Gene detail

Detailed information of OS493_001627-T1 in Lophelia pertusa

Genomic Location: scaffold_3:6757986...6771308
NR annotation: KAJ7381483.1, hypothetical protein OS493_001627 [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
Q9P0L0	Vesicle-associated membrane protein-associated protein A OS=Homo sapiens OX=9606 GN=VAPA PE=1 SV=3
Q9WV55	Vesicle-associated membrane protein-associated protein A OS=Mus musculus OX=10090 GN=Vapa PE=1 SV=2
Q5R601	Vesicle-associated membrane protein-associated protein A OS=Pongo abelii OX=9601 GN=VAPA PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006268 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00635 all species →	Motile_Sperm	MSP (Major sperm protein) domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR008962 all species →	Homologous_superfamily	PapD-like superfamily	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR000535 all species →	Domain	Major sperm protein (MSP) domain	Interproscan
IPR016763 all species →	Family	Vesicle-associated membrane-protein-associated protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10809 all species →	VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005789 all species →	Cellular Component	endoplasmic reticulum membrane	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0033149 all species →	Molecular Function	FFAT motif binding	Interproscan
GO:0061817 all species →	Biological Process	endoplasmic reticulum-plasma membrane tethering	Interproscan
GO:0090158 all species →	Biological Process	endoplasmic reticulum membrane organization	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_001627-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_001627-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

225.7Max TPM

122.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	112.77	145.30
polyp at pH7 6	18	18	121.88	150.36
coral polyp · control treatment	16	16	133.68	225.72
coral polyp · oil and dispersant treatment	16	16	150.01	219.90
coral polyp · oil treatment	16	16	120.17	142.04
coral polyp · dispersant treatment	16	16	104.90	139.91
Polyp	10	10	112.74	130.21

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	145.30
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	140.88
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	135.16
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	134.78
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	125.88
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	116.49
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	114.09
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	110.78
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	108.90
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	108.75
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	103.38
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	102.06
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	101.43
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	100.41
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	100.41
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	95.79
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	95.75
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	89.56
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	150.36
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	147.58
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	138.23
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	133.12
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	132.09
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	130.76
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	130.01
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	129.98
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	127.90
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	126.84
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	116.19
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	115.45
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	110.68
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	105.88
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	103.87
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	101.41
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	99.01
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	94.40
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	225.72
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	166.56
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	147.67
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	147.53
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	143.46
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	138.91
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	134.37
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	131.56
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	127.31
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	124.97
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	122.99
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	122.48
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	115.29
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	107.73
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	101.25
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	81.11
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	219.90
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	186.13
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	162.80
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	161.10
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	160.09
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	150.46
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	148.50
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	148.44
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	147.74
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	144.40
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	142.82
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	140.66
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	135.84
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	128.59
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	126.12
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	96.52
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	142.04
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	141.49
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	134.20
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	132.56
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	132.26
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	131.67
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	127.47
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	126.84
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	125.90
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	124.48
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	119.14
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	109.75
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	103.84
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	99.14
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	95.45
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.49
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	139.91
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	135.04
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	129.20
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	129.01
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	116.93
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	115.66
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	114.33
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	111.92
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	110.36
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	110.04
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	105.20
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	96.92
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	85.20
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	79.53
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.28
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.89
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	130.21
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	127.13
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	126.08
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	124.11
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	119.89
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	115.29
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	110.32
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	106.94
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	98.29
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	69.15

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.