Gene detail

Detailed information of OS493_018668-T1 in Lophelia pertusa

Genomic Location: scaffold_62:892692...894280
NR annotation: KAJ7384979.1, E3 ubiquitin-protein ligase march6 [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
O60337	E3 ubiquitin-protein ligase MARCHF6 OS=Homo sapiens OX=9606 GN=MARCHF6 PE=1 SV=2
Q5R9W1	E3 ubiquitin-protein ligase MARCHF6 OS=Pongo abelii OX=9601 GN=MARCHF6 PE=2 SV=1
Q6ZQ89	E3 ubiquitin-protein ligase MARCHF6 OS=Mus musculus OX=10090 GN=Marchf6 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005387 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_018668-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

No InterPro signature was detected for OS493_018668-T1. This gene does have a gene model — the search simply returned no hit.

PANTHER

PANTHER term	Description	Source
PTHR13145 all species →	SSM4 PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0030176 all species →	Cellular Component	obsolete integral component of endoplasmic reticulum membrane	Interproscan
GO:0030433 all species →	Biological Process	obsolete ubiquitin-dependent ERAD pathway	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

No KEGG orthology assignment for OS493_018668-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_018668-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

48.2Max TPM

20.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	17.26	28.05
polyp at pH7 6	18	17	16.68	26.59
coral polyp · control treatment	16	16	22.95	40.91
coral polyp · oil and dispersant treatment	16	16	21.96	47.99
coral polyp · oil treatment	16	16	21.22	28.61
coral polyp · dispersant treatment	16	16	19.41	29.09
Polyp	10	10	26.77	48.20

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.05
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.45
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.43
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.61
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.47
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.43
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.97
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.83
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.52
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.21
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.07
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.51
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.25
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.60
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.62
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.15
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.59
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.59
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.55
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.23
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.85
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.55
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.64
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.54
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.86
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.65
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.85
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.68
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.93
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.87
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.14
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.02
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.07
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.16
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.91
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.24
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.79
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.28
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.99
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.86
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.25
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.19
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.79
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.72
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.41
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.02
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.48
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.30
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.24
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.69
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.99
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.28
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.63
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.08
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.88
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.81
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.20
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.24
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.90
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.84
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.53
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.10
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.77
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.35
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.73
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.07
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.61
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.80
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.94
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.73
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.56
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.07
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.65
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.25
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.11
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.10
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.01
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.71
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.58
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.13
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.09
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.23
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.09
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.06
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.16
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.01
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.48
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.03
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.18
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.69
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.18
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.04
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.36
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.09
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.65
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.34
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.97
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.25
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	48.20
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	37.06
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	35.63
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	29.47
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	27.08
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	24.46
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	19.13
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	18.38
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	14.17
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	14.10

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.