Gene detail

Detailed information of OS493_011179-T1 in Lophelia pertusa

Genomic Location: scaffold_28:1315615...1318970
NR annotation: KAJ7373574.1, hypothetical protein OS493_011179 [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)	OG0000365 (this species only)
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
IPR020472 all species →	Repeat	G-protein beta WD-40 repeat	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR011047 all species →	Homologous_superfamily	Quinoprotein alcohol dehydrogenase-like superfamily	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR19848 all species →	WD40 REPEAT PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	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_011179-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_011179-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

101TPM > 0

7Conditions

4.8Max TPM

1.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	1.96	4.77
polyp at pH7 6	18	17	1.63	2.86
coral polyp · control treatment	16	16	1.19	2.07
coral polyp · oil and dispersant treatment	16	13	0.33	0.78
coral polyp · oil treatment	16	16	1.21	2.67
coral polyp · dispersant treatment	16	14	0.83	3.23
Polyp	10	7	1.95	4.19

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.77
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.65
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.88
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.28
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.16
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.72
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.68
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.64
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.44
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.42
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.39
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.35
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.18
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.08
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.77
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.73
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.14
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.86
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.57
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.51
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.50
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.97
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.95
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.83
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.78
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.59
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.50
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.44
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.40
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.26
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.24
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.08
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.06
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.74
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.07
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.96
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.82
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.70
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.54
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.52
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.39
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.35
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.30
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.25
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.82
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.75
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.59
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.52
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.30
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.20
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.78
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.68
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.65
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.62
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.59
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.50
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.38
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.30
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.25
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.21
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.14
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.12
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.05
SRR16705977	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
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.67
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.39
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.73
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.72
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.56
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.56
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.06
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.03
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.91
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.89
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.85
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.75
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.66
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.64
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.50
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.38
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.23
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.70
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.51
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.20
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.19
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.16
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.99
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.85
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.60
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.22
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.21
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.16
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.12
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.08
SRR16705953	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
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.19
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.73
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.26
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.55
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.39
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.29
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.13
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	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.