Additional File 1:

Sequences of alternative first exons of the dystrophin and utrophin genes. Alignments of: A) N-terminal translation of Dp260 transcript (Dp260 first exon and exon 30), B) first exon and part of exon 45 of Dp140 transcript, C) N-terminal translation of Dp116 transcript (Dp116 first exon and exon 56) and G-utrophin transcript (G-utrophin first exon and exon 56), D) N-terminal translation of Dp71 transcript (Dp71 first exon and exons 63 and 64). Vertical lines denote exon boundaries. Accession numbers: Dp260, H. sapiens [GenBank:U27203], M. musculus [GenBank:CX568898], X. laevis [GenBank:DQ831004]; Dp140, H. sapiens [GenBank:L35854], M. musculus [GenBank:CJ185327], X. laevis [GenBank:DQ831006]; Dp116, H. sapiens [GenBank:S62617], M. musculus [GenBank:AK149002], R. norvegicus [GenBank:S76214], D. rerio [GenBank:DQ788695]; G-utrophin, H. sapiens [GenBank:BP282211], M. musculus [GenBank:X83506], R. norvegicus [GenBank:CB546060], D. rerio [GenBank:DQ788696], D. rerio pseudogene [GenBank:DQ831005]; Dp71, H. sapiens [GenBank:M92650], Canis familiaris [GenBank:AY566609], M. musculus [GenBank:S62620], R. norvegicus [GenBank:X69767], G. gallus [GenBank:CN223681], X. laevis [GenBank:BC082429], D. rerio [GenBank:AF339032], Squalus acanthias [GenBank:CV798132]. Sequences without accession numbers are predicted from genomic sequence alone.

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Additional File 2:

Pyrimidine +3 and alternative splicing of vertebrate dystrophin and dystrobrevin transcripts. A) Alignment of genomic context of dystrophin exon 78, which shows conservation of alternative splicing across vertebrates. Arrow shows the unusual pyrimidine at position +3. B) Alignment of genomic context of exon 13 of the vertebrate dystrobrevin exon 13, which shows alternative splicing across vertebrates in the α- and β-dystrobrevins, but not the γ-dystrobrevins. Arrow shows that a pyrimidine occurs at position +3 in the genes that undergo alternative splicing; this is replaced by a purine in those genes (the γ-dystrobrevins) which constitutively include exon 13. All sequences derived from Ensembl genome databases except S. canicula exon 78 (this work) [GenBank:DQ641922]. Upper case and yellow boxes – exons; lower case – introns.

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Additional File 3:

High Ka/Ks values in the dystrotelin family. Ka/Ks values for the six main vertebrate dystrophin-related proteins (γ-dystrobrevin is only found in fish). The three columns show the degree of pressure to conserve amino acid sequence within rodents, mammals and vertebrates, respectively. High Ka/Ks values suggest weak negative selection or partial positive selective pressures acting on dystrotelin, particularly in the C-terminal region (shaded). All other family members show Ka/Ks < 0.2, indicative of strong purifying selection acting at the amino acid level.

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Additional File 4:

Oligonucleotide primers used in this study. Not all primers are given, but these represent the majority of those used for RT-PCR and genomic PCR. Sequences of primers used for internal sequencing and construct generation are available on request.

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