Gene detail

Detailed information of OS493_017057-T1 in Lophelia pertusa

Genomic Location: scaffold_54:200512...205503
NR annotation: KAJ7333520.1, 26S proteasome non-ATPase regulatory subunit 4 [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
P55036	26S proteasome non-ATPase regulatory subunit 4 OS=Homo sapiens OX=9606 GN=PSMD4 PE=1 SV=1
Q58DA0	26S proteasome non-ATPase regulatory subunit 4 OS=Bos taurus OX=9913 GN=PSMD4 PE=2 SV=1
O35226	26S proteasome non-ATPase regulatory subunit 4 OS=Mus musculus OX=10090 GN=Psmd4 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007625 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13519 all species →	VWA_2	von Willebrand factor type A domain	Domain	Interproscan
PF02809 all species →	UIM	Ubiquitin interaction motif	Motif	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002035 all species →	Domain	von Willebrand factor, type A	Interproscan
IPR003903 all species →	Conserved_site	Ubiquitin interacting motif	Interproscan
IPR036465 all species →	Homologous_superfamily	von Willebrand factor A-like domain superfamily	Interproscan
IPR049590 all species →	Domain	PSMD4, RAZUL domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10223 all species →	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0008540 all species →	Cellular Component	proteasome regulatory particle, base subcomplex	Interproscan
GO:0031593 all species →	Molecular Function	polyubiquitin modification-dependent protein binding	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	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
K03029	PSMD4, RPN10; 26S proteasome regulatory subunit N10	-	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_017057-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

221.2Max TPM

70.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	50.01	67.75
polyp at pH7 6	18	18	60.89	120.83
coral polyp · control treatment	16	16	66.63	115.11
coral polyp · oil and dispersant treatment	16	16	107.03	158.19
coral polyp · oil treatment	16	16	63.59	91.01
coral polyp · dispersant treatment	16	16	59.45	132.33
Polyp	10	10	103.20	221.21

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	-	67.75
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.79
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.56
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.17
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.63
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.37
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.24
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.88
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.19
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.94
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.76
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.60
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.50
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.83
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.85
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.38
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.93
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.72
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	120.83
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	105.30
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.24
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.36
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.32
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.12
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.87
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.71
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.30
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.93
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.36
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.39
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.23
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.08
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.59
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.19
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.43
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.72
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	115.11
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	94.80
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.06
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.55
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.09
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.00
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.42
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.35
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.76
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.00
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.62
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.68
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.03
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.39
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.94
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.32
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	158.19
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	147.43
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	141.50
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	123.95
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	123.90
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	119.89
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	112.86
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	111.77
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	97.62
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	95.77
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	95.00
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	89.58
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	82.01
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	78.36
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.90
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.77
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	91.01
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.52
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.00
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.53
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	72.85
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	68.63
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.28
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.09
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.90
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.99
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.94
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.84
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.17
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.07
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.19
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.38
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	132.33
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	93.17
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	86.92
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	85.57
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.81
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.52
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.55
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.24
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.89
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.33
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.11
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.44
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.24
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.55
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.28
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.23
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	221.21
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	177.83
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	133.39
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	126.82
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	107.47
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	67.12
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	64.47
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	48.34
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	45.55
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	39.77

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.