Table 1.
Features of the coding sequences of black grouse MHC-B genes and sequence comparisons with homologous genes in chicken, turkey, quail and pheasant
| Gene | Position | Strand | Gene length (bp) | Exons | Exons verified* | Average coverage per nucleotide |
Comparison with other galliformMHCs |
dN/dS | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Chicken |
Turkey |
Quail |
Pheasant |
||||||||||||
| Nucleotide identity | Amino Acid Identity | Nucleotide identity | Amino Acid Identity | Nucleotide identity | Amino Acid Identity | Nucleotide identity | Amino Acid Identity | ||||||||
| BTN1(partial) |
112-4076 |
+ |
786 |
14 |
1 |
34.6 |
|
|
|
|
|
|
|
|
|
| BTN2 |
7150-10374 |
+ |
921 |
8 |
0 |
0 |
0.797 |
0.738 |
0.913 |
0.894 |
/ |
/ |
/ |
/ |
0.470 |
| BG1 |
12132-16240 |
- |
804 |
14 |
1 |
1.0 |
0.881 |
0.826 |
0.851 |
0.800 |
0.832 |
0.771 |
/ |
/ |
0.335 |
| Blec2 |
18188-20712 |
- |
825 |
6 |
1 |
5.8 |
0.698 |
0.595 |
0.706 |
0.593 |
0.705 |
0.607 |
/ |
/ |
0.433 |
| Blec1 |
23007-24547 |
+ |
471 |
5 |
1 |
1.0 |
0.934 |
0.917 |
0.949 |
0.942 |
0.927 |
0.894 |
0.958 |
0.947 |
0.230 |
| BLB1** |
25386-26738 |
- |
792 |
6 |
3 |
18.1 |
0.920 |
0.863 |
0.932 |
0.886 |
0.884 |
0.826 |
0.934 |
0.890 |
0.805 |
| TAPBP |
27591-31078 |
+ |
1296 |
8 |
7 |
21.5 |
0.920 |
0.882 |
0.951 |
0.935 |
0.891 |
0.856 |
0.942 |
0.919 |
0.301 |
| BLB2** |
32031-33413 |
+ |
792 |
6 |
5 |
10.6 |
0.933 |
0.897 |
0.928 |
0.875 |
0.890 |
0.818 |
0.943 |
0.902 |
0.924 |
| BRD2 |
34798-40437 |
- |
2340 |
12 |
12 |
8.7 |
0.957 |
0.996 |
0.976 |
0.996 |
0.934 |
0.995 |
0.971 |
0.997 |
0.011 |
| DMA |
44248-46392 |
+ |
789 |
4 |
3 |
12.2 |
0.913 |
0.889 |
0.937 |
0.924 |
0.856 |
0.817 |
0.943 |
0.928 |
0.375 |
| DMB1 |
46628-48880 |
+ |
1020 |
8 |
2 |
1.0 |
0.864 |
0.794 |
0.851 |
0.793 |
0.847 |
0.774 |
0.923 |
0.876 |
0.496 |
| DMB2 |
49322-52121 |
+ |
777 |
6 |
5 |
23.0 |
0.921 |
0.911 |
0.951 |
0.938 |
0.859 |
0.822 |
0.952 |
0.955 |
0.235 |
| BF1*** |
52919-54907 |
+ |
1056 |
8 |
5 |
1.3 |
0.858 |
0.769 |
0.879 |
0.789 |
0.835 |
0.734 |
0857 |
0.770 |
0.733 |
| TAP2 |
56357-59553 |
- |
2106 |
9 |
6 |
2.2 |
0.927 |
0.934 |
0.952 |
0.950 |
0.897 |
0.893 |
0.940 |
0.932 |
0.186 |
| TAP1 |
60134-64265 |
+ |
1755 |
11 |
2 |
1.0 |
0.932 |
0.938 |
0.957 |
0.966 |
0.905 |
0.915 |
0.954 |
0.949 |
0.195 |
| BF2*** |
65364-67372 |
- |
1077 |
8 |
6 |
16.1 |
0.860 |
0.749 |
0.888 |
0.802 |
0.826 |
0.737 |
0.870 |
0.767 |
0.767 |
| C4 |
68440-82244 |
+ |
4875 |
38 |
4 |
1.4 |
0.911 |
0.940 |
0.933 |
0.958 |
/ |
/ |
0.963 |
0.963 |
0.207 |
| CenpA |
82653-84175 |
+ |
429 |
4 |
0 |
0 |
0.967 |
0.993 |
/ |
/ |
/ |
/ |
0.968 |
0.979 |
0.037 |
| CYP21(partial) | 84680-88358 | + | 1326 | 10 | 2 | 1.0 | |||||||||
* Expression verified by 454 transcriptome sequencing, **BLB = MHC Class IIB genes, *** BF = MHC Class I genes.