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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.
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Retrovirology

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