Gene detail

Detailed information of OS493_026233-T1 in Lophelia pertusa

Genomic Location: scaffold_134:248080...254157
NR annotation: KAJ7383703.1, F-box/WD repeat-containing protein 2 [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
B2RZ17	F-box/WD repeat-containing protein 2 OS=Rattus norvegicus OX=10116 GN=Fbxw2 PE=2 SV=1
Q58D00	F-box/WD repeat-containing protein 2 OS=Bos taurus OX=9913 GN=FBXW2 PE=2 SV=1
Q9UKT8	F-box/WD repeat-containing protein 2 OS=Homo sapiens OX=9606 GN=FBXW2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009690 (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\|DWD · 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
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036047 all species →	Homologous_superfamily	F-box-like domain superfamily	Interproscan
IPR042627 all species →	Family	F-box/WD repeat-containing protein 2	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan
IPR001810 all species →	Domain	F-box domain	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR020472 all species →	Repeat	G-protein beta WD-40 repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR44436 all species →	F-BOX/WD REPEAT-CONTAINING PROTEIN 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K10261	FBXW2, MD6; F-box and WD-40 domain protein 2	-	Ubiquitin system	ko04121	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_026233-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

15.6Max TPM

3.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	3.05	6.98
polyp at pH7 6	18	16	2.53	4.30
coral polyp · control treatment	16	16	5.08	12.66
coral polyp · oil and dispersant treatment	16	15	3.36	8.99
coral polyp · oil treatment	16	16	6.17	15.56
coral polyp · dispersant treatment	16	16	3.50	9.98
Polyp	10	8	3.16	10.64

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	-	6.98
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.28
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.67
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.24
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.83
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.67
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.48
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.14
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.11
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.75
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.75
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.59
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.54
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.40
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.97
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.46
SRR11359495	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
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.30
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.24
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.92
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.24
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.18
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.14
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.10
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.04
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.02
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.57
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.36
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.24
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.89
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.79
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.43
SRR11359513	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	12.66
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.90
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.12
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.87
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.69
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.76
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.85
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.01
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.01
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.70
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.32
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.26
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.09
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.01
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.30
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.80
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.99
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.88
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.03
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.90
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.43
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.88
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.54
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.86
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.69
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.42
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.86
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.64
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.00
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.94
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.63
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.56
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.56
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.87
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.26
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.59
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.84
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.54
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.27
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.04
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.99
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.80
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.46
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.69
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.57
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.29
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.38
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.98
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.22
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.75
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.52
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.31
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.30
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.26
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.20
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.17
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.01
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.74
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.27
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.08
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.04
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.73
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.35
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	10.64
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.54
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.33
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.83
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.58
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.25
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.00
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.43
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.