.1ACBE01427750.1 44805 11784 19379-27642 10858-2531 381 489 0.046/16 0.063/22 10/4.6/1.9 13.7/6.3/2.6  
X 0 [0-4] 0.043 (0.004) Felis, Lg, Lco, tiger [10 MY] ACBE01234963.1 AANG02117711.1 12498 14995 2151-9706 4735-14409 632 626 0.023/14 0.013/08 5/2.3/0.96 2.8/1.3/0.54  
XI 2 [0-4] 0.072 Felis, Py, Lgu, Lwi, LP, Pco, tiger [10 MY] AANG02106789.1 17944 1- 5793 348 0.086/26 18.7/8.6/3.6  
  1. aMedian [min-max] values.
  2. bNucleotide distances within lineages.
  3. cTime based on Johnson et al. [16]. The abbreviations of species’ names in column 4 are as in the legend of Figure 3.
  4. dOnly representatives of full-length ERVs from the domestic cat and tiger genomes are in column 5.
  5. eGenetic distances (Kimura 2 parameter model) between LTRs.
  6. fNumber of differences between the 5′ and 3′LTRs.
  7. gThe three depicted values are based on mutation rates of 2.3e-9, 5e-9 and 1.2e-8 substitutions/site/year (see text for details), respectively. MY, million years; ND, not dated.