Gene detail

Detailed information of OS493_012704-T1 in Lophelia pertusa

Genomic Location: scaffold_33:2174664...2176185
NR annotation: KAJ7379942.1, Exosome component 5 [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)	OG0006435 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03725 all species →	RNase_PH_C	3' exoribonuclease family, domain 2	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036345 all species →	Homologous_superfamily	Exoribonuclease, PH domain 2 superfamily	Interproscan
IPR050080 all species →	Family	Ribonuclease PH	Interproscan
IPR027408 all species →	Homologous_superfamily	PNPase/RNase PH domain superfamily	Interproscan
IPR015847 all species →	Domain	Exoribonuclease, phosphorolytic domain 2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11953 all species →	EXOSOME COMPLEX COMPONENT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000176 all species →	Cellular Component	nuclear exosome (RNase complex)	Interproscan
GO:0000177 all species →	Cellular Component	cytoplasmic exosome (RNase complex)	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0016075 all species →	Biological Process	rRNA catabolic process	Interproscan
GO:0034427 all species →	Biological Process	obsolete nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'	Interproscan
GO:0034475 all species →	Biological Process	U4 snRNA 3'-end processing	Interproscan
GO:0071028 all species →	Biological Process	nuclear mRNA surveillance	Interproscan
GO:0071051 all species →	Biological Process	poly(A)-dependent snoRNA 3'-end processing	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_012704-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_012704-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

91TPM > 0

7Conditions

9.4Max TPM

2.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	12	2.43	5.27
polyp at pH7 6	18	11	2.97	8.88
coral polyp · control treatment	16	16	3.43	6.11
coral polyp · oil and dispersant treatment	16	14	2.36	6.59
coral polyp · oil treatment	16	15	3.68	6.66
coral polyp · dispersant treatment	16	14	1.72	4.61
Polyp	10	9	3.45	9.45

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.27
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.65
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.50
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.32
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.23
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.10
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.90
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.37
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.71
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.53
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.33
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.81
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.88
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.34
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.25
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.01
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.89
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.21
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.99
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.93
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.89
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.10
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.01
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.11
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.08
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.64
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.30
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.72
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.21
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.96
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.76
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.21
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.48
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.12
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.91
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.70
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.47
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.28
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.93
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.59
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.71
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.07
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.66
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.78
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.64
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.87
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.63
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.62
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.50
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.32
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.17
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.70
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.56
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.66
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.52
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.34
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.18
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.68
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.52
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.88
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.85
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.02
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.89
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.80
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.74
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.62
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.13
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.61
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.80
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.80
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.54
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.41
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.30
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.02
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.19
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.13
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.07
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.00
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.81
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.47
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.43
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	9.45
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.63
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.62
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.50
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.34
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.10
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.29
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.59
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.