The exon 1B structure/function in C3H/10T1/2 cells. (A) Lack of the exon 1B-included Gli1 variants in the C3H/10T1/2 cell line. Gli1 variants in C3H/10T1/2 cells, treated with methanol (MeOH) or SAG, were analyzed by real-time RT-PCR. Data are presented as relative Ct (C ycle t hreshold) values (ΔCt), that is the Ct of individual transcripts minus the Ct of the housekeeping gene Arp. A logarithmic plot of the 2-ΔCt values is shown. The PCR primer sets used are the ones depicted in Figure 2A. The error bars indicate the standard deviation and the statistical significance between the L and L+M as well as the E1B and ΔE1B transcripts is shown (*: p < 0.05, **: p < 0.01, Student's t-test). ND, non-detected, the signal is below the sensitivity limit of the assay. (B) Comparison of the genomic structure of the Gli1 exon 1B region in C3H/10T1/2 and wtMEF cells. The white box indicates the exon 1B, while the orange and blue boxes the "AAAAATCACCTAGG" and "GGGATGTTTCTTCTT" sequences, respectively, which are duplicated by the B1 SINE (orange rhomb) and B2 SINE (blue rhomb) insertions in C3H/10T1/2 cells. The vertical black bars in C3H/10T1/2 represent the intronic boundaries of exon 1B. The scale of the genomic sequence, 100 base pairs, is indicated by a double arrow. (C) Genomic sequence of the exon 1B region in C3H/10T1/2 cells. The SINE insertions and the duplicated regions are highlighted by the same colors as in (B). The triangles indicate the intronic boundaries of exon 1B.