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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.