Gene detail

Detailed information of OS493_027435-T1 in Lophelia pertusa

Genomic Location: scaffold_149:708160...720963
NR annotation: KAJ7356038.1, Synaptic vesicle membrane protein VAT-1 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8JFV8	Synaptic vesicle membrane protein VAT-1 homolog OS=Danio rerio OX=7955 GN=vat1 PE=2 SV=1
Q3MIE4	Synaptic vesicle membrane protein VAT-1 homolog OS=Rattus norvegicus OX=10116 GN=Vat1 PE=1 SV=1
Q99536	Synaptic vesicle membrane protein VAT-1 homolog OS=Homo sapiens OX=9606 GN=VAT1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009493 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08240 all species →	ADH_N	Alcohol dehydrogenase GroES-like domain	Domain	Interproscan
PF13602 all species →	ADH_zinc_N_2	Zinc-binding dehydrogenase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013154 all species →	Domain	Alcohol dehydrogenase-like, N-terminal	Interproscan
IPR011032 all species →	Homologous_superfamily	GroES-like superfamily	Interproscan
IPR036291 all species →	Homologous_superfamily	NAD(P)-binding domain superfamily	Interproscan
IPR020843 all species →	Domain	Polyketide synthase, enoylreductase domain	Interproscan
IPR052100 all species →	Family	Synaptic vesicle ATPase and mitochondrial regulator	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR44054 all species →	SYNAPTIC VESICLE MEMBRANE PROTEIN VAT-1 HOMOLOG-LIKE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

No KEGG orthology assignment for OS493_027435-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_027435-T1 across 110 RNA-seq samples of Lophelia pertusa. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

110Samples

110TPM > 0

7Conditions

118.0Max TPM

44.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	51.25	79.26
polyp at pH7 6	18	18	55.69	92.39
coral polyp · control treatment	16	16	47.19	91.92
coral polyp · oil and dispersant treatment	16	16	46.32	118.00
coral polyp · oil treatment	16	16	43.69	109.09
coral polyp · dispersant treatment	16	16	38.68	98.71
Polyp	10	10	14.59	27.35

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	79.26
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	77.68
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	76.26
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	75.35
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.97
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	61.88
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.91
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.51
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.63
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.64
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.31
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.92
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.23
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.37
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.64
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.14
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.19
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.57
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	92.39
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	91.26
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	79.72
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	79.17
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.82
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.50
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.91
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.48
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.51
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.42
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.85
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.15
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.99
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.74
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.06
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.22
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.21
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.06
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	91.92
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	82.89
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.21
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.33
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.14
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.63
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.57
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.37
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.11
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.43
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.73
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.59
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.21
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.87
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.24
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.85
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	118.00
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.55
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	65.30
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.01
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.55
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.88
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.91
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.04
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.39
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.65
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.52
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.05
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.87
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.34
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.94
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.15
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	109.09
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	104.56
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	67.96
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	67.90
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.14
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.78
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.02
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.34
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.64
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.16
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.00
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.32
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.66
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.07
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.19
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.25
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	98.71
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.68
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.67
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.55
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.89
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.55
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.11
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.67
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.99
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.65
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.22
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.67
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.45
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.41
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.37
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.22
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	27.35
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	22.45
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	21.57
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	18.96
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	17.18
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	16.67
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	7.66
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.18
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.78
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	4.12

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.