Table 1.
Comparison of frequency of repetitive elements
| Results |
AF020503 and U66722
|
BAC 18C17
|
Intron 4 (and 3) (total 308 kb) | Intron 5 (total 150 kb) | Intron 5–7 (total 411 kb) | |||
|---|---|---|---|---|---|---|---|---|
| 0–60 | 60–120 | 120–180 | 180–240 | 240–308 | ||||
| SINEs | ||||||||
| Alus | 2,640 (4.4)* | 3,893 (6.5) | 3,748 (6.2) | 2,540 (4.2) | 5,309 (7.8) | 18,130 (5.9) | 8,370 (5.6) | 27,855 (6.8) |
| MIRs | 1,440 (2.4) | 1,216 (2.0) | 776 (1.3) | 1,734 (2.9) | 1,585 (2.3) | 6,751 (2.2) | 4,630 (3.1) | 11,800 (2.9) |
| LINEs: | ||||||||
| L1 | 9,056 (15.1) | 6,937 (11.6) | 21,806 (36.3) | 3,313 (5.5) | 9,956 (14.6) | 51,068 (16.6) | 22,679 (15.1) | 27,458 (6.7) |
| L2 | 1,227 (2.0) | 1,002 (1.7) | 70 (0.1) | 3,362 (5.6) | 2,423 (3.5) | 8,084 (2.6) | 2,078 (1.4) | 15,913 (3.9) |
| LTR elements | ||||||||
| MaLRs | 0 (0) | 1,260 (2.1) | 1,632 (2.7) | 369 (0.6) | 2,738 (4.0) | 5,999 (2.0) | 3,173 (2.1) | 17,174 (4.2) |
| Retroviral | 207 (0.3) | 457 (0.8) | 1,181 (2.0) | 3,434 (5.7) | 638 (0.9) | 5,917 (1.9) | 1,083 (0.7) | 3,248 (0.8) |
| DNA elements | ||||||||
| MER1 | 1,442 (2.4) | 621 (1.0) | 1,625 (2.7) | 890 (1.4) | 875 (1.3) | 5,453 (1.8) | 2,451 (1.6) | 8,048 (2.0) |
| MER2 | 2,845 (4.7) | 0 (0) | 3,181 (5.3) | 960 (1.6) | 641 (0.9) | 7,627 (2.5) | 2,779 (1.9) | 3,060 (0.7) |
| Mariners | 0 (0) | 66 (0.1) | 79 (0.1) | 0 (0) | 0 (0) | 145 (0) | 1,368 (0.9) | 91 (0) |
| Unclassified | 779 (1.3) | 0 (0) | 526 (0.9) | 763 (1.3) | 525 (0.8) | 2,593 (0.8) | 1,028 (0.7) | 0 (0) |
| Total repeats | 20,290 (33.8) | 15,757 (26.3) | 35,013 (58.4) | 20,022 (33.4) | 29,032 (42.4) | 120,114 (38.9) | 49,986 (33.3) | 128,170 (31.2) |
| GC content, % | 38.9 | 38.9 | 36.8 | 40.3 | 38.2 | 38.6 | 38.3 | 38.6 |
Data are shown as total and percentage of (in parentheses) nucleotides. The sequence of the 0- to 120-kb region of intron 4 was reported previously (accession nos. AF020503 and U66722). The 120- to 308-kb region represents the newly sequenced region. Alu sequences are most frequent in the 240- to 308-kb region (7.8%). LINE1 sequences are notably more frequent in the 120- to 180-kb region (36.3%) than in other regions. The total LINE1 content is higher in intron 4 (16.6%) than in the previously sequenced region of intron 5 (15.1%). Long terminal repeat (LTR/retroviral) elements are most frequent (5.7%) in the 180- to 240-kb region, especially in clusters around exon 4. MIR, mammalian-wide interspersed repeat; SINE, short interspersed nuclear elements; MaLR, mammalian LTR retrosequences; MER, medium reiteration frequency element.