Gene detail

Detailed information of OS493_039870-T1 in Lophelia pertusa

Genomic Location: scaffold_1507:1084...4185
NR annotation: KAJ7388094.1, hypothetical protein OS493_039870 [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
Q28104	Coatomer subunit epsilon OS=Bos taurus OX=9913 GN=COPE PE=1 SV=3
Q5RFR8	Coatomer subunit epsilon OS=Pongo abelii OX=9601 GN=COPE PE=2 SV=1
O14579	Coatomer subunit epsilon OS=Homo sapiens OX=9606 GN=COPE PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005637 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04733 all species →	Coatomer_E	Coatomer epsilon subunit	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR006822 all species →	Family	Coatomer, epsilon subunit	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10805 all species →	COATOMER SUBUNIT EPSILON	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005198 all species →	Molecular Function	structural molecule activity	Interproscan
GO:0006888 all species →	Biological Process	endoplasmic reticulum to Golgi vesicle-mediated transport	Interproscan
GO:0006890 all species →	Biological Process	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	Interproscan
GO:0006891 all species →	Biological Process	intra-Golgi vesicle-mediated transport	Interproscan
GO:0030126 all species →	Cellular Component	COPI vesicle coat	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_039870-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_039870-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

80TPM > 0

7Conditions

40.6Max TPM

13.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	18.39	35.90
polyp at pH7 6	18	15	19.15	34.33
coral polyp · control treatment	16	10	7.68	39.07
coral polyp · oil and dispersant treatment	16	8	7.82	31.95
coral polyp · oil treatment	16	9	6.39	29.73
coral polyp · dispersant treatment	16	10	8.20	34.00
Polyp	10	10	27.49	40.61

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.90
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.62
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.79
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.64
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.90
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.25
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.58
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.11
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.81
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.24
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.12
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.40
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.31
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.61
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.17
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.96
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.95
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.67
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.33
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.92
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.46
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.99
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.71
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.32
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.56
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.39
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.90
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.87
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.61
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.75
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.66
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.53
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.75
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
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.07
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.34
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.34
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.34
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.08
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.66
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.91
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.78
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.24
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.11
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.95
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.71
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.37
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.16
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.73
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.44
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.43
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.37
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.73
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.02
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.78
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.04
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.45
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.09
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.90
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.68
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.57
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.00
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.24
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.30
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.82
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.09
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.13
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.02
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.87
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.44
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.27
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	40.61
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	39.15
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	32.08
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	31.60
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	31.38
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	30.75
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	26.90
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	21.63
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	20.39
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.38

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.