Gene detail

Detailed information of OS493_015430-T1 in Lophelia pertusa

Genomic Location: scaffold_46:1715563...1722940
NR annotation: KAJ7372965.1, rRNA-processing endoribonuclease [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
Q9JJT0	RNA 3'-terminal phosphate cyclase-like protein OS=Mus musculus OX=10090 GN=Rcl1 PE=2 SV=1
Q2KHX8	RNA 3'-terminal phosphate cyclase-like protein OS=Bos taurus OX=9913 GN=RCL1 PE=2 SV=1
Q9Y2P8	RNA 3'-terminal phosphate cyclase-like protein OS=Homo sapiens OX=9606 GN=RCL1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005462 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05189 all species →	RTC_insert	RNA 3'-terminal phosphate cyclase (RTC), insert domain	Domain	Interproscan
PF01137 all species →	RTC	RNA 3'-terminal phosphate cyclase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR037136 all species →	Homologous_superfamily	RNA 3'-terminal phosphate cyclase domain superfamily	Interproscan
IPR013791 all species →	Domain	RNA 3'-terminal phosphate cyclase, insert domain	Interproscan
IPR023797 all species →	Domain	RNA 3'-terminal phosphate cyclase domain	Interproscan
IPR000228 all species →	Family	RNA 3'-terminal phosphate cyclase	Interproscan
IPR013792 all species →	Homologous_superfamily	RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11096 all species →	RNA 3' TERMINAL PHOSPHATE CYCLASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000479 all species →	Biological Process	endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	Interproscan
GO:0004521 all species →	Molecular Function	RNA endonuclease activity	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0003824 all species →	Molecular Function	catalytic 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

No KEGG orthology assignment for OS493_015430-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_015430-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

62TPM > 0

7Conditions

12.5Max TPM

2.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	2	0.37	4.70
polyp at pH7 6	18	3	0.51	3.17
coral polyp · control treatment	16	15	3.64	12.46
coral polyp · oil and dispersant treatment	16	15	2.70	6.01
coral polyp · oil treatment	16	13	3.02	7.90
coral polyp · dispersant treatment	16	9	2.57	9.17
Polyp	10	5	1.58	5.30

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.70
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.90
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
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	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
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359511	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
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359521	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
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.17
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.09
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.97
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	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
SRR11359526	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
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.46
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.79
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.93
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.72
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.75
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.60
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.56
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.34
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.09
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.95
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.52
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.25
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.23
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.87
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.24
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.01
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.40
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.38
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.30
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.20
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.80
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.63
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.45
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.28
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.05
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.03
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.75
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.47
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.39
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.13
SRR16705948	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	7.90
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.14
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.65
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.20
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.98
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.72
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.54
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.95
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.93
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.84
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.56
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.44
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.40
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.17
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.20
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.23
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.62
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.21
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.45
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.88
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.11
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.21
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.30
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.92
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.21
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.70
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.63
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.00
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.