Gene detail

Detailed information of OS493_004920-T1 in Lophelia pertusa

Genomic Location: scaffold_10:1032943...1043445
NR annotation: KAJ7374582.1, hypothetical protein OS493_004920 [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
A9JTG5	RanBP-type and C3HC4-type zinc finger-containing protein 1 OS=Danio rerio OX=7955 GN=rbck1 PE=2 SV=1
E6ZIJ1	RanBP-type and C3HC4-type zinc finger-containing protein 1 OS=Dicentrarchus labrax OX=13489 GN=rbck1 PE=3 SV=1
Q9WUB0	RanBP-type and C3HC4-type zinc finger-containing protein 1 OS=Mus musculus OX=10090 GN=Rbck1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003398 (this species only)
Ubiquitin family	UBD\|ZnF\|NZF · all ubiquitin genes in this species
Ubiquitin family	ULD\|UFD/UBQ\|UBQ_Other · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 activity\|RBR · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00097 all species →	zf-C3HC4	Zinc finger, C3HC4 type (RING finger)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR044066 all species →	Domain	TRIAD supradomain	Interproscan
IPR051628 all species →	Family	Linear Ubiquitination-Associated E3 Ligases	Interproscan
IPR001876 all species →	Domain	Zinc finger, RanBP2-type	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR036443 all species →	Homologous_superfamily	Zinc finger, RanBP2-type superfamily	Interproscan
IPR047558 all species →	Domain	Heme-oxidized IRP2 ubiquitin ligase 1, BRcat domain	Interproscan
IPR047557 all species →	Domain	Heme-oxidized IRP2 ubiquitin ligase 1, Rcat domain	Interproscan
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan
IPR029071 all species →	Homologous_superfamily	Ubiquitin-like domain superfamily	Interproscan
IPR047559 all species →	Domain	Heme-oxidized IRP2 ubiquitin ligase 1, modified RING finger, HC subclass	Interproscan
IPR018957 all species →	Domain	Zinc finger, C3HC4 RING-type	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22770 all species →	UBIQUITIN CONJUGATING ENZYME 7 INTERACTING PROTEIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000151 all species →	Cellular Component	ubiquitin ligase complex	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0043130 all species →	Molecular Function	ubiquitin binding	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	Interproscan
GO:0097039 all species →	Biological Process	protein linear polyubiquitination	Interproscan
GO:0046872 all species →	Molecular Function	metal ion 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
K10630	RBCK1, HOIL1; RanBP-type and C3HC4-type zinc finger-containing protein 1	EC:2.3.2.31	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_004920-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

67.7Max TPM

31.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	28.11	36.82
polyp at pH7 6	18	18	27.76	34.65
coral polyp · control treatment	16	16	44.44	67.70
coral polyp · oil and dispersant treatment	16	16	40.75	62.48
coral polyp · oil treatment	16	16	31.87	49.91
coral polyp · dispersant treatment	16	16	25.72	38.57
Polyp	10	10	16.93	32.18

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.82
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.67
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.74
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.64
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.25
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.77
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.59
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.12
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.32
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.24
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.67
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.44
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.12
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.49
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.98
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.41
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.32
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.40
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.65
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.18
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.82
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.69
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.83
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.72
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.47
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.99
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.94
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.50
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.40
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.80
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.60
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.35
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.56
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.94
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.56
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.68
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.70
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.85
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.84
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.77
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.98
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.73
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.14
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.92
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.18
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.03
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.75
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.86
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.11
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.35
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.57
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.23
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.48
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.41
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.37
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.11
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.54
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.19
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.88
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.62
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.36
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.35
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.22
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.61
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.72
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.60
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.53
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.97
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.91
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.73
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.73
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.19
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.21
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.75
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.25
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.26
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.79
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.71
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.00
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.75
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.61
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.18
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.57
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.36
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.57
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.39
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.42
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.68
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.57
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.20
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.75
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.10
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.55
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.98
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.44
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.19
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.54
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.32
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.18
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.61
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	32.18
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	31.76
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	20.85
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	19.37
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	14.86
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	13.26
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.71
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	9.34
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	8.85
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	7.07

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.