Gene detail

Detailed information of OS493_028995-T1 in Lophelia pertusa

Genomic Location: scaffold_172:533944...536499
NR annotation: KAJ7370920.1, Guanine nucleotide exchange factor vav2, partial [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
P52735	Guanine nucleotide exchange factor VAV2 OS=Homo sapiens OX=9606 GN=VAV2 PE=1 SV=2
Q60992	Guanine nucleotide exchange factor VAV2 OS=Mus musculus OX=10090 GN=Vav2 PE=1 SV=1
Q1ZXH8	Guanine exchange factor for Rac 30 OS=Dictyostelium discoideum OX=44689 GN=gxcDD PE=4 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002902 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00621 all species →	RhoGEF	RhoGEF domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000219 all species →	Domain	Dbl homology (DH) domain	Interproscan
IPR035899 all species →	Homologous_superfamily	Dbl homology (DH) domain superfamily	Interproscan
IPR001331 all species →	Conserved_site	Guanine-nucleotide dissociation stimulator, CDC24, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45818 all species →	PROTEIN VAV	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005085 all species →	Molecular Function	guanyl-nucleotide exchange factor activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0016477 all species →	Biological Process	cell migration	Interproscan
GO:0043087 all species →	Biological Process	regulation of GTPase activity	Interproscan
GO:0035556 all species →	Biological Process	intracellular signal transduction	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_028995-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_028995-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

105TPM > 0

7Conditions

202.0Max TPM

41.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	17.47	30.31
polyp at pH7 6	18	15	16.82	28.76
coral polyp · control treatment	16	16	43.05	129.00
coral polyp · oil and dispersant treatment	16	16	99.71	201.98
coral polyp · oil treatment	16	16	43.73	75.87
coral polyp · dispersant treatment	16	16	52.65	115.19
Polyp	10	9	8.90	18.31

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	-	30.31
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.09
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.88
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.92
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.32
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.07
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.49
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.47
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.96
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.45
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.25
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.87
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.42
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.37
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.64
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.42
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.53
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.76
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.18
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.78
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.55
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.35
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.99
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.84
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.78
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.50
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.48
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.63
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.37
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.32
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.67
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.56
SRR11359513	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
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	129.00
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	78.89
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.17
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.28
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.67
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.32
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.83
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.05
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.11
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.30
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.44
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.87
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.11
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.95
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.91
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.90
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	201.98
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	164.96
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	150.44
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	145.20
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	139.10
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	126.82
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	115.28
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	109.75
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.75
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	70.70
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.69
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.78
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.32
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.67
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.38
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.56
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	75.87
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.74
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.21
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.84
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.90
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.82
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.16
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.99
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.01
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.39
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.78
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.97
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.92
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.55
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.48
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.08
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	115.19
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	107.02
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	103.95
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.50
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.29
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.58
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.83
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.48
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.11
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.22
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.77
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.63
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.88
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.58
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.99
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.38
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	18.31
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	14.50
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.27
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	11.49
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	10.15
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.81
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	8.44
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.79
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.27
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.