Gene detail

Detailed information of OS493_021542-T1 in Lophelia pertusa

Genomic Location: scaffold_83:638389...644515
NR annotation: KAJ7358765.1, Ribosome production factor 1 [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
Q8AVP1	Ribosome production factor 1 OS=Xenopus laevis OX=8355 GN=rpf1 PE=2 SV=1
Q9H9Y2	Ribosome production factor 1 OS=Homo sapiens OX=9606 GN=RPF1 PE=1 SV=2
Q5R631	Ribosome production factor 1 OS=Pongo abelii OX=9601 GN=RPF1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001859 (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
IPR044281 all species →	Family	U3 snoRNP protein/Ribosome production factor 1	Interproscan
IPR007109 all species →	Domain	Brix domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22734 all species →	U3 SMALL NUCLEOLAR RIBONUCLEOPROTEIN PROTEIN IMP4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000460 all species →	Biological Process	maturation of 5.8S rRNA	Interproscan
GO:0000470 all species →	Biological Process	maturation of LSU-rRNA	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0006364 all species →	Biological Process	rRNA processing	Interproscan
GO:0030687 all species →	Cellular Component	preribosome, large subunit precursor	Interproscan
GO:0042134 all species →	Molecular Function	rRNA primary transcript binding	Interproscan
GO:0019843 all species →	Molecular Function	rRNA binding	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
K14846	RPF1; ribosome production factor 1	-	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_021542-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

108TPM > 0

7Conditions

20.5Max TPM

7.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.29	11.90
polyp at pH7 6	18	17	7.56	13.05
coral polyp · control treatment	16	16	10.65	17.17
coral polyp · oil and dispersant treatment	16	16	8.60	20.46
coral polyp · oil treatment	16	16	8.59	16.10
coral polyp · dispersant treatment	16	16	6.19	11.14
Polyp	10	9	6.14	11.59

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	-	11.90
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.23
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.99
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.78
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.33
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.21
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.74
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.72
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.28
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.23
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.91
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.35
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.06
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.80
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.64
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.18
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.67
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.21
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.05
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.73
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.35
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.37
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.98
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.93
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.81
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.73
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.71
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.47
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.31
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.22
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.87
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.37
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.05
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.22
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.17
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.77
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.83
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.22
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.57
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.56
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.25
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.95
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.78
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.13
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.87
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.80
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.82
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.62
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.47
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.62
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.46
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.22
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.00
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.59
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.97
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.60
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.13
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.78
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.99
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.85
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.36
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.71
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.48
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.67
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.16
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.70
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.10
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.06
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.63
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.53
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.48
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.01
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.73
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.43
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.92
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.84
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.72
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.16
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.46
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.28
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.38
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.74
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.14
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.60
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.68
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.02
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.09
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.90
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.52
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.25
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.08
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.47
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.33
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.93
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.78
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.92
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.80
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.53
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.59
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	7.53
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	7.39
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.13
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	7.10
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	6.24
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.84
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.53
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.08
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.