Gene detail

Detailed information of OS493_009825-T1 in Lophelia pertusa

Genomic Location: scaffold_23:3052628...3056797
NR annotation: KAJ7363663.1, rRNA-binding ribosome biosynthesis protein rpf2 [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
Q2YDN6	Ribosome production factor 2 homolog OS=Bos taurus OX=9913 GN=RPF2 PE=2 SV=1
Q9H7B2	Ribosome production factor 2 homolog OS=Homo sapiens OX=9606 GN=RPF2 PE=1 SV=2
Q9JJ80	Ribosome production factor 2 homolog OS=Mus musculus OX=10090 GN=Rpf2 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005457 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04427 all species →	Brix	Brix domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007109 all species →	Domain	Brix domain	Interproscan
IPR039770 all species →	Family	Ribosome biogenesis protein Rpf2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12728 all species →	BRIX DOMAIN CONTAINING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006364 all species →	Biological Process	rRNA processing	Interproscan
GO:0019843 all species →	Molecular Function	rRNA binding	Interproscan
GO:0000027 all species →	Biological Process	ribosomal large subunit assembly	Interproscan
GO:0000463 all species →	Biological Process	maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	Interproscan
GO:0000470 all species →	Biological Process	maturation of LSU-rRNA	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	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
K14847	RPF2; ribosome production factor 2	-	Ribosome biogenesis	ko03009	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_009825-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

110TPM > 0

7Conditions

65.0Max TPM

30.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	36.53	55.54
polyp at pH7 6	18	18	42.76	64.34
coral polyp · control treatment	16	16	27.32	60.45
coral polyp · oil and dispersant treatment	16	16	22.10	51.82
coral polyp · oil treatment	16	16	23.72	31.96
coral polyp · dispersant treatment	16	16	18.47	36.65
Polyp	10	10	40.97	64.99

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.54
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.40
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.63
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.52
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.51
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.10
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.74
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.04
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.55
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.73
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.54
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.49
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.81
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.65
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.96
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.24
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.63
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.54
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.34
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.71
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	60.95
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.97
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.34
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.58
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.96
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.58
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.21
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.23
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.99
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.89
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.24
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.33
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.32
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.69
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.24
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.13
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.45
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.50
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.82
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.73
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.74
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.52
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.80
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.95
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.91
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.15
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.73
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.29
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.04
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.00
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.12
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.30
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.82
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.20
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.35
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.29
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.98
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.33
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.00
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.75
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.40
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.78
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.33
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.72
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.95
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.94
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.36
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.35
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.96
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.31
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.56
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.42
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.72
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.38
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.29
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.20
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.06
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.20
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.13
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.89
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.84
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.78
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.71
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.09
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.65
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.90
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.15
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.99
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.17
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.58
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.85
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.09
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.04
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.84
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.36
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.97
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.78
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.78
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.45
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.95
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	64.99
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	55.55
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	45.63
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	45.28
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	45.13
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	40.76
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	37.70
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	34.32
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	20.49
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	19.84

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.