Gene detail

Detailed information of OS493_012688-T1 in Lophelia pertusa

Genomic Location: scaffold_33:2059313...2060422
NR annotation: KAJ7379927.1, COP9 signalosome complex subunit 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
Q6IR75	COP9 signalosome complex subunit 2 (Fragment) OS=Xenopus laevis OX=8355 GN=csn2 PE=2 SV=1
P61201	COP9 signalosome complex subunit 2 OS=Homo sapiens OX=9606 GN=COPS2 PE=1 SV=1
P61202	COP9 signalosome complex subunit 2 OS=Mus musculus OX=10090 GN=Cops2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006683 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01399 all species →	PCI	PCI domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR000717 all species →	Domain	Proteasome component (PCI) domain	Interproscan
IPR050871 all species →	Family	26S Proteasome and COP9 Signalosome Components	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10678 all species →	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 11/COP9 SIGNALOSOME COMPLEX SUBUNIT 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000338 all species →	Biological Process	protein deneddylation	Interproscan
GO:0008180 all species →	Cellular Component	COP9 signalosome	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
K12176	COPS2, CSN2, TRIP15; COP9 signalosome complex subunit 2	-	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_012688-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

47.5Max TPM

15.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	14.38	27.11
polyp at pH7 6	18	18	17.05	22.67
coral polyp · control treatment	16	16	20.75	47.46
coral polyp · oil and dispersant treatment	16	16	21.75	38.70
coral polyp · oil treatment	16	16	15.49	30.87
coral polyp · dispersant treatment	16	16	8.97	19.58
Polyp	10	10	6.66	13.27

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.11
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.34
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.57
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.23
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.86
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.15
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.87
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.74
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.23
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.21
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.92
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.08
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.46
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.09
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.09
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.98
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.80
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.08
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.67
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.04
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.36
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.44
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.46
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.28
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.20
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.13
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.97
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.82
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.80
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.64
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.58
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.43
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.30
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.24
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.25
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.28
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.46
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.69
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.53
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.59
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.47
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.11
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.13
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.13
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.51
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.34
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.77
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.18
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.99
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.58
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.15
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.34
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.70
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.18
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.27
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.19
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.32
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.81
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.68
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.70
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.64
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.51
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.35
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.08
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.19
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.39
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.87
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.06
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.87
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.85
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.23
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.85
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.65
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.37
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.22
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.10
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.84
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.28
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.02
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.77
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.75
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.68
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.34
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.09
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.58
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.09
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.95
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.77
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.38
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.20
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.79
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.47
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.40
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.52
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.19
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.95
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.81
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.17
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.19
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.08
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	13.27
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.56
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.22
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	7.06
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.80
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.76
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.13
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.39
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.32
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.06

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.