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Table 2 QTL genes with nonsynonymous changes

From: In silicodiscovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases

(a) Altered genes within the chronic alcohol withdrawal QTL on proximal chromosome 1

 

Gene

In silico percent coverage*

Amino-acid variations

Symbol

Gene ID

Location

B6

D2

Both

 
 

mCG55019

30,510,903 - 30,520,321

100

100

100

M72V†

 

mCG52566

31,637,483 - 31,666,730

95

95

95

S6A

 

mCG49360

32,140,873 - 32,141,648

100

87

87

P74L†, C123R†

 

mCG66997

36,796,676 - 36,805,521

100

100

100

stop61Y

 

mCG4911

39,571,491 - 39,572,134

54

100

54

R74H, E79D

Slc5a7

NM_022025

Uncertain

100

99 (100)

99 (100)

R38H†

(b) Altered genes within the sex-limited chronic alcohol withdrawal QTL on chromosome 13

 

Gene

In silico percent coverage*

Amino-acid variations

Symbol

Gene ID

Location

B6

D2

Both

 
 

mCG22018

54,248,540 - 54,266,542

100

86

86

I155F

Ptch

mCG21490

54,702,052 - 54,733,739

79

68

68

T1267N

 

mCG67381

54,910,868 - 54,921,322

95

95

95

N48D

 

mCG49128

55,141,914 - 55,156 036

82

100

82

S38G, H96R

Hsd17b3

NM_008291

55,258,374 - 55,287,747

69 (100)

61 (100)

45 (100)

C95R†

 

mCG67239

55,349,545 - 55,350,013

100

100

100

T47M, P124R‡

Habp4

NM_019986

55,358,811 - 55,383,494

89 (96)

90 (96)

84 (96)

A65-(in/del)†, P187L†, A266T†

 

mCG65010

55,397,330 - 55,399,305

84

100

84

S48N†, R76W†

 

mCG51118

55,652,165 - 55,652,438

31

100

31

F6L‡

 

mCG50935

55,841,328 - 55,842,516

100

100

100

A210V

 

mCG50411

56,005,687 - 56,054,181

100

66

66

G200E†

 

mCG55714

56,067,926 - 56,074,495

96

90

90

S99P‡, L361S‡, Q557R‡, A851V‡

 

mCG59053

56,106,754 - 56,107,033

84

100

84

S64G‡

 

mCG59052

56,122,823 - 56,169,063

93

86

79

W53R, M62V, T17I, V197A, T198P, A324S, D645N, R728G, W846R†

Nrif-2

AJ319726

56,376,102 - 56,425,620

96 (100)

78 (100)

74 (100)

A491T†, Q593R†, I679V†

Ptdss1

mCG67987

57,190,261 - 57,251,587

100

89

89

G322C†

 

mCG67995

57,426,346 - 57,427,146

100

83

83

G4E

 

mCG67997

57,732,668 - 57,740,675

53 (100)

100

53 (100)

K24T†, L30R†, S36P†, I48S†, K62R†, V89E†, N94T†

Srd5a1

mCG7698

58,982,812 - 59,009,801

78 (100)

78 (100)

78 (100)

R7C†, V142I†, E176D†

  1. Gene IDs beginning with the letters mCG are Celera gene ID numbers; all other gene ID numbers are GenBank accession numbers for transcript sequences. Although genes are identified by the Celera genomic (mCG) ID, transcript sequence was used as query for the BLAST searches for each gene. All data were retrieved from Celera and NCBI between August 2001 and April 2002. Only changes where the reading frame is known and sequence is available in both B6 and D2 are displayed. The B6 amino acid is given first, then the position, followed by the D2 amino acid. *Numbers in parentheses indicate percent coverage after in-house sequencing. †These changes were verified by in-house sequencing. ‡These changes are supported by only a single read in either B6 or D2 and have not been verified by in-house sequencing.