Gene detail

Detailed information of OS493_034511-T1 in Lophelia pertusa

Genomic Location: scaffold_293:65344...73093
NR annotation: KAJ7351907.1, positive regulation of proteasomal ubiquitin-dependent protein catabolic process [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)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008077 (this species only)
Ubiquitin family	ULD\|UFD/UBQ\|UBQ_Other · all ubiquitin genes in this species
Ubiquitin family	ULD\|UFD/UBQ\|UBQ_PIM · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF18037 all species →	Ubiquitin_5	Ubiquitin-like domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029071 all species →	Homologous_superfamily	Ubiquitin-like domain superfamily	Interproscan
IPR039749 all species →	Family	NEDD8 ultimate buster 1	Interproscan
IPR000626 all species →	Domain	Ubiquitin-like domain	Interproscan
IPR041207 all species →	Domain	NEDD8 ultimate buster 1, ubiquitin-like domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12948 all species →	NEDD8 ULTIMATE BUSTER-1 BS4 PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:2000058 all species →	Biological Process	regulation of ubiquitin-dependent protein catabolic process	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

No KEGG orthology assignment for OS493_034511-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_034511-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

103TPM > 0

7Conditions

52.0Max TPM

9.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	15	2.50	4.85
polyp at pH7 6	18	14	3.09	8.51
coral polyp · control treatment	16	16	17.95	51.99
coral polyp · oil and dispersant treatment	16	16	16.13	42.17
coral polyp · oil treatment	16	16	11.59	26.55
coral polyp · dispersant treatment	16	16	14.33	31.21
Polyp	10	10	3.27	9.81

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.85
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.40
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.12
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.57
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.56
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.34
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.09
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.94
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.74
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.31
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.21
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.14
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.12
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.03
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.67
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.51
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.23
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.97
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.56
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.01
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.99
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.43
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.34
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.12
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.10
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.04
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.94
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.26
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.05
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.99
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.60
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.72
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.54
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.93
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.55
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.31
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.25
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.26
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.35
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.89
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.45
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.75
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.35
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.19
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.17
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.81
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.17
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.66
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.09
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.18
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.38
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.29
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.22
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.66
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.63
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.47
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.84
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.17
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.87
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.43
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.55
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.66
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.31
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.52
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.99
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.89
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.55
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.47
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.28
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.47
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.40
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.08
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.95
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.58
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.52
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.27
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.21
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.47
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.97
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.52
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.57
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.67
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.43
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.69
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.48
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.46
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.84
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.66
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.27
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.06
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.48
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.58
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	9.81
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.14
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.19
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.07
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.88
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.87
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.42
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.33
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.72
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.24

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.