Gene detail

Detailed information of OS493_002191-T1 in Lophelia pertusa

Genomic Location: scaffold_4:6462315...6462656
NR annotation: KAJ7375426.1, hypothetical protein OS493_002191 [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)	OG0009263 (this species only) · gene tree & orthology

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
IPR039588 all species →	Family	F-box only protein 4	Interproscan
IPR036047 all species →	Homologous_superfamily	F-box-like domain superfamily	Interproscan
IPR032675 all species →	Homologous_superfamily	Leucine-rich repeat domain superfamily	Interproscan
IPR001810 all species →	Domain	F-box domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR16008 all species →	F-BOX ONLY PROTEIN 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
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_002191-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_002191-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

100TPM > 0

7Conditions

8.1Max TPM

1.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	1.10	2.35
polyp at pH7 6	18	14	1.36	3.72
coral polyp · control treatment	16	16	2.78	5.31
coral polyp · oil and dispersant treatment	16	15	2.38	8.08
coral polyp · oil treatment	16	15	1.55	5.71
coral polyp · dispersant treatment	16	15	2.61	6.33
Polyp	10	8	0.34	0.70

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.35
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.17
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.99
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.69
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.45
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.35
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.35
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.14
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.01
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.83
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.80
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.80
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.77
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.77
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.52
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.41
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.37
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.72
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.61
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.42
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.39
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.11
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.92
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.83
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.64
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.47
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.16
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.90
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.75
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.31
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.18
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	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
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.31
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.26
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.65
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.59
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.43
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.41
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.38
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.45
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.89
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.68
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.67
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.64
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.62
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.43
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.02
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.12
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.08
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.02
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.44
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.85
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.97
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.76
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.21
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.02
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.42
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.94
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.67
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.22
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.22
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.17
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.06
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.71
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.51
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.15
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.56
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.52
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.17
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.12
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.06
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.77
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.66
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.57
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.40
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.39
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.15
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.08
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.33
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.62
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.12
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.39
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.81
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.63
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.62
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.55
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.32
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.26
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.02
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.41
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.39
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.16
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.06
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.70
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.69
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.57
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.55
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.32
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.26
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.18
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.16
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
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.