Gene detail

Detailed information of OS493_027328-T1 in Lophelia pertusa

Genomic Location: scaffold_148:323771...328031
NR annotation: KAJ7371214.1, RING-box protein 1 [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
Q8QG64	E3 ubiquitin-protein ligase RBX1 OS=Salmo salar OX=8030 GN=rbx1 PE=2 SV=2
P62877	E3 ubiquitin-protein ligase RBX1 OS=Homo sapiens OX=9606 GN=RBX1 PE=1 SV=1
P62878	E3 ubiquitin-protein ligase RBX1 OS=Mus musculus OX=10090 GN=Rbx1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002208 (this species only)
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12678 all species →	zf-rbx1	RING-H2 zinc finger domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR024766 all species →	Domain	Zinc finger, RING-H2-type	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR051031 all species →	Family	RING-box E3 Ubiquitin Ligase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11210 all species →	RING BOX	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0031461 all species →	Cellular Component	cullin-RING ubiquitin ligase complex	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	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
K03868	RBX1, ROC1; E3 ubiquitin-protein ligase RBX1	EC:2.3.2.32	DNA repair and recombination proteins	ko03400	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_027328-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

480.3Max TPM

150.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	142.60	223.79
polyp at pH7 6	18	18	161.26	251.74
coral polyp · control treatment	16	16	147.18	434.60
coral polyp · oil and dispersant treatment	16	16	139.97	403.79
coral polyp · oil treatment	16	16	126.72	170.29
coral polyp · dispersant treatment	16	16	95.56	150.81
Polyp	10	10	290.49	480.29

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	-	223.79
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	202.17
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	158.25
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	157.37
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	155.45
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	151.55
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	144.79
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	143.92
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	143.74
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	139.39
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	132.04
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	130.09
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	126.98
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	119.71
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	118.89
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	116.39
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	107.99
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	94.38
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	251.74
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	245.36
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	222.45
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	202.22
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	169.42
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	167.51
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	161.01
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	153.88
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	150.78
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	150.66
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	146.91
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	146.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	144.93
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	131.11
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	120.92
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	119.89
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	113.61
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	104.24
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	434.60
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	180.60
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	167.28
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	159.96
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	155.29
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	146.11
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	125.72
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	124.15
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	124.09
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	118.32
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	116.69
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	112.73
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	109.07
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	97.68
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	97.13
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	85.38
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	403.79
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	167.37
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	159.78
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	156.92
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	134.18
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	120.76
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	120.08
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	118.44
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	117.99
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	114.15
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	112.75
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	111.13
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	109.99
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	108.99
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	92.87
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	90.40
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	170.29
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	158.08
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	147.75
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	140.58
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	133.56
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	125.70
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	122.82
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	121.96
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	121.47
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	120.73
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	119.02
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	110.40
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	109.87
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	109.39
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	108.30
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	107.65
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	150.81
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	133.38
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	130.14
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	116.77
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	103.94
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	100.53
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	100.30
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	93.59
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	91.59
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	89.27
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	84.84
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	79.29
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.57
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.68
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.54
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.79
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	480.29
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	460.77
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	417.72
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	312.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	289.82
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	259.01
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	240.89
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	186.68
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	139.07
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	118.69

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.