Table 2.
TE effect on the mouse transcriptome
| RE | Total | Intronic | TE in introns of UCSC annotated genesa | TE in introns of non-annotated genesa | TE exonization in UCSC annotated genesa | TE exonization in non-annotated genesa |
| B1 | 506,528 | 331,015 (65%) | 189,268 | 141,747 | 134 (0.07%) | 96 (0.07%) |
| MIR | 116,355 | 66,597 (63%) | 41,853 | 24,744 | 27 (0.06%) | 14 (0.06%) |
| B2 | 338,642 | 215,264 (63%) | 118,646 | 96,618 | 81 (0.07%) | 80 (0.08%) |
| B4 | 345,646 | 216,550 (66%) | 119,827 | 96,723 | 62 (0.05%) | 72 (0.07%) |
| ID | 45,955 | 30,285 (57%) | 18,022 | 12,263 | 8 (0.04%) | 3 (0.02%) |
| L1 | 820,434 | 457,705 (56%) | 181,292 | 276,413 | 102 (0.07%) | 189 (0.07%) |
| L2 | 56,518 | 34,923 (62%) | 18,963 | 15,960 | 9 (0.05%) | 5 (0.03%) |
| CR1 | 11,812 | 7,167 (61%) | 3,779 | 3,388 | 0 (0%) | 1 (0.03%) |
| LTR | 756,324 | 396,226 (52%) | 156,690 | 239,536 | 72 (0.05%) | 243 (0.1%) |
| DNA | 124,202 | 75,200 (60%) | 40,428 | 34,772 | 11 (0.02%) | 19 (0.05%) |
| Total | 3,122,416 | 1,830,932 (58%) | 888,768 | 942,164 | 506 (0.06%) | 722 (0.08%) |
Insertions of transposed elements (TEs) within the mouse genome. The different classes of the examined TEs are shown in the left column. 'Total' (second column) indicates the overall amount of each TE within the human and mouse genomes. 'Intronic' (third column) indicates the number of TEs within intronic regions, and the percentage of TEs within introns relative to the total amount of TEs is shown in parentheses. The fourth and fifth columns show the number of TEs within introns of University of California, Santa Cruz (UCSC) knownGene list (version mm6) and those inserted within genes not listed within UCSC knownGene list. The sixth and seventh columns show the numbers of exonized TEs within the UCSC knownGene list and those exonized within genes not listed within UCSC knownGene list. In brackets are indicated the percentage of exonized TEs. The lower row shows the total number of all TEs. aGene annotation is based on the annotations of the known gene list in the UCSC genome browser (version hg17). LTR, long terminal repeat; MIR, mammalian interspersed repeat; RE, retroelement.