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Table 2 Genes in vertebrate skin development and pigmentation identified in the Atlantic halibut skin transcriptome

From: The transcriptome of metamorphosing flatfish

Contig ID Protein name Acronym Accession no. Species E-value Biological role
lcst_c59341 Transcription factor ap-2 alpha (activating enhancer binding protein 2 alpha) tfap2c A2APA8 Mus musculus 3E-38 Skin development
lcst_c6882 Epithelial discoidin domain-containing receptor 1 ddr1 B0V2H8 Mus musculus 2E-71
lcst_c52199 Adenomatosis polyposis coli, isoform CRA_a apc B2RUG9 Mus musculus 8E-28
lcst_c5213 T-cell factor-4 variant L tcf7l2 E2GH26 Homo sapiens 1E-39
lcst_c348 Desmoplakin dsp E9Q557 Mus musculus 0
lcst_c611 Collagen, type V. Alpha 2 col5a2 F1LQ00 Rattus norvegicus 1E-124
lcst_rep_c10540 Keratin, type I cytoskeletal 9 krt9 F1M7K4 Rattus norvegicus 2E-59
lcst_c88 Sratifin (14-3-3 protein sigma) sfn O70456 Mus musculus 4E-74
lcst_c38806 Steryl-sulfatase sts P15589 Rattus norvegicus 2E-61
lcst_c1342 Gap junction beta-3 protein gjb3 P28231 Mus musculus 2E-56
lcst_c5669 Macrophage migration inhibitory factor mif P30904 Rattus norvegicus 3E-30
lcst_c7497 Cellular tumor antigen p53 Trp63 Q569E5 Mus musculus 8E-48
lcst_c26088 Transcription factor 15 tcf15 Q60756 Mus musculus 4E-31
lcst_c32091 Copper-transporting atpase 1 atp7a Q64430 Mus musculus 8E-47
lcst_c62343 Calcium release channel (Ryanodine receptor 1) crc1, ryr1 Q6LAA3 Sus scrofa 3E-26
lcst_c54854 Lethal(2) giant larvae protein homolog 2 llgl2 Q7SZE3 Danio rerio 8E-58
lcst_c28836 Extracellular matrix protein FRAS1 fras1 Q80T14 Mus musculus 1E-70
lcst_c6455 Alanine-trna ligase, cytoplasmic aars Q8BGQ7 Mus musculus 0
lcst_c50366 Nerve growth factor receptor (TNFR superfamily, member 16) ngfr Q8CFT3 Mus musculus 7E-34
lcst_c1016 Delta(24)-sterol reductase dhcr24 Q8VCH6 Mus musculus 0
lcst_c60747 Long-chain fatty acid transport protein 4 slc27a4 Q91VE0 Mus musculus 2E-121
lcst_c28754 Platelet-derived growth factor subunit A pdgfa Q99L56 Mus musculus 1E-29
lcst_c4164 Collagen, type I, alpha 2 Col1a2 Q91VL4 Mus musculus 9E-91
lcst_c27614 B-cell lymphoma/leukemia 11B bcl11b Q99PV8 Mus musculus 2E-58
lcst_rep_c10461 Junction plakoglobin jup Q9PVF7 Danio rerio 4E-180
lcst_c57261 Suppressor of fused homolog sufu Q9Z0P7 Mus musculus 3E-64
lcst_c27807 Serum response factor srf Q9JM73 Mus musculus 9E-58 Skin morphogenesis
lcst_c6845 Collagen, type I, alpha 1 col1a1 Q99LL6 Mus musculus 1E-117
lcst_c4164 Collagen, type I, alpha 2 col1a2 Q91VL4 Mus musculus 9E-91
lcst_c25461 Fibroblast growth factor receptor 1-A fgfr1a Q90Z00 Danio rerio 6E-112
lcst_c7432 Transformation related protein 63 trp63 Q5CZX0 Mus musculus 2E-131
lcst_c34953 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3b erbb3b F1Q4T5 Danio rerio 2E-83 Developmental pigmentation
lcst_c23922 ATPase, H+ transporting, V0 subunit B atp6v0b F1QYM3 Danio rerio 1E-82
lcst_c4704 Melanocyte protein pmel-like pmela Q4VW61 Danio rerio 1E-56
lcst_c40663 Macrophage colony-stimulating factor 1 receptor csf1r Q9I8N6 Danio rerio 1E-40
lcst_c24693 Vacuolar protein sorting-associated protein 18 homolog vps18 P59015 Danio rerio 5E-139 Endosome to pigment granule transport
lcst_c52806 Mediator of RNA polymerase II transcription subunit 12 med12 Q2QCI8 Danio rerio 3E-122 Iridophore differentiation
lcst_c7916 Forkhead box D3 foxd3 Q502Q4 Danio rerio 2E-107
lcst_c467 Rab escort protein 1 chm Q6RFG0 Danio rerio 1E-114
lcst_c8298 Mindbomb E3 ubiquitin protein ligase 2 mib2 A0AR23 Danio rerio 1E-138 Melanosome differentiation
lcst_c2918 Transcription factor Sox-10 sox10 A4IIJ8 Xenopus tropicalis 1E-49
lcst_rep_c15027 Mindbomb E3 ubiquitin protein ligase 1 mib1 B3DGQ0 Danio rerio 9E-66
lcst_c31755 Transient receptor potential cation channel, subfamily M, member 7 trpm7 B3DK48 Danio rerio 5E-82
lcst_c8173 Glutamine-fructose-6-phosphate transaminase 1 gfpt1 Q3S344 Danio rerio 2E-117
lcst_c8009 vacuolar protein sorting-associated protein 11 homolog vps11 Q4G0A0 Danio rerio 1E-135
lcst_c31151 RNA polymerase-associated protein LEO1 leo1 Q6NYV9 Danio rerio 1E-50
lcst_c366 Histone deacetylase hdac1 Q8JIY7 Danio rerio 0
lcst_c1665 Transcription factor AP2 alpha 2 tfap2a Q8UVE5 Danio rerio 3E-55
lcst_c24989 Microphthalmia-associated transcription factor a mitfa Q9PWC2 Danio rerio 5E-24
lcst_rep_c15543 Presenilin-1 psen1 Q9W6T7 Danio rerio 2E-62
lcst_c2922 Adaptor-related protein complex AP-1, mu subunit 1 ap1m1 Q3UG16 Mus musculus 1E-81 Melanosome organization
lcst_c31194 Tyrosinase related protein tyrp1 Q6DGE4 Danio rerio 1E-84
lcst_c60613 ras-related protein rab-8a rab8a A4FVK4 Danio rerio 8E-99 Melanosome transport
lcst_c1994 Inositol-pentakisphosphate 2-kinase ippk Q4JL91 Danio rerio 2E-33
lcst_c2227 RAB11a, member RAS oncogene family rab11a Q5U3E1 Danio rerio 7E-75
lcst_c43921 Tetratricopeptide repeat protein 8 ttc8 Q6P5I7 Danio rerio 8E-66
lcst_rep_c10145 Chaperonin containing TCP1, subunit 2 (Beta) cct2 Q6PBW6 Danio rerio 0
lcst_c6090 Synembryn-B ric8b Q6DRJ9 Danio rerio 3E-77 Pigment cell development
lcst_c1817 Cadherin-2 cdh2 Q90275 Danio rerio 0
lcst_c2222 N-ethylmaleimide-sensitive factor Nsfa Q7ZU50 Danio rerio 0 Pigment granule localization
lcst_c31478 Dedicator of cytokinesis protein 7 dock7 A2A9M4 Mus musculus 9E-84 Pigmentation
lcst_c30539 Dopachrome tautomerase dct A3KDL7 Sus scrofa 1E-36
lcst_c2174 RNA polymerase-associated protein Ctr9 homolog ctr9 A3KDM3 Danio rerio 0
lcst_c307 Phosphoribosylglycinamide formyltransferase gart Q9I9E6 Danio rerio 0
lcst_c45538 Lysosomal-trafficking regulator lyst Q9Z2X9 Rattus norvegicus 6E-86
lcst_c2408 Apoptosis regulator BAX bax Q07813 Mus musculus 6E-34 Positive regulation of developmental pigmentation
lcst_c8805 A disintegrin and metalloproteinase with thrombospondin motifs 9 adamts9 E9PYV8 Mus musculus 4E-67 Positive regulation of melanocyte differentiation
lcst_c546 Ras-related protein ralb-A ralb-a Q9YH09 Xenopus laevis 3E-65 Regulation of developmental pigmentation
lcst_c6473 Guanine nucleotide binding protein, alpha 11 gna11 Q3UPA1 Mus musculus 1E-131 Regulation of melanocyte differentiation
lcst_c4062 Beta-adrenergic receptor kinase 2 adrbk2 P26819 Rattus norvegicus 6E-144 Rhodopsin metabolic process
  1. Transcripts identified in the Atlantic halibut skin transcriptome that are involved in vertebrate skin development/morphogenesis and pigmentation. The contig ID of the skin transcriptome assembly, Protein name, acronym, accession number (no.), organism and e-value are shown for each protein and they are grouped by biological function (when identified)