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Additional supporting information may be found in the online version of this article.

FilenameFormatSizeDescription
jezb22469-sup-0001-figure1.tif576KSupplemental Fig. 1. Multiple sequence alignment of the Dlx3 proteins of mammals. Protein sequences were deduced from genomic sequences based on conserved exon-intron boundary information. Hyphens indicate gaps.
jezb22469-sup-0001-figure2.tif488KSupplemental Fig. 2. Multiple sequence alignment of the Dlx4 proteins of mammals. Protein sequences were deduced from genomic sequences based on conserved exon-intron boundary information. Hyphens indicate gaps. Note that the hedgehog second and third exon harbored nucleotide deletions that caused frame shifts (resulting amino acid gap positions are indicated by the # in the amino acid sequence), thus hedgehog Dlx4 exhibited a severely altered protein sequence and is a presumptive pseudogene. Here we show a reconstructed putative original hedgehog amino acid sequence maximizing homology to other Dlx4 genes for a purpose of comparison. Putative platypus first exon derived from the non-orthologous sequence was not alignable, therefore only exon 2 and exon 3 are shown in the alignment.
jezb22469-sup-0001-figure3.tif320KSupplemental Fig. 3. A predicted coding sequence and amino acid sequence of platypus Dlx4. Three exons (exon 1 and 3 are underlined) and the homeodomain (red) are shown. The predictions were made using GeneScan and GenomeScan, both of which produced the identical result.
jezb22469-sup-0001-figure4.tif1269KSupplemental Fig. 4. PIP diagram for 14 mammalian species. Reference genome sequence is human, and its percent identities to baboon, lemur, dog, cow, pig, bat, rabbit, mouse, rat, hedgehog, armadillo, opossum, and platypus sequences are shown as horizontal bars. Black and gray boxes with numbers (1, 2 and 3) on the top indicate locations of protein coding regions and UTRs respectively in exons for Dlx3 and Dlx4. Triangles on the top denote repetitive sequences. Background colors in the PIP diagram indicate: green for exon, yellow for gene, red for 5' upstream conserved noncoding element, and orange for intergenic conserved noncoding element. Sequence position in human Dlx3-4 PAC clone is shown at the bottom.
jezb22469-sup-0001-figure5.tif1283KSupplemental Fig. 5. External ear transverse section of E13.5 embryo of Tg-(Dlx37-lacZ-79kb) mouse line. Arrows indicate the position of external auditory meatus. LacZ reporter expression was observed in external ear region along external auditory meatus.

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