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Table 1 Zebrafish orthologs of human muscular dystrophy genes and their genomic locations.

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
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.
  1. MD-Muscular Dystrophy, LGMD-Limb Girdle Muscular Dystrophy, CMD-Congenital Muscular Dystrophy, nt-nucleotides.