Gene detail

Detailed information of OS493_015910-T1 in Lophelia pertusa

Genomic Location: scaffold_48:1763901...1767577
NR annotation: KAJ7333818.1, hypothetical protein OS493_015910 [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
Q5ZIR9	E3 ubiquitin-protein ligase RNF185 OS=Gallus gallus OX=9031 GN=RNF185 PE=2 SV=1
Q6PC78	E3 ubiquitin-protein ligase RNF185 OS=Danio rerio OX=7955 GN=rnf185 PE=2 SV=1
Q96GF1	E3 ubiquitin-protein ligase RNF185 OS=Homo sapiens OX=9606 GN=RNF185 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006199 (this species only)
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 activity RING\|U-box · 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
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR018957 all species →	Domain	Zinc finger, C3HC4 RING-type	Interproscan
IPR045103 all species →	Family	E3 ubiquitin-protein ligase RNF5/RNF185-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12313 all species →	E3 UBIQUITIN-PROTEIN LIGASE RNF5-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0005783 all species →	Cellular Component	endoplasmic reticulum	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0044390 all species →	Molecular Function	ubiquitin-like protein conjugating enzyme binding	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	Interproscan
GO:0071712 all species →	Biological Process	obsolete ER-associated misfolded protein catabolic process	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
K10666	RNF5_185; E3 ubiquitin-protein ligase RNF5/185	EC:2.3.2.27	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_015910-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

93.8Max TPM

46.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	37.91	49.08
polyp at pH7 6	18	18	38.99	57.10
coral polyp · control treatment	16	16	59.39	93.76
coral polyp · oil and dispersant treatment	16	16	55.74	81.77
coral polyp · oil treatment	16	16	48.22	60.96
coral polyp · dispersant treatment	16	16	49.71	91.57
Polyp	10	10	29.66	49.26

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.08
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.33
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.01
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.64
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.83
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.61
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.68
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.62
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.82
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.85
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.43
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.59
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.81
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.61
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.89
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.35
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.20
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.10
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.21
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.24
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.06
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.22
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.59
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.20
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.94
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.18
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.94
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.21
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.53
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.49
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.03
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.34
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.97
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.69
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.84
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.76
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	81.09
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	74.11
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.76
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	71.02
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.61
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.22
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.31
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.14
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.28
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.88
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.25
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.49
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.62
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.24
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.53
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.77
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.47
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.32
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	67.74
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.58
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.31
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.62
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.81
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.15
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.43
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.45
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.18
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.08
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.78
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.76
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.42
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	60.96
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.26
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.36
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.00
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.16
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.79
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.71
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.99
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.83
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.20
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.76
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.85
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.74
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.30
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.21
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.35
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	91.57
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	85.25
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.05
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.16
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.73
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.76
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.78
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.15
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.57
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.51
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.00
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.63
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.43
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.78
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.73
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.20
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	49.26
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	41.25
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	36.83
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	34.95
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	34.09
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	26.19
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	22.87
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	19.30
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	18.47
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	13.42

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.