Gene detail

Detailed information of OS493_033818-T1 in Lophelia pertusa

Genomic Location: scaffold_274:324915...326169
NR annotation: KAJ7370193.1, E3 ubiquitin-protein ligase Zswim2 [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
Q9M622	Receptor homology region, transmembrane domain- and RING domain-containing protein 1 OS=Arabidopsis thaliana OX=3702 GN=RMR1 PE=1 SV=1
Q8LFY8	RING-H2 finger protein ATL54 OS=Arabidopsis thaliana OX=3702 GN=ATL54 PE=2 SV=2
Q9SLC4	RING-H2 finger protein ATL40 OS=Arabidopsis thaliana OX=3702 GN=ATL40 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007859 (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
PTHR46539 all species →	E3 UBIQUITIN-PROTEIN LIGASE ATL42	Interproscan

Gene Ontology

No Gene Ontology signature was detected for OS493_033818-T1. This gene does have a gene model — the search simply returned no hit.

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_033818-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_033818-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

37.1Max TPM

9.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	12.65	26.34
polyp at pH7 6	18	18	9.72	18.16
coral polyp · control treatment	16	16	8.26	23.81
coral polyp · oil and dispersant treatment	16	16	5.75	10.95
coral polyp · oil treatment	16	16	6.77	12.37
coral polyp · dispersant treatment	16	16	4.23	10.00
Polyp	10	10	21.83	37.14

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.34
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.80
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.18
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.00
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.82
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.10
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.26
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.91
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.56
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.82
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.94
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.04
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.39
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.60
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.09
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.62
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.14
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.16
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.54
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.08
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.57
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.02
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.25
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.25
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.12
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.64
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.61
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.89
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.07
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.83
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.47
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.10
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.01
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.77
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.66
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.81
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.26
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.01
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.97
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.60
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.82
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.48
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.16
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.07
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.80
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.77
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.40
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.32
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.90
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.30
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.51
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.95
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.87
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.92
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.06
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.00
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.70
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.58
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.95
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.93
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.79
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.42
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.23
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.58
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.22
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.97
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.81
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.37
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.79
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.75
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.50
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.41
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.26
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.13
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.78
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.48
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.00
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.68
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.61
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.24
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.08
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.99
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.24
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.00
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.16
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.10
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.00
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.71
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.16
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.46
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.34
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.03
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.55
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.14
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.58
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.97
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.92
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.77
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.87
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	37.14
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	30.21
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	28.02
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	26.09
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	19.61
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	19.41
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	19.07
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	18.66
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	15.13
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.02

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.