Gene detail

Detailed information of OS493_011708-T1 in Lophelia pertusa

Genomic Location: scaffold_30:344792...352882
NR annotation: KAJ7336503.1, WD repeat-containing protein 6 [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
Q5RB07	tRNA (34-2'-O)-methyltransferase regulator WDR6 OS=Pongo abelii OX=9601 GN=WDR6 PE=2 SV=1
A7Z052	tRNA (34-2'-O)-methyltransferase regulator WDR6 OS=Bos taurus OX=9913 GN=WDR6 PE=2 SV=1
Q9NNW5	tRNA (34-2'-O)-methyltransferase regulator WDR6 OS=Homo sapiens OX=9606 GN=WDR6 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004784 (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
IPR051973 all species →	Family	tRNA Anticodon Loop Methyltransferase Regulator	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14344 all species →	WD REPEAT PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0030488 all species →	Biological Process	tRNA methylation	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_011708-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_011708-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

105TPM > 0

7Conditions

7.7Max TPM

2.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	3.05	6.14
polyp at pH7 6	18	18	3.92	7.48
coral polyp · control treatment	16	15	2.52	7.75
coral polyp · oil and dispersant treatment	16	16	1.60	4.72
coral polyp · oil treatment	16	15	2.47	6.28
coral polyp · dispersant treatment	16	15	1.56	6.55
Polyp	10	9	1.94	4.58

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.14
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.23
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.38
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.87
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.83
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.75
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.64
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.39
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.38
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.08
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.63
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.51
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.32
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.16
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.03
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.28
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.19
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.48
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.27
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.13
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.12
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.69
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.49
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.25
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.94
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.76
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.22
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.28
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.10
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.99
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.95
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.70
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.67
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.38
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.18
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.75
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.37
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.77
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.78
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.99
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.33
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.00
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.91
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.61
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.60
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.56
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.39
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.14
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.76
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.31
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.72
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.74
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.35
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.07
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.77
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.71
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.56
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.48
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.46
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.36
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.28
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.75
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.68
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.66
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.55
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.51
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.28
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.57
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.30
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.29
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.86
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.46
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.45
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.34
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.89
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.83
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.83
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.52
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.41
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.32
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.19
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.55
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.47
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.86
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.74
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.71
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.57
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.56
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.45
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.35
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.12
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.96
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.87
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.82
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.60
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.30
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.58
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.78
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.72
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.67
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.10
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.63
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.09
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.97
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.87
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.