Gene detail

Detailed information of OS493_028591-T1 in Lophelia pertusa

Genomic Location: scaffold_166:465013...482755
NR annotation: KAJ7370976.1, E3 ubiquitin-protein ligase rnf38 [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
Q8BI21	E3 ubiquitin-protein ligase RNF38 OS=Mus musculus OX=10090 GN=Rnf38 PE=2 SV=2
Q9H0F5	E3 ubiquitin-protein ligase RNF38 OS=Homo sapiens OX=9606 GN=RNF38 PE=1 SV=4
Q4V7B8	RING finger protein 44 OS=Rattus norvegicus OX=10116 GN=Rnf44 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007387 (this species only)
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13639 all species →	zf-RING_2	Ring finger domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
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
PTHR46171 all species →	GH10160P	Interproscan

Gene Ontology

GO term	Category	Description	Source
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

No KEGG orthology assignment for OS493_028591-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_028591-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

115.5Max TPM

23.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	17.01	32.88
polyp at pH7 6	18	18	15.54	24.59
coral polyp · control treatment	16	16	29.59	115.51
coral polyp · oil and dispersant treatment	16	16	36.10	86.66
coral polyp · oil treatment	16	16	22.23	30.76
coral polyp · dispersant treatment	16	16	28.72	56.12
Polyp	10	10	11.11	16.74

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	-	32.88
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.47
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.86
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.74
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.99
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.86
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.79
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.38
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.09
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.70
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.76
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.61
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.90
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.27
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.22
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.03
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.01
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.60
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.59
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.83
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.54
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.52
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.47
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.34
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.22
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.18
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.03
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.00
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.10
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.74
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.71
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.25
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.03
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.03
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.59
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.62
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	115.51
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.38
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.83
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.76
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.02
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.68
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.00
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.79
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.48
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.50
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.93
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.69
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.27
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.96
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.41
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.22
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	86.66
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.02
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.46
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.59
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.66
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.44
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.47
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.46
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.48
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.44
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.95
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.81
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.35
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.14
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.40
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.20
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.76
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.31
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.92
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.80
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.41
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.54
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.35
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.70
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.06
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.56
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.11
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.38
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.69
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.36
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.17
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.59
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	56.12
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.82
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.79
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.23
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.84
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.68
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.57
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.56
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.51
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.66
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.47
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.43
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.01
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.28
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.69
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.91
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	16.74
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	15.58
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	15.28
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	14.52
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	12.73
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	12.24
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.29
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.91
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.46
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.31

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.