Gene detail

Detailed information of OS493_028996-T1 in Lophelia pertusa

Genomic Location: scaffold_172:536975...542232
NR annotation: KAJ7370921.1, 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
Q9R0C8	Guanine nucleotide exchange factor VAV3 OS=Mus musculus OX=10090 GN=Vav3 PE=1 SV=2
Q9UKW4	Guanine nucleotide exchange factor VAV3 OS=Homo sapiens OX=9606 GN=VAV3 PE=1 SV=1
Q08DN7	Proto-oncogene vav OS=Bos taurus OX=9913 GN=VAV1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002927 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00307 all species →	CH	Calponin homology (CH) domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001715 all species →	Domain	Calponin homology domain	Interproscan
IPR035899 all species →	Homologous_superfamily	Dbl homology (DH) domain superfamily	Interproscan
IPR036872 all species →	Homologous_superfamily	CH domain superfamily	Interproscan
IPR000219 all species →	Domain	Dbl homology (DH) domain	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: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_028996-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_028996-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

163.4Max TPM

35.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	13.80	25.00
polyp at pH7 6	18	18	13.30	19.64
coral polyp · control treatment	16	16	37.37	105.88
coral polyp · oil and dispersant treatment	16	16	84.93	163.37
coral polyp · oil treatment	16	16	36.73	70.81
coral polyp · dispersant treatment	16	16	49.57	120.56
Polyp	10	10	7.48	13.34

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.00
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.26
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.62
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.58
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.53
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.21
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.23
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.65
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.56
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.41
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.25
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.47
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.20
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.53
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.63
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.09
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.82
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.37
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.64
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.62
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.50
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.43
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.91
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.88
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.85
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.34
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.20
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.50
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.48
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.35
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.35
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.07
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.05
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.45
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.63
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.10
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	105.88
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.21
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.32
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.24
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.80
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.55
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.79
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.02
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.34
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.17
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.53
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.99
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.33
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.32
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.10
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.39
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	163.37
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	140.41
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	124.00
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	120.86
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	118.21
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	116.48
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	99.57
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	95.70
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.27
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.61
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.02
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.57
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.34
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.89
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.37
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.24
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	70.81
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.29
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.02
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.19
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.64
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.41
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.68
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.60
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.29
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.89
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.40
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.82
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.93
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.34
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.71
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.61
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	120.56
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	99.51
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	83.42
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.64
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.83
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.03
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.74
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.61
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.28
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.94
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.43
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.26
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.64
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.86
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.40
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.03
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.34
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	11.16
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.90
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	8.78
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	7.33
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.14
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6.02
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.27
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.83
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.02

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.