Table 3

The representative amino acid patterns of the conserved transmembrane motifs of pig, dog and rat OR genes
Pattern no. Transmembrane domain Pattern
Pig TMII H-X-P-M-Y-F-F-L-X-[NS]-L-S-[FL]-[AV]-D
1
2 TMIII L-X(2,3)-M-[AV]-Y-D-[RS]-F-[LV]-A-I_C-H-P-L-H-Y
3 TMIII L-X(2,4)-M-[AGS]-X-D-X(2,3)-A-[IV]-X(2)-[LP]-[FIL]
4 TMVI K-A-[FL]-S-T-C-X-S-H-L-X-V
5 TMVII P-M-[LM]-N-P-F-[IV]-Y-[NS]-L-X-N-[KR]-[DN]
Dog
1 TMII P-M-Y-X-[FL]-L-X(2)-[FL]-[AMS]-X(2)-[DE]
2 TMIII L-X(3)-M-X(0,1)-Y-X-[FLR]-[LY]-X(2)-[FILV]-[ACS]
3 TMIII L-X(1,3)-M-X-[FILY]-D-R-X(2)-A-[IV]-[CS]-X-P-L-X-[HY]-X(3)-[ILM]
4 TMVI K-X-[FL]-[AGHNST]-T-C-X-[AS]-H-X(3)-[AIV]
5 TMVII N-P-[FILMV]-[IV]-Y-[AGST]-[AILMV]-[KR]-X(2)-[DEKQ]
Rat
1 TMII L-[HKNQR]-X-P-M-[FY]-X-[FIL]-L-X(2)-L-X(3)-[DEY]
2 TMIII M-[AS]-[FLY]-D-R-[FHY]-[AILMV]-A-[IV]-X(2)-P-L-X-[HY]-X(3)-[FILMV]-[DGHKNPRST]
3 TMV S-Y-X(2)-I-[FILV]-X-[AST]-[FIV]
4 TMVI K-X-[FILMV]-X-T-C-X-[ACPST]-H-[FILMV]-X(2)-[FILMV]
5 TMVII P-X-[LMV]-N-P-[FILMV]-X-Y-[ACGST]-X-[KNR]-X-[KNQRT]-[DEKPQ]-[FILMV]

Note: The pattern for dogs and rats was taken from Quignon et al.[16]. [XYZ] means X or Y or Z. The lower case letter “X” can be used as a pattern element to denote any amino acid. X(m) is equivalent to the repetition of X exactly m times. X(m,n) is equivalent to the repetition of X exactly k times for any integer k satisfying: m ≤ k ≤ n.

Nguyen et al.

Nguyen et al. BMC Genomics 2012 13:584   doi:10.1186/1471-2164-13-584

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