Gene detail

Detailed information of OS493_002602-T1 in Lophelia pertusa

Genomic Location: scaffold_5:5197668...5212212
NR annotation: KAJ7365879.1, E3 ubiquitin-protein ligase arih1 [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
B1H1E4	E3 ubiquitin-protein ligase arih1 OS=Xenopus tropicalis OX=8364 GN=arih1 PE=2 SV=1
A2VEA3	E3 ubiquitin-protein ligase ARIH1 OS=Bos taurus OX=9913 GN=ARIH1 PE=2 SV=1
Q9Z1K5	E3 ubiquitin-protein ligase ARIH1 OS=Mus musculus OX=10090 GN=Arih1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002408 (this species only)
Ubiquitin family	E3\|E3 activity\|RBR · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01485 all species →	IBR	IBR domain, a half RING-finger domain	Domain	Interproscan
PF19422 all species →	Ariadne	Ariadne domain	Domain	Interproscan
PF21235 all species →	ARI1_UBAl	E3 ubiquitin-protein ligase ARIH1, UBA-like domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002867 all species →	Domain	IBR domain	Interproscan
IPR045840 all species →	Domain	Ariadne domain	Interproscan
IPR048962 all species →	Domain	E3 ubiquitin-protein ligase ARIH1-like, UBA-like domain	Interproscan
IPR031127 all species →	Family	E3 ubiquitin ligase RBR family	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR044066 all species →	Domain	TRIAD supradomain	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11685 all species →	RBR FAMILY RING FINGER AND IBR DOMAIN-CONTAINING	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0000151 all species →	Cellular Component	ubiquitin ligase complex	Interproscan
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0031624 all species →	Molecular Function	ubiquitin conjugating enzyme binding	Interproscan
GO:0032436 all species →	Biological Process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	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
K11968	ARIH1; ariadne-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_002602-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

267.7Max TPM

87.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	56.94	67.56
polyp at pH7 6	18	18	62.12	74.80
coral polyp · control treatment	16	16	87.18	136.59
coral polyp · oil and dispersant treatment	16	16	130.40	191.89
coral polyp · oil treatment	16	16	78.30	104.74
coral polyp · dispersant treatment	16	16	137.91	267.74
Polyp	10	10	51.55	73.34

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	-	67.56
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	65.80
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	65.08
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.52
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.38
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.12
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	61.99
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	59.91
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	59.08
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.59
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.09
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.59
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.76
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.60
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.65
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.64
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.55
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.09
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	74.80
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	73.27
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	72.31
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.53
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.90
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.04
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.59
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.37
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.80
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.74
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.75
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.73
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.51
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.14
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.39
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.38
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.81
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.08
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	136.59
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	129.80
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	104.31
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	99.95
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	96.90
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.08
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	85.04
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	81.63
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	80.81
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	76.47
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	75.91
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	74.08
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.73
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.30
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.99
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.34
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	191.89
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	154.68
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	151.20
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	149.47
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	147.87
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	146.59
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	136.36
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	134.89
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	134.12
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	129.50
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	123.86
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	115.46
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	113.43
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	95.00
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.63
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.53
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	104.74
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	99.23
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	90.72
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	89.07
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	86.20
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	86.19
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.52
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	78.69
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	77.50
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	77.15
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.21
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	69.39
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.88
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.11
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.81
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.43
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	267.74
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	222.54
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	206.25
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	193.31
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	183.15
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	163.66
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	136.81
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	120.50
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	120.41
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	119.16
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	119.14
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	100.54
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	87.96
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	84.22
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.79
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.47
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	73.34
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	69.32
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	64.64
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	63.47
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	60.68
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	49.83
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	45.08
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	37.94
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	32.12
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	19.13

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.