Supplemental Table 1:

The collection of Runx genes used in this study. This table indicates the sources of Runx gene sequences from selected species, and additional references that were used in the analysis. The C. intestinalis Runx gene (CiRunt) was derived from a contig assembled using shot-gun sequence segments queried from NCBI's trace archive. The accession number given can be used as a seed for querying the database start the retrieval of necessary sequence. Vector NTI ContigXpress was used to assemble the sequence. Verification of CiRunt was performed by comparing the gDNA to cDNA available on-line at the Nori Satoh Laboratory web page. Only the first cDNA sequence accession number is given and can be used as a seed to extract the remaining sequences. There was 2 × coverage of the cDNA. A special note needs to be made about the sequence upstream from the start of the Runt domain. The sequence from the start of the runt gene to the start of the Runt domain is theoretical. No cDNA could be found to verify this segment. The T. rubripes Runx genes were derived from scaffolds available on-line at the MRC HGMP-RC site. M. musculus Runx2 and D. rerio runtb were used to identify T. rubripes Runx2 and Runx3, respectively. T. rubripes Runx2 was verified by a published report [11]. D. rerio runta was used to identify T. rubripes Runx1. The sea urchin gene SpRunt has not yet been completely sequenced, and sequence is currently available only for the SpRunt-1 cDNA [9] and for the termini of the exons and introns [10]. ND, not determined.

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Supplemental Table 2:

Sequence length of Runx genes from selected species. This table indicates the total and intron length in nucleotides of the sequences of each of the collected Runx genes from the proximal promoters. Exon lengths (bold numbers) are given in amino acids. Note that the nucleotide lengths of the S. purpuratus gene and introns are approximate (based on the lengths estimated for PCR products by gel electrophoresis), as these have not yet been completely sequenced.

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Supplemental Figure 1:

Comparison of relative exon-intron positions and splice sites among Runx genes. Details of exon-intron structure of genes analysed in this study. Exons are represented as boxes, and the number in the box indicates the number of amino acids. The central bold boxes represent the C-terminus of the Runt domain, which are contained in a single compact exon in all of the genes except for DmRunt and AgRunt, which lack the intron that borders the N-terminal end of this exon that is found in all of the other genes. The nucleotide sequences of the splice site termini are indicated: the junctions between exon and intron are represented by two dots (..), while the intervening intron sequence is indicated by a dash (-). The lengths of the introns in nucleotide number are indicated in parentheses. For the vertebrate Runx genes, only exons downstream of the proximal promoters are shown. The gene and intron lengths for the sea urchin gene SpRunt are approximate and based on PCR products obtained from a BAC clone [10] that has not yet been completely sequenced.

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