Table 3. Chr6 QTL candidate genes with SNPs fitting haplotype B≠C and A≠C.
| Gene | ID | Introns | Non-syn | Syn | UTR | PosMed | Microarray FC 4m | Microarray FC 8m | qRT–PCR FC 4m | qRT–PCR FC 8 m | N criteria |
|---|---|---|---|---|---|---|---|---|---|---|---|
|
Fbln2 |
Mm.249146 |
4 |
|
|
|
Yes |
1.8 |
1 |
|
|
2 |
|
Ctnna2 |
Mm.34637 |
5 |
|
|
|
Yes |
NP |
NP |
|
|
1 |
|
Lrrtm4 |
Mm.94135 |
27 |
|
|
|
No |
1 |
1 |
|
|
0 |
|
Tacr1 |
Mm.8055 |
13 |
|
|
|
Yes |
NP |
NP |
|
|
1 |
|
Hk2 |
Mm.255848 |
7 |
|
|
|
Yes |
1 |
1 |
0.5* |
1 |
1 |
|
Sema4f |
Mm.270543 |
5 |
|
|
|
Yes |
NP |
NP |
|
|
1 |
|
Dok1 |
Mm.156 |
1 |
|
|
|
Yes |
1 |
1 |
1.2* |
2.1* |
1 |
|
Htra2 |
Mm.21880 |
2 |
|
|
|
Yes |
1 |
1 |
1 |
1.3 |
1 |
|
Vax2 |
Mm.307165 |
1 |
|
|
|
Yes |
NP |
NP |
|
|
1 |
|
Cyp26b1 |
Mm.255246 |
1 |
2 |
|
|
Yes |
NP |
NP |
|
|
1 |
|
Rab11fip5 |
Mm.220334 |
1 |
|
|
No |
1 |
1 |
|
|
0 |
|
|
Alms1 |
Mm.246967 |
1 |
|
|
Yes |
1 |
1 |
|
|
1 |
|
|
Tgfa |
Mm.137222 |
3 |
|
|
|
Yes |
1.4 |
1.8 |
|
|
2 |
|
Gmcl1 |
Mm.321452 |
4 |
|
|
|
No |
1 |
1.3 |
|
|
1 |
|
Anxa4 |
Mm.259702 |
32 |
|
|
1 |
No |
1 |
1 |
|
|
0 |
|
Aak1 |
Mm.221038 |
133 |
1 |
|
3 |
Yes |
1 |
1 |
|
|
1 |
|
Nfu1 |
Mm.23809 |
11 |
1 |
|
1 |
No |
1 |
0.8 |
|
|
1 |
|
Gfpt1 |
Mm.19893 |
59 |
1 |
|
|
Yes |
0.5 |
0.5 |
|
|
2 |
|
Antxr1** |
Mm.232525 |
432 |
|
1 |
|
Yes |
1.4 |
1 |
1 |
1 |
2 |
|
Gkn1 |
Mm.46414 |
2 |
|
|
|
No |
1 |
0.9 |
|
|
1 |
|
Arhgap25 |
Mm.119564 |
85 |
|
1 |
|
No |
NP |
NP |
|
|
0 |
|
Ccdc48 |
Mm.333229 |
1 |
1 |
1 |
|
NP |
NP |
|
|
0 |
|
|
Cnbp |
Mm.290251 |
1 |
|
|
|
1 |
1 |
|
|
0 |
|
|
Isy1 |
Mm.241546 |
20 |
|
|
1 |
No |
NP |
NP |
|
|
0 |
|
Gata2 |
Mm.476843 |
|
|
1 |
|
1 |
1 |
|
|
1 |
|
|
Eefsec |
Mm.333237 |
43 |
|
|
|
Yes |
1 |
1 |
1 |
1 |
1 |
|
Wnt7a |
Mm.56964 |
1 |
|
|
|
Yes |
NP |
NP |
|
|
1 |
|
Slc6a6 |
Mm.395650 |
1 |
|
|
|
Yes |
0.8 |
1 |
|
|
2 |
| Grip2 | Mm.333264 | 1 | No | NP | NP | 0 |
Number of criteria met for each gene (regulation found by microarray or presence in PosMed list) is indicated. FC ratios are C/B6a. NP represents not present in the microarray. **: Out of the 10 genes sequenced in exons, only the silent single nucleotide polymorphism (SNP) in Antxr1 fit the haplotype. *: Significant difference (p<0.05) in expression between strains obtained by qRT–PCR. Non-syn: nonsynonymous SNP. Syn represents synonymous SNP.