Gene detail

Detailed information of OS493_031640-T1 in Lophelia pertusa

Genomic Location: scaffold_222:358796...363137
NR annotation: KAJ7323441.1, RING finger and WD repeat domain-containing protein 2 [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
Q8NHY2	E3 ubiquitin-protein ligase COP1 OS=Homo sapiens OX=9606 GN=COP1 PE=1 SV=1
Q9R1A8	E3 ubiquitin-protein ligase COP1 OS=Mus musculus OX=10090 GN=Cop1 PE=1 SV=2
Q9T014	Protein SPA1-RELATED 2 OS=Arabidopsis thaliana OX=3702 GN=SPA2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006674 (this species only)
Ubiquitin family	UBD\|Other\|Beta-prp · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR042755 all species →	Family	E3 ubiquitin-protein ligase COP1	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR44080 all species →	E3 UBIQUITIN-PROTEIN LIGASE COP1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	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_031640-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_031640-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

29.7Max TPM

7.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	8.33	15.64
polyp at pH7 6	18	15	6.76	15.02
coral polyp · control treatment	16	16	8.41	29.72
coral polyp · oil and dispersant treatment	16	16	5.70	17.66
coral polyp · oil treatment	16	16	8.63	15.20
coral polyp · dispersant treatment	16	13	4.09	11.98
Polyp	10	9	8.62	14.46

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.64
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.46
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.92
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.25
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.53
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.00
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.86
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.46
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.83
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.23
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.88
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.74
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.52
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.32
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.21
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.05
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.05
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.02
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.57
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.26
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.53
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.10
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.95
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.59
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.34
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.40
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.55
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.27
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.20
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.60
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.39
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.87
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
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.72
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.73
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.09
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.49
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.41
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.36
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.60
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.50
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.28
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.14
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.02
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.86
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.70
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.02
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.85
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.82
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.66
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.61
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.40
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.19
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.58
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.51
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.37
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.36
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.85
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.73
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.50
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.45
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.39
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.61
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.54
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.50
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.20
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.69
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.13
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.51
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.25
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.01
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.23
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.17
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.58
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.60
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.32
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.08
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.36
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.24
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.61
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.12
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.98
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.07
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.45
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.00
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.08
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.08
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.79
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.97
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.75
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.18
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.15
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.82
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.12
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	14.46
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	14.21
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	12.78
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.54
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	11.34
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.60
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.13
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.81
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.34
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.