Gene detail

Detailed information of OS493_012180-T1 in Lophelia pertusa

Genomic Location: scaffold_31:2828672...2836588
NR annotation: KAJ7392509.1, E3 ubiquitin-protein ligase rnf4 [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)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009025 (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
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan
IPR047134 all species →	Family	E3 ubiquitin-protein ligase RNF4	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23041 all species →	RING FINGER DOMAIN-CONTAINING	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008134 all species →	Molecular Function	transcription factor binding	Interproscan
GO:0045944 all species →	Biological Process	positive regulation of transcription by RNA polymerase II	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
K22651	RNF4; E3 ubiquitin-protein ligase RNF4	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_012180-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

62.1Max TPM

13.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.08	12.69
polyp at pH7 6	18	18	8.83	11.69
coral polyp · control treatment	16	16	18.19	48.40
coral polyp · oil and dispersant treatment	16	16	22.77	62.12
coral polyp · oil treatment	16	16	13.82	22.59
coral polyp · dispersant treatment	16	16	11.39	17.05
Polyp	10	10	6.48	9.26

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.69
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.04
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.26
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.29
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.97
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.78
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.30
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.50
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.92
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.03
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.66
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.53
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.30
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.73
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.67
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.51
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.22
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.14
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.69
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.69
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.12
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.94
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.46
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.89
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.71
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.42
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.90
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.88
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.73
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.94
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.42
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.38
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.09
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.75
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.63
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.40
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.40
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.90
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.04
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.90
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.37
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.27
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.12
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.85
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.45
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.74
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.18
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.91
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.93
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.83
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.68
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.48
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.12
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.41
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.29
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.77
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.33
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.27
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.25
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.61
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.15
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.09
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.02
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.91
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.89
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.19
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.78
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.20
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.59
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.80
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.59
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.11
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.37
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.55
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.59
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.05
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.22
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.96
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.73
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.53
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.61
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.05
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.80
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.60
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.05
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.15
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.59
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.73
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.65
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.42
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.53
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.22
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.37
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.19
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.40
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.78
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.27
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.46
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.89
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.53
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	9.26
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	8.43
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.41
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.32
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	7.06
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.76
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	6.08
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.45
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.31
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	1.73

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.