Gene detail

Detailed information of OS493_031623-T1 in Lophelia pertusa

Genomic Location: scaffold_222:134642...148281
NR annotation: KAJ7323426.1, 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
Q9R1A8	E3 ubiquitin-protein ligase COP1 OS=Mus musculus OX=10090 GN=Cop1 PE=1 SV=2
Q8NHY2	E3 ubiquitin-protein ligase COP1 OS=Homo sapiens OX=9606 GN=COP1 PE=1 SV=1
P93471	E3 ubiquitin-protein ligase COP1 OS=Pisum sativum OX=3888 GN=COP1 PE=2 SV=1

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
Ubiquitin family	E3\|E3 adaptor Cullin RING\|CDC20 · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 activity RING\|U-box · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|DWD · 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
PF13923 all species →	zf-C3HC4_2	Zinc finger, C3HC4 type (RING finger)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan
IPR042755 all species →	Family	E3 ubiquitin-protein ligase COP1	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	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_031623-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_031623-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

108TPM > 0

7Conditions

41.1Max TPM

8.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.87	11.33
polyp at pH7 6	18	17	7.76	11.86
coral polyp · control treatment	16	16	11.24	41.09
coral polyp · oil and dispersant treatment	16	16	7.50	33.73
coral polyp · oil treatment	16	16	8.55	13.58
coral polyp · dispersant treatment	16	16	7.57	17.23
Polyp	10	9	5.71	10.58

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.33
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.07
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.89
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.68
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.26
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.12
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.51
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.07
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.94
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.76
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.74
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.18
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.84
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.59
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.18
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.15
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.84
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.54
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.86
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.81
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.10
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.07
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.71
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.04
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.95
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.77
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.64
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.51
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.31
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.07
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.85
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.33
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.41
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.76
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.52
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.09
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.72
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.34
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.23
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.12
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.24
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.48
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.30
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.00
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.69
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.34
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.05
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.23
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.03
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.10
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.85
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.73
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.59
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.72
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.63
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.76
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.55
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.20
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.14
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.10
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.04
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.01
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.78
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.35
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.68
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.38
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.31
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.58
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.22
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.95
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.47
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.37
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.09
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.12
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.87
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.43
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.77
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.30
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.04
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.81
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.11
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.66
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.05
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.23
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.23
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.01
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.98
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.23
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.35
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.02
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.47
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.38
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.34
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.97
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.17
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.96
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.96
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.53
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.33
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	10.58
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	9.90
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.65
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	7.68
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.69
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.89
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.69
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.57
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.48
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.