Table 2.
Polymorphism in cattle
| Nucleotide | 189 | 202 | 455 | 467 | 631 | 681 | 914 | 925 | 978 | 989 |
|---|---|---|---|---|---|---|---|---|---|---|
| Amino acid | 63 | 68 | 152 | 156 | 211 | 227 | 305 | 309 | 326 | 330 |
| Domain | LRR1 | LRR1 | LRR5 | LRR5 | LRR7 | LRR8 | LRR10 | LRR11 | LRR11 | LRR11 |
| Blosum62 | 2 | 0 | 1 | -3 | 3 | 0 | -2 | 1 | 0 | 1 |
| P (all) | 0.922 | 0.735 | 0.22 | 0.005 | 0.942 | 0 | 1 | 0 | 0.982 | 0.018 |
| Class (all) | 3 | 3 | 2 | 2 | 3 | 1 | 3 | 1 | 3 | 2 |
| Class (ruminants) | 2 | 3 | 2 | 3 | 2 | 3 | 3 | 2 | 3 | 2 |
| Codon_wildtype | gag | ggc | cgg | gta | gtt | tta | cac | gtg | cat | agt |
| Codon_mutant | gat | agc | cag | gga | aat | ttt | ccc | atg | caa | aat |
| AA_wildtype | E | G | R | V | V | L | H | V | H | S |
| AA_mutant | D | S | Q | G | I | F | P | M | Q | N |
| dbSNP_ID (ss#) | 95214853 | 95214854 | 95214855 | 95214856 | 95214857 | 95214858 | 95214858 | 95214859 | 95214861 | 95214862 |
| AA | t | g | g | t | a | t | a | g | t | g |
| FB | t | g | g | t | g/a | t | a | g | t | a |
| BP | t | g | g | g | g/a | t | a | g | t | g |
| GA | g/t | g/a | g | t | g | t | a | g | t | g |
| FV | t | g | g/a | t | g/a | t | a | g/a | t | g |
| HF | t | g | g | t | a | t | a | g | t | g |
| LI | t | g | g | t | g/a | t | a | g | t | g |
| NE | g/t | g/a | g | t | g | a | a | g | a/t | g |
| SW | g | a | g | t | g | a | c | g | a | g |
| BH | g | g/a | g | t | g | a/t | a | g | a | g |
| Nucleotide | 1010 | 1214 | 1250 | 1457 | 1504 | 1688 | 1814 | 1962 | 1995 | 2149 |
| Amino acid | 337 | 405 | 417 | 486 | 502 | 563 | 605 | 654 | 665 | 717 |
| Domain | LRR11 | LRR14 | LRR15 | LRR18 | LRR19 | LRRCT | MEM | TIR | TIR | TIR |
| Blosum62 | 2 | -1 | 1 | 2 | 1 | 0 | -1 | -2 | 0 | 2 |
| P (all) | 0.972 | 0 | 0.352 | 0 | 0.998 | 0.776 | 0.578 | 0 | 0.011 | 0 |
| Class (all) | 3 | 1 | 2 | 1 | 3 | 3 | 3 | 1 | 2 | 1 |
| Class (ruminants) | 2 | 2 | 2 | 2 | 2 | 3 | 2 | 2 | 2 | 2 |
| Codon_wildtype | aaa | acg | aac | aga | tca | cgc | acg | tgg | cac | ctg |
| Codon_mutant | aga | atg | agc | aaa | gca | cac | atg | tgt | cag | atg |
| AA_wildtype | K | T | N | R | S | R | T | W | H | L |
| AA_mutant | R | M | S | K | A | H | M | C | Q | M |
| dbSNP_ID (ss#) | 95214863 | 95214864 | 95214865 | 95214867 | 95214868 | 95214869 | 95214873 | 95214874 | 95214875 | 95214878 |
| AA | g | c | a | g | t | g/a | c | g | c | c |
| FB | g | c | a | g | t | g | c | g | c | c |
| BP | g | c | a | g | t | g | c | g | c | c |
| GA | g/a | c | a | g | t | g/a | c | g | c | c |
| FV | g | c | a | g | t | g | c | g | c | c |
| HF | g | c | a | g | t | g | c | g/t | c | a/c |
| LI | g | c | a | g/a | t | g | c | g | c | c |
| NE | a | c | g/a | g | g/t | g/a | c/t | g | g/c | c |
| SW | a | t | g | g | g | a | c/t | g | g | c |
| BH | a | c | g | g | t | a | c | g | g | c |
Nucleotide: position of the polymorphism in the nucleotide sequence, Amino acid: affected amino acid site, Domain: domain in which the polymorphic site is located, LRRCT: Leucine Rich Repeat C-terminal domain, MEM: transmembrane domain, Blosum62: Blosum62 matrix score of the particular AA exchange, P (all): probablitiy of class assignment in the complete dataset, Class (all): class assignment in the complete dataset (1: purifying selection, 2: neutral, 3: positive selection), Class (ruminants): class assignment in the ruminant subset, dbSNP_ID (ss#): accession number in dbSNP database, AA: Aberdeen Angus, FB: Fighting Bull, BP: Black Pied Gene Reserve, GA: German Angus, FV: Fleckvieh, HF: Holstein Friesian, LI: Limousin, NE: Nelore, SW: Sahiwal, BH: Brahman. The last three breeds are Bos indicus breeds.