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Table 2 Zebrafish orthologs of human congenital muscular dystrophy and selected myopathy genes and their genomic locations. Genes associated with both non-congenital and congenital muscular dystrophies are in Table 2-1.

From: Zebrafish orthologs of human muscular dystrophy genes

      Fish Genomic Location Fish BAC Loc   
Gene Symbol Associated Disease Fish EST Notes Scaffold location Clone Location Gene location Notes BAC Name Notes Synteny Notes
Collagen 6A1 Col6A1 Bethlem myopathy, Ullrich CMD XM_693161, partial   1607 CR925698 Chr11 35.3 Mb   zK287I12   On one side Syntenic with Col6A2 on genome and BAC.
Collagen 6A2 Col6A2 Bethlem myopathy, Ullrich CMD XM_691072 The first 320 bases are likely not part of this transcript. 1607 CR925698-BX323597 Chr11 35.2 Mb The first 320 bases are located in multiple places on other chromosomes zK287I12 – zC227N13 The first 320 bases are located on zC184B9. On one side Syntenic with Col6A1 on genome and BAC.
Collagen 6A3 Col6A3 Bethlem myopathy, Ullrich CMD XM_679796 XM_687365 is also orthologous to mammalian Col6A3, but is more similar to a second predicted Col6A3 mammalian locus. 1361-1360 No data Chr9 19.0 Mb and 15.0 Mb The beginning is located on scaffold 1361, the repeating middle elements are on both scaffolds, and the end is on 1360. Note that the genomic locus may be misorganized. zC5M6 Unfinished BAC covers entire transcript on various fragments Yes Syntenic with MLPH on Chr9 and with COPS8 on Chr9 and clone zC5M6.
Desmin DES DCM1, CMD1I, several skeletal and/or cardio-myopathies NM_130963   1342 No data Chr9 7.3 Mb Several loci are orthologous to human desmin. Most ruled out due to closer homology with other proteins. Additional loci on Chr20 (scaffold 2945), and Chr13 (scaffold 1885) could not be ruled out and may be duplications. None Homologous sequences were found, but none were near-exact matches to the zebrafish transcript sequence. No Chr9 locus is not syntenic with the other desmin-like genes, either.
Fukutin FCMD Fukuyama CMD XM_686729, partial   792, 793 CR753888, CT027618, BX072578 Chr5 78.4–79.0 Mb Full match on the first two clones, partial match on the third. Likely a genomic misalignment. zC286A10, zC154E10 Full coverage of the partial transcript on both On one side FSD1CL is syntenic on both genome and BAC.
Filamin C FLNC Myofibrillar myopathy XM_693754, XM_687344, partial Duplicated. Divergent nucleotide sequences. First contains the Human FLNC unique region. Second transcript is only partial. 505, 3643 AL954190, No data Chr4 7.5 Mb, Chr25 32.9 Mb Human FLNC unique region is not part of XM_687344, but is located immediately after it on Chr25. zC284B12, zK3006 Both BACs match XM_693754. No BACs for XM_687344 On one side Chr4 locus not syntenic, though flanking genes are elsewhere on Chr4. Partial NAG6 matches on Chr25.
Integrin Alpha 7 ITGA7 CMD with integrin deficiency None found Closest EST is a closer match to mammalian ITGA6 1560 No data Chr11 2.5 Mb Location identified using human ITGA7 only zC245G15 Used human ITGA7 No Flanking genes are not syntenic with each other, either
Acetyl-glucosaminyl-transferase-like protein LARGE MDC1D NM_001004537 LARGE1B (NM_001004538) is highly orthologous. 570 No data Chr4 39.4 Mb LARGE1B located on Chr18, scaffold 2725, clone BX908385. None LARGE1B located on both zC282N12 & zC206G24 No The closest flanking genes are predictions
Laminin alpha 2 LAMA2 Merosin-deficient CMD XM_694983 Partial, predicted 2875 No data Chr20 3.8 Mb Aligns with LAMA2 predicted transcripts GenScan01065 and FGENESH78171 None   On one side Syntenic with ARHGAP18, but NOT the highly similar LAMA1 locus (on Chr24)
Polyadenylate-binding protein, nuclear 1 PABPN1 Oculo-pharyngeal MD BC079522 NM_213259 also matches but diverges over the 3' non-coding end. NM_213259 3' end is discontinuous with its 5' end on the genome and BACs and may not represent a real transcript. 3471 BX294113 and CT583644 Chr24 21.4 Mb and 21.6 Mb Duplication on Chr24 clones is likely due to genomic misalignment since clones overlap in the Sanger fingerprinted contigs. zKp73G8   No SLC22A17 is located on Chr24, but not in the same region.
Protein O-Mannose Beta-1,2-N-Acetyl-glucosaminyl-transferase POMGNT1 Muscle-eye-brain (MEB) BC097123   985 No data Chr6 69.0 Mb   zK170G13, zC156B18 Sequencing of first BAC is unfinished On one side Syntenic with TSPAN1 on both genome and BAC
Protein-O-mannosyl-transferase 1 POMT1 LGMD2K, Walker Warburg syndrome XM_693177   723 BX511209 and No data Chr5 56.2 Mb & 56.3 Mb Split between 3 loci. Exons 1–3 at first location, exons 3–17 at second location. Exons 17–22 potentially on Chr17 at 37.47 Mb. zC129A6 Covers only first 3 exons. No matches for other exons. No  
Sarcoglycan epsilon SGCE Myoclonic dystonia NM_001002594 Close homology with SCGA 2827 BX640469 Chr19 41.07 Mb   zK104M9   On one side Syntenic with CASD1 on both genome and BAC
Selenoprotein N, 1 SEPN1 Rigid spine MD1 (RSMD1), Multiminicore disease NM_001004294   2451 BX323794 & R626962 Chr17 1.8 Mb & 2.3 Mb Duplication likely due to genome misalignment since the BACs overlap. Both clones have full transcript coverage. zC247C16, zC15D5 BACs overlap, suggesting that the genomic duplication is a misalignment. On one side Syntenic with FAM54B on genome and BAC
  1. CMD/DCM-Congenital Muscular Dystrophy, MD-Muscular Dystrophy, nt-nucleotides.