Gene detail

Detailed information of OS493_035816-T1 in Lophelia pertusa

Genomic Location: scaffold_336:80210...90999
NR annotation: KAJ7319506.1, Exosome complex component RRP41 [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
Q921I9	Exosome complex component RRP41 OS=Mus musculus OX=10090 GN=Exosc4 PE=1 SV=3
Q7YRA3	Exosome complex component RRP41 OS=Bos taurus OX=9913 GN=EXOSC4 PE=2 SV=3
Q9NPD3	Exosome complex component RRP41 OS=Homo sapiens OX=9606 GN=EXOSC4 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001803 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01138 all species →	RNase_PH	3' exoribonuclease family, domain 1	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027408 all species →	Homologous_superfamily	PNPase/RNase PH domain superfamily	Interproscan
IPR001247 all species →	Domain	Exoribonuclease, phosphorolytic domain 1	Interproscan
IPR050080 all species →	Family	Ribonuclease PH	Interproscan
IPR020568 all species →	Homologous_superfamily	Ribosomal protein uS5 domain 2-type superfamily	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_035816-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_035816-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

31.0Max TPM

8.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.18	11.82
polyp at pH7 6	18	18	9.04	13.20
coral polyp · control treatment	16	16	8.55	18.21
coral polyp · oil and dispersant treatment	16	15	7.92	15.95
coral polyp · oil treatment	16	16	7.04	10.52
coral polyp · dispersant treatment	16	16	9.45	31.00
Polyp	10	10	11.59	22.77

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.82
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.97
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.33
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.01
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.64
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.53
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.26
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.59
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.43
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.90
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.42
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.24
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.96
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.88
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.30
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.70
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.60
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.74
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.20
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.55
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.54
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.23
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.21
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.85
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.37
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.34
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.54
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.22
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.12
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.86
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.45
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.77
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.59
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.59
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.58
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.67
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.21
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.53
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.84
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.02
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.96
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.13
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.57
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.22
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.78
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.63
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.33
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.30
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.78
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.36
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.34
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.88
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.95
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.86
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.53
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.14
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.79
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.66
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.64
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.84
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.70
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.36
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.28
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.95
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.68
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.99
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.40
SRR16705977	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	10.52
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.36
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.12
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.07
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.24
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.06
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.03
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.66
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.36
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.24
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.91
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.62
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.35
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.34
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.01
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.67
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.00
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.40
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.50
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.34
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.03
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.99
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.23
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.09
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.86
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.47
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.02
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.14
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.45
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.48
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.11
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.01
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	22.77
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	16.34
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	13.29
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	11.79
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	11.34
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	11.06
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.73
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.53
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	7.61
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.43

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.