Gene detail

Detailed information of OS493_022289-T1 in Lophelia pertusa

Genomic Location: scaffold_90:1338297...1341057
NR annotation: KAJ7330674.1, hypothetical protein OS493_022289 [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
Q7T308	E3 ubiquitin-protein ligase rnf168 OS=Danio rerio OX=7955 GN=rnf168 PE=2 SV=1
B0BLU1	E3 ubiquitin-protein ligase rnf168 OS=Xenopus tropicalis OX=8364 GN=rnf168 PE=2 SV=1
Q6INS5	E3 ubiquitin-protein ligase rnf168 OS=Xenopus laevis OX=8355 GN=rnf168 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007018 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00097 all species →	zf-C3HC4	Zinc finger, C3HC4 type (RING finger)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR018957 all species →	Domain	Zinc finger, C3HC4 RING-type	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR051657 all species →	Family	RNF168/RNF169 E3 ubiquitin-protein ligase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23328 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006302 all species →	Biological Process	double-strand break repair	Interproscan
GO:0031491 all species →	Molecular Function	nucleosome binding	Interproscan
GO:0035861 all species →	Cellular Component	site of double-strand break	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
K20779	RNF168; E3 ubiquitin-protein ligase RNF168	EC:2.3.2.31	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_022289-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

107TPM > 0

7Conditions

68.1Max TPM

3.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	3.52	5.46
polyp at pH7 6	18	16	3.73	7.92
coral polyp · control treatment	16	16	7.07	68.13
coral polyp · oil and dispersant treatment	16	16	4.67	44.22
coral polyp · oil treatment	16	16	3.04	5.39
coral polyp · dispersant treatment	16	16	1.65	5.22
Polyp	10	9	3.34	7.02

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	-	5.46
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.39
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.15
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.96
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.81
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.35
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.27
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.20
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.67
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.36
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.95
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.87
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.62
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.59
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.28
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.01
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.36
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.07
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.92
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.25
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.76
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.79
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.76
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.76
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.54
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.17
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.15
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.02
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.66
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.26
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.87
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.58
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.21
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.46
SRR11359513	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	68.13
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.46
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.37
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.10
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.24
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.18
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.04
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.87
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.74
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.70
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.49
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.45
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.08
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.85
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.73
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.72
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.22
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.35
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.08
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.03
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.51
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.28
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.15
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.08
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.91
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.85
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.82
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.70
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.61
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.45
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.10
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.51
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.39
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.02
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.87
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.80
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.28
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.49
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.28
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.06
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.49
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.92
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.92
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.91
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.83
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.80
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.50
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.06
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.22
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.22
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.14
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.81
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.61
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.49
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.47
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.30
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.26
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.23
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.13
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.96
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.69
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.42
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.25
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.17
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	7.02
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.87
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.51
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.59
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.58
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.59
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.35
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.86
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.08
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.