1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
|---|
artifical sequence | Locus-Assigner | # diff's | # recom's | loci involved | recom region | # diff's to locus | p value | # diff's after recom |
|---|
B86_B107
| 22_012 |
37
| 1 | 22_012 7_450 | 282 – 307 | 4 0 | 0,001 | 4 |
B112_B131
| 7_450 |
34
| 1 | 7_450 6_324/3_496 | 282 – 307 | 1 0 | 0,001 | 1 |
B2_B15_B2
| 4_742 |
26
| 2 | 4_742 10_019 4_742 | 317 – 384 583 – 603 | 0 0 0 | 0,003 0,001 | 0 |
B443_B474
| 10_019 |
18
| 2 | 10_019 3_385 | 388 – 436 | 3 2 | 0,001 |
5
|
B86_B44
| 22_012 |
8
| 1 | 10_310 1_504 | 59 – 191 503 – 639 | 0 4 |  |
4
|
B86_B44
| 22_012 |
8
| 0 | 22_012 | Â | 8 | Â |
8
|
B44_B45_B187
| 11_424/3_610/5 544/7_345 |
6
| 0 | 11_424/3_610/5_544/7_345 | Â | 6 | Â |
6
|
- Test sequences were created in silico by combining sequence regions of assignable HML-2 cDNA sequences, with the aim to construct recombination events between transcripts from corresponding HML-2 loci. Pairwise comparisons, using the in-house Bio-Python script Locus-Assigner, were then performed for test and reference sequences. Column 1 denotes the cDNA sequence name. Column 2: best matching HML-2 proviral locus according to pairwise sequence comparisons with Locus-Assigner. The numbers given here disregard the PCR primer binding regions, and therefore are, for HERV-KX sequences B262, B12 and 93, below the <18 nt differences-threshold initially set for HERV-KX (see text). Due to the lack of a HERV taxonomy, and for the sake of simplicity, HML-2 proviral loci have been numbered artificially in this paper, with the first number indicating chromosomal location of the locus, and the second number being a consecutive number without further connotation. Column 3: nucleotide differences to best match. Column 4: number of recombinations according to RECCO. Column 5: proviral loci involved in recombination(s). More than one locus is given when different loci displayed identical (dis)similarities. Column 6: regions where recombination(s) occured, with the 5' end of the RT-PCR product being defined as nucleotide +1. Column 7: nucleotide differences to individual HML-2 loci. Column 8: p-values of particular predicted recombinations. Column 9: nucleotide differences remaining after considering recombination(s) (see text).
