Gene detail

Detailed information of OS493_005994-T1 in Lophelia pertusa

Genomic Location: scaffold_12:3338142...3342232
NR annotation: KAJ7339591.1, Exosome complex component RRP4 [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
Q2KID0	Exosome complex component RRP4 OS=Bos taurus OX=9913 GN=EXOSC2 PE=2 SV=1
Q8VBV3	Exosome complex component RRP4 OS=Mus musculus OX=10090 GN=Exosc2 PE=1 SV=1
Q13868	Exosome complex component RRP4 OS=Homo sapiens OX=9606 GN=EXOSC2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006821 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF15985 all species →	KH_6	KH domain	Domain	Interproscan
PF14382 all species →	ECR1_N	Exosome complex exonuclease RRP4 N-terminal region	Domain	Interproscan
PF21266 all species →	RRP4_S1	RRP4, S1 domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR004088 all species →	Domain	K Homology domain, type 1	Interproscan
IPR026699 all species →	Family	Exosome complex RNA-binding protein 1/RRP40/RRP4	Interproscan
IPR048565 all species →	Domain	RRP4, S1 domain	Interproscan
IPR036612 all species →	Homologous_superfamily	K Homology domain, type 1 superfamily	Interproscan
IPR025721 all species →	Domain	Exosome complex component, N-terminal domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21321 all species →	PNAS-3 RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0000176 all species →	Cellular Component	nuclear exosome (RNase complex)	Interproscan
GO:0000177 all species →	Cellular Component	cytoplasmic exosome (RNase complex)	Interproscan
GO:0000178 all species →	Cellular Component	exosome (RNase complex)	Interproscan
GO:0000467 all species →	Biological Process	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	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:0043928 all species →	Biological Process	obsolete exonucleolytic catabolism of deadenylated mRNA	Interproscan
GO:0071034 all species →	Biological Process	CUT catabolic process	Interproscan
GO:0071035 all species →	Biological Process	nuclear polyadenylation-dependent rRNA catabolic process	Interproscan
GO:0071038 all species →	Biological Process	TRAMP-dependent tRNA surveillance pathway	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K03679	RRP4, EXOSC2; exosome complex component RRP4	-	Messenger RNA biogenesis	ko03019	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_005994-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

27.8Max TPM

8.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	9.93	14.93
polyp at pH7 6	18	18	10.42	15.63
coral polyp · control treatment	16	16	9.87	23.35
coral polyp · oil and dispersant treatment	16	16	5.54	11.89
coral polyp · oil treatment	16	16	9.01	15.46
coral polyp · dispersant treatment	16	16	5.38	14.77
Polyp	10	9	11.84	27.76

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	-	14.93
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.65
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.35
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.96
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.83
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.00
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.66
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.38
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.57
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.39
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.93
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.89
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.09
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.64
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.16
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.11
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.71
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.40
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.63
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.51
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.33
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.27
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.13
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.83
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.66
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.41
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.67
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.22
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.87
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.68
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.29
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.25
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.23
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.95
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.94
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.59
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.35
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.80
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.00
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.30
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.90
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.17
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.75
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.03
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.47
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.93
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.17
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.68
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.63
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.00
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.53
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.24
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.89
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.29
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.82
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.12
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.48
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.10
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.88
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.35
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.19
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.89
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.87
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.22
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.78
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.42
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.39
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.92
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.46
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.26
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.78
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.12
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.58
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.66
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.32
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.85
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.14
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.85
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.28
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.90
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.75
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.96
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.46
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.84
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.77
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.80
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.22
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.54
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.04
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.88
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.04
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.97
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.75
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.92
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.49
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.69
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.16
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.38
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.25
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.09
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	27.76
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	15.78
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	15.11
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	14.02
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	13.42
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	10.61
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.08
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.48
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.10
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.