early conceptus |
embryo ectoderm |
embryo endoderm |
embryo mesoderm |
embryo mesenchyme |
extraembryonic component |
alimentary system |
auditory system |
branchial arches |
cardiovascular system |
connective tissue |
endocrine system |
exocrine system |
hemolymphoid system |
integumental system |
limbs |
liver and biliary system |
musculoskeletal system |
nervous system |
olfactory system |
reproductive system |
respiratory system |
urinary system |
visual system |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Transcription Start Site | Location | Distance from Gene 5'-end |
| Tssr129899 | Chr14:79539063-79539081 (-) | 3 bp |
| Tssr129898 | Chr14:79538514-79538532 (-) | 552 bp |
| Tssr129897 | Chr14:79538492-79538502 (-) | 578 bp |
| Tssr129896 | Chr14:79538480-79538483 (-) | 593 bp |
| Tssr129895 | Chr14:79538454-79538466 (-) | 615 bp |
| Tssr129891 | Chr14:79529430-79529438 (-) | 9,641 bp |
| QTL | Genetic Location* | Genome Location (GRCm39) | Reference | QTL Note |
| Ccmsa2 | Chr14, syntenic | J:276654 | To evaluate candidate genes, the authors used the QTLMiner module of GeneNetwork (Alberts and Schughart, 2010), which evaluates all genes in an interval against neocortical gene expression databases within GeneNetwork. The authors used QTLMiner to rank potential candidates among the 48 genes in the Ccmsa2 interval based on the presence of non-synonymous SNPs, of expression levels in mRNA databases (in this case, three neocortical mRNA expression databases: P3, P14, and P60), and cis-eQTL. Using sequence data and QTLMiner, the authors were able to narrow down eight positional and plausible biological candidate genes within the Ccmsa2 interval: The authors first isolated those genes with non-synonymous SNPs or indels, reasoning that only genes with allelic differences between the two parent strains could account for the QTL. Of the 48 genes in the interval, 14 had SNPs between B6 and D2 (4921530L21Rik [Spertl; MGI:1913982], AU017455 [Zfp957; MGI:2145729], Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], EG629734 [Gm6999; MGI:3647443], Kiaa0564 [Vwa8; MGI:1919008], Klhl1 [MGI:2136335], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh8 [MGI:1306800], Pcdh9 [MGI:1306801], Pcdh20 [MGI:2443376], Tdrd3 [MGI:2444023], Tnfsf11 [MGI:1100089]). The authors next identified those genes that had moderate to high expression in forebrain at some stage of development - values above the average of 8 in at least one neocortical expression database (Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], Kiaa0564 [Vwa8; MGI:1919008], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh20 [MGI:2443376], Pcd8*, Pcdh9 [MGI:1306801], Tdrd3 [MGI:2444023]). Of these, seven were identified as having cis-eQTL in at least one of the expression databases: Dgkh (MGI:2444188), Kiaa0564 (Vwa8; MGI:1919008), Naa16 (MGI:1914147), Mtrf1 (MGI:2384815), Diap3 (Diaph3; MGI:1927222), Tdrd3 (MGI:2444023), and Pcdh9 (MGI:1306801). Finally, the authors examined the interval for genes without non-synonymous SNPs but with significant cis-eQTL, and identified Rgc32 (Rgcc; 1190002H23Rik; MGI:1913464) as another potential candidate (Table 1; Figure 3A). Gene expression of these candidates is highly intercorrelated and their expression correlates with MSACC (Figure 3B). * Curator Note: Pcd8 is not in MGD. The authors may have been referring to Pcdh8 (MGI:1306800). |
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO) |
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last database update 12/10/2024 MGI 6.24 |
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