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Table 4 Genes and transcripts associated with the MHC complex affected by CNVs as predicted by a hidden Markov model

From: Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels

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