Gene detail

Detailed information of OS493_030083-T1 in Lophelia pertusa

Genomic Location: scaffold_189:406055...407285
NR annotation: KAJ7377272.1, hypothetical protein OS493_030083 [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
Q9SS90	E3 ubiquitin-protein ligase RGLG1 OS=Arabidopsis thaliana OX=3702 GN=RGLG1 PE=1 SV=1
Q8LB88	E3 ubiquitin-protein ligase RGLG5 OS=Arabidopsis thaliana OX=3702 GN=RGLG5 PE=1 SV=1
Q9LY87	E3 ubiquitin-protein ligase RGLG2 OS=Arabidopsis thaliana OX=3702 GN=RGLG2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008947 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07002 all species →	Copine	Copine	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR052079 all species →	Family	E3 ubiquitin-ligases/Copine domain-containing protein	Interproscan
IPR036465 all species →	Homologous_superfamily	von Willebrand factor A-like domain superfamily	Interproscan
IPR010734 all species →	Domain	Copine, C-terminal	Interproscan
IPR002035 all species →	Domain	von Willebrand factor, type A	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45751 all species →	COPINE FAMILY PROTEIN 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K16280	RGLG; E3 ubiquitin-protein ligase RGLG	EC:2.3.2.27	Ubiquitin system	ko04121	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_030083-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

13.9Max TPM

6.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	9.02	11.70
polyp at pH7 6	18	18	8.18	13.95
coral polyp · control treatment	16	16	7.49	12.45
coral polyp · oil and dispersant treatment	16	16	3.89	8.31
coral polyp · oil treatment	16	16	6.63	12.05
coral polyp · dispersant treatment	16	16	3.52	8.89
Polyp	10	10	7.05	11.49

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.70
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.37
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.17
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.95
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.87
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.71
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.32
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.23
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.20
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.16
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.16
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.57
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.55
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.49
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.47
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.53
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.72
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.11
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.95
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.85
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.52
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.35
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.10
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.45
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.86
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.00
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.92
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.83
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.59
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.32
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.19
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.17
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.14
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.91
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.88
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.26
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.45
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.52
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.66
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.64
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.03
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.62
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.61
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.23
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.94
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.32
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.01
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.32
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.84
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.58
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.13
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.90
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.31
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.52
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.82
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.66
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.64
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.60
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.20
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.13
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.04
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.35
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.98
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.84
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.68
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.46
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.52
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.44
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.05
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.87
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.52
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.31
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.51
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.04
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.86
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.39
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.23
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.84
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.71
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.31
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.97
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.52
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.37
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.56
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.89
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.51
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.42
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.35
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.23
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.75
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.35
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.09
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.92
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.53
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.40
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.34
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.21
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.54
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.90
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.86
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	11.49
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	10.53
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	9.30
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.13
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.66
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.84
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	6.60
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.29
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.88
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.79

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.