Gene detail

Detailed information of OS493_011917-T1 in Lophelia pertusa

Genomic Location: scaffold_30:3161145...3163158
NR annotation: KAJ7336695.1, F-box/WD repeat-containing protein 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)

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

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007622 (this species only) · gene tree & orthology
Ubiquitin family	E3\|E3 adaptor Cullin RING\|F-box · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12937 all species →	F-box-like	F-box-like	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR052301 all species →	Family	SCF Complex F-box/Wd Repeat-Containing Protein	Interproscan
IPR001810 all species →	Domain	F-box domain	Interproscan
IPR036047 all species →	Homologous_superfamily	F-box-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14381 all species →	DACTYLIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0019005 all species →	Cellular Component	SCF ubiquitin ligase complex	Interproscan
GO:0031146 all species →	Biological Process	SCF-dependent proteasomal 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_011917-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_011917-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

22.9Max TPM

10.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.72	19.65
polyp at pH7 6	18	17	12.37	19.49
coral polyp · control treatment	16	16	11.81	21.33
coral polyp · oil and dispersant treatment	16	16	7.64	12.66
coral polyp · oil treatment	16	16	11.29	22.91
coral polyp · dispersant treatment	16	16	6.25	15.92
Polyp	10	9	9.93	16.58

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.65
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.90
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.82
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.47
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.43
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.99
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.53
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.74
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.98
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.12
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.18
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.08
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.40
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.16
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.78
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.49
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.85
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.35
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.49
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.01
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.83
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.08
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.03
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.39
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.31
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.78
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.41
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.36
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.86
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.65
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.85
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.71
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.47
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.39
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.10
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.33
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.73
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.61
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.20
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.88
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.12
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.92
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.26
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.50
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.36
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.59
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.96
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.90
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.68
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.45
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.51
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.66
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.60
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.75
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.28
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.40
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.25
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.32
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.85
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.36
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.47
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.07
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.85
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.72
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.58
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.12
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.04
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.91
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.16
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.91
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.76
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.23
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.84
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.97
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.57
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.68
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.12
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.24
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.12
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.70
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.11
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.88
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.40
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.92
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.69
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.54
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.45
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.42
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.52
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.82
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.13
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.61
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.43
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.79
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.60
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.50
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.30
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.28
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	16.58
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	15.81
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	15.33
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	14.51
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	12.00
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.58
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.25
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.50
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.70
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.