Gene detail

Detailed information of OS493_002078-T1 in Lophelia pertusa

Genomic Location: scaffold_4:4836944...4845502
NR annotation: KAJ7375327.1, E3 ubiquitin-protein ligase ubr3 [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
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
Q6ZT12	E3 ubiquitin-protein ligase UBR3 OS=Homo sapiens OX=9606 GN=UBR3 PE=1 SV=2

Gene family

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

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF18995 all species →	PRT6_C	Proteolysis_6 C-terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039164 all species →	Family	E3 ubiquitin-protein ligase UBR1-like	Interproscan
IPR044046 all species →	Domain	E3 ubiquitin-protein ligase UBR-like, C-terminal	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_002078-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_002078-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

176.9Max TPM

25.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	27.22	50.11
polyp at pH7 6	18	18	25.03	45.29
coral polyp · control treatment	16	16	28.02	55.16
coral polyp · oil and dispersant treatment	16	16	24.50	47.92
coral polyp · oil treatment	16	16	28.10	48.36
coral polyp · dispersant treatment	16	16	16.01	27.49
Polyp	10	10	34.43	176.87

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.11
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.22
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.93
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.03
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.17
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.58
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.57
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.10
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.45
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.25
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.74
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.55
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.26
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.51
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.63
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.48
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.40
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.95
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.29
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.79
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.07
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.24
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.71
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.70
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.51
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.67
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.53
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.06
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.51
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.27
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.75
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.52
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.23
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.55
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.55
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.62
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.16
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.29
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.99
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.81
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.19
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.92
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.69
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.52
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.68
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.51
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.57
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.51
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.01
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.36
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.09
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.97
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.92
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.84
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.36
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.53
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.24
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.36
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.91
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.65
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.25
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.09
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.67
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.45
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.54
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.25
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.75
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.23
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.36
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.07
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.28
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.84
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.18
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.10
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.81
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.38
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.95
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.29
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.82
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.19
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.36
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.80
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.59
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.61
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.49
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.76
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.61
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.67
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.32
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.84
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.84
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.72
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.34
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.07
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.02
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.00
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.98
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.22
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.31
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	176.87
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	78.31
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	22.08
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	17.08
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	14.47
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.35
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.80
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.54
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.87
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.89

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.