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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