Gene detail

Detailed information of OS493_004564-T1 in Lophelia pertusa

Genomic Location: scaffold_9:1641653...1657245
NR annotation: KAJ7380972.1, WD repeat-containing protein 76 [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
Q4KLQ5	WD repeat-containing protein 76 OS=Xenopus laevis OX=8355 GN=wdr76 PE=2 SV=1
B2KIQ4	WD repeat-containing protein 76 OS=Rhinolophus ferrumequinum OX=59479 GN=WDR76 PE=3 SV=2
A6PWY4	WD repeat-containing protein 76 OS=Mus musculus OX=10090 GN=Wdr76 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003214 (this species only)
Ubiquitin family	UBD\|Other\|Beta-prp · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|DWD · 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
IPR050853 all species →	Family	WD repeat-containing DNA damage-binding protein	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14773 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:2000001 all species →	Biological Process	regulation of DNA damage checkpoint	Interproscan
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_004564-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_004564-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

94TPM > 0

7Conditions

5.4Max TPM

1.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	15	1.68	4.29
polyp at pH7 6	18	10	0.87	2.25
coral polyp · control treatment	16	16	1.45	3.45
coral polyp · oil and dispersant treatment	16	15	1.05	4.10
coral polyp · oil treatment	16	16	1.18	3.11
coral polyp · dispersant treatment	16	14	1.40	5.36
Polyp	10	8	1.41	4.48

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.29
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.30
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.99
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.32
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.14
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.11
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.96
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.95
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.78
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.65
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.43
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.32
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.25
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.18
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.67
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
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.25
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.09
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.77
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.64
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.45
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.42
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.41
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.40
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.20
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.01
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
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	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
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.45
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.54
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.10
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.05
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.81
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.69
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.67
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.59
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.30
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.26
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.15
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.86
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.80
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.48
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.21
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.20
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.10
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.71
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.15
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.56
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.33
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.29
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.58
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.51
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.46
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.43
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.43
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.36
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.34
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.33
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.26
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.11
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.10
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.94
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.71
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.58
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.23
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.09
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.03
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.02
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.84
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.81
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.68
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.64
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.62
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.36
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.18
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.36
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.33
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.13
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.80
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.67
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.56
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.36
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.30
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.14
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.09
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.96
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.70
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.58
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.50
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.48
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.78
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.80
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.68
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.58
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.79
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.68
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.32
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.