Gene detail

Detailed information of OS493_000290-T1 in Lophelia pertusa

Genomic Location: scaffold_1:3594590...3602593
NR annotation: KAJ7394479.1, Coatomer subunit beta' [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
O55029	Coatomer subunit beta' OS=Mus musculus OX=10090 GN=Copb2 PE=1 SV=2
P35605	Coatomer subunit beta' OS=Bos taurus OX=9913 GN=COPB2 PE=1 SV=3
P35606	Coatomer subunit beta' OS=Homo sapiens OX=9606 GN=COPB2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004164 (this species only)
Ubiquitin family	UBD\|Other\|Beta-prp · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|CDC20 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR050844 all species →	Family	Coatomer complex subunit	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR19876 all species →	COATOMER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0006886 all species →	Biological Process	intracellular protein transport	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_000290-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_000290-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

109TPM > 0

7Conditions

69.6Max TPM

33.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	22.58	33.77
polyp at pH7 6	18	18	25.01	33.99
coral polyp · control treatment	16	16	42.30	67.68
coral polyp · oil and dispersant treatment	16	16	45.60	62.50
coral polyp · oil treatment	16	16	32.84	69.57
coral polyp · dispersant treatment	16	16	45.67	64.60
Polyp	10	9	12.79	25.54

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	-	33.77
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.53
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.43
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.41
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.85
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.58
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.14
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.02
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.98
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.82
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.60
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.41
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.81
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.46
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.04
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.64
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.87
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.11
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.99
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.59
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.32
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.21
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.18
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.29
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.86
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.50
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.65
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.32
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.60
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.53
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.42
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.03
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.71
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.81
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.91
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.28
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.68
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.11
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.56
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.66
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.57
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.47
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.95
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.29
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.58
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.82
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.58
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.57
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.46
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.58
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.24
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.75
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.50
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.95
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.23
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.05
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.15
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.02
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.36
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.83
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.60
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.85
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.42
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.04
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.27
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.90
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.77
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.57
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	69.57
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.84
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.87
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.29
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.81
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.09
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.84
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.74
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.69
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.50
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.28
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.35
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.06
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.18
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.72
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.60
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.60
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.65
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.75
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	56.50
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	56.43
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.65
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.25
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.91
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.11
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.81
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.42
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.05
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.22
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.90
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.48
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	25.54
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	19.96
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	16.16
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	15.86
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	13.09
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.79
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	8.56
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	8.55
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.40
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.