Table 3.
Specific and predominant single nucleotide polymorphisms in regulatory and/or coding regions harbored by shared genes among DEGs and DEPs related to skeletal muscle development
| Chrom | Position | SNP type | Gene name | Ref allele | Alt allele | Allele frequency of Alt allele | ΔAF | |
|---|---|---|---|---|---|---|---|---|
|
| ||||||||
| TIBP | LWP | |||||||
| 1 | 108,987,504 | 3′ Prime UTR | TPM1 | T | C | 0.91 | 0.11 | 0.81 |
| 1 | 128,960,185 | 3′ Prime UTR | CAPN3 | G | A | 0.93 | 0.05 | 0.88 |
| 1 | 129,012,944 | Synonymous | CAPN3 | C | A | 0.87 | 0.03 | 0.85 |
| 1 | 129,013,136 | Synonymous | CAPN3 | C | T | 0.86 | 0.03 | 0.83 |
| 1 | 129,013,139 | Synonymous | CAPN3 | T | C | 0.86 | 0.03 | 0.83 |
| 1 | 129,013,184 | Synonymous | CAPN3 | G | A | 0.84 | 0.03 | 0.82 |
| 1 | 129,013,317 | 5′ Prime UTR | CAPN3 | T | C | 0.89 | 0.03 | 0.86 |
| 1 | 129,013,319 | 5′ Prime UTR | CAPN3 | C | T | 0.89 | 0.03 | 0.86 |
| 1 | 129,013,515 | Upstream | CAPN3 | G | T | 0.89 | 0.03 | 0.86 |
| 1 | 129,013,788 | Upstream | CAPN3 | G | T | 0.85 | 0.03 | 0.83 |
| 1 | 129,014,494 | Upstream | CAPN3 | T | C | 0.85 | 0.03 | 0.82 |
| 8 | 121,866,237 | Upstream | RAP1GDS1 | G | A | 0.90 | 0.03 | 0.87 |
| 8 | 121,866,622 | Upstream | RAP1GDS1 | A | G | 0.91 | 0.05 | 0.86 |
| 8 | 121,867,490 | 3′ Prime UTR | RAP1GDS1 | T | C | 0.91 | 0.03 | 0.88 |
| 8 | 121,868,433 | 3′ Prime UTR | RAP1GDS1 | A | C | 0.88 | 0.03 | 0.85 |
| 12 | 16,774,572 | Upstream | MYL4 | G | A | 0.93 | 0.00 | 0.93 |
| 14 | 76,452,928 | 5′ Prime UTR | MYOZ1 | A | C | 0.06 | 0.97 | 0.91 |
| 15 | 33,537,058 | Splice region & intron | MYOM2 | G | A | 0.86 | 0.00 | 0.86 |
| 15 | 33,569,852 | Synonymous | MYOM2 | T | C | 0.86 | 0.05 | 0.81 |
| 15 | 33,574,636 | Synonymous | MYOM2 | T | C | 0.86 | 0.05 | 0.81 |
| 15 | 33,577,752 | Synonymous | MYOM2 | T | C | 0.86 | 0.05 | 0.81 |
| 15 | 33,577,812 | Synonymous | MYOM2 | C | T | 0.93 | 0.11 | 0.82 |
| 15 | 33,606,405 | Synonymous | MYOM2 | T | C | 0.87 | 0.05 | 0.82 |
| 15 | 33,607,063 | Downstream | MYOM2 | G | A | 0.88 | 0.05 | 0.83 |
| 15 | 33,607,875 | Downstream | MYOM2 | C | T | 0.89 | 0.06 | 0.83 |
| 18 | 48,694,221 | 5′ Prime UTR Premature start codon gain | PGAM2 | G | A | 0.83 | 0.00 | 0.83 |
| 18 | 48,694,249 | 5′ Prime UTR | PGAM2 | A | G | 0.86 | 0.00 | 0.86 |
| 18 | 48,694,283 | 5′ Prime UTR | PGAM2 | T | A | 0.82 | 0.00 | 0.82 |
| 18 | 48,701,904 | 5′ Prime UTR | PGAM2 | C | A | 0.03 | 0.95 | 0.91 |
| 18 | 48,709,016 | 5′ Prime UTR | PGAM2 | G | A | 0.04 | 0.97 | 0.93 |
| 18 | 48,709,414 | 5′ Prime UTR | PGAM2 | C | G | 0.02 | 0.94 | 0.92 |
| 18 | 48,710,042 | 5′ Prime UTR Premature start codon gain | PGAM2 | C | T | 0.04 | 0.84 | 0.81 |
| 18 | 48,710,267 | 5′ Prime UTR | PGAM2 | C | G | 0.04 | 0.97 | 0.93 |
| 18 | 48,712,707 | Synonymous | PGAM2 | C | A | 0.04 | 0.94 | 0.90 |
DEGs, differentially expressed genes; DEPs, differentially expressed proteins; SNP, single nucleotide polymorphism; TIBP, Tibetan pig; LWP, Large White pig; UTR, untranslated regions; AF, allele frequency differences.