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.
| Â | Â | Â | Â | Â | Fish Genomic Location | Fish BAC Loc | Â | Â | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | Â | 1607 | CR925698 | Chr11 35.3 Mb | Â | zK287I12 | Â | 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 | Â | 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 | Â | 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 | Â | 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 | Â | 985 | No data | Chr6 69.0 Mb | Â | 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 | Â | zK104M9 | Â | On one side | Syntenic with CASD1 on both genome and BAC |
Selenoprotein N, 1 | SEPN1 | Rigid spine MD1 (RSMD1), Multiminicore disease | NM_001004294 | Â | 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 |