Gene detail

Detailed information of OS493_016415-T1 in Lophelia pertusa

Genomic Location: scaffold_50:1096373...1102278
NR annotation: KAJ7385338.1, GTPase-activating protein and VPS9 domain-containing protein 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
A5D794	GTPase-activating protein and VPS9 domain-containing protein 1 OS=Bos taurus OX=9913 GN=GAPVD1 PE=2 SV=1
A2RV61	GTPase-activating protein and VPS9 domain-containing protein 1 OS=Xenopus laevis OX=8355 GN=gapvd1 PE=2 SV=1
Q14C86	GTPase-activating protein and VPS9 domain-containing protein 1 OS=Homo sapiens OX=9606 GN=GAPVD1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006034 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF18151 all species →	DUF5601	Domain of unknown function (DUF5601)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003123 all species →	Domain	VPS9 domain	Interproscan
IPR037191 all species →	Homologous_superfamily	VPS9 domain superfamily	Interproscan
IPR045046 all species →	Family	Vacuolar protein sorting-associated protein 9-like	Interproscan
IPR041545 all species →	Domain	RABX5, catalytic core helical domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23101 all species →	RAB GDP/GTP EXCHANGE FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005085 all species →	Molecular Function	guanyl-nucleotide exchange factor activity	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0030139 all species →	Cellular Component	endocytic vesicle	Interproscan
GO:0031267 all species →	Molecular Function	small GTPase binding	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_016415-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_016415-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

57.8Max TPM

22.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	20.81	36.12
polyp at pH7 6	18	18	18.96	29.02
coral polyp · control treatment	16	16	29.91	57.84
coral polyp · oil and dispersant treatment	16	16	26.52	39.50
coral polyp · oil treatment	16	16	25.19	44.59
coral polyp · dispersant treatment	16	16	23.40	33.42
Polyp	10	10	9.51	14.57

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.12
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.22
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.97
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.41
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.82
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.98
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.69
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.36
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.24
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.93
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.66
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.27
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.50
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.06
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.64
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.35
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.20
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.09
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.02
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.30
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.16
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.93
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.03
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.47
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.45
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.29
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.12
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.83
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.42
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.10
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.07
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.53
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.49
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.39
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.74
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.84
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.76
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.75
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.93
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.13
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.59
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.28
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.40
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.79
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.87
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.18
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.81
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.43
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.85
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.20
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.75
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.50
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.36
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.75
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.98
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.48
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.01
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.00
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.85
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.21
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.77
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.74
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.24
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.63
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.75
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.57
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.43
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.59
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.34
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.36
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.76
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.56
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.78
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.75
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.74
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.56
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.46
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.85
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.03
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.35
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.05
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.60
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.31
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.42
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.99
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.73
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.86
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.59
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.45
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.28
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.14
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.06
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.77
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.12
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.40
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.94
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.65
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.52
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.54
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	14.57
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	13.53
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.72
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.49
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	10.38
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.30
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	7.62
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.36
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.48
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.64

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.