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. 2013 Jan 8;8(1):e53171. doi: 10.1371/journal.pone.0053171

Table 3. Selection of novel rainbow trout genes grouped by functional categories.

Putative Name and Function Size, bp Hit Acc. No. E-Value Blastx Muscle
Growth and Myogenic Factors
fibroblast growth factor 1 (acidic) [D. rerio] 659 NP_001098748 4.88E−31 Drerio R
follistatin-like 1b [D. rerio] 539 NP_001034710 8.02E−89 Drerio W
growth arrest-specific 7 [X laevis] 574 NP_001090555 4.02E−72 RefSeq R
heparin-binding EGF-like growth factor [D. rerio] 1024 NP_001104696 5.52E−31 Drerio R, W
insulin-like growth factor binding protein 5a [D. rerio] 565 NP_001119935 4.26E−43 Drerio R
insulin-like growth factor binding protein 6b [D. rerio] 500 NP_001154874 3.11E−73 Drerio W
insulin-like growth factor-binding protein 3 [B. taurus] 593 NP_776981 2.04E−37 RefSeq W
myocyte enhancer factor 2ca [D. rerio] 600 NP_571387 1.23E−59 Drerio R, W
myocyte-specific enhancer factor 2C [D. rerio] 634 NP_001124434 1.06E−35 Drerio R
myogenic factor 6 [D. rerio] 562 NP_001003982 7.14E−67 Drerio R, W
protein Wnt-2 [D. rerio] 2633 NP_878296 2.62E−128 Drerio R
angiopoietin-1 [D. rerio] 1023 NP_571888 5.88E−57 Drerio R, W
Receptors
androgen receptor [D. rerio] 624 NP_001076592 1.38E−32 Drerio W
cation-independent mannose-6-phosphate receptor [D. rerio] 1107 NP_001034716 3.81E−81 Drerio W
TGF-beta receptor type-2 [D. rerio] 658 NP_878275 8.17E−95 Drerio R
vascular endothelial growth factor receptor 1 [D. rerio] 536 NP_001014829 6.43E−11 Drerio R
frizzled homolog 3-like [D. rerio] 512 NP_001074070 1.85E−52 Drerio R
bone morphogenetic protein receptor, type 1a [D. rerio] 661 NP_571696 6.21E−39 Drerio R
leukemia inhibitory factor receptor alpha [D. rerio] 1278 NP_001014328 2.68E−89 Drerio W
ryanodine receptor 1b (skeletal) [D. rerio] 3716 NP_001096041 0.0 Drerio R, W
ryanodine receptor 3 [G. gallus] 845 NP_996757 2.46E−111 RefSeq R, W
acetylcholine receptor subunit alpha [D. rerio] 1860 NP_571520 0.0 Drerio R, W
acetylcholine receptor subunit beta [M. musculus] 520 NP_033731 2.60E−50 RefSeq W
acetylcholine receptor subunit delta [D. rerio] 606 NP_996947 2.40E−18 Drerio R, W
Structural and Cytoskeletal Elements
myosin heavy chain, cardiac muscle isoform [G. gallus] 603 NP_990097 5.02E−52 RefSeq R
myosin-binding protein C, slow-type [D. rerio] 782 NP_001007323 1.21E−111 Drerio R
myosin-Va [D. rerio] 1990 NP_001074428 0 Drerio R
myosin-VI [D. rerio] 500 NP_001004110 2.24E−68 Drerio R
dystrophin [D. rerio] 624 NP_571860 7.21E−18 Drerio R
actin-binding protein IPP [D. rerio] 1013 NP_001107093 1.83E−02 Drerio W
actin-binding Rho-activating protein [D. rerio] 805 NP_001003986 1.10E−74 Drerio W
actin-related protein 3B [D. rerio] 780 NP_001083025 1.76E−113 Drerio W
alpha-actinin-2 [D. rerio] 1369 NP_001032662 0 Drerio R
ankyrin 1, erythrocytic [D. rerio] 643 NP_001005969 9.70E−21 Drerio R, W
ankyrin 3, epithelial isoform 1 [R. norvegicus] 1195 NP_113993 1.70E−04 RefSeq W
huntingtin [D. rerio] 580 NP_571093 4.42E−91 Drerio R
supervillin [D. rerio] 1705 NP_001030338 0.0 Drerio R, W
synaptopodin-2 [R. norvegicus] 513 NP_001178892 1.14E−23 RefSeq R
synemin [D. rerio] 655 NP_001038340 1.40E−46 Drerio R, W
tensin 1 [R. norvegicus] 603 NP_001178739 6.56E−48 RefSeq W
troponin I, skeletal, slow like [D. rerio] 696 NP_001002101 2.83E−45 Drerio R
troponin T type 1 (skeletal, slow) [X laevis] 1067 NP_001086207 3.06E−67 RefSeq R
troponin T2a, cardiac [D. rerio] 891 NP_690853 5.36E−61 Drerio R
Protein Kinases and Phosphatases
5′-AMP-activated protein kinase alpha-2 [G. gallus] 613 NP_001034694 1.83E−89 RefSeq R
mitogen-activated protein kinase kinase kinase 5 [D. rerio] 764 NP_001155222 1.82E−107 Drerio R, W
protein kinase C, theta [D. rerio] 667 NP_001082839 4.76E−90 Drerio W
striated muscle preferentially expressed protein kinase [D. rerio] 2086 NP_001007110 1.10E−141 Drerio R, W
protein phosphatase 1 regulatory subunit 3C [D. rerio] 616 NP_957128 7.79E−81 Drerio R, W
protein phosphatase 1L [D. rerio] 1119 NP_001071068 0.0 Drerio W
protein phosphatase inhibitor 2 [G. gallus] 723 NP_001026484 1.17E−06 RefSeq W
Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform [S. salar] 649 NP_001135322 4.11E−122 RefSeq R
serine/threonine-protein phosphatase 5 [D. rerio] 1291 NP_001014372 0.0 Drerio R, W
hepatocyte growth factor-regulated tyrosine kinase substrate [D. rerio] 725 NP_956162 1.62E−119 Drerio W
Metabolism
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 [D. rerio] 772 NP_956102 1.09E−104 Drerio R
brain creatine kinase [D. rerio] 737 NP_001070631 4.68E−04 Drerio R, W
acetyl-CoA carboxylase beta [X. tropicalis] 1947 NP_001131086 0 RefSeq R
acetyl-coenzyme A synthetase, cytoplasmic [D. rerio] 575 NP_001002641 1.15E−59 Drerio W
glycogen phosphorylase, muscle form [D. rerio] 568 NP_001018464 6.92E−99 Drerio R
glycogenin 1 [D. rerio] 509 NP_998675 3.52E−85 Drerio R
mitochondrial uncoupling protein 2 [D. rerio] 1737 NP_571251 5.97E−130 Drerio R, W
phosphoglycerate kinase 1 [D. rerio] 690 NP_998552 3.05E−79 Drerio W
phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform [R. norvegicus] 634 NP_072148 2.67E−41 RefSeq W
Cell adhesion/Extracellular Matrix
laminin subunit alpha-1 [D. rerio] 3762 NP_001030158 0.0 Drerio W
laminin subunit beta-1 [D. rerio] 752 NP_775382 5.48E−40 Drerio R, W
integrin alpha-6 [D. rerio] 1086 NP_001138253 2.65E−96 Drerio W
integrin, beta 1a [D. rerio] 551 NP_001030143 5.60E−61 Drerio R, W
collagen type IV alpha1 [O. latipes] 657 NP_001170943 8.53E−14 RefSeq R
collagen type IX alpha I [D. rerio] 1653 NP_998429 8.32E−49 Drerio R, W
collagen, type IV, alpha 2 [G. gallus] 569 NP_001155862 1.51E−63 RefSeq R, W
collagen, type XI, alpha 1 [D. rerio] 1718 NP_001077313 2.05E−90 Drerio R, W
basement membrane-specific heparan sulfate proteoglycan core protein [D. rerio] 521 NP_001120939 7.01E−71 Drerio R, W
A disintegrin and metalloproteinase with thrombospondin motifs 10 [D. rerio] 582 NP_001116746 1.70E−99 Drerio R
Ion channels
potassium voltage-gated channel subfamily A member 6 [D. rerio] 1103 NP_001124098 5.48E−81 Drerio W
sodium- and chloride-dependent creatine transporter 1 isoform 3 [M. musculus] 1370 NP_001136282 1.15E−155 RefSeq W
sodium channel protein type 4 subunit alpha A [D. rerio] 753 NP_001034914 7.36E−77 Drerio W
sodium channel, voltage gated, type XII, alpha a [D. rerio] 707 NP_001038387 1.15E−110 Drerio R
sodium channel, voltage-gated, type IV, beta a [D. rerio] 522 NP_001071038 1.54E−57 Drerio W
voltage-dependent calcium channel gamma-6 subunit [D. rerio] 650 NP_001076560 3.54E−18 Drerio R, W
voltage-dependent calcium channel subunit alpha-2/delta-1 [D. rerio] 920 NP_001038425 4.99E−110 Drerio R
calcium channel, voltage-dependent, L type, alpha 1S subunit, a [D. rerio] 2299 NP_001139622 0.0 Drerio R, W
Protein degradation
E3 ubiquitin/ISG15 ligase TRIM25 [B. taurus] 538 NP_001093806 1.68E−07 RefSeq R
E3 ubiquitin-protein ligase HECTD1 [D. rerio] 582 NP_001002504 1.20E−11 Drerio W
E3 ubiquitin-protein ligase MARCH5 [D. rerio] 730 NP_956033 5.41E−37 Drerio R, W
E3 ubiquitin-protein ligase mib1 [D. rerio] 506 NP_775393 3.30E−86 Drerio W
E3 ubiquitin-protein ligase NEDD4 [D. rerio] 770 NP_001029358 6.72E−126 Drerio W
E3 ubiquitin-protein ligase RING2 [D. rerio] 727 NP_571288 2.21E−107 Drerio W
E3 ubiquitin-protein ligase SMURF1 [D. rerio] 726 NP_001001943 2.12E−110 Drerio W
E3 ubiquitin-protein ligase TRIM32 [D. rerio] 873 NP_001107066 1.94E−10 Drerio W
ubiquilin-4 [D. rerio] 600 NP_998521 7.89E−22 Drerio W
ubiquitin carboxyl-terminal hydrolase 25 [D. rerio] 1575 NP_001001886 0.0 Drerio R, W
ubiquitin specific peptidase 47 [R. norvegicus] 610 NP_001101012 5.83E−80 RefSeq R
ubiquitin specific peptidase 7 (herpes virus-associated) [X. laevis] 537 NP_001121282 6.28E−58 RefSeq W
ubiquitin-associated protein 2-like [D. rerio] 520 NP_001076535 1.37E−50 Drerio W
ubiquitin-conjugating enzyme E2 E3 [D. rerio] 598 NP_957215 1.21E−14 Drerio R, W
ubiquitin-like modifier-activating enzyme 1 [D. rerio] 815 NP_998227 1.34E−127 Drerio W
ubiquitin-protein ligase E3A [D. rerio] 1101 NP_001007319 2.68E−18 Drerio W
26S proteasome non-ATPase regulatory subunit 2 [D. rerio] 523 NP_956840 2.60E−81 Drerio W
26S proteasome non-ATPase regulatory subunit 4 [M. domestica] 797 NP_001130032 2.54E−22 RefSeq W
calpain 1, (mu/I) large subunit a [D. rerio] 779 NP_956739 4.42E−142 Drerio R, W
Calpain-3 [S. salar] 2559 NP_001158880 0.0 RefSeq W
cathepsin Z [X laevis] 500 NP_001088101 4.86E−48 RefSeq W
cationic trypsin-3 [D. rerio] 509 NP_571783 6.69E−55 Drerio W
Immune Factors
interferon regulatory factor 4 [D. rerio] 1202 NP_001116182 5.61E−46 Drerio R
leukocyte receptor cluster member 8 homolog [D. rerio] 820 NP_001082988 4.38E−118 Drerio R, W
NF-kappa-B inhibitor epsilon [D. rerio] 539 NP_001073558 8.99E−40 Drerio W
nuclear factor NF-kappa-B p100 subunit [S. salar] 1084 NP_001167054 2.68E−130 RefSeq W
scavenger receptor class B, member 2 [D. rerio] 1631 NP_775366 9.74E−135 Drerio R, W
signal transducer and activator of transcription 2 [S. salar] 1072 NP_001138896 3.69E−124 RefSeq W
signal transducer and activator of transcription 5.1 [D. rerio] 1168 NP_919368 0.0 Drerio W
thymosin beta [D. rerio] 574 NP_991144 1.17E−03 Drerio R, W