Gene detail

Detailed information of OS493_028235-T1 in Lophelia pertusa

Genomic Location: scaffold_160:815251...818942
NR annotation: KAJ7371071.1, E3 ubiquitin-protein ligase ubr2 [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)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003166 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_028235-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: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_028235-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_028235-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

97TPM > 0

7Conditions

22.4Max TPM

8.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	14	4.35	9.41
polyp at pH7 6	18	12	5.36	14.85
coral polyp · control treatment	16	16	11.81	22.37
coral polyp · oil and dispersant treatment	16	16	12.73	18.92
coral polyp · oil treatment	16	16	9.79	19.13
coral polyp · dispersant treatment	16	15	10.55	19.82
Polyp	10	8	2.40	5.08

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.41
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.86
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.89
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.48
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.23
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.97
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.50
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.64
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.42
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.31
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.85
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.66
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.12
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.88
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
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.85
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.16
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.10
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.17
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.89
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.71
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.38
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.60
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.53
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.18
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.43
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.52
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
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
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
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.37
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.44
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.67
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.83
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.65
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.05
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.79
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.52
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.01
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.12
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.46
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.09
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.47
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.02
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.35
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.14
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.92
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.99
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.64
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.24
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.64
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.83
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.44
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.82
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.48
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.43
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.66
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.48
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.94
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.78
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.18
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.20
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.13
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.68
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.76
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.00
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.66
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.34
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.09
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.38
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.18
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.04
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.40
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.33
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.84
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.80
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.23
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.69
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.82
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.04
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.94
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.31
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.50
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.40
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.10
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.86
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.51
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.19
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.95
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.89
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.61
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.15
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.47
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.08
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.03
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.49
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.02
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.79
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.75
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.89
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.97
SRR7746667	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.