Gene detail

Detailed information of OS493_039522-T1 in Lophelia pertusa

Genomic Location: scaffold_1227:6132...9113
NR annotation: KAJ7375695.1, suppressor of kinetochore protein mutant, partial [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
G5ECU1	Skp1-related protein OS=Caenorhabditis elegans OX=6239 GN=skr-1 PE=1 SV=1
Q3ZCF3	S-phase kinase-associated protein 1 OS=Bos taurus OX=9913 GN=SKP1 PE=1 SV=1
P63209	S-phase kinase-associated protein 1 OS=Cavia porcellus OX=10141 GN=SKP1 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004214 (this species only)
Ubiquitin family	E3\|E3 adaptor Cullin RING\|SKP1 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01466 all species →	Skp1	Skp1 family, dimerisation domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR016897 all species →	Family	S-phase kinase-associated protein 1	Interproscan
IPR011333 all species →	Homologous_superfamily	SKP1/BTB/POZ domain superfamily	Interproscan
IPR016072 all species →	Domain	SKP1 component, dimerisation	Interproscan
IPR036296 all species →	Homologous_superfamily	SKP1-like, dimerisation domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11165 all species →	SKP1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0031146 all species →	Biological Process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	Interproscan
GO:0097602 all species →	Molecular Function	cullin family 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_039522-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_039522-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

101TPM > 0

7Conditions

297.6Max TPM

29.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	12	7.44	33.89
polyp at pH7 6	18	15	8.55	24.26
coral polyp · control treatment	16	16	51.58	297.57
coral polyp · oil and dispersant treatment	16	16	54.73	267.98
coral polyp · oil treatment	16	16	30.87	83.57
coral polyp · dispersant treatment	16	16	33.93	70.45
Polyp	10	10	24.22	54.05

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	-	33.89
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.33
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.99
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.49
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.59
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.65
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.06
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.83
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.81
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.56
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.36
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.29
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	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
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.26
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.41
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.85
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.51
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.23
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.52
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.57
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.41
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.65
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.44
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.39
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.18
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.05
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.47
SRR11359513	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
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	297.57
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	77.61
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.04
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.88
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.80
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.33
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.54
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.97
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.61
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.07
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.22
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.69
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.12
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.74
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.34
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.76
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	267.98
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.10
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.06
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.45
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.06
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.93
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.19
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.26
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.09
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.44
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.84
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.54
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.22
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.65
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.74
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.20
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	83.57
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.38
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.88
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	60.86
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.32
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.85
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.70
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.90
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.65
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.64
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.39
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.31
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.91
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.20
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.56
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.79
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.45
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.87
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.82
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.97
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.98
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.71
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.65
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.74
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.30
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.77
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.38
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.36
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.73
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.47
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.72
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.01
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	54.05
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	53.90
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	36.47
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	21.68
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	20.69
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	15.82
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	11.56
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	10.82
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	10.01
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	7.21

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.