Gene detail

Detailed information of OS493_026834-T1 in Lophelia pertusa

Genomic Location: scaffold_140:791660...796871
NR annotation: KAJ7383648.1, Glutamate-rich WD repeat-containing protein 1 [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
Q1JQD2	Glutamate-rich WD repeat-containing protein 1 OS=Bos taurus OX=9913 GN=GRWD1 PE=2 SV=1
Q9BQ67	Glutamate-rich WD repeat-containing protein 1 OS=Homo sapiens OX=9606 GN=GRWD1 PE=1 SV=1
Q5XI13	Glutamate-rich WD repeat-containing protein 1 OS=Rattus norvegicus OX=10116 GN=Grwd1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004805 (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
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
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR020472 all species →	Repeat	G-protein beta WD-40 repeat	Interproscan
IPR051972 all species →	Family	Glutamate-rich WD repeat-containing	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45903 all species →	GLUTAMATE-RICH WD REPEAT-CONTAINING PROTEIN 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0042254 all species →	Biological Process	ribosome biogenesis	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K14848	RRB1, GRWD1; ribosome assembly protein RRB1	-	Ribosome biogenesis	ko03009	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_026834-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

11.4Max TPM

3.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	3.45	5.04
polyp at pH7 6	18	17	4.11	6.48
coral polyp · control treatment	16	16	5.19	11.45
coral polyp · oil and dispersant treatment	16	16	2.92	3.95
coral polyp · oil treatment	16	16	4.66	8.70
coral polyp · dispersant treatment	16	16	3.03	8.17
Polyp	10	9	3.01	6.82

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.04
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.57
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.42
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.29
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.09
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.03
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.90
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.88
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.78
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.75
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.70
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.44
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.13
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.12
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.65
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.37
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.93
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.48
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.65
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.29
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.98
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.94
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.92
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.72
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.67
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.63
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.21
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.87
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.64
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.62
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.41
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.15
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.11
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.66
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.45
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.40
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.87
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.84
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.45
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.76
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.47
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.45
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.37
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.83
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.43
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.12
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.02
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.69
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.04
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.92
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.95
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.86
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.71
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.70
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.50
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.28
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.17
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.14
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.74
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.63
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.63
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.48
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.17
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.06
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.89
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.81
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.70
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.64
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.47
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.69
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.30
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.24
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.19
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.05
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.05
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.78
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.76
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.72
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.59
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.71
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.68
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.07
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.17
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.13
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.76
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.09
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.04
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.96
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.49
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.93
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.32
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.14
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.93
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.77
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.63
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.98
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.62
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.51
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6.82
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.79
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.77
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.67
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.37
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.16
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.94
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.49
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.13
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.