Table 3 Descriptions of the significant CNVRs associated with wrinkled skin cases.
From: Genome-wide identification of copy number variations in wrinkled skin cases of Xiang pigs
CNVR ID | Location | Type | Overlap gene | Fst | Impact on gene |
|---|---|---|---|---|---|
CNVR_0012 | 1:2305601–2,307,600 | LOSS | RPS6KA2 | 0.18 | Intron 3 deletion |
CNVR_0558 | 1:168793801–168,814,200 | LOSS | THSD4 | 0.17 | Intron 3 deletion |
CNVR_1114 | 2:62575001–62,577,000 | LOSS | CCDC105 | 0.16 | Intron 2 deletion |
CNVR_1251 | 2:101763601–101,791,200 | LOSS | MCTP1 | 0.18 | Intron 1 deletion |
CNVR_1435 | 3:3243801–3,246,600 | LOSS | SDK1 | 0.17 | Intron 47 deletion |
CNVR_2707 | 6:10396201–10,410,600 | LOSS | ENSSSCG00000034356|ADAMTS18 | 0.19 | Intron 2 deletion |
CNVR_4513 | 9:131467001–131,468,400 | LOSS | LPGAT1 | 0.26 | Intron 4 deletion |
CNVR_5619 | 13:107584201–107,678,400 | LOSS | ENSSSCG00000035525 | 0.44 | Intron 16 − 3’UTR deletion |
CNVR_5906 | 14:9239401–9,244,200 | LOSS | DOCK5 | 0.23 | Intron 1 deletion |
CNVR_7427 | X:27,429,401–27,441,400 | LOSS | DMD | 0.17 | Intron 5 deletion |
CNVR_1195 | 2:78188001–79,688,400 | GAIN | MAPK9|SQSTM1|ADAMTS2… | 0.21 | Whole-gene duplication |
CNVR_1233 | 2:91356201–91,612,000 | LOSS | VCAN|ENSSSCG00000045510|ENSSSCG00000056442 | 0.29 | Partial deletion in 5’ end |
CNVR_1241 | 2:97898801–97,903,000 | LOSS | ADGRV1 | 0.21 | Intron 49-exon 50 deletion |
CNVR_1854 | 3:129356201–130,543,800 | GAIN | SOX11|ENSSSCG00000047407 | 0.18 | Whole-gene duplication |
CNVR_2313 | 5:10172601–10,323,800 | LOSS | LGALS2|GGA1|CARD10|CDC42EP1|MFNG|PDXP | 0.15 | Whole-gene duplication |
CNVR_3562 | 7:90242601–90,785,800 | LOSS | CCDC196|GPHN | 0.19 | Intron 1–3’UTR deletion (CCDC1); 5’UTR to intron10 deletion (GPHN) |
CNVR_4222 | 9:33886601–34,045,200 | LOSS | DYNC2H1 | 0.16 | Intron 71-exon 90 − 3’UTR Deletion |
CNVR_4865 | 11:14662401–16,377,400 | GAIN | FOXO1|NEK3|NEK5… | 0.27 | Whole-gene duplication |
CNVR_5972 | 14:29207001–29,214,000 | LOSS | DNAH10 | 0.17 | Intron 13-exon 14-intron 14-exon15-intron 15 deletion |
CNVR_7238 | 18:8296401–8,303,600 | LOSS | AGK | 0.17 | Intron 10 deletion |
CNVR_7368 | 18:50886201–51,012,600 | LOSS | YKT6|GCK|CAMK2B | 0.25 | Intron 2-exon 22 − 3’UTR deletion (CAMK2B); exon 1-intron 1 deletion (GCK); whole-gene deletion (YKT6) |
CNVR_7451 | X:42,077,601–42,115,600 | LOSS | ARAF|SYN1|TIMP1 | 0.20 | Whole-gene deletion |
