Drosophila Euchromatic LTR Retrotransposons are Much Younger Than the Host Species in Which They Reside

Table 3.

LTR Retrotransposons Characterized in This Study

Element Accession # Genomic location ITR DTR LTR length (bp) Inserted element length LTR % identity Element age in millions of years
17.6-1 AC005860 2R/47D1 AG/TT ATAT/ATAT 512 7202 100 0
17.6-2 AC005894 2R/46A1-46B2 AG/TT ATAT/ATAT 512 7200 100 0
17.6-3 AC004333 3L/62A1-62A4 AG/TT ATAT/ATAT 512 7245 100 0
17.6-4 AE003471 3L AG/TT ATAT/ATAT 514 6505 100 0
17.6-5 AE003082 2R AG/TT ATAT/ATAT 512 6329 99.419 0.181563
17.6-6 AE003545 3L AG/TT ATAT/ATAT 517 6509 99.189 0.253438
297-1 AC006303 2L/35E-36A AG/CT ATAT/ATAT 414 6808 100 0
297-2 AC007176 2L-2R/37C1-46B2 AG/CT ATAT/ATAT 414 6791 100 0
297-3 AC005558 2L/23A1-23B2 AG/CT ATAT/ATAT 414 6336 100 0
297-4 AC005720 3L/79F1-80A2 AG/CT ATAT/ATAT 414 6730 100 0
297-5 AC004306 2R/51E1-51E2 AG/CT ATAT/ATAT 414 6805 100 0
297-6 AC002441 2L/35F3-35F6 AG/CT ATAT/ 414/3′ LTR  DELETION 6809 100
297-7 AE003413 2L/34C4-36A7 AG/CT ATAT/ATAT 414 6808 100 0
297-8 AE003574 X AG/CT ATAT/ATAT 414 5708 100
297-9 AE003415 SL/34C4-36A7 AG/CT ATAT/ATAT 415 6809 100 0
297-10 AE003599 3L AG/CT ATAT/ATAT 414 5549 99.193 0.252188
412-1 AC005847 3L/61F3-62A2 TG/CT ATAT/ACAG 571 7592 99.789 0.065938
412-2 AC005639 2R/59E3-59F4 TG/CA AGGG/AGGG 481 7519 100 0
412-3 AC005267 3L/60A2-60B2 TG/CA ATAT/ATAT 514 7566 100 0
412-4 AL050231 X/1A-1B TG/TA CAAT/TATC 512 7572 100 0
412-6 AE003417 X TG/TA CCAAT/TCGAC 514 7578 99.415 0.182813
412-7 AE003429 X TG/CA TGAA/TGAA 515 99.610 0.121875
412-8 AE003553 3L TG/CA GGGAGA/TGGCGA 514 7582 99.805 0.060938
412-9 AE003709 3R TG/CA CTAC/CTAC 517 7558 99.368 0.197500
412-10 AE003461 2R TG/CA AGGG/AGGG 481 7452 100 0
412-11 AE003462 2R TG/CA ATAT/ATAT 518 7492 99.364 0.198750
412-12 AE003463 2R TG/CA ATAG/ATAG 482 7454 100 0
412-13 AE003463 2R TG/CA CGAT/CGAT 484 7461 99.583 0.130313
412-14 AE003464 2R TG/CA AGTATG/CTAGAG 472 7446 100 0
412-15 AE003470 3L TG/CA GTCCTT/CAAGTC 518 7529 100 0
412-16 AE003470 3L TG/CA GATATA/ACAGCA 572 7576 99.786 0.066875
412-17 AE003511 X TG/CA AAAC/AAAC 514 7520 100 0
412-18 AE003523 3L TG/CA GTGG/GTGG 514 7520 99.790 0.065625
412-19 AE003718 3R TG/CA ACAG/ACAG 483 7550 100 0
antonia-1 AC005891 2L/33F3-34A2 AG/TT ATAT/ATAT 659 6953 100 0
antonia-2 AC004362 2L/35E3-35E6 AG/TT ATAT/ATAT 659 6943 100 0
antonia-3 AE003640 2L AG/TT ATAT/ATAT 661 6170 99.697 0.094688
antonia-4 AE003786 2R AG/TT ATAT/ATAT 661 6116 98.573 0.445938
blastopia-1 AC007177 2R/59C1-59C5 TG/CA TATA/TATA 276 5029 100 0
blastopia-2 AC006402 2L/38C-38D TG/CA TATA/TATA 276 5029 100 0
blastopia-3 AC005638 2R/47E1-47E3 TG/CA TTTA/TTTA 276 4264 100 0
blastopia-4 AL033125 DISTAL X TG/CA TATA/TATA 276 4645 100 0
blastopia-5 AE003417 X TG/CA TACA/TACA 276 4272 100 0
blastopia-6 AE003489 X TG/CA TGTA/TGTA 275 3851 100 0
blood-1 AC002474 2L/38D1-38D2 TG/CA GTAC/GTAC 399 7411 100 0
blood-2 AC005734 2L/31A1-31B1 TG/CA AAGG/AAGG 401 7413 100 0
blood-3 AC004442 2L/22A3-22A7 TG/CA GTGG/GTGG 399 7408 100 0
blood-4 AC005130 2L/39C1-39D1 TG/CA AGCA/AGCA 399 7415 100 0
blood-5 AC007082 2L/37D TG/CA CCTG/CCTG 401 7417 100 0
blood-6 L49394 2L/35E1-35E2 TG/CA AGGG/AGGG 399 7411 100 0
blood-7 AC004115 2L/27B7-21C2 TG/CA GAAT/GAAT 415 7443 99.758 0.07563
blood-8 AC003727 3R TG/CA ATAT/AGTC 395 7425 99.500 0.15625
blood-9 AE003413 2L/34C4-36A7 TG/CA AGGG/AGGG 399 7411 100 0
blood-10 AE003647 2L TG/CA AGGG/AGGG 399 7421 100 0
blood-11 AE003718 3R TG/CA ATAC/ATAC 399 7421 100 0
blood-12 AE003775 3R TG/CA GTAC/GTAC 399 7421 100 0
blood-13 AE003555 3L TG/CA ACAT/ACAT 400 7422 99.750 0.078125
blood-14 AE003667 2L TG/CA GTAC/GTAC 400 7420 99.748 0.078750
blood-15 AE003670 2L TG/CA AGCA/AGCA 400 7420 99.751 0.077813
blood-16 AE003633 2L TG/CA GCAG/GCAG 400 7422 100 0
blood-17 AE003709 3R TG/CA ACAG/ACAG 401 7425 100 0
blood-18 AE003598 3L TG/CA CTGC/CTGC 401 7423 100 0
blood-19 AE003780 3R TG/CA CTAC/CTAC 402 7427 100 0
blood-20 AE003589 2L TG/CA GAAT/GAAT 415 7452 99.758 0.075625
blood-21 AE003638 2L TG/CA GTAC/GTAC 377 7403 99.24 0.237500
burdock-1 AE002976 2R/41C-41D AG/TT TATA/TATA 276 6425 100 0
copia-1 AC007146 2L/33A TG/CA GATCC/GATCC 276 5146 100 0
copia-2 AC001657 2L/35B7-35C1 TG/CA GTTTC/GTTTC 276 5145 100 0
copia-3 AC004445 2L/22A3-22A5 TG/CA GTTGG/GTTGG 276 5145 100 0
copia-4 AC005554 2L/23C4-23D4 TG/CA TTATC/TTATC 276 5145 100 0
copia-5 AC004276 2L/22E1-22E2 TG/CA GTATC/GTATC 276 5147 100 0
copia-6 AC005647 2R/53C7-53C14 TG/CA TATGT/TATGT 276 5151 100 0
copia-7 AC002501 2L/35F1-35F2 TG/CA AAAAT/AAAAT 276 5149 100 0
copia-8 AC004735 2L/38A7-39C9 TG/CA GAGCA/GAGCA 276 5144 100 0
copia-9 AC003053 2L/24A3-24C2 TG/CA ATCAC/ATCAC 276 5145 100 0
copia-10 AC011662 2L/36D TG/CA ATAAC/ATAAC 275 5145 100 0
copia-11 AC006215 2L/38C1-38C2 TG/CA ACTGC/ACTGC 275 5252 100 0
copia-12 AE003494 X TG/CA TTGAC/TTGAC 276 4835 99.638 0.113125
copia-14 AE003794 2R TG/CA GGTTC/GGTTC 276 4837 100 0
copia-15 AE003804 2R TG/CA ACGCC/ACGCC 276 4742 100 0
copia-16 AE003777 3R TG/CA GATGG/GATGG 277 4836 100 0
copia-17 AE003806 2R TG/CA TATGT/TATGT 277 4511 99.628 0.116250
copia-18 AE003579 2L TG/CA ATCAC/ATCAC 277 4747 100 0
copia-19 AE003729 3R TG/CA AAAAC/AAAAC 277 4506 100 0
copia-21 AE003466 2R TG/CA CTTTG/CTCAG 278 5176 100 0
copia-22 AE003783 2L TG/CA AACAC/AACAC 278 4509 100 0
copia-23 AE003526 3L TG/CA AATAT/AATAT 288 4564 100 0
copia-24 AE003778 3R TG/CA ATTAT/ATTAT 307 4741 98.536 0.457500
copia-25 AE003473 3L TG/CA AGAAC/AGAAC 276 4120 100 0
hamilton-1 AC006215 2L/38C1-38C2 AG/TT TGTA/TGTA 495 6973 100 0
hamilton-2 AC006215 2L/38C1-38C2 495 6973 100 0
HMS Beagle-1 AC004563 2R/56D11-56E6 AG/CT TATA/TATA 266 6883 100 0
HMS Beagle-2 AC007977 2L/27C AG/CT TATA/TATA 266 6885 100 0
HMS Beagle-3 AL121804 DISTAL X AG/CT TATA/TATT 266 6887 100 0
HMS Beagle-4 AE003116 3L AG/CT TATA/TATA 332 7180 99.034 0.301875
HMS Beagle-5 AE003574 X AG/CT TGTA/TGTA 332 7008 99.698 0.094375
HMS Beagle-6 AE003600 3R AG/CT TATA/TATA 332 7217 100 0
HMS Beagle-7 AE003679 AG/CT TGCA/TGCA 266 4441 100 0
HMS Beagle-8 AE003651 2L AG/CT TGTA/TGTA 266 6906 100 0
mazi-1 AC004377 2R/58E8-58F4 TG/CA ATGCTT/ATGGAA 224 6112 100 0
mazi-2 AE003482 3L TG/CA AAGGG/AAGGG 245 6150 100 0
mazi-3 AE003615 2L TG/CA GCTGG/GCTGG 245 6148 100 0
mazi-4 AE003777 3R TG/CA AGTGT/AGTGT 245 6149 100 0
mdg1-1 AL138971 DISTAL X TG/CA CTAG/CTAG 442 7355 100 0
mdg1-2 AE003736 3R TG/CA CTCC/CTCC 442 8170 99.582 0.130625
mdg1-3 AE003828 2R TG/CA TCAC/TCAC 444 7420 99.320 0.212500
mdg1-4 AE002943 TG/CA CTAT/CTAT 425 8213 100 0
mdg3-1 AC004574 2L/22B1-22B2 TG/AA GTAG/GTAG 267 5519 100 0
mdg3-2 AC004735 2L/38A7-38C9 TG/AA GCAC/GCAC 267 5504 100 0
mdg3-3 AE003607 3R TG/AA ATTG/ATTG 265 5526 100 0
mdg3-4 AE003492 X TG/AA ATGT/ATGT 267 5399 100 0
mdg3-5 AE003514 3L TG/AA GTAT/GTAT 267 5331 100 0
mdg3-6 AE003604 3R TG/AA CCAT/CCAT 267 5330 100 0
mdg3-7 AE003686 3R TG/AA GTTG/GTTG 267 5526 100 0
mdg3-8 AE003502 X TG/AA TACT/TACT 268 5529 99.247 0.235313
micropia-1 AE003672 3R TG/CA TATA/TATA 514 5124 99.405 0.185938
nik AE003485 X AG/TT CCAG/CCAG 430 6938 100 0
nomad-1 AE003411 2L/35B4-35C1 AG/CT TTATA/TATA 518 7389 100 0
nomad-2 AC004716 2L/22C1-22C2 AG/CT TTTA/TTTA 518 7473 100 0
nomad-3 AC005111 2L/31F5-32A1 AG/CT TTCA/TTCA 518 7473 100 0
nomad-4 AL121805 DISTAL X AG/CT TATA/TATA 517 7475 100 0
roo-1 AC005333 2L/26A1-26A3 TG/CA GGTAC/GGTAC 428 8067 100 0
roo-2 AC004728 2L/29D1 TG/CA AGCGC/AGCGC 429 8218 100 0
roo-3 AC001647 2R/35A1 TG/CA GTTAT/GTTAT 428 8211 100 0
roo-4 AC001659 2L/34D1-34D4 TG/CA CTAAC/CTAAC 429 8209 99.528 0.147500
roo-5 AC007453 2R/49D1-49D3 TG/CA TGGCC/TGGCC 428 7411 100 0
roo-6 AC004438 3L/68C2-68C3 TG/CA CATTT/CATTT 428 8251 99.766 0.073125
roo-7 AC004767 3L/65A6-65A10 TG/CA AACGG/AACGG 428 8211 99.766 0.073125
roo-8 AC004245 2L/21D1-21D2 TG/CA GCCCC/GCCCC 428 8087 100 0
roo-9 AC005974 2R/46E1-46F6 TG/CA TGTAT/TGTAT 428 8215 99.766 0.073125
roo-10 AC011662 2L/36D TG/CA CCCCC/CCCCC 428 8209 100 0
roo-11 AC006415 2L/40B-40C TG/CA GCTTCC/GCTTCC 428 8212 100 0
roo-12 AL035311 DISTAL TIP OF X TG/CA GCATC/GCATC 427 7788 100 0
roo-13 AL121805 DISTAL TIP OF X TG/CA TTAAT/TTAAT 428 8197 100 0
roo-14 AC004349 3L/65B1-65B2 TG/CA TAATA/ 428/3′ END   DELETION 5895 100 0
roo-16 AL031366 DISTAL TIP OF X TG/CA ATTA/ATTA 428 7758 100 0
roo-17 AL138971 DISTAL X TG/CA GGGAC/GGGAC 428 7593 100 0
roo-19 AE003606 3R TG/CA ATAAG/ATAAG 429 8211 100 0
roo-21 AE003428 X TG/CA CATAC/CCAGA 429 8086 99.532 0.146250
roo-22 AE003703 3R TG/CA AGAC/AGAC 429 8317 99.766 0.073125
roo-23 AE003497 X TG/CA GTCAT/GTCAT 429 8087 100 0
roo-24 AE003552 3L TG/CA TGGAG/TGGAG 429 8086 100 0
roo-25 AE003421 X TG/CA CAGCT/CAGCT 430 8251 100 0
roo-26 AE003773 3R TG/CA CAAAT/CAAAT 430 7332 99.767 0.072813
roo-27 AE003753 3R TG/CA AGGGC/AGGGC 430 8229 99.765 0.073438
roo-28 AE003756 3R TG/CA ATAGT/ATAGT 430 8229 99.766 0.073125
roo-29 AE003455 2R TG/CA ACTAC/ACTAC 431 8089 99.523 0.149063
roo-30 AE003544 3L TG/CA CATTT/CATTT 431 8086 99.769 0.072188
roo-31 AE003679 3R TG/CA GCCGG/GCCGG 431 8240 99.768 0.072500
roo-32 AE003738 3R TG/CA AGACC/AGACC 431 8240 99.766 0.073125
roo-33 AE003529 3L TG/CA ATAGG/ATAGG 431 8087 100 0
roo-34 AE003470 3L TG/CA ATAA/ATAA 432 8144 99.295 0.220313
roo-35 AE003455 2R TG/CA GCCAG/GCCAG 432 8086 99.766 0.073125
roo-36 AE003519 2R TG/CA GAAGG/GAAGG 432 8090 99.768 0.072500
roo-37 AE003520 3L TG/CA AATAG/AATAG 432 8089 99.766 0.073125
roo-38 AE003467 3L TG/CA TAAAC/TAAAC 433 8241 99.769 0.072188
roo-39 AE003515 3L TG/CA CTTGC/CTTGC 433 8091 99.761 0.074688
roo-40 AE003419 X TG/CA TTAC/TTAC 434 8090 99.529 0.147188
roo-41 AE003781 2L TG/CA ATAAC/ATAAC 431 8251 100 0
roo-42 AE003463 2R TG/CA CTTTA/CTTTA 430 8088 100 0
roo-43 AE003410 2L, REGION 34C4-36A7 TG/CA ATAAC/ATAAC 428 8142 100 0
tirant-1 AC005444 2L/36D3 AG/CT CGCG/CGCG 417 8109 100 0
tirant-2 AC004759 2L/38E1-38E9 AG/CT CCCG/CCCG 417 7399 100 0
tirant-3 AE003829 2R AG/CT CGTG/CGTG 418 8016 100 0
tirant-4 AE003601 3R AG/CT CCCG/CCCG 418 8016 100 0
tirant-5 AE003593 3L AG/CT CGCG/CGCG 418 8016 100 0
tirant-6 AE003843 4 AG/CT CGCT/CGAT 419 8017 100 0
transpac-1 AC006302 2L/34C4-34D2 AG/CT ATAT/ATAT 330 5249 100 0
transpac-2 AE003426 X AG/CT ATAT/ATAT 330 5251 100 0
transpac-3 AE003762 3R AG/CT ATAT/ATAT 330 5247 100 0
transpac-4 AE003508 X AG/CT ATAT/ATAT 331 5253 100 0
wolfman-1 AC007146 2L/33A-33A TG/CA AAGC/AAGC 506 7345 100 0
wolfman-2 AE003439 X TG/CA CCTG/CCTG 506 7231 100 0
unclassified AE002665 3L TG/CA AATG/AATG 266 7436 100 0
unclassified AE002987 X AG/TT TATA/TATA 414 8437 99.510 0.153125
unclassified AE003268 AG/CT TATA/TATA 416 7185 99.760 0.075120
unclassified AE003450 X AG/TT TATA/TATA 405 6538 100 0
unclassified AL035631 DISTAL X AG/TT TCTA/TCTA 353 5023 99.433 0.177054

This Article

  1. Published in Advance August 16, 2001, doi: 10.1101/gr.164201 Genome Res. 11: 1527-1540

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