Gene detail

Detailed information of OS493_000196-T1 in Lophelia pertusa

Genomic Location: scaffold_1:2189520...2191706
NR annotation: KAJ7394387.1, Cullin-5 [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
Q93034	Cullin-5 OS=Homo sapiens OX=9606 GN=CUL5 PE=1 SV=4
Q5RB36	Cullin-5 OS=Pongo abelii OX=9601 GN=CUL5 PE=2 SV=3
Q9JJ31	Cullin-5 OS=Rattus norvegicus OX=10116 GN=Cul5 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000554 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10557 all species →	Cullin_Nedd8	Cullin protein neddylation domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR019559 all species →	Domain	Cullin protein, neddylation domain	Interproscan
IPR045093 all species →	Family	Cullin	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11932 all species →	CULLIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0019005 all species →	Cellular Component	SCF ubiquitin ligase complex	Interproscan
GO:0030674 all species →	Molecular Function	protein-macromolecule adaptor activity	Interproscan
GO:0031146 all species →	Biological Process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	Interproscan
GO:0031461 all species →	Cellular Component	cullin-RING ubiquitin ligase complex	Interproscan
GO:0031466 all species →	Cellular Component	Cul5-RING ubiquitin ligase complex	Interproscan
GO:0031625 all species →	Molecular Function	ubiquitin protein ligase 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_000196-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_000196-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

110TPM > 0

7Conditions

58.7Max TPM

18.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	16.29	25.71
polyp at pH7 6	18	18	19.30	28.06
coral polyp · control treatment	16	16	22.69	58.75
coral polyp · oil and dispersant treatment	16	16	24.25	56.25
coral polyp · oil treatment	16	16	18.75	31.56
coral polyp · dispersant treatment	16	16	16.38	27.98
Polyp	10	10	10.47	22.09

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.71
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.48
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.96
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.82
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.07
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.02
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.90
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.84
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.75
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.53
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.60
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.53
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.27
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.19
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.66
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.30
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.86
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.75
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.06
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.23
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.84
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.36
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.68
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.24
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.92
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.33
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.90
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.77
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.61
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.21
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.94
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.54
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.35
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.06
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.69
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.59
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.75
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.17
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.89
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.04
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.70
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.22
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.78
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.80
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.54
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.29
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.57
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.23
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.04
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.11
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.84
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.04
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.25
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.00
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.50
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.26
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.66
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.21
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.91
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.76
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.07
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.00
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.13
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.77
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.90
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.03
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.58
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.01
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.56
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.66
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.84
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.38
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.24
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.91
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.65
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.62
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.22
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.00
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.54
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.38
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.78
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.35
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.04
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.79
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.98
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.58
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.35
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.10
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.28
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.21
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.54
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.32
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.31
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.18
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.60
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.68
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.18
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.96
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.88
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.86
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	22.09
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.65
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	12.08
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	11.62
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	11.15
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.97
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	9.60
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.89
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.80
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.83

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.