Gene detail

Detailed information of OS493_002258-T1 in Lophelia pertusa

Genomic Location: scaffold_4:7672478...7680807
NR annotation: KAJ7375484.1, 26S proteasome non-ATPase regulatory subunit 11 [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
F6P3G4	26S proteasome non-ATPase regulatory subunit 11A OS=Danio rerio OX=7955 GN=psmd11a PE=2 SV=1
F6XBL2	26S proteasome non-ATPase regulatory subunit 11 OS=Xenopus tropicalis OX=8364 GN=psmd11 PE=3 SV=2
Q8BG32	26S proteasome non-ATPase regulatory subunit 11 OS=Mus musculus OX=10090 GN=Psmd11 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005612 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF18503 all species →	RPN6_C_helix	26S proteasome subunit RPN6 C-terminal helix domain	Domain	Interproscan
PF18055 all species →	RPN6_N	26S proteasome regulatory subunit RPN6 N-terminal domain	Repeat	Interproscan
PF01399 all species →	PCI	PCI domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR050871 all species →	Family	26S Proteasome and COP9 Signalosome Components	Interproscan
IPR000717 all species →	Domain	Proteasome component (PCI) domain	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR040780 all species →	Domain	6S proteasome subunit Rpn6, C-terminal helix domain	Interproscan
IPR040773 all species →	Domain	26S proteasome regulatory subunit Rpn6, N-terminal	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	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:0005198 all species →	Molecular Function	structural molecule activity	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0008541 all species →	Cellular Component	proteasome regulatory particle, lid subcomplex	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	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
K03036	PSMD11, RPN6; 26S proteasome regulatory subunit N6	-	Proteasome	ko03051	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_002258-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

285.1Max TPM

75.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	55.59	100.64
polyp at pH7 6	18	18	71.90	97.49
coral polyp · control treatment	16	16	71.61	121.23
coral polyp · oil and dispersant treatment	16	16	102.86	134.76
coral polyp · oil treatment	16	16	64.20	92.43
coral polyp · dispersant treatment	16	16	57.24	125.53
Polyp	10	10	131.14	285.09

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	100.64
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	96.14
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	72.98
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	70.86
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.20
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.08
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.72
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.17
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.40
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.07
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.09
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.07
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.68
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.41
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.73
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.05
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.36
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.96
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	97.49
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	97.48
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	90.18
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	89.67
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	87.21
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	86.55
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	82.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	78.92
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	72.85
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	71.30
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	71.02
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.69
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.76
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.67
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.49
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.48
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.55
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.43
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	121.23
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	104.10
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	94.56
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	92.14
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	90.30
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	75.47
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.92
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.62
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.62
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.12
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.21
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.73
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.53
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.85
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.67
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.62
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	134.76
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	129.67
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	128.26
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	119.32
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	112.16
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	111.44
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	109.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	108.86
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	98.03
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	95.88
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	93.69
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	90.16
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	87.99
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	79.32
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	78.50
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.70
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	92.43
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	92.16
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	88.89
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	78.17
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	77.64
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.32
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	61.70
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.73
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.18
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.40
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.82
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.52
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.70
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.17
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.54
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.90
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	125.53
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	115.74
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	81.11
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.72
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.61
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.26
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.42
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.57
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.69
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.10
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.81
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.30
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.94
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.46
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.73
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.89
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	285.09
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	227.89
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	170.26
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	158.29
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	156.70
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	96.52
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	87.35
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	50.90
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	42.28
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	36.15

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.