Gene detail

Detailed information of OS493_014260-T1 in Lophelia pertusa

Genomic Location: scaffold_40:1441050...1452461
NR annotation: KAJ7373112.1, Rap1 GTPase-GDP dissociation stimulator 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
O93614	Rap1 GTPase-GDP dissociation stimulator 1-A OS=Xenopus laevis OX=8355 GN=rap1gds1-a PE=1 SV=1
Q5PPZ9	Rap1 GTPase-GDP dissociation stimulator 1-B OS=Xenopus laevis OX=8355 GN=rap1gds1-b PE=2 SV=1
E9Q912	Rap1 GTPase-GDP dissociation stimulator 1 OS=Mus musculus OX=10090 GN=Rap1gds1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005265 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_014260-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan
IPR040144 all species →	Family	Rap1 GTPase-GDP dissociation stimulator 1	Interproscan
IPR000225 all species →	Repeat	Armadillo	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10957 all species →	RAP1 GTPASE-GDP DISSOCIATION STIMULATOR 1	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:0043547 all species →	Biological Process	positive regulation of GTPase activity	Interproscan
GO:0005515 all species →	Molecular Function	protein 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_014260-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_014260-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

102TPM > 0

7Conditions

12.5Max TPM

3.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	2.81	4.68
polyp at pH7 6	18	14	2.68	5.20
coral polyp · control treatment	16	16	4.46	12.51
coral polyp · oil and dispersant treatment	16	16	3.22	7.07
coral polyp · oil treatment	16	16	4.05	6.15
coral polyp · dispersant treatment	16	16	3.53	9.87
Polyp	10	8	1.54	4.54

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.68
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.39
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.24
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.23
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.14
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.74
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.52
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.42
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.81
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.63
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.51
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.37
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.15
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.98
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.97
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.81
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.20
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.13
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.27
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.21
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.12
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.87
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.83
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.57
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.47
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.15
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.53
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.47
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.72
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.75
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.51
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.30
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.10
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.55
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.28
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.22
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.91
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.89
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.63
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.41
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.95
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.88
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.74
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.24
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.67
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.16
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.07
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.73
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.65
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.17
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.65
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.58
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.32
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.28
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.80
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.79
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.56
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.48
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.20
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.70
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.33
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.18
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.15
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.12
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.03
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.68
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.95
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.54
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.39
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.25
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.86
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.76
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.75
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.33
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.24
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.54
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.70
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.59
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.87
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.15
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.71
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.53
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.44
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.39
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.78
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.75
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.59
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.58
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.49
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.47
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.23
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.01
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.81
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.62
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.54
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.12
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.07
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.04
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.62
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.39
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.02
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.64
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.