Table 4.
Genes and transcripts associated with the MHC complex affected by CNVs as predicted by a hidden Markov model
| Gene | Transcript | Type | Strain | Exons |
|---|---|---|---|---|
| 2410017I17Rik | ENSMUST00000090537 | Gain | A/J | 1- 7 |
| ENSMUST00000090537 | Loss | CAST/Ei | 1-6 | |
| CR974462.5-201 | ENSMUST00000087244 | Gain | CAST/Ei | 1-5 |
| H2-D1 | ENSMUST00000087173 | Gain | A/J | 1-8 |
| ENSMUST00000078966 | Gain | A/J | 1-7 | |
| ENSMUST00000087173 | Gain | CAST/Ei | 1-8 | |
| ENSMUST00000078966 | Gain | CAST/Ei | 1-7 | |
| H2-DMb2 | ENSMUST00000114232 | Gain | A/J | 1-6 |
| H2-K1 | ENSMUST00000114311 | Gain | A/J | 1-7 |
| ENSMUST00000087189 | Gain | A/J | 1-9 | |
| ENSMUST00000025181 | Gain | A/J | 1-8 | |
| ENSMUST00000046131 | Gain | A/J | 1-7 | |
| ENSMUST00000114311 | Gain | CAST/Ei | 1-7 | |
| ENSMUST00000087189 | Gain | CAST/Ei | 1-9 | |
| ENSMUST00000025181 | Gain | CAST/Ei | 1-8 | |
| ENSMUST00000046131 | Gain | CAST/Ei | 1-7 | |
| H2-M10.5 | ENSMUST00000041531 | Gain | A/J | 1 |
| H2-M10.6 | ENSMUST00000041398 | Gain | CAST/Ei | 1, 2 |
| H2-Q1 | ENSMUST00000105041 | Gain | A/J | 1-3 |
| ENSMUST00000073208 | Gain | A/J | 1-8 | |
| ENSMUST00000074806 | Gain | A/J | 1-7 | |
| ENSMUST00000078205 | Loss | A/J | 1-8 | |
| ENSMUST00000113887 | Loss | A/J | 6, 7 | |
| ENSMUST00000081435 | Loss | A/J | 5, 6 | |
| ENSMUST00000078205 | Gain | CAST/Ei | 1-3 | |
| ENSMUST00000105041 | Gain | CAST/Ei | 2 | |
| ENSMUST00000073208 | Gain | CAST/Ei | 4-8 | |
| ENSMUST00000113887 | Gain | CAST/Ei | 1-4 | |
| ENSMUST00000081435 | Gain | CAST/Ei | 1-3 | |
| ENSMUST00000074806 | Gain | CAST/Ei | 1-7 | |
| ENSMUST00000078205 | Loss | CAST/Ei | 1-8 | |
| ENSMUST00000113887 | Loss | CAST/Ei | 6, 7 | |
| ENSMUST00000081435 | Loss | CAST/Ei | 5, 6 | |
| H2-Q10 | ENSMUST00000056774 | Gain | A/J | 1-4 |
| ENSMUST00000068291 | Gain | A/J | 1-3 | |
| ENSMUST00000040279 | Gain | A/J | 1-3 | |
| ENSMUST00000056774 | Gain | CAST/Ei | 1-4 | |
| ENSMUST00000068291 | Gain | CAST/Ei | 1-3 | |
| ENSMUST00000040279 | Gain | CAST/Ei | 1-3 | |
| H2-Q2 | ENSMUST00000040240 | Gain | A/J | 1-6 |
| H2-Q7 | ENSMUST00000071951 | Gain | A/J | 7 |
| H2-Q7 | ENSMUST00000076256 | Gain | A/J | 7, 8 |
| H2-T10 | ENSMUST00000074201 | Loss | A/J | 1-10 |
| H2-T18 | ENSMUST00000025312 | Gain | A/J | 1-6 |
| ENSMUST00000095300 | Gain | A/J | 1-4 | |
| ENSMUST00000097329 | Gain | A/J | 1, 2 | |
| ENSMUST00000113714 | Gain | A/J | 1-4 | |
| ENSMUST00000102675 | Gain | A/J | 1-6 | |
| ENSMUST00000025312 | Gain | CAST/Ei | 1-6 | |
| ENSMUST00000095300 | Gain | CAST/Ei | 1-4 | |
| ENSMUST00000097329 | Gain | CAST/Ei | 1, 2 | |
| ENSMUST00000113714 | Gain | CAST/Ei | 1-4 | |
| ENSMUST00000102675 | Gain | CAST/Ei | 1-6 | |
| H2-T9 | ENSMUST00000058801 | Loss | A/J | 1-9 |
| ENSMUST00000077960 | Loss | A/J | 1-10 | |
| ENSMUST00000080015 | Loss | A/J | 1-9 | |
| NM_001025208.1 | ENSMUST00000064686 | Gain | A/J | 1-9 |
| ENSMUST00000064686 | Gain | CAST/Ei | 1-9 |