Table 2 Numts detected in the chicken nuclear genome, and parameters of alignments returned on BLASTN searches. Start and end indicates positions of alignments in the chicken mitochondrial (mtDNA) and chromosomal (chrom) sequences. Orientation corresponds to whether integration in the nuclear genome is 5' > 3' (+) or 3' > 5' (-). E-val and % ID are respectively expected value and % of identity for each returned alignment. Some Numts were identified by more than one alignment.
Numt # | Genes included | start mtDNA | End mtDNA | Orientation | chromosome | Start on chrom. | End on chrom. | Orientation | Blast score | E-val | %ID | Length of alignment | Length of Numt |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ND4 | 12341 | 12585 | + | 1 | 13059619 | 13059865 | - | 610 | 5.9e-32 | 74.10 | 251 | 848 |
| Â | ND4 | 11738 | 12327 | + | 1 | 13059865 | 13060448 | - | 536 | 5.9e-32 | 58.65 | 607 | - |
2 | tRNAGlu – CR – tRNAPhe – 12S | 1063 | 1342 | + | 1 | 18250179 | 18250453 | - | 370 | 1.9e-05 | 61.97 | 284 | 1536 |
|  | tRNAGlu – CR – tRNAPhe – 12S | 563 | 1139 | + | 1 | 18250273 | 18250834 | - | 743 | 2.4e-22 | 62.29 | 586 | - |
|  | tRNAGlu – CR – tRNAPhe – 12S | 16582 | 16748 | + | 1 | 18250802 | 18250966 | - | 364 | 3.5e-05 | 69.46 | 167 | - |
3 | tRNASer – tRNALeu | 12941 | 13069 | - | 1 | 132949128 | 132949256 | + | 397 | 3.8e-05 | 80.15 | 131 | 131 |
4 | ND4 – tRNAHis – tRNASer | 12572 | 12980 | - | 2 | 48703806 | 48704212 | + | 1598 | 5.8e-61 | 88.83 | 412 | 412 |
5 | ND5 | 13569 | 13804 | + | 2 | 88002064 | 88002298 | + | 460 | 2.2e-08 | 67.78 | 239 | 239 |
6 | tRNATrp – tRNAAla | 6274 | 6404 | - | 4 | 1975588 | 1975719 | - | 381 | 6.2e-06 | 79.26 | 135 | 135 |
7 | 16S – tRNALeu – ND1 | 3314 | 3389 | + | 4 | 22850352 | 22850426 | + | 257 | 5.5e-70 | 82.89 | 76 | 1182 |
|  | 16S – tRNALeu – ND1 | 3695 | 4169 | + | 4 | 22850419 | 22850882 | + | 1101 | 5.5e-70 | 73.50 | 483 | - |
|  | 16S – tRNALeu – ND1 | 4200 | 4498 | + | 4 | 22850879 | 22851175 | + | 737 | 5.5e-70 | 74.01 | 304 | - |
8a | ND5 – cyt b | 14548 | 14983 | - | 4 | 47771664 | 47772104 | + | 1005 | 3.8e-34 | 72.67 | 450 | 1733 |
8b | ND5 | 13251 | 13612 | + | 4 | 47772159 | 47772520 | + | 426 | 5.8e-08 | 63.52 | 381 | - |
9 | CR | 476 | 842 | - | 4 | 72432412 | 72432775 | + | 572 | 1.1e-14 | 65.96 | 379 | 782 |
| Â | CR | 141 | 608 | - | 4 | 72432642 | 72433107 | + | 405 | 4.3e-07 | 60.37 | 492 | - |
| Â | CR | 61 | 526 | - | 4 | 72432662 | 72433124 | + | 458 | 1.7e-09 | 60.33 | 484 | - |
10 | ND4 | 11603 | 11748 | + | 9 | 21658995 | 21659139 | - | 436 | 1.7e-07 | 78.08 | 146 | 146 |
11 | CR | 309 | 505 | + | 15 | 7657960 | 7658157 | + | 479 | 1.9e-10 | 73.76 | 202 | 202 |
12 | Cyt b | 15247 | 15565 | - | 19 | 5161850 | 5162161 | - | 797 | 7.6e-25 | 73.67 | 319 | 319 |
13 | CO2 – tRNALys – ATP8/6 | 9192 | 9883 | + | 27 | 2160604 | 2161286 | - | 2022 | 3.1e-81 | 77.92 | 693 | 1204 |
|  | CO2 – tRNALys – ATP8/6 | 8680 | 9630 | + | 27 | 2160837 | 2161782 | - | 1393 | 4.0e-52 | 65.21 | 986 | - |