Gene detail

Detailed information of OS493_032056-T1 in Lophelia pertusa

Genomic Location: scaffold_232:375601...381366
NR annotation: XP_020611660.1, S-phase kinase-associated protein 1 isoform X1 [Orbicella faveolata]
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
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
Q5ZKF5	S-phase kinase-associated protein 1 OS=Gallus gallus OX=9031 GN=SKP1 PE=2 SV=1

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
PF03931 all species →	Skp1_POZ	Skp1 family, tetramerisation domain	Domain	Interproscan
PF01466 all species →	Skp1	Skp1 family, dimerisation domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036296 all species →	Homologous_superfamily	SKP1-like, dimerisation domain superfamily	Interproscan
IPR016897 all species →	Family	S-phase kinase-associated protein 1	Interproscan
IPR001232 all species →	Family	S-phase kinase-associated protein 1-like	Interproscan
IPR011333 all species →	Homologous_superfamily	SKP1/BTB/POZ domain superfamily	Interproscan
IPR016073 all species →	Domain	SKP1 component, POZ domain	Interproscan
IPR016072 all species →	Domain	SKP1 component, dimerisation	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11165 all species →	SKP1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K03094	SKP1, CBF3D; S-phase kinase-associated protein 1	-	Chromosome and associated proteins	ko03036	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_032056-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

458.7Max TPM

126.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	104.25	176.52
polyp at pH7 6	18	18	127.50	231.51
coral polyp · control treatment	16	16	142.80	458.75
coral polyp · oil and dispersant treatment	16	16	148.31	444.01
coral polyp · oil treatment	16	16	111.85	155.13
coral polyp · dispersant treatment	16	16	97.68	198.61
Polyp	10	10	173.50	267.27

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	176.52
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	158.24
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	119.06
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	116.52
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	112.95
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	111.31
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	108.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	104.13
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	103.33
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	99.71
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	99.08
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	97.63
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	86.72
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	83.20
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	81.83
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	79.70
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	71.13
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	67.51
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	231.51
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	183.61
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	157.33
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	139.69
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	133.84
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	129.07
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	128.49
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	127.03
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	126.64
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	122.33
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	122.19
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	108.03
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	107.36
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	106.77
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	101.34
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	99.88
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	92.04
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	77.80
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	458.75
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	169.15
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	167.79
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	165.31
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	149.57
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	142.54
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	134.36
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	126.91
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	115.73
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	108.18
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	106.04
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	104.81
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	89.70
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	89.24
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	88.59
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	68.11
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	444.01
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	179.26
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	174.57
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	163.91
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	144.12
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	142.14
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	137.33
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	135.77
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	134.06
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	127.93
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	123.88
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	119.38
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	96.59
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	86.81
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.41
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	77.74
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	155.13
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	155.11
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	144.17
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	138.98
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	129.26
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	124.94
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	118.40
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	114.29
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	106.13
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	100.50
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	97.50
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	90.73
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	88.49
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	85.24
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	72.44
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	68.35
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	198.61
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	130.73
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	123.89
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	116.89
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	107.79
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	102.91
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	101.18
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	98.80
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	87.11
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	86.29
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	82.53
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	77.24
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.75
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.15
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.83
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.13
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	267.27
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	252.31
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	235.65
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	159.40
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	158.47
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	155.72
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	154.30
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	125.17
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	116.05
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	110.65

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.