Gene detail

Detailed information of OS493_035061-T1 in Lophelia pertusa

Genomic Location: scaffold_307:389421...390779
NR annotation: KAJ7388913.1, hypothetical protein OS493_035061 [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)	OG0001705 (this species only)
Ubiquitin family	UBD\|Other\|Beta-prp · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|CDC20 · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|SOCS · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|DWD · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07525 all species →	SOCS_box	SOCS box	Domain	Interproscan
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan
PF07676 all species →	PD40	WD40-like Beta Propeller Repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001496 all species →	Domain	SOCS box domain	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR051983 all species →	Family	WD repeat and SOCS box domain-containing protein	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR011659 all species →	Repeat	WD40-like beta propeller	Interproscan
IPR036036 all species →	Homologous_superfamily	SOCS box-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15622 all species →	WD40 REPEAT PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0035556 all species →	Biological Process	intracellular signal transduction	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_035061-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_035061-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

108TPM > 0

7Conditions

12.4Max TPM

4.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.68	7.69
polyp at pH7 6	18	18	4.57	7.08
coral polyp · control treatment	16	16	5.99	12.41
coral polyp · oil and dispersant treatment	16	16	5.10	10.92
coral polyp · oil treatment	16	16	4.85	8.65
coral polyp · dispersant treatment	16	15	2.53	5.33
Polyp	10	9	2.65	5.18

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.69
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.13
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.54
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.21
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.69
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.44
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.41
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.31
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.01
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.88
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.79
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.27
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.07
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.60
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.46
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.43
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.59
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.81
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.08
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.51
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.46
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.25
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.10
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.19
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.95
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.86
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.81
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.71
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.22
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.20
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.95
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.62
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.47
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.44
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.38
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.11
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.41
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.16
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.95
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.91
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.41
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.08
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.06
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.68
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.38
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.48
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.16
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.15
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.72
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.68
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.73
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.97
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.92
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.00
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.60
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.03
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.96
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.92
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.12
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.79
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.71
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.15
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.81
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.04
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.95
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.93
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.35
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.28
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.65
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.99
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.29
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.47
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.75
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.51
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.77
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.60
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.43
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.31
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.30
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.92
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.64
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.48
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.69
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.78
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.33
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.92
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.90
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.32
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.90
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.87
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.69
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.62
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.54
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.34
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.60
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.47
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.12
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.87
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.18
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.39
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.34
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.70
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.99
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.93
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.69
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.17
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.11
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.