The transcriptome of metamorphosing flatfish

Alves, Ricardo N.; Gomes, Ana S.; Stueber, Kurt; Tine, Mbaye; Thorne, M. A. S.; Smáradóttir, H.; Reinhard, Richard; Clark, M. S.; Rønnestad, Ivar; Power, Deborah M.

doi:10.1186/s12864-016-2699-x

BMC Genomics

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	Melanosome organization
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	Pigment cell development
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

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)

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ISSN: 1471-2164

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