Table 1.
Zebrafish orthologs of human muscular dystrophy genes and their genomic locations.
| 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 |
| Calpain-3 | CAPN3 | LGMD2A | NM_001004571 | 2601 | NA-BX322589 | Chr17 62.6 Mb and 63.1 Mb | By blasts and synteny, appears split,. The first ~ 1550 nt has no corresponding BAC. | N/A – zC283F6 | Human CAPN3 matches well with zK12H9 | Yes | Syntenic with GANC on genome and ZFP106 on genome and BAC (zC283F6) | |
| Caveolin 3 | CAV3 | LGMD1C, hyperCKemia, Rippling muscle disease | NM_205738 | 879 | BX664752 | Chr6 33.2 Mb | Organized in 2 exons, similar to human CAV3 | zKp111E5 | On one side | Syntenic with OXTR on BAC and genome. | ||
| Dystrophin | DMD | Duchenne MD, Becker MD | XM_678461, XM_678362, XM_678552, partial | All three are partial transcripts, but in order, cover most of the DMD coding region | 42 | BX004756, CT033808 | Chr1 9.6 Mb-9.4 Mb | Duplications within gene likely incorrect. Additional partial sequence located on Chr1 scaffold 49 at 10.5 Mb | zC59A4, zC274B7 | Transcripts span these two overlapping BACs | No | |
| Dysferlin | DYSF | LGMD2B, Miyoshi Myopathy, Distal myopathy with anterior tibial onset | XM_684324 | Many transcripts are similar to dysferlin, but this is the only one that aligns closer to dysferlin (rather than myoferlin or otoferlin) on reciprocal blast | 1155 | CR847843 | Chr7 83.3 Mb-83.5 Mb | Human dysferlin also identifies Chr12 (BC063743, likely fish myoferlin) and Chr13 (XM_682373, similar to myoferlin, dysferlin, and otoferlin) | zKp78E10 – bZ50C18 | The first BAC contains the 5' ~ 1/7th while the second BAC overlaps and gives coverage to the transcript end | No | Flanking genes are on Chr7 but not in the same region or on the same scaffold as dysferlin |
| Emerin | EMD | Emery-Dreifuss MD | XM_685843, XM_549369 | Identical except for a single 7nt internal fragment. Likely alternatively spliced variants. Poor homology to mammalian emerin. | 3352 | No data | Chr23 18.96 MB | Duplication of last 4/5 of transcript on Chr7 39.54 Mb, scaffold 1085. No synteny with Chr7. | zC133L21 | Identical matches on unfinished BACs zK233H12, zK181F15, and zK93L1. | Yes | RPL10 and FLNA are at 19.1 Mb and 19.0 Mb, on Chr23 Both are syntenic on BACs. |
| Fukutin related protein | FKRP | MDC1C, LGMD2I | XM_695011, partial | 2206 | No data | Chr15 26.6 Mb | zK31C13 | Yes | STRN4 and SLC1A5 are syntenic on the genome and the BAC. | |||
| Lamin A/C | LMNA | Emery-Dreifuss MD, LGMD1B, CMD1A, etc. | NM_152971 | 2371 | CR848742 | Chr16 37.8 Mb | zK181C1 | No | Flanking genes are not syntenic with each other, either | |||
| Myotilin | TTID | LGMD1A, myofibrillar myopathy | None found | Closest match is Zv5 predicted transcript ENSDARG015348 | 1999 | CT573287 | Chr14 12.2 Mb & 10.8 Mb | ENSDARG015348 split between two loci in Zv6. Genome incorrect. | zK101K8 | Complete and contiguous BAC coverage | No | Flanking genes are not syntenic with each other, either |
| Sarcoglycan alpha | SGCA | LGMD2D | XM_680178 | Close homology with SCGE | 1664 | BX548040 | Chr12 870 Kb | zC190L11 | On one side | Syntenic with Col1A1 on both genome and BAC | ||
| Sarcoglycan beta | SGCB | LGMD2E | NM_001034973 | First half of transcript aligns with full length of human SGCB | 2974 | CT583700 | Chr20 59.8 Mb | Second half of EST is located on Chr25 1.3 Mb (Scaffold 3566) | zC253J24 | Yes | Both genes syntenic on genome and BAC | |
| Sarcoglycan delta | SGCD | LGMD2F, CMD1L | NM_001001816 | 3106 | BX294656 | Chr21 39.0–38.7 Mb | zC238M13 | First 300nt located on zK189O20 | On one side | Syntenic with MRPL22 | ||
| Sarcoglycan gamma | SGCG | LGMD2C | NM_001003748 | 2184 | BX927291 | Chr15 20.2 Mb | Incomplete coverage. Duplicate exon also on scaffold 2184 but not on BAC. | zC261A10 | Complete coverage | On one side | Syntenic with SACS on both genome and BAC | |
| Telethonin | TCAP | LGMD2G, Dilated cardio-myopathy (CMD1N) | XM_679011 | 371 | CR387996 | Chr3 19.9 Mb | Human TCAP also identifies a locus on Chr16 scaffold 2377 but coverage is less complete and exons are not contiguous | zK183N6 | No | |||
| Tripartite Motif-containing protein 32 | TRIM32 | LGMD2H | XM_686142 | Human TRIM32 only has one coding exon. | NA688 | No data | No data | Coding sequence on scaffold NA688. Putative 5' UTR exons are located in duplicate on Chr8, scaffold 1244 | None | Putative 5' UTR exons are located on zK72L14 & zK65O14 | Yes | ASTN2 spans the both the human and the zebrafish TRIM32 loci on Scaffold NA688 |
| Titin | TTN | LGMD2J, Tibial MD, Hereditary Myopathy with early respiratory failure | XM_679005 (TTN2, partial), XM_678144 (TTN1, partial) | Locus is duplicated. Only partial transcripts available | 3186 | BX640499, BX571737, BX640465 | Chr9 41.8 Mb-42.2 Mb | Locus duplications are in tandem. Duplicate genes are divergent in sequence and likely to be true duplicates. | zKp67D2, dZ258D18, zK190I10, dZ249N21, zC198B21 | BACs overlap to cover the entire titin locus. | Yes | Syntenic with FLJ39502 and FKBP7 on genome and BAC. |
MD-Muscular Dystrophy, LGMD-Limb Girdle Muscular Dystrophy, CMD-Congenital Muscular Dystrophy, nt-nucleotides.