Gene detail

Detailed information of OS493_012412-T1 in Lophelia pertusa

Genomic Location: scaffold_32:1967572...1976361
NR annotation: KAJ7386076.1, E3 ubiquitin-protein ligase marchf8 [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
Q5T0T0	E3 ubiquitin-protein ligase MARCHF8 OS=Homo sapiens OX=9606 GN=MARCHF8 PE=1 SV=1
Q9DBD2	E3 ubiquitin-protein ligase MARCHF8 OS=Mus musculus OX=10090 GN=Marchf8 PE=2 SV=1
Q0VD59	E3 ubiquitin-protein ligase MARCHF8 OS=Bos taurus OX=9913 GN=MARCHF8 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001027 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12906 all species →	RINGv	RING-variant domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011016 all species →	Domain	Zinc finger, RING-CH-type	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45981 all species →	LD02310P	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0002495 all species →	Biological Process	antigen processing and presentation of peptide antigen via MHC class II	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005764 all species →	Cellular Component	lysosome	Interproscan
GO:0006955 all species →	Biological Process	immune response	Interproscan
GO:0031901 all species →	Cellular Component	early endosome membrane	Interproscan
GO:0031902 all species →	Cellular Component	late endosome membrane	Interproscan
GO:0042287 all species →	Molecular Function	MHC protein binding	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
K10656	MARCH1_8; E3 ubiquitin-protein ligase MARCH1/8	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_012412-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

201.9Max TPM

64.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	44.07	75.69
polyp at pH7 6	18	18	45.94	75.79
coral polyp · control treatment	16	16	75.39	171.91
coral polyp · oil and dispersant treatment	16	16	104.19	153.63
coral polyp · oil treatment	16	16	61.77	110.14
coral polyp · dispersant treatment	16	16	87.05	201.86
Polyp	10	10	21.54	40.02

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	-	75.69
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	75.58
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.36
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.18
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.63
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.74
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.50
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.79
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.49
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.84
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.98
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.61
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.58
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.54
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.92
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.07
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.76
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.96
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	75.79
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	73.79
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.55
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.81
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.53
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.23
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.29
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.22
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.66
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.63
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.20
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.41
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.51
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.25
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.32
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.74
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.72
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.29
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	171.91
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	111.46
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	100.89
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	94.85
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	85.07
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	76.47
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.01
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.72
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	68.86
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.06
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.95
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.11
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.15
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.87
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.81
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.04
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	153.63
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	150.71
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	128.19
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	124.86
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	119.92
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	114.63
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	113.77
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	110.35
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	108.40
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	107.05
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	95.27
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	91.00
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.87
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.92
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.65
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.77
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	110.14
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	83.51
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	83.11
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	72.60
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	71.95
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	70.94
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	69.96
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	67.58
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.69
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.89
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.69
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.72
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.61
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.22
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.20
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.47
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	201.86
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	182.94
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	129.32
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	112.68
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	111.87
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	96.14
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	83.97
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	82.21
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	80.81
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	75.99
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	56.18
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.43
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.95
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.76
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.60
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.18
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	40.02
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	35.44
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	31.55
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	24.41
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	18.92
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	16.92
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	16.15
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	13.23
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	10.51
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	8.21

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.