Gene detail

Detailed information of OS493_002081-T1 in Lophelia pertusa

Genomic Location: scaffold_4:4866088...4869822
NR annotation: KAJ7375330.1, hypothetical protein OS493_002081 [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
Q6ZT12	E3 ubiquitin-protein ligase UBR3 OS=Homo sapiens OX=9606 GN=UBR3 PE=1 SV=2
Q5U430	E3 ubiquitin-protein ligase UBR3 OS=Mus musculus OX=10090 GN=Ubr3 PE=1 SV=3
F1QJX5	E3 ubiquitin-protein ligase ubr3 OS=Danio rerio OX=7955 GN=ubr3 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002540 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_002081-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR039164 all species →	Family	E3 ubiquitin-protein ligase UBR1-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21497 all species →	UBIQUITIN LIGASE E3 ALPHA-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000151 all species →	Cellular Component	ubiquitin ligase complex	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	Interproscan
GO:0071596 all species →	Biological Process	ubiquitin-dependent protein catabolic process via the N-end rule 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_002081-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_002081-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

94TPM > 0

7Conditions

42.8Max TPM

4.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	12	2.64	6.35
polyp at pH7 6	18	12	3.01	10.22
coral polyp · control treatment	16	16	4.91	15.22
coral polyp · oil and dispersant treatment	16	16	5.65	30.13
coral polyp · oil treatment	16	16	4.20	9.31
coral polyp · dispersant treatment	16	15	3.50	9.03
Polyp	10	7	5.26	42.85

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.35
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.14
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.75
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.63
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.31
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.74
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.65
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.61
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.42
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.39
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.35
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.12
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	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
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.22
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.70
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.70
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.67
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.74
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.39
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.32
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.01
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.66
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.54
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.94
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.36
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359504	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
SRR11359524	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	15.22
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.56
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.38
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.16
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.12
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.25
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.86
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.65
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.46
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.20
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.95
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.99
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.92
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.68
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.38
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.81
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.13
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.77
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.42
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.55
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.89
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.37
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.75
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.06
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.44
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.41
SRR16705947	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	1.98
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.95
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.89
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.45
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.11
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.31
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.82
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.96
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.24
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.57
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.44
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.26
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.26
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.59
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.20
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.09
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.86
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.41
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.02
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.89
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.31
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.03
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.95
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.43
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.63
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.19
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.07
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.72
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.36
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.35
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.82
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.55
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.88
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.16
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.06
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.76
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	42.85
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.83
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.26
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.78
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.16
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.97
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.74
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.