Table 3

List of paralogues identified in the gilthead sea bream skeletal muscle transcriptome
Paralogue Gene name Gene Function

Fraction of CDS (%)

Paralogue1/ paralogue2

Coverage

Paralogue1/ Paralogue2

Paralogues identity (%) Nomenclature
Acethylcoline receptor subunit alpha 1 Ion-conducting channel 50/50 8/12 85 Alpha 1.a/1.b
Adp/atp translocase (Solute carrier family 25, SLC25) Catalyzes the exchange of ADP and ATP across the mitochondrial inner membrane 100/100 43/87 92 SLC25 member 5 and 6
Calpain small subunit 1 Calcium-regulated thiol-protease involved in cytoskeletal remodeling 100/100 10/11 79 Calpain subunit 1a/b
Carnitine O- acetyltransferase Carnitine acetylase is specific for short chain fatty acids 100/67 23/7 67 Carnitine O-acetyltransferase a1/a2
Dehydrogenase reductase member 7c Putative oxidoreductase 100/99 59/32 60 DHR7SC-A/DHR7SC-B
Dysferlin interacting protein 1 Sarcolemma repair mechanism of both skeletal muscle and cardiomyocytes 90/90 39/11 71 Dysferlin1a/b
Epithelial membranse protein 3 Probably involved in cell proliferation and cell-cell interactions 100/100 4/14 68 EMP3a/b
Glioblastoma amplified sequence Widely expressed. Most abundant in heart and skeletal muscle 100/100 39/10 80 Nipsnap2a/b
High mobility group box 1 DNA binding proteins that associates with chromatin 88/60/87 439/7/9 60 HMG1a/b HMG2
Microglobulin beta-2 Component of the class I major histocompatibility complex (MHC) 100/100 57/90 60 B2ma/b
Myomesin 185 kDa Major component of the vertebrate myofibrillar M band 98/90 170/54 65 Myomesin1a/b
Serine threonine-protein phosphatase Essential for cell division, and participates in muscle contractility and protein synthesis 50/50 3/4 89 Subunit alpha/gamma
Solute carrier family 38 member 5 Sodium-dependent, pyrimidine- and purine-selective. Involved in the homeostasis of endogenous nucleosides 100/90 14/5 73 Member 5a/b
Tyrosine 3 monooxigenase Enzyme function 90/100 5/5 74 Ywhab/ywhag2
Set and mynd domain- containing protein 1 Acts as a transcriptional repressor. Essential for cardiomyocyte differentiation 95/97 154/127 76 Smyd1a/b
Dual specificity phosphatase and pro Isomerase domain containing 1 Catalyse reaction: Protein tyrosine phosphate + H2O = protein tyrosine + phosphate. 95/100 7/7 51 DUPD1a/b
Metalloproteinase inhibitor 2 precursor Complexes with metalloproteinases and irreversibly inactivates them 80/60 4/4 62 TIMP2b/a
Retinoid x gamma Rreceptor for retinoic acid 100/100 21/10 73 Gamma/beta
Junctophilin 1 Contributes to the stabilization of the junctional membrane complexes 85/87 7/10 65 Junctophilin 1a/b
60s ribosomal protein l5 Required for rRNA maturation and formation of the 60 S ribosomal subunits 100/100 58/186 91 Rpl5a/b
Trans-2,3-enoyl-CoA reductase Reduces trans-2,3-stearoyl-CoA to stearoyl-CoA of long and very long chain fatty acids 98/98 11/61 75 Trec.a/b
Methylmalonate- semialdehyde Dehydrogenase Plays a role in valine and pyrimidine metabolism. Binds fatty acyl-CoA 100/100 26/12 86 Aldha1.a/a1.b
Eukaryotic translation initiation factor 4e type 3 Its translation stimulation activity is repressed by binding to the complex CYFIP1-FMR1 100/100 28/15 73 EIF4E3a/b
Fk506-binding protein 1a May play a role in modulation of ryanodine receptor isoform-1 (RYR-1) 100/100 52/12 82 FKBP1A.1/A.2
Splicing arginine serine-rich 11 May function in pre-mRNA splicing. 95/95 11/25 82 Srf11a/b
Kelch repeat and btb domain containing 10 Substrate-specific adapter of an E3 ubiquitin-protein ligase complex 95/100 38/15 53 Kbtb5/kbtb10

Garcia de la serrana et al.

Garcia de la serrana et al. BMC Genomics 2012 13:181   doi:10.1186/1471-2164-13-181

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