TABLE 2.
Grouping and characterization of recent Pol-containing ERV integrations in the Homo (hg16) and Pan (PanTro1) genomes
| Sequence from Pol putein tree (Score > 300, LTR nonidentity < 2%) (species “unique”)a | Genomic positions (PanTro1/hg16)b | Nucleotide frequency (%)
|
Chain (genus) | PBS | Stops and frameshifts (genus)
|
LTR nonidentity (%) | BLAT 5′ and 3′ LTRs >98% of max. score | Best Pol hits in tBLASTn (against nr database) | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A | T | G | C | gag | pro | pol | env | |||||||
| PtG1a | 26.5 | 21.7 | 23.7 | 28.2 | Using 75% Pol consensus | |||||||||
| pt01Chr1_162576402_493 | chr1: 162576402/(−) | 28.4 | 23.2 | 21.6 | 26.8 | gamma (C) | 12 (C) | 6 (C) | 1.58 | 4 | AC148703Macaca mulatta | |||
| pt01Chr1_65005019_528 | chr1: 65005019/(−?) | 26.1 | 22 | 23.4 | 28.5 | gamma (C) | 9 (C) | 4 (C) | 0.48 | 4 | AC093133Papio anubis | |||
| pt01Chr10_6018423_610 | chr10: 6018423/(−) | 27.3 | 22.5 | 22.4 | 27.8 | gamma (C) | P | 11 (C) | 4 (C) | 0.53 | 9 | AF142988Papio cynocephalus | ||
| pt01Chr10r_17119458_1920 | chr10: 17111172/(−) | 26.9 | 21.5 | 23.6 | 28 | gamma (C) | P | 2 (C) | 0 (C) | 7 (C) | 3 (C) | 1.99 | 2 | |
| pt01Chr12_86282276_907 | chr12: 86282276/(−) | 26.2 | 21.5 | 24 | 28.3 | gamma (C) | P | 4 (C) | 8 (C) | 2 (C) | 0.98 | 19 | ||
| pt01Chr12_86988340_584 | chr12: 86981358/(−) | 26.0 | 21.8 | 23.8 | 28.4 | gamma (C) | 10 (C) | 1 (C) | 0.27 | 19 | ||||
| pt01Chr18_10653851_529 | chr18: 10646172/(−) | 25.6 | 21.6 | 24.5 | 28.3 | gamma (C) | 8 (C) | 4 (C) | 0.97 | 20 | ||||
| pt01Chr2_96744750_613 | chr2: 96737061/(−) | 24.3 | 22.1 | 25.1 | 28.4 | gamma (C) | 0 (C) | 7 (C) | 3 (C) | 0.5 | 2 | |||
| pt01Chr20_29149338_571 | chr20: 29142410/(−) | 27.1 | 21.6 | 23.3 | 28 | gamma (C) | 3 (C) | 11 (C) | 1.22 | 4 | ||||
| pt01Chr4_59045395_660 | chr4: 59038147/(−) | 26.1 | 21.6 | 24.1 | 28.1 | gamma (C) | 5 (C) | 4 (C) | 1.23 | 8 | ||||
| pt01Chr4_73583587_915 | chr4: 73584507/(−) | 26.7 | 21.4 | 23.6 | 28.3 | gamma (C) | 4 (C) | 6 (C) | 8 (C) | 0.52 | 13 | |||
| pt01Chr5r_11234345_1097 | chr5r: 11234345/(−) | 25.9 | 21.5 | 24.2 | 28.4 | gamma (C) | P | 3 (C) | 3 (C) | 2 (C) | 0.76 | 17 | ||
| pt01Chr6_37617641_1629 | chr6: 37617641/(−) | 26.7 | 21.5 | 23.5 | 28.3 | gamma (C) | 4 (C) | 0 (C) | 8 (C) | 5 (C) | 0.79 | 4 | ||
| pt01Chr6_44854470_567 | chr6: 44854470/(−) | 26.8 | 21.7 | 23.2 | 28.3 | gamma (C) | 4 (C) | 7 (C) | 7 (C) | 1.06 | 2 | |||
| pt01Chr7_74967707_1011 | chr7: 74960368/(−) | 27.2 | 21.4 | 23.4 | 28.1 | gamma (C) | P | 2 (C) | 4 (C) | 2 (C) | 0.79 | 8 | ||
| pt01Chr8_43813694_459 | chr8: 43806427/(−) | 27.7 | 21.4 | 23 | 27.9 | gamma (C) | 11 (C) | 5 (C) | 0.95 | 3 | ||||
| pt01Chr8_62466624_970 | chr8: 62466624/(−) | 25.2 | 21.2 | 24.9 | 28.7 | gamma (C) | P | 5 (C) | 1 (C) | 0.73 | 25 | |||
| pt01Chr9_95940431_611 | chr9: 95940431/(−) | 26.2 | 21.6 | 24.1 | 28.2 | gamma (C) | 7 (C) | 9 (C) | 0.98 | 8 | ||||
| PtG1b | 25.4 | 22.4 | 24.2 | 28.0 | Using pt01Chr6_139921967_779 | |||||||||
| pt01Chr10_72581664_733 | chr10: 72573964/(−) | 25.6 | 22 | 24.2 | 28.2 | gamma (C) | 4 (C) | 7 (C) | 8 (C) | 0 | 4 | AC148703Macaca mulatta | ||
| pt01Chr6_139921967_779 | chr6: 139915850/(−) | 24.9 | 22.5 | 24.6 | 28 | gamma (C) | 2 (C) | 7 (C) | 2 (C) | 0.74 | 11 | AC091754Papio anubis | ||
| pt01Chr6_50486605_639 | chr6:50486605/(−) | 25.7 | 22.6 | 23.9 | 27.8 | gamma (C) | 7 (C) | 3 (C) | 0.49 | 5 | AF142988Papio cynocephalus | |||
| PtG2a | 25.9 | 21.4 | 23.9 | 28.9 | Using pt01Chr5_53871501_226 | |||||||||
| pt01ChrY_13806832_1804 | chrY: 13806832/(−) | 25.7 | 21.1 | 23.9 | 29.3 | gamma (C) | P | 10 (C) | 0 (C) | 3 (C) | 0 | 2 | AF142988Papio cynocephalus | |
| pt01Chr1_24412696_1251 | chr1: 24412696/(−) | 26.3 | 20.9 | 24.1 | 28.7 | gamma (C) | P | 3 (C) | 1 (C) | 7 (C) | 4 (C) | 0.29 | 4 | AC148703Macaca mulatta |
| pt01Chr5_53871501_2266 | chr5: 53871501/(−) | 25.7 | 22.1 | 23.6 | 28.6 | gamma (C) | P | 6 (C) | 0 (C) | 9 (C) | 1 (C) | 1.67 | 4 | AC091754Papio anubis |
| PtG2b | Using pt01Chr12_34847717_1068 | |||||||||||||
| pt01Chr12_34847717_1068 | chr12: 34840755/(−) | 25.9 | 22 | 23.6 | 28.5 | gamma (C) | P | 1 (C) | 1 (C) | 8 (C) | 0.79 | 4 | AC148703Macaca mulatta | |
| AC091754 Papio anubis | ||||||||||||||
| AF142988 Papio cynocephalus | ||||||||||||||
| HML2 | 32.2 | 26.1 | 21.3 | 20.4 | Using pt01Chr10_4757815_326 | |||||||||
| pt01Chr10_4757815_3269 | chr10: 4757815/(−) | 32.1 | 26 | 21.2 | 20.6 | beta (B) | K | 6 (B) | 3 (B) | 6 (B) | 10 (B) | 0.63 | 4 | AC016577Homo sapiens |
| hg16Chr1_152822428_3843 | (−?)/1q22 | 32.2 | 26.2 | 21.3 | 20.3 | beta (B) | K | 3 (B) | 0 (B) | 1 (B) | 0 (B) | 0.21 | 28 | |
| hg16Chr11_101103511_3881 | (−)/11q22 | 32.2 | 26 | 21.3 | 20.5 | beta (B) | K | 3 (B) | 0 (B) | 1 (B) | 1 (B) | 0.41 | 61 | |
| hg16Chr11_118138535_3044 | (−?)/11q22 | 32.1 | 26.2 | 21.4 | 20.3 | beta (B) | K | 3 (B) | 0 (B) | 7 (B) | 2 (B) | 0.41 | 4 | |
| hg16Chr12_57016965_3699 | (−)/12q14 | 32.3 | 26 | 21.2 | 20.5 | beta (B) | K | 2 (B) | 0 (B) | 4 (B) | 0 (B) | 0.41 | 58 | |
| hg16Chr22_17300741_3451 | (−?)/22q11 | 32.2 | 26.1 | 21.3 | 20.4 | beta (B) | 2 (B) | 1 (B) | 3 (B) | 0 (B) | 0.41 | 21 | ||
| hg16Chr3_114073183_3522 | (−)/3q13 | 32.3 | 26.1 | 21.3 | 20.4 | beta (B) | K | 2 (B) | 2 (B) | 2 (B) | 1 (B) | 0 | 106 | |
| hg16Chr3_186610428_4007 | (−)/3q27 | 32.2 | 26.2 | 21.1 | 20.4 | beta (B) | K | 2 (B) | 1 (B) | 1 (B) | 1 (B) | 0.31 | 11 | |
| hg16Chr5_156074791_3951 | (−)/5q33 | 32.2 | 26.2 | 21.3 | 20.3 | beta (B) | K | 2 (B) | 0 (B) | 1 (B) | 1 (B) | 0.21 | 24 | |
| hg16Chr6_78431679_3161 | (−)/6q14 | 32.2 | 25.9 | 21.4 | 20.5 | beta (B) | K | 2 (B) | 0 (B) | 3 (B) | 0 (B) | 0.31 | 33 | |
| hg16Chr7_4376621_3310 | (−?)/7q22 | 32.1 | 26.1 | 21.4 | 20.5 | beta (B) | 3 (B) | 0 (B) | 1 (B) | 0 (B) | 0.86 | 4 | ||
| hg16Chr7_4384369_3828 | (−?)/7q22 | 32.4 | 25.8 | 21.3 | 20.5 | beta (B) | K | 3 (B) | 1 (B) | 1 (B) | 0 (B) | 0.21 | 4 | |
| hg16Chr8_7352269_3797 | (−?)/8p23 | 32.3 | 25.9 | 21.3 | 20.5 | beta (B) | 2 (B) | 1 (B) | 1 (B) | 0 (B) | 1.36 | 16 | ||
| HERV-H like | 24.2 | 28.1 | 15.3 | 32.4 | Using pt01Chr12_68612294_457 | |||||||||
| pt01Chr12_68612294_457 | chr12: 68612294/2p14 | 25.5 | 29.6 | 16.2 | 28.7 | gamma (C) | 2 (C) | 13 (C) | 1.55 | 15 | AC003009Homo sapiens | |||
| pt01Chr3_171348113_448 | chr3: 171342431/4q31.3 | 24.4 | 28.4 | 14.6 | 32.6 | gamma (C) | H | 15 (C) | 1.26 | 2 | ||||
| hg16Chr13_107615439_763 | chr14: 92137066/13q33 | 23.5 | 28.5 | 14.7 | 33.2 | gamma (C) | 0 (C) | 18 (C) | 1.16 | 2 | ||||
| hg16Chr18_52888720_999 | chr17: 49759585/18q21 | 24.1 | 28.6 | 14.9 | 32.5 | gamma (C) | H | 8 (C) | 4 (C) | 16 (C) | 3 (C) | 1.33 | 2 | |
| hg16Chr2_216989568_637 | (−?)/2q35 | 24.5 | 27.5 | 14.7 | 33.3 | gamma (C) | H | 6 (C) | 19 (C) | 1.98 | 2 | |||
| hg16Chr2_71367277_635 | (−?)/2p13 | 23.2 | 27.3 | 17.8 | 31.7 | gamma (C) | H | 6 (C) | 16 (C) | 1.39 | 2 | |||
| hg16Chr20_12321779_626 | chr21: 12124144/20p12 | 24.4 | 28.1 | 14.7 | 32.8 | gamma (C) | H | 7 (C) | 33 (C) | 0.6 | 3 | |||
| hg16Chr4_154245926_660 | chr4: 171342440/4q31 | 24.3 | 28 | 14.8 | 32.9 | gamma (C) | H | 9 (C) | 13 (C) | 1.36 | 2 | |||
| hg16Chr5_103482398_993 | chr4: 109273559/5q21 | 24.8 | 27.7 | 15 | 32.5 | gamma (C) | H | 11 (C) | 12 (C) | 1.33 | 2 | |||
| hg16Chr6_125192129_682 | (−?)/6q22 | 23.7 | 26.5 | 17.3 | 32.5 | gamma (C) | 7 (C) | 2 (C) | 22 (C) | 1.62 | 2 | |||
| hg16Chr6_127150561_671 | chr5: 129741796/6q22 | 24.8 | 28.6 | 14.5 | 32.1 | gamma (C) | H | 8 (C) | 17 (C) | 1.39 | 2 | |||
| hg16Chr6_78371754_1345 | chr5: 79852317/6q14 | 24.4 | 28 | 14.7 | 32.9 | gamma (C) | H | 11 (C) | 5 (C) | 1 (C) | 1.8 | 2 | ||
| hg16ChrX_5657489_573 | chrX: 6014174/Xp22 | 23.5 | 28 | 15.1 | 33.4 | gamma (C) | H | 8 (C) | 2 (C) | 17 (C) | 1.71 | 2 | ||
a
Sequences are referred according to their chromosomal start positions and RetroTector scores. Species-unique integrations are underlined. BLAT results for uncertain species-unique integrations are presented in Fig. S6 in the supplemental material.
b
(−) indicates no detected proviral integration. (−?) indicates uncertain proviral integration or possible deletion.