Table 4.
Variants identified by Sanger sequencing of MC1R and the haplotypes associated with imperial (black) and native (gray) nose phenotypes
| Position (bp) | Observed haplotypes | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| UMD 3.1 | ARS- UCD 1.2 | Variant ID | Ref | Alt | Imperial | Native 1 | Native 2 | Native 3 | Variant position (predicted consequence), annotation |
| 14757353 | 14705114 | . | G | A | G | A | A | A | 5′ UTR, c.-262G>A |
| 14757486 | 14705247 | rs525922202 | T | C | T | C | C | C | 5′ UTR, c.-129T>C |
| 14757488 | 14705249 | . | A | C | A | C | C | C | 5′ UTR, c.-127A>C |
| 14757509 | 14705270 | rs460981838 | C | T | C | T | T | T | 5′ UTR, gain of start (Low), c.-106C>T |
| 14757910b | 14705671 | ss974293047 | T | C | T | T | T | T | Missense (Moderate), c.296T>C, p.Leu99Pro |
| 14757924b | 14705685 | rs110710422 | GG | G | GG | GG | GG | GG | Frameshift (High), c.311delG, p.Gly104fs |
| 14757954 | 14705715 | . | C | A | A | C | C | C | Missense (Moderate), c.340C>A, p.Gln114Lys |
| 14757989a | 14705750 | . | C | T | C | T | T | T | Synonymous, c.375C>T |
| 14758256 | 14706017 | rs442354353 | C | G | C | C | G | C | Synonymous, c.642C>G |
| 14758277 | 14706038 | rs525311468 | T | C | T | C | C | C | Synonymous, c.663T>C |
| 14758485 a | 14706246 | rs135181132 | G | A | A | G | G | G | Missense (Moderate), c.871G>A, p.Ala291Thr |
| 14758691 | 14706452 | rs481591010 | C | T | C | T | C | C | 3′ UTR, c.*123C>T |
| 14758692 | 14706453 | rs442584695 | T | G | T | G | G | G | 3′ UTR, c.*124T>G |
| 14758896 | 14706657 | TG | T | TG | T | T | T | 3′ UTR, c.*334delG | |
| 14758950a | 14706711 | G | A | G | A | A | A | 3′ UTR, c.*482A>G | |
Reference (Ref) and Alternative (Alt) alleles are defined with respect to UMD3.1. Variants (bp) shown in bold were described in the Y1 haplotype of Chen et al. (2009).
aVariants included in the MALDI genotyping assay.
bVariants found only in domestic cattle.