Gene detail

Detailed information of OS493_034910-T1 in Lophelia pertusa

Genomic Location: scaffold_303:268993...283392
NR annotation: KAJ7376388.1, E3 ubiquitin-protein ligase rad18 [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
Q9NS91	E3 ubiquitin-protein ligase RAD18 OS=Homo sapiens OX=9606 GN=RAD18 PE=1 SV=2
Q9QXK2	E3 ubiquitin-protein ligase RAD18 OS=Mus musculus OX=10090 GN=Rad18 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004694 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13923 all species →	zf-C3HC4_2	Zinc finger, C3HC4 type (RING finger)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan
IPR039577 all species →	Family	E3 ubiquitin-protein ligase Rad18	Interproscan
IPR006642 all species →	Domain	Rad18, zinc finger UBZ4-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14134 all species →	E3 UBIQUITIN-PROTEIN LIGASE RAD18	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003697 all species →	Molecular Function	single-stranded DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006301 all species →	Biological Process	postreplication repair	Interproscan
GO:0006513 all species →	Biological Process	protein monoubiquitination	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	Interproscan
GO:0097505 all species →	Cellular Component	Rad6-Rad18 complex	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	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
K10627	RAD18; E3 ubiquitin-protein ligase RAD18	EC:2.3.2.27	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_034910-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

109TPM > 0

7Conditions

13.7Max TPM

2.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	2.98	5.03
polyp at pH7 6	18	18	2.83	4.99
coral polyp · control treatment	16	16	2.96	13.67
coral polyp · oil and dispersant treatment	16	16	2.13	11.87
coral polyp · oil treatment	16	16	2.32	4.28
coral polyp · dispersant treatment	16	16	2.56	4.60
Polyp	10	9	2.70	8.38

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.03
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.36
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.94
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.63
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.53
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.52
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.52
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.96
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.79
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.65
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.56
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.52
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.49
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.41
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.05
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.92
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.81
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.99
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.61
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.88
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.71
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.37
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.89
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.87
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.82
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.78
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.66
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.65
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.22
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.17
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.11
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.06
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.95
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.60
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.60
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.67
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.99
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.26
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.18
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.14
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.00
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.59
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.56
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.53
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.48
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.16
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.54
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.21
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.15
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.57
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.35
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.87
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.88
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.17
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.91
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.78
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.77
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.69
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.49
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.47
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.13
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.06
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.00
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.91
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.73
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.65
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.48
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.28
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.94
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.20
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.86
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.82
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.65
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.64
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.43
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.43
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.27
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.91
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.79
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.21
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.19
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.07
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.45
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.60
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.32
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.74
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.58
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.38
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.93
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.78
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.51
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.50
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.32
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.86
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.72
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.54
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.45
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.06
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.72
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	8.38
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.79
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.75
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.76
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.45
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.99
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.78
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.37
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.71
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.