Table 3. The contribution of LTR-retrotransposons to C. quinquefasciatus gene organization.
| Element | Interaction | Description | GENE ID | Supercont:position |
| Cqgypsy_2 | Within intron | Dual specificity tyrosine-phosphorylation-regulated kinase | CPIJ004687 | 3.72: 556,787–583,090 |
| Exon-Intron junction | 5′-3′ exoribonuclease, putative | CPIJ016423 | 3.746: 154,787–166,602 | |
| 1–2 Kbp upstream | fimbrin/plastin | CPIJ004008 | 3.57: 387,682–393,342 | |
| 2–3 Kbp downstream | allergen, putative | CPIJ018993 | 3.1504: 58,993–71,374 | |
| 0–1 Kbp downstream | Adenylyltransferase and sulfurtransferase MOCS3 | CPIJ001621 | 3.19: 246,047–247,568 | |
| Cqgypsy_3 | 0–1 Kbp downstream | disulfide oxidoreductase | CPIJ018966 | 3.1505: 2,834–13,165 |
| Cqgypsy_5 | 1–2 Kbp downstream | chaperonin | CPIJ013429 | 3.475: 239,574–242,207 |
| Exon-Intron junction | 40 S ribosomal protein S2 | CPIJ012693 | 3.480: 10,936–19,727 | |
| 4–5 Kbp upstream | serine threonine-protein kinase | CPIJ018896 | 3.1443: 17,857–21,694 | |
| Cqgypsy_7 | Within intron | Brahma associated protein 170 kD, putative | CPIJ002241 | 3.30: 656,859–677,280 |
| Overlap first exon | ribosomal protein L23a | CPIJ016489 | 3.858: 52,166–53,573 | |
| Cqgypsy_8 | 1–2 Kbp upstream | suppressor of ty3 | CPIJ014381 | 3.539: 307,272–309,528 |
| 1–2 Kbp downstream | suppressor of ty3 | CPIJ014381 | 3.539: 307,272–309,528 | |
| intron | suppressor of ty3 | CPIJ014381 | 3.539: 307,272–309,528 | |
| Cqgypsy_13 | 0–1 Kbp downstream | transcription factor IIIB 90 kDa subunit | CPIJ008270 | 3.167: 169,563–182,965 |
| Cqgypsy_15 | Within intron | dystrophin major muscle isoform | CPIJ013032 | 3.423: 50,593–185,416 |
| Cqgypsy_20 | 0–1 Kbp downstream | histone-lysine n-methyltransferase | CPIJ000732 | 3.6: 1,790,053–1,797,972 |
| Cqgypsy_21 | 0–1 Kbp upstream | flotillin-2 | CPIJ007626 | 3.148: 169,798–180,783 |
| Cqgypsy_25 | Exon-Intron junction | phd finger protein | CPIJ014131 | 3.545: 75,916–92,572 |
| Cqgypsy_29 | 3–4 Kbp downstream | protein phosphatase-1 | CPIJ008212 | 3.168: 687,712–708,602 |
| 0–1 Kbp downstream | helicase | CPIJ019431 | 3.1585: 41,788–51,610 | |
| Cqgypsy_37 | 1–2 Kbp downstream | sphingomyelin synthetase | CPIJ002233 | 3.30: 541,656–542,535 |
| 2–3 Kbp downstream | DEAD box ATP-dependent RNA helicase | CPIJ006204 | 3.118: 567,640–586,793 | |
| Cqgypsy_47 | 2–3 Kbp downstream | sodium/iodide cotransporter | CPIJ002364 | 3.33: 789,851–792,666 |
| 4–5 Kbp upstream | serine protease inhibitor, serpin | CPIJ012013 | 3.346: 385,437–397,533 | |
| 3–4 Kbp downstream | pre-mrna splicing factor prp17 | CPIJ011807 | 3.365: 424,340–426,137 | |
| 1–2 KbpUpstream | uridine cytidine kinase i | CPIJ016204 | 3.736: 44,070–45,560 | |
| 1–2 Kbp downstream | uridine cytidine kinase i | CPIJ016204 | 3.736: 44,070–45,560 | |
| 1–2 Kbp downstream | coatomer | CPIJ014834 | 3.606: 201,807–202,272 | |
| 1–2 Kbp downstream | poly a polymerase | CPIJ014835 | 3.606: 205,341–209,830 | |
| Cqgypsy_51 | 1–2 Kbp upstream | zinc finger protein | CPIJ009854 | 3.243: 281,133–285,737 |
| 2–3 Kbp upstream | DNA replication licensing factor MCM7 | CPIJ009855 | 3.243: 295,787–306,221 | |
| 2–3 Kbp downstrean | mitochondrial 39 S ribosomal protein L3 | CPIJ017407 | 3.941: 86,591–87,964 | |
| 1–2 Kbp downstream | 26 S protease regulatory subunit 6a | CPIJ017405 | 3.941: 78,697–79,175 | |
| Cqgypsy_53 | 3–4 Kbp downstream | esterase B1 precursor | CPIJ016336 | 3.777: 170,027–172,021 |
| 4–5 Kbp upstream | ATP synthase D chain, mitochondrial | CPIJ011691 | 3.328: 179,978–180,887 | |
| 2–3 Kbp downstream | Eftud2 protein, putative | CPIJ000064 | 3.1: 1,221,757–1,228,225 | |
| 1–2 Kbp upstream | cell division protein kinase 5 | CPIJ000065 | 3.1: 1,233,232–1,234,222 | |
| Exon-Intron junction | sarcolemmal associated protein-2, putative | CPIJ011313 | 3.310: 56,964–69,006 | |
| Cqgypsy_56 | Exon-Intron junction | semaphorin | CPIJ001593 | 3.17: 1,304,933–1,339,494 |
| Exon-Intron junction | microfibrillar-associated protein, putative | CPIJ020039 | 3.2342: 8,606–17,792 | |
| Exon-Intron junction | male-specific doublesex protein | CPIJ004057 | 3.59: 681,384–685,772 | |
| 1–2 Kbp downstream | polypeptide of 976aa, putative | CPIJ018525 | 3.1222: 14,705–19,317 | |
| Cqgypsy_59 | 1 Kbp upstream | negative elongation factor E | CPIJ000025 | 3.1: 727,264–728,238 |
| 4–5 Kbp downstream | semaphorin | CPIJ000027 | 3.1: 744,915–761,147 | |
| 4–5 Kbp downstream | superoxide dismutase, putative | CPIJ005173 | 3.91: 822,776–823,755 | |
| Within intron | enhancer of polycomb | CPIJ018246 | 3.1131: 70,175–80,884 | |
| Cqgypsy_60 | Overlaps last exon | serine protease inhibitors putative | CPIJ007021 | 3.133: 747,858–748,701 |
| 0–1 Kbp upstream | serine protease inhibitor | CPIJ007023 | 3.133: 758,924–759,336 | |
| 1 Kbp downstream | nucleoporin | CPIJ013031 | 3.426: 362,618–363,727 | |
| 0–1 Kbp upstream | 40 S ribosomal protein S14-A | CPIJ012110 | 3.400: 69,850–70,191 | |
| Cqgypsy_61 | Overlaps last exon | cytochrome c oxidase subunit I | CPIJ016836 | 3.816: 17,796–33,791 |
| Cqgypsy_63 | Within intron | Dual specificity tyrosine-phosphorylation-regulated kinase | CPIJ004687 | 3.72: 556,787–583,090 |
| Exon-Intron junction | 5′-3′ exoribonuclease, putative | CPIJ016423 | 3.746: 154,787–166,602 | |
| 4–5 Kbp upstream | alanine-glyoxylate aminotransferase | CPIJ006409 | 3.128: 202,128–218,875 | |
| Cqgypsy_64 | Exon-Intron junction | arsenite inducible RNA associated protein aip-1 | CPIJ005006 | 3.82: 520,914–524,059 |
| Exon-Intron junction | nk homeobox protein | CPIJ019260 | 3.1511: 40,639–44,852 | |
| 2–3 Kbp downstream | 60 S ribosomal protein L7 | CPIJ017548 | 3.961: 25,320–28,131 |
For each insertions detected in proximity (+/− 5 Kbp) or into genes are reported the kind of interaction (upstream, downstream, exon, intron), the Vectorbase identifier of the gene, its description and its position in the supercontig.