Gene detail

Detailed information of OS493_005985-T1 in Lophelia pertusa

Genomic Location: scaffold_12:3142853...3146003
NR annotation: KAJ7339582.1, hypothetical protein OS493_005985 [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
A0A0R4I9Y1	E3 ubiquitin-protein ligase rnf213-beta OS=Danio rerio OX=7955 GN=rnf213b PE=3 SV=1
A0A0R4IBK5	E3 ubiquitin-protein ligase rnf213-alpha OS=Danio rerio OX=7955 GN=rnf213a PE=3 SV=1
Q63HN8	E3 ubiquitin-protein ligase RNF213 OS=Homo sapiens OX=9606 GN=RNF213 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000236 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_005985-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR031248 all species →	Family	E3 ubiquitin-protein ligase RNF213	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22605 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0002040 all species →	Biological Process	sprouting angiogenesis	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:2000051 all species →	Biological Process	negative regulation of non-canonical Wnt signaling pathway	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_005985-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_005985-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

96TPM > 0

7Conditions

18.1Max TPM

5.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	7.25	17.20
polyp at pH7 6	18	14	4.03	9.80
coral polyp · control treatment	16	15	7.74	18.06
coral polyp · oil and dispersant treatment	16	15	4.83	9.09
coral polyp · oil treatment	16	16	4.72	14.16
coral polyp · dispersant treatment	16	15	5.97	16.02
Polyp	10	5	1.03	5.05

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.20
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.49
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.21
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.45
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.96
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.53
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.38
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.23
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.14
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.78
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.63
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.80
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.87
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.47
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.56
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.89
SRR11359494	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
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.80
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.04
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.38
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.15
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.73
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.70
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.30
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.64
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.59
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.55
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.74
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.02
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.90
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
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	18.06
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.92
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.67
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.60
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.16
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.62
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.08
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.03
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.90
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.22
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.21
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.18
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.31
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.11
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.71
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.09
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.37
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.49
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.84
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.83
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.95
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.54
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.85
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.69
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.27
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.06
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.65
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.85
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.81
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.06
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.16
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.31
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.38
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.80
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.54
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.20
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.14
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.03
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.76
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.08
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.74
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.59
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.83
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.57
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.56
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.79
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.02
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.11
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.40
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.46
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.02
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.32
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.07
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.00
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.69
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.29
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.19
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.11
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.51
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.84
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.51
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.05
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.14
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.20
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.98
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.97
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.00
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.