Gene detail

Detailed information of OS493_039781-T1 in Lophelia pertusa

Genomic Location: scaffold_1440:7048...12288
NR annotation: KAJ7312347.1, Vesicle-associated membrane protein 3 [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
Q15836	Vesicle-associated membrane protein 3 OS=Homo sapiens OX=9606 GN=VAMP3 PE=1 SV=3
Q4R8T0	Vesicle-associated membrane protein 3 OS=Macaca fascicularis OX=9541 GN=VAMP3 PE=3 SV=1
P63024	Vesicle-associated membrane protein 3 OS=Mus musculus OX=10090 GN=Vamp3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001916 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00957 all species →	Synaptobrevin	Synaptobrevin	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001388 all species →	Family	Synaptobrevin-like	Interproscan
IPR042855 all species →	Domain	v-SNARE, coiled-coil homology domain	Interproscan
IPR016444 all species →	Family	Synaptobrevin/Vesicle-associated membrane protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45701 all species →	SYNAPTOBREVIN FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0005484 all species →	Molecular Function	SNAP receptor activity	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0006906 all species →	Biological Process	vesicle fusion	Interproscan
GO:0019905 all species →	Molecular Function	syntaxin binding	Interproscan
GO:0031201 all species →	Cellular Component	SNARE complex	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_039781-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_039781-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

201.6Max TPM

97.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	109.22	201.57
polyp at pH7 6	18	18	105.97	171.28
coral polyp · control treatment	16	16	92.42	129.70
coral polyp · oil and dispersant treatment	16	16	99.06	138.50
coral polyp · oil treatment	16	16	88.87	132.48
coral polyp · dispersant treatment	16	16	92.33	178.55
Polyp	10	10	93.59	173.76

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	201.57
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	191.24
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	187.67
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	169.19
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	141.37
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	138.86
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	131.84
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	123.02
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	111.58
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	100.58
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	99.32
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	73.38
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	66.65
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	59.78
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.92
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.84
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.70
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.50
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	171.28
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	167.62
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	167.42
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	164.47
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	136.23
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	134.44
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	132.48
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	123.61
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	122.73
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	113.04
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	88.24
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	82.38
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.35
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.77
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.60
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.23
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.56
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.06
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	129.70
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	124.75
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	115.01
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	105.37
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	104.96
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	101.76
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	100.56
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	96.44
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	94.50
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	92.03
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	82.08
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	79.24
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	75.44
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	69.07
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.83
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.94
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	138.50
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	132.66
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	120.34
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	119.41
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	111.69
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	110.04
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	108.79
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	106.90
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	103.46
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	93.47
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	87.93
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	87.14
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	86.22
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.94
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.32
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.08
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	132.48
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	120.19
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	111.54
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	105.10
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	104.58
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	103.44
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	97.65
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	94.72
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	85.58
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.40
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	79.20
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	77.23
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	72.55
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	67.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.28
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.95
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	178.55
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	121.89
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	118.29
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	111.62
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	107.50
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	102.40
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	101.51
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	101.16
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	96.16
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	92.14
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	79.34
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	75.83
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.54
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	69.26
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.79
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.33
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	173.76
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	146.06
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	133.04
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	107.81
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	95.05
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	81.46
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	76.59
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	62.30
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	30.30
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	29.56

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.