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 3 Genes of the vertebrate digestive system identified in the Atlantic halibut GI-tract transcriptome

From: The transcriptome of metamorphosing flatfish

Contig ID	Protein name	Acronym	Accession no.	Organism	E-value	Biological role
lcgut_c14148	Adenosine deaminase	Ada	Q4FK28	Mus musculus	1E-41	Embryonic digestive tract development
lcgut_c24687	Protein kinase domain-containing protein, cytoplasmic	Pkdcc	Q5RJI4	Mus musculus	2E-46
lcgut_c25681	Transforming growth factor beta receptor type 3 isoform b precursor	Tgfbr3	Q90998	Gallus gallus	4E-36
lcgut_c26069	Sal-like protein 1	Sall1	Q6P5E3	Mus musculus	1E-67
lcgut_c31048	Forkhead box protein F1	Foxf1	Q28BS5	Xenopus tropicalis	1E-55
lcgut_c34421	Proprotein convertase subtilisin/kexin type 5	Pcsk5	Q04592	Mus musculus	1E-152
lcgut_c17559	Ribosomal protein S6 kinase	Rps6ka3a	Q7ZVH8	Danio rerio	5E-75	Digestive tract development
lcgut_c33030	TGF-beta receptor type-2	Tgfbr2	P38438	Rattus norvegicus	9E-40
lcgut_c35109	G2/mitotic-specific cyclin-B1	Ccnb1	P24860	Mus musculus	7E-43
lcgut_c901	Cytochrome P450 family 1 subfamily a polypeptide 1	Cyp1a1	Q05A20	Mus musculus	3E-156
lcgut_c17435	Retinoid X nuclear receptor alpha	Nr2b1	F1D8Q5	Homo sapiens	1E-76	Midgut development
lcgut_c186	Retinal dehydrogenase 1	Aldh1a1	P24549	Mus musculus	2E-179
lcgut_c24118	Ornithine transcarbamylase, isoform CRA_a	Otc	Q543H3	Mus musculus	3E-72
lcgut_c2518	Arginase-2, mitochondrial	Arg2	O08691	Mus musculus	2E-56
lcgut_c2565	Proto-oncogene tyrosine-protein kinase receptor Ret	Ret	P07949	Homo sapiens	3E-35
lcgut_rep_c3756	Hydroxymethylglutaryl-coa synthase, mitochondrial	Hmgcs2	P54869	Mus musculus	5E-171
lcgut_c25668	Homeobox protein Nkx-3.2	Nkx3-2	P97503	Mus musculus	6E-35	Intestinal epithelial cell development
lcgut_c374	GATA-binding protein 6	Gata6	ENSDARP00000051997	Danio rerio	0
lcgut_c981	Protein-tyrosine kinase 6	Ptk6	Q64434	Mus musculus	9E-64
lcgut_rep_c3687	Anterior gradient protein 2 homolog	Agr2	Q5RZ65	Danio rerio	7E-66
lcgut_rep_c15924	Polypyrimidine tract binding protein 1a	Ptbp1a	Q503D3	Danio rerio	7E-112	Intestinal epithelial structure maintenance
lcgut_c2805	Heart and neural crest derivatives expressed transcript 2	Hand2	Q5XJD8	Danio rerio	7E-49	Determination of intestine left/right asymmetry
lcgut_c17287	Platelet-derived growth factor receptor alpha	Pdgfra	P26618	Mus musculus	4E-86	Embryonic digestive tract morphogenesis
lcgut_c2545	Sonic hedgehog protein A	Shha	Q92008	Danio rerio	2E-41
lcgut_c30553	DNA-binding protein inhibitor ID-2	Id2	Q6PBD7	Xenopus tropicalis	8E-44
lcgut_c32097	GATA binding protein 4	Gata4	ENSDARP00000090333	Danio rerio	2E-42
lcgut_c37022	Transcription factor 21	Tcf21	Q32PV5	Danio rerio	4E-69
lcgut_c17569	Hepatocyte nuclear factor 1-beta-A	Hnf1ba	A1L1N5	Danio rerio	5E-66	Digestive tract morphogenesis
lcgut_c19328	Caudal type homeobox 1	Cdx1	ENSP00000367043	Homo sapiens	3E-31
lcgut_c20926	Mib protein	Mib	B3DGQ0	Danio rerio	8E-45
lcgut_c22447	Ephrin type-B receptor 3	Ephb3	P54754	Mus musculus	1E-39
lcgut_c22825	Probable rna-binding protein 19	Rbm19	Q6DRI6	Danio rerio	3E-32
lcgut_c25556	Vang-like 2 (Van gogh, Drosophila), isoform CRA_b	Vangl2	D3YY75	Mus musculus	4E-38
lcgut_c26	Claudin 15 like	Cldn15a	Q7T2E7	Danio rerio	3E-82
lcgut_c27711	Secreted frizzled-related protein 1	Sfrp1	Q8C4U3	Mus musculus	1E-49
lcgut_c38245	Protein kinase C iota type	Prkci	Q90XF2	Danio rerio	2E-87
lcgut_c14247	Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 3	Gcnt3	Q5JCT0	Mus musculus	2E-57	Intestinal absorption
lcgut_c14318	2-acylglycerol O-acyltransferase 2	Mogat2	Q80W94	Mus musculus	8E-73
lcgut_c425	Sodium/glucose cotransporter 1	Slc5a1	F6XY79	Mus musculus	6E-142
lcgut_rep_c3628	Fatty acid binding protein 2, intestinal	Fabp2	Q53YP5	Mus musculus	9E-47
lcgut_rep_c38188	Fatty acid binding protein 1, liver	Fabp1	Q3V2F7	Mus musculus	9E-35
lcgut_c2583	ATP-binding cassette sub-family G member 5	Abcg5	Q99PE8	Mus musculus	6E-168	Intestinal cholesterol absorption
lcgut_c280	Niemann-Pick C1-like protein 1	Npc1l1	Q6T3U4	Mus musculus	6E-140
lcgut_c30941	Caveolin	Cav1	Q6YLH9	Danio rerio	3E-65
lcgut_c3243	Pancreatic triacylglycerol lipase	Pnlip	Q6P8U6	Mus musculus	6E-99
lcgut_c34406	Sterol O-acyltransferase 2	Soat2	O75908	Homo sapiens	1E-89
lcgut_c508	ATP-binding cassette sub-family G member 8	Abcg8	Q9DBM0	Mus musculus	0
lcgut_rep_c3552	Pancreatic lipase	pl	D4P6H2	Sus scrofa	4E-83
lcgut_rep_c3840	Annexin	Anxa2b	Q6DHD8	Danio rerio	2E-133
lcgut_c20773	Cholecystokinin receptor type A	Cckar	O08786	Mus musculus	1E-47	Gastric acid secretion/Regulation
lcgut_c14119	Pepsinogen A form iib precursor	Pep2b	AAD56284	Pseudopleuronectes americanus	0	Gastric acid secretion/Regulation
lcgut_c1099	Bone morphogenetic protein 2a	Bmp2a	ENSDARP00000013686	Danio rerio	3E-35
lcgut_c17255	Histamine N-methyltransferase	Hnmt	ENSORLP00000025386	Oryzias latipes	1E-87
lcgut_c17921	MAD homolog 9	Smad9	ENSDARP00000031108	Danio rerio	1E-85
lcgut_c20823	Histamine receptor H2	Hrh2	ENSORLP00000004946	Oryzias latipes	2E-24
lcgut_c22281	Epidermal growth factor receptor a	Egfra	ENSDARP00000125265	Danio rerio	4E-42
lcgut_c25854	SRY-box containing gene 2	Sox2	ENSDARP00000095266	Danio rerio	2E-21
lcgut_c28926	Forkhead box A1 (HNF3?)	Foxa1	ENSDARP00000002213	Danio rerio	7E-44
lcgut_rep_c6868	Protein wntmber 5a	Wnt5a	F1Q8M2	Danio rerio	5E-26

List of candidate genes in the Atlantic halibut GI-tract transcriptome assembly that are involved in vertebrate digestive system development and morphogenesis. The contig ID of the GI-tract 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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