Gene detail

Detailed information of OS493_002924-T1 in Lophelia pertusa

Genomic Location: scaffold_6:2274678...2284527
NR annotation: KAJ7340193.1, hypothetical protein OS493_002924 [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
Q3TEL6	E3 ubiquitin ligase Rnf157 OS=Mus musculus OX=10090 GN=Rnf157 PE=1 SV=2
Q96PX1	E3 ubiquitin ligase RNF157 OS=Homo sapiens OX=9606 GN=RNF157 PE=1 SV=3
Q5XIQ4	E3 ubiquitin-protein ligase MGRN1 OS=Rattus norvegicus OX=10116 GN=Mgrn1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006794 (this species only) · gene tree & orthology
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species

Pfam domain

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

InterPro

InterPro term	Type	Description	Source
IPR045195 all species →	Domain	LOG2-like, modified RING finger, C3HC5-type	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR045194 all species →	Family	E3 ubiquitin-protein ligase MGRN1/RNF157-like	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22996 all species →	MAHOGUNIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	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
K25192	RNF157; E3 ubiquitin-protein ligase RNF157	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_002924-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

114.2Max TPM

41.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	23.02	33.39
polyp at pH7 6	18	18	23.72	32.23
coral polyp · control treatment	16	16	53.01	106.02
coral polyp · oil and dispersant treatment	16	16	75.75	114.20
coral polyp · oil treatment	16	16	43.33	62.02
coral polyp · dispersant treatment	16	16	49.00	100.72
Polyp	10	10	17.30	29.49

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	-	33.39
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.87
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.04
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.50
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.55
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.62
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.12
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.32
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.62
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.93
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.69
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.37
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.99
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.44
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.28
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.12
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.90
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.56
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.23
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.77
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.31
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.25
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.24
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.14
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.63
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.78
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.19
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.67
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.38
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.01
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.85
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.20
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.25
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.44
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.41
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.18
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	106.02
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.14
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.92
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.67
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.47
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.19
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.30
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.88
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.50
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.36
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.32
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.33
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.54
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.01
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.51
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	114.20
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	107.46
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	105.66
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	104.69
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	87.83
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.62
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	84.67
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	83.64
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	79.72
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.00
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.71
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.28
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.38
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.67
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.90
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.63
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.02
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.63
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.99
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.80
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.41
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.61
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.49
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.68
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.13
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.21
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.19
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.07
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.47
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.84
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.11
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.60
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	100.72
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.92
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	68.89
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.21
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.78
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.25
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.61
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.51
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.74
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.50
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.55
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.71
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.42
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.11
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.10
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	29.49
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	24.13
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	21.13
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	18.47
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	15.39
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	15.31
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	13.33
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	12.77
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	12.45
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	10.49

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.