Gene detail

Detailed information of OS493_012942-T1 in Lophelia pertusa

Genomic Location: scaffold_34:1490895...1507336
NR annotation: KAJ7373350.1, COP9 signalosome complex subunit 3 [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
Q6P2U9	COP9 signalosome complex subunit 3 OS=Danio rerio OX=7955 GN=cops3 PE=2 SV=1
O88543	COP9 signalosome complex subunit 3 OS=Mus musculus OX=10090 GN=Cops3 PE=1 SV=3
Q9UNS2	COP9 signalosome complex subunit 3 OS=Homo sapiens OX=9606 GN=COPS3 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005579 (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
IPR000717 all species →	Domain	Proteasome component (PCI) domain	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR050756 all species →	Family	COP9 signalosome complex subunit 3	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10758 all species →	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3/COP9 SIGNALOSOME COMPLEX SUBUNIT 3	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	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
K12177	COPS3, CSN3; COP9 signalosome complex subunit 3	-	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_012942-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

93.1Max TPM

41.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	38.56	55.57
polyp at pH7 6	18	18	39.28	57.85
coral polyp · control treatment	16	16	44.87	69.00
coral polyp · oil and dispersant treatment	16	16	29.82	49.92
coral polyp · oil treatment	16	16	47.02	67.38
coral polyp · dispersant treatment	16	16	38.13	92.24
Polyp	10	10	65.34	93.12

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	-	55.57
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.50
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.39
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.19
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.77
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.94
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.53
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.71
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.38
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.14
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.01
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.70
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.50
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.40
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.05
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.86
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.66
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.83
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.85
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.70
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.55
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.58
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.02
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.98
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.19
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.17
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.67
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.52
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.27
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.93
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.39
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.69
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.11
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.51
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.38
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.54
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	69.00
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.96
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.68
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.86
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.41
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.76
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.79
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.80
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.66
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.47
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.85
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.89
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.32
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.14
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.76
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.53
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.92
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.29
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.91
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.99
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.95
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.38
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.43
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.55
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.67
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.24
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.65
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.07
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.26
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.08
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.67
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.08
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	67.38
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.21
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.55
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.32
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.82
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.47
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.27
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.70
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.86
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.83
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.73
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.03
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.32
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.57
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.22
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.00
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	92.24
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.26
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.26
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.20
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.89
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.67
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.73
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.32
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.23
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.01
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.49
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.06
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.20
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.19
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.19
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.13
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	93.12
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	85.05
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	81.55
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	77.23
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	73.97
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	69.74
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	54.65
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	44.09
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	37.96
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	36.08

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.