Gene detail

Detailed information of OS493_032066-T1 in Lophelia pertusa

Genomic Location: scaffold_232:481739...493724
NR annotation: KAJ7370500.1, DDB1- and CUL4-associated factor 13 [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
Q6NVS5	DDB1- and CUL4-associated factor 13 OS=Xenopus tropicalis OX=8364 GN=dcaf13 PE=2 SV=1
Q7ZYQ6	DDB1- and CUL4-associated factor 13 OS=Xenopus laevis OX=8355 GN=dcaf13 PE=2 SV=1
Q803X4	DDB1- and CUL4-associated factor 13 OS=Danio rerio OX=7955 GN=dcaf13 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006768 (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

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan
PF04158 all species →	Sof1	Sof1-like domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR051733 all species →	Family	WD repeat-containing DCAF13/WDSOF1	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR007287 all species →	Domain	Sof1-like protein	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22851 all species →	U3 SMALL NUCLEOLAR RNA U3 SNORNA ASSOCIATED PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
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:0032040 all species →	Cellular Component	small-subunit processome	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K11806	DCAF13, WDSOF1; DDB1- and CUL4-associated factor 13	-	Ubiquitin system	ko04121	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_032066-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

16.8Max TPM

6.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	5.61	9.31
polyp at pH7 6	18	18	7.15	9.30
coral polyp · control treatment	16	16	8.50	13.89
coral polyp · oil and dispersant treatment	16	16	6.64	16.42
coral polyp · oil treatment	16	16	7.79	12.05
coral polyp · dispersant treatment	16	16	6.51	16.78
Polyp	10	10	3.79	9.34

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.31
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.25
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.37
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.88
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.68
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.37
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.16
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.93
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.52
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.29
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.10
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.82
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.81
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.61
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.46
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.86
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.51
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.09
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.30
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.92
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.69
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.33
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.94
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.63
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.52
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.52
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.40
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.19
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.05
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.83
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.62
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.20
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.15
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.12
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.96
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.31
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.89
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.89
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.19
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.61
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.43
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.14
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.79
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.82
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.47
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.31
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.02
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.93
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.86
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.75
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.32
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.57
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.42
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.90
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.91
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.67
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.71
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.08
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.90
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.57
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.64
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.17
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.10
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.04
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.34
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.14
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.85
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.78
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.05
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.70
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.61
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.30
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.82
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.65
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.45
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.45
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.52
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.22
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.99
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.82
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.24
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.95
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.89
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.05
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.78
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.87
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.46
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.31
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.64
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.73
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.16
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.06
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.40
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.06
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.39
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.34
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.98
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.60
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.60
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.75
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	9.34
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.11
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.98
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.87
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.43
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.28
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.99
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.20
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.91
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.83

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.