Gene detail

Detailed information of OS493_014327-T1 in Lophelia pertusa

Genomic Location: scaffold_40:2157481...2162857
NR annotation: KAJ7373179.1, Ubiquitin conjugation factor E4 A [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)	OG0003372 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_014327-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR045132 all species →	Family	Ubiquitin conjugation factor E4	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13931 all species →	UBIQUITINATION FACTOR E4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000151 all species →	Cellular Component	ubiquitin ligase complex	Interproscan
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0030433 all species →	Biological Process	obsolete ubiquitin-dependent ERAD pathway	Interproscan
GO:0034450 all species →	Molecular Function	ubiquitin-ubiquitin ligase activity	Interproscan
GO:0036503 all species →	Biological Process	ERAD 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_014327-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_014327-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

193.5Max TPM

31.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	10.88	20.63
polyp at pH7 6	18	17	14.35	22.34
coral polyp · control treatment	16	16	29.83	69.56
coral polyp · oil and dispersant treatment	16	15	84.39	193.54
coral polyp · oil treatment	16	16	24.35	50.80
coral polyp · dispersant treatment	16	16	46.16	155.76
Polyp	10	9	6.71	16.95

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	-	20.63
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.78
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.94
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.44
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.13
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.45
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.24
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.75
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.91
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.72
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.02
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.38
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.09
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.00
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.38
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.20
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.37
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.34
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.68
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.36
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.12
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.60
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.56
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.82
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.26
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.17
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.80
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.32
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.96
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.26
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.02
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.51
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.49
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.98
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	69.56
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.88
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.57
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.91
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.07
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.52
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.35
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.78
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.77
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.37
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.10
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.20
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.92
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.23
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.02
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.06
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	193.54
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	149.17
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	138.21
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	129.04
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	112.44
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	94.71
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.28
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	83.65
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.97
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.95
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.20
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.79
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.97
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.05
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.26
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.80
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.31
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.14
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.11
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.58
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.83
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.65
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.52
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.57
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.42
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.99
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.40
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.09
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.62
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.88
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.62
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	155.76
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	109.66
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	79.16
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	69.61
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.18
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.14
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.55
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.40
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.28
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.87
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.53
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.27
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.90
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.54
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.65
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.07
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	16.95
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.29
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	9.80
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	6.86
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.39
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.58
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.09
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.04
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.12
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.