Gene detail

Detailed information of OS493_039508-T1 in Lophelia pertusa

Genomic Location: scaffold_1217:4410...11250
NR annotation: KAJ7348212.1, hypothetical protein OS493_039508, partial [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
Q149N8	E3 ubiquitin-protein ligase SHPRH OS=Homo sapiens OX=9606 GN=SHPRH PE=1 SV=2
Q7TPQ3	E3 ubiquitin-protein ligase SHPRH OS=Mus musculus OX=10090 GN=Shprh PE=1 SV=1
Q9UTL9	Uncharacterized ATP-dependent helicase C144.05 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=SPAC144.05 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003108 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00271 all species →	Helicase_C	Helicase conserved C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR052583 all species →	Family	ATP-dependent Helicase/E3 Ubiquitin Ligase	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR049730 all species →	Domain	SNF2/RAD5-like, C-terminal helicase domain	Interproscan
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45865 all species →	E3 UBIQUITIN-PROTEIN LIGASE SHPRH FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006974 all species →	Biological Process	DNA damage response	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
K23460	CHM, CHML; Rab proteins geranylgeranyltransferase component A	-	Membrane trafficking	ko04131	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_039508-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

12.5Max TPM

4.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	6.32	12.18
polyp at pH7 6	18	18	6.51	12.53
coral polyp · control treatment	16	16	5.02	12.11
coral polyp · oil and dispersant treatment	16	16	3.02	5.62
coral polyp · oil treatment	16	16	5.36	10.53
coral polyp · dispersant treatment	16	16	2.92	6.32
Polyp	10	9	3.19	4.61

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.18
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.59
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.45
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.57
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.32
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.50
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.28
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.06
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.79
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.75
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.70
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.78
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.30
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.18
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.13
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.06
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.01
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.11
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.53
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.09
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.89
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.79
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.48
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.39
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.36
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.37
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.15
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.06
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.04
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.74
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.64
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.48
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.10
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.07
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.05
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.11
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.85
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.86
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.71
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.67
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.46
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.17
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.13
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.72
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.03
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.85
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.30
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.98
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.72
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.49
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.31
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.62
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.35
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.34
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.03
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.85
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.64
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.22
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.04
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.01
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.93
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.27
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.25
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.73
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.29
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.91
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.85
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.53
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.17
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.15
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.64
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.11
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.78
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.66
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.11
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.82
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.40
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.28
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.15
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.05
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.97
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.02
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.95
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.32
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.92
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.87
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.48
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.21
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.01
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.87
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.81
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.45
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.43
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.33
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.18
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.12
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.85
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.45
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.35
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.61
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.53
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.33
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.10
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.25
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.11
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.07
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.57
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.30
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.