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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.
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Genome Biology

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