Gene detail

Detailed information of OS493_028392-T1 in Lophelia pertusa

Genomic Location: scaffold_163:649893...654415
NR annotation: KAJ7389927.1, nucleolar pre-ribosomal-associated protein 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)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002500 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF11707 all species →	Npa1	Ribosome 60S biogenesis N-terminal	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039844 all species →	Family	Nucleolar pre-ribosomal-associated protein 1	Interproscan
IPR021714 all species →	Domain	Nucleolar pre-ribosomal-associated protein 1, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13500 all species →	NUCLEOLAR PRERIBOSOMAL-ASSOCIATED PROTEIN 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000463 all species →	Biological Process	maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	Interproscan
GO:0000466 all species →	Biological Process	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 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

No KEGG orthology assignment for OS493_028392-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_028392-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

78TPM > 0

7Conditions

11.9Max TPM

1.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	7	0.58	3.81
polyp at pH7 6	18	8	0.53	1.97
coral polyp · control treatment	16	14	1.56	3.78
coral polyp · oil and dispersant treatment	16	15	2.17	5.99
coral polyp · oil treatment	16	15	2.47	11.92
coral polyp · dispersant treatment	16	14	1.96	5.92
Polyp	10	5	0.73	2.45

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.81
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.38
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.07
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.89
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.85
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.71
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.67
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
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
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
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.97
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.91
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.30
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.18
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.13
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.05
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.61
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.43
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
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
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
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.78
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.33
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.55
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.31
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.92
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.90
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.83
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.72
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.39
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.16
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.05
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.89
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.81
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.32
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.99
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.80
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.09
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.11
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.60
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.54
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.02
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.86
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.44
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.20
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.93
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.83
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.59
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.42
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.23
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.92
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.88
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.47
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.93
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.25
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.70
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.73
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.56
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.44
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.10
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.08
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.68
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.43
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.25
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.14
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.92
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.05
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.42
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.65
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.39
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.97
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.90
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.86
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.59
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.57
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.46
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.25
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.80
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.56
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
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.45
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.13
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.84
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.59
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.30
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.