Expression of Gli1 variants during embryogenesis. (A) Schematic representation of the variant-specific primer sets for real-time RT-PCR used to detect the alternative Gli1 transcripts. Gray, black and white arrows indicate the alternative transcription start sites TSS-L, TSS-M and TSS-S of the Gli1 mRNAs. The initiator methionine codon (ATG) in exon 2 is also shown. The positions of the forward and reverse primers for detection of the L (E1L-F, E1L/M-R), L+M (E1M-F, E1L/M-R), ΔE1B (E1A-F, E1B-R), and ΔE1B (E1A-F, E2/1A-R) transcripts are indicated by white and black triangles, respectively. Exons are shown by boxes. (B) Gli1 expression profile in mouse embryos. The L, L+M, E1B, and ΔE1B variants were quantified by real-time RT-PCR using SYBR Green in two 8.5 d.p.c. and two 9.5 d.p.c. mouse embryos. Data are presented as relative Ct (C ycle t hreshold, the number of PCR cycles that reaches an arbitrary threshold) values (ΔCt), that is the Ct of the individual transcripts minus the Ct of the housekeeping gene Arp. A logarithmic plot of the 2-ΔCt values is shown. 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).