TABLE 2.
Summary of the frequency of retrotransposons and estimates about the number of open reading frames for their encoded proteins.
| LTR | LINE | SINE | References | |
| % Human genome | 9% | 21% | 14% | Lander et al., 2001 |
| Integration mechanism | dsDNA + IN | TPRT + EN | TPRT + EN (from L1) | |
| # of potential coding loci | Predicted in1:12779 | Predicted in1:21187 | 0 | 1 Nakagawa and Takahashi, 2016 |
| Predicted in2 ≈ 3000 Pol ORFs | 2 Seifarth et al., 2005 | |||
| # of TEs with coding potential | Predicted in3:42 HERVs regions with 29 Env, 13 Pol, 17 Gag ORFs | Predicted in6:146 flL1 with complete ORF1p and ORF2p ORFs, 107 ORF2-only | Not coding | 3 Villesen et al., 2004 |
| Predicted in5:15 Env, 14 Pol, 25 | 4Garcia-Montojo et al., 2018, 2021 | |||
| Gag, 11 Rec, 12 Np94, 8 IN | 5 Bray et al., 2016 | |||
| 6 Penzkofer et al., 2017 | ||||
| 7 Mills et al., 2007 |
LINEs are the most represented subclass in the human genome covering 21% of the human genome with about 500,000 copies (Lander et al., 2001) of which only a small fraction of the LINE-1 family is mobile. HERVs are thought to have lost mobility, but some HERV families still encode functional proteins. LINE-1 integration is mediated by the LINE-1 encoded EN via a mechanism called targeted primed reverse transcription, TPRT. HERV elements integrate via a pre-integration complex formed by the IN protein, viral dsDNA, and host proteins. Non-autonomous SINEs do not encode protein as they use the retrotransposition machinery and form an RNP with their RNA and the LINE-1 encoded ORF1 and ORF2 for integration. Listed are predictions for the number of potential coding loci for HERV and LINE-1 elements using different sources. Of note, TEs are polymorphic in populations and these predictions are mostly based on reference genomes.