Gene detail

Detailed information of OS493_002539-T1 in Lophelia pertusa

Genomic Location: scaffold_5:3607610...3610203
NR annotation: KAJ7365818.1, hypothetical protein OS493_002539 [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
P34147	Rho-related protein racA OS=Dictyostelium discoideum OX=44689 GN=racA PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002834 (this species only)
Ubiquitin family	E3\|E3 adaptor Cullin RING\|BTB · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00651 all species →	BTB	BTB/POZ domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000210 all species →	Domain	BTB/POZ domain	Interproscan
IPR011333 all species →	Homologous_superfamily	SKP1/BTB/POZ domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24413 all species →	SPECKLE-TYPE POZ PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0030162 all species →	Biological Process	regulation of proteolysis	Interproscan
GO:0031625 all species →	Molecular Function	ubiquitin protein ligase binding	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	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_002539-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_002539-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

95TPM > 0

7Conditions

261.7Max TPM

33.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	25.15	60.33
polyp at pH7 6	18	13	21.83	46.52
coral polyp · control treatment	16	13	27.22	48.53
coral polyp · oil and dispersant treatment	16	15	47.50	117.52
coral polyp · oil treatment	16	14	29.83	54.32
coral polyp · dispersant treatment	16	15	56.05	261.69
Polyp	10	9	28.80	60.82

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.33
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.67
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.21
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.36
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.55
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.60
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.05
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.72
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.22
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.09
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.86
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.65
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.78
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.59
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.26
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.71
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.52
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.85
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.68
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.53
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.32
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.61
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.37
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.29
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.41
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.01
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.47
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.65
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.25
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
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.53
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.90
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.13
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.50
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.42
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.67
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.68
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.65
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.41
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.98
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.16
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.24
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.19
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	117.52
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	91.89
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	88.89
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	70.22
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.08
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.00
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.11
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.03
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.01
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.21
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.01
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.87
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.00
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.66
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.47
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.32
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.36
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.68
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.87
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.76
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.17
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.38
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.64
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.64
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.98
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.77
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.96
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.44
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.35
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	261.69
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	122.08
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	76.18
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.20
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.84
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.19
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.12
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.95
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.63
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.88
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.79
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.59
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.78
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.64
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.22
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	60.82
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	58.21
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	42.04
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	37.56
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	34.44
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	32.12
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	20.68
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.08
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.04
SRR23025710	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.