Gene detail

Detailed information of OS493_034066-T1 in Lophelia pertusa

Genomic Location: scaffold_280:329949...337842
NR annotation: KAJ7370137.1, WD repeat-containing protein 46 [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
Q9P4X3	Probable U3 small nucleolar RNA-associated protein 7 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=utp7 PE=3 SV=1
O15213	WD repeat-containing protein 46 OS=Homo sapiens OX=9606 GN=WDR46 PE=1 SV=3
Q9Z0H1	WD repeat-containing protein 46 OS=Mus musculus OX=10090 GN=Wdr46 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005689 (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
PF08149 all species →	BING4CT	BING4CT (NUC141) domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012952 all species →	Domain	BING4, C-terminal domain	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan
IPR040315 all species →	Family	WD repeat-containing protein WDR46/Utp7	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

PANTHER

PANTHER term	Description	Source
PTHR14085 all species →	WD-REPEAT PROTEIN BING4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000462 all species →	Biological Process	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0030686 all species →	Cellular Component	90S preribosome	Interproscan
GO:0032040 all species →	Cellular Component	small-subunit processome	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
K14768	UTP7, WDR46; U3 small nucleolar RNA-associated protein 7	-	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_034066-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

110TPM > 0

7Conditions

47.7Max TPM

15.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	17.61	29.17
polyp at pH7 6	18	18	20.68	40.83
coral polyp · control treatment	16	16	15.06	23.79
coral polyp · oil and dispersant treatment	16	16	9.93	23.17
coral polyp · oil treatment	16	16	14.21	19.29
coral polyp · dispersant treatment	16	16	7.47	16.38
Polyp	10	10	24.49	47.75

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.17
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.69
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.08
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.61
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.82
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.62
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.41
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.21
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.13
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.88
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.85
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.69
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.93
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.65
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.64
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.17
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.03
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.33
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.83
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.50
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.93
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.20
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.20
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.12
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.03
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.61
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.48
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.47
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.84
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.41
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.28
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.13
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.34
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.31
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.93
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.63
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.79
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.01
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.61
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.39
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.69
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.32
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.30
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.96
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.27
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.23
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.79
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.50
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.14
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.07
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.75
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.18
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.17
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.18
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.22
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.21
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.17
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.14
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.72
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.01
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.86
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.82
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.65
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.83
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.45
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.40
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.12
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.99
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.29
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.09
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.47
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.40
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.37
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.32
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.83
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.72
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.05
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.78
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.64
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.45
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.04
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.40
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.00
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.57
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.38
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.56
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.32
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.39
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.32
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.80
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.76
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.63
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.45
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.27
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.57
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.19
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.38
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.15
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.97
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.45
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	47.75
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	38.79
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	37.11
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	29.48
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	28.67
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	21.31
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	15.59
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	14.71
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	8.14
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.40

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.