Gene detail

Detailed information of OS493_004146-T1 in Lophelia pertusa

Genomic Location: scaffold_8:2766571...2773002
NR annotation: KAJ7387179.1, hypothetical protein OS493_004146 [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
Q969K3	E3 ubiquitin-protein ligase RNF34 OS=Homo sapiens OX=9606 GN=RNF34 PE=1 SV=1
Q5NVC7	E3 ubiquitin-protein ligase RNF34 OS=Pongo abelii OX=9601 GN=RNF34 PE=2 SV=2
Q99KR6	E3 ubiquitin-protein ligase RNF34 OS=Mus musculus OX=10090 GN=Rnf34 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008993 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13920 all species →	zf-C3HC4_3	Zinc finger, C3HC4 type (RING finger)	Domain	Interproscan
PF01363 all species →	FYVE	FYVE zinc finger	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036361 all species →	Homologous_superfamily	SAP domain superfamily	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR051728 all species →	Family	RING-FYVE domain-containing E3 ubiquitin-protein ligase	Interproscan
IPR000306 all species →	Domain	FYVE zinc finger	Interproscan
IPR017455 all species →	Domain	Zinc finger, FYVE-related	Interproscan
IPR011011 all species →	Homologous_superfamily	Zinc finger, FYVE/PHD-type	Interproscan
IPR013087 all species →	Domain	Zinc finger C2H2-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14879 all species →	CASPASE REGULATOR, RING FINGER DOMAIN-CONTAINING	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	Interproscan
GO:0070936 all species →	Biological Process	protein K48-linked ubiquitination	Interproscan
GO:1902042 all species →	Biological Process	negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	Interproscan
GO:2001271 all species →	Biological Process	obsolete negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis	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
K20804	RNF34; E3 ubiquitin-protein ligase RNF34	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_004146-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

109TPM > 0

7Conditions

57.9Max TPM

18.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	10.48	17.87
polyp at pH7 6	18	17	10.67	18.12
coral polyp · control treatment	16	16	24.89	47.59
coral polyp · oil and dispersant treatment	16	16	26.83	43.94
coral polyp · oil treatment	16	16	17.81	27.52
coral polyp · dispersant treatment	16	16	31.48	57.90
Polyp	10	10	6.67	12.08

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	-	17.87
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.94
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.51
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.36
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.40
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.28
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.57
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.67
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.29
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.95
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.71
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.71
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.51
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.33
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.87
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.86
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.84
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.97
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.12
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.54
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.67
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.12
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.53
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.67
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.43
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.05
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.35
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.62
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.17
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.75
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.70
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.57
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.50
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.18
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.03
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.59
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.47
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.26
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.57
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.05
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.35
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.02
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.26
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.64
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.99
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.16
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.18
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.55
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.69
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.59
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.79
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.94
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.65
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.89
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.02
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.49
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.82
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.92
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.69
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.22
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.70
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.97
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.59
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.58
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.42
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.37
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.02
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.52
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.89
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.22
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.21
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.41
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.00
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.56
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.29
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.83
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.55
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.00
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.86
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.31
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.85
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.64
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.86
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.90
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.49
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.26
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.32
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.10
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.62
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.77
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.72
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.32
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.35
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.96
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.63
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.16
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.80
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.18
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.06
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.08
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.70
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.46
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	6.29
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.57
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.48
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.87
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.59
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	4.35
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.33

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.