TABLE 2.
Inferring codon changing SNPs between SM and NZB by examining SNPs between highly sequenced strains
| Highly sequenced strains, e.g., C57BL/6, DBA/2, etc.
|
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Chr 6 gene | SNP | i | ii | iii | iv | v | vi | SM | NZB | SM and NZB are |
| Syn2 | UTR | A | A | A | G | G | G | G | G | IBD |
| Syn2 | Cs | T | T | T | C | C | C | |||
| Syn2 | Cs | G | G | G | A | A | A | A | G | Non-IBD |
| C | C | C | T | T | T | |||||
| Pparg | UTR | A | A | A | G | G | G | |||
| Pparg | Cn | T | T | T | C | C | C | c | t | Inferred Cn between SM and NZB |
| Pparg | Cs | G | G | G | A | A | A | |||
| Pparg | Cs | C | C | C | T | T | T | |||
| Pparg | Cs | A | A | A | G | G | G | G | A | Non-IBD |
| T | T | T | C | C | C | |||||
| G | G | G | A | A | A | |||||
| Tsen2 | UTR | C | C | C | T | T | T | |||
| Tsen2 | Cs | C | C | C | G | G | G | C | G | Non-IBD |
| Tsen2 | Cs | T | T | T | C | C | C | |||
| Tsen2 | Cs | G | G | G | A | A | A | |||
| Tsen2 | Cs | C | C | C | T | T | T | T | T | IBD |
Italic nucleotides indicate an alternative haplotype present in common inbred strains that can be used to infer the origin of polymorphisms from less well characterized strains. Although SM and NZB are not as well sequenced as other strains, missing SNPs between SM and NZB can be inferred by examining the haplotypes of the other strains. For the Cn in Pparg (underlined), SM is inferred to be “C” and NZB is inferred to be “T.” Cs, coding synonymous; Cn, coding nonsynonymous; IBD, identical by descent.