Fig. 1

(A) The positions of the six exons of the hoxb3a gene (light blue boxes) and the three exons of the hoxb4a gene (orange boxes) within the hoxba cluster are illustrated. The first exon is shared between the hoxb3a and hoxb4a genes (light blue/orange box). Hoxb3a transcript I (1646 bp; exons 4–6), transcript II (1728 bp; exons 1, 2, 3, 5, and 6), and transcript III (exons 2, 3, 5, 6) code for the same protein. In contrast, the shorter of the two hoxb4a transcripts (II; exons 1 and 3) gives rise to an N-terminal truncated protein. The positions of experimentally verified promoters of hoxb3a and hoxb4a are indicated. (B) Schematic showing from which regions of the cluster sequence the primer pairs were chosen to detect the exon composition of hoxb3a transcripts I and II and hoxb4a transcript II. (C) RT-PCR analyses of hoxb3a and hoxb4a transcripts. PCR results for primer combinations L1 with R2 (hoxb3a transcript II) and L4 with R2 (hoxb3a transcript I) were shown previously (Hadrys et al., 2004). With primer set L5/R3 hoxb3a transcript I sequences corresponding to exons 4–6 were amplified from cDNA preparation. cDNA fragments of transcript II were amplified with primers L6/R3 (exons 2, 3, 5, and 6) and L7/R3 (exons 3, 5, and 6). No PCR products were obtained when using exon 1, exon 2, or exon 3 forward primers (L1, L6, and L7) and an exon 4 reverse primer (R4), indicating that transcripts of these exon compositions, at least in developmental stages 12 hpf, 24 and 33 hpf, do not exist. Hoxb4a transcript II sequences (containing exons 1 and 3, but not exon 2) were amplified using the primers L1/R5, L2/R5, L1/R6, and L2/R6.