Gene detail

Detailed information of OS493_024612-T1 in Lophelia pertusa

Genomic Location: scaffold_116:104631...111985
NR annotation: KAJ7383927.1, DDB1- and CUL4-associated factor 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
Q58WW2	DDB1- and CUL4-associated factor 6 OS=Homo sapiens OX=9606 GN=DCAF6 PE=1 SV=1
Q5R9B8	DDB1- and CUL4-associated factor 6 OS=Pongo abelii OX=9601 GN=DCAF6 PE=2 SV=2
Q9DC22	DDB1- and CUL4-associated factor 6 OS=Mus musculus OX=10090 GN=Dcaf6 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006990 (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
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR045151 all species →	Family	DDB1- and CUL4-associated factor 8-like	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15574 all species →	WD REPEAT DOMAIN-CONTAINING FAMILY	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:0030374 all species →	Molecular Function	nuclear receptor coactivator activity	Interproscan
GO:0045944 all species →	Biological Process	positive regulation of transcription by RNA polymerase II	Interproscan
GO:0080008 all species →	Cellular Component	Cul4-RING E3 ubiquitin ligase complex	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
K11795	DCAF6, IQWD1, NRIP, ARCAP; DDB1- and CUL4-associated factor 6	-	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_024612-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

39.8Max TPM

9.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	10.82	17.01
polyp at pH7 6	18	18	9.28	13.50
coral polyp · control treatment	16	16	12.16	39.79
coral polyp · oil and dispersant treatment	16	16	8.90	32.93
coral polyp · oil treatment	16	16	10.52	15.93
coral polyp · dispersant treatment	16	16	6.52	17.10
Polyp	10	10	6.60	11.18

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	-	17.01
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.69
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.09
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.99
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.80
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.40
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.96
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.81
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.06
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.66
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.62
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.42
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.01
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.50
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.87
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.47
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.34
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.08
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.50
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.23
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.58
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.16
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.13
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.94
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.79
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.76
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.75
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.06
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.97
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.72
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.62
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.34
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.26
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.17
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.42
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.72
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.79
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.36
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.43
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.03
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.01
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.81
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.59
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.40
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.14
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.88
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.22
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.96
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.08
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.87
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.12
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.96
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.93
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.53
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.33
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.10
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.79
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.44
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.91
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.84
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.39
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.19
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.34
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.27
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.83
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.37
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.26
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.83
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.93
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.55
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.55
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.35
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.09
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.91
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.42
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.40
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.18
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.16
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.94
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.65
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.34
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.12
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.41
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.28
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.10
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.02
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.56
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.27
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.51
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.46
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.03
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.64
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.44
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.66
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.60
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.15
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.60
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.06
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.59
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.59
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.18
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.54
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.33
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	8.02
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.70
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.15
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.04
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.88
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.86
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.27

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.