TABLE 2.
Satellite junction regions identified in theA. gambiae genome sequence
| Scaffold
|
Coordinates on scaffold
|
Mate pair information
|
||||||
|---|---|---|---|---|---|---|---|---|
| StDNA | Name | Length | Adjacent sequence similar to (expect value) |
53-bp satellite |
Adjacent sequence |
Junction-spanning fragment (orientation)a |
Insert size (kb) | Mate sequence similar to (expect value) |
| AgY53A | 4063 | 1330 | Repetitiveb; no similarity to known TEs | 1–351 | 352–1330 | 55433665 (+/+) | 10 | AgY53A |
| 6929 | 11068 | AgY373 stDNA | 675–11068c | 5–281 | 55794517 (+/+) | 10 | AgY53A | |
| 3901 | 2570 | ENSANGP00000018025, A. gambiae (8e-36)d | 2006–2570 | 10–660 | 56838282 (+/−) | 10 | AgY53B/AgY53A junction | |
| 1–456 | 56521932 (+/+) | 10 | AgY53A | |||||
| 4621 | 1276 | pygopus gene, D. melanogaster (2e-04)e | 355–1276 | 164–322 | 56037571 (+/−) | 10 | AgY53A | |
| 17–355 | 55582724 (+/+) | 10 | AgY53A | |||||
| AgY53B | 4339 | 1310 | AgY477 stDNA | 503–1310 | 1–497 | 59870233 (+/−) | 50 | AgY477 |
| 47452583 (+/+) | 2.5 | AgY53B | ||||||
| Ag53C | 3553 | 1113 | Transposon Tsessebe III; A. gambiae (0.0) | 623–1113 | 1–624 | 46844423 (+/+) | 2.5 | agCP7415, A. gambiae (e-140); blastopia |
| Polyprotein, D. melanogaster (1.2) | ||||||||
| 56602027 (+/−) | 10 | Ag53C | ||||||
| 4593 | 1340 | Repetitivef; no similarity to known TEs | 1–1137 | 1150–1340 | 55141577 (+/+) | 2.5 | Retrotransposon R2 gag polyprotein, Nasonia vitripennis (5e-05) |
|
| 7835 | 2991 | Repetitiveg; no similarity to known TEs | 692–2991 | 1–691 | 46910563 (+/+) | 2.5 | Ag53C | |
| 2370 | 1444 | Complex-B satellite | 1–289 | 303–1444 | 55518933 (+/−) | 10 | Ag53C | |
| 59577007h (+/+) | 15 | Complex-B | ||||||
| 5564 | 1216 | Complex-B satellite | 405–1216 | 1–403 | 117434796 (+/−) | 14 | Complex-B | |
| 56786386 (+/+) | 10 | Ag53C | ||||||
Fragment names are from the NCBI Trace Archive at http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi; Orientation, +/+, forward, with mate sequence positioned downstream from the junction; +/−, reverse, with mate sequence upstream from the junction. Where available, mate-pair information provided for two clones to reveal the nature of sequences at both flanks of the junction.
At least 60 hits.
The 6829 scaffold encompasses a sequence gap between positions 2054 and 9833.
Similar to putative transposase from Oryza sativa (expected value 1.8).
Similar to the T1-1 transposon, A. gambiae (expected value 0.018).
Three hits, including the 4593 scaffold.
At least 20 hits.
The fragment shows slight sequence discrepancies when compared to the junction sequence on the scaffold and it may represent another, but nearly identical, junction.