Gene detail

Detailed information of OS493_027798-T1 in Lophelia pertusa

Genomic Location: scaffold_154:332787...335589
NR annotation: KAJ7371110.1, ribosomal protein S9, S4 [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
A6QLG5	Small ribosomal subunit protein uS4 OS=Bos taurus OX=9913 GN=RPS9 PE=2 SV=1
P46781	Small ribosomal subunit protein uS4 OS=Homo sapiens OX=9606 GN=RPS9 PE=1 SV=3
Q6ZWN5	Small ribosomal subunit protein uS4 OS=Mus musculus OX=10090 GN=Rps9 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007374 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01479 all species →	S4	S4 domain	Domain	Interproscan
PF00163 all species →	Ribosomal_S4	Ribosomal protein S4/S9 N-terminal domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002942 all species →	Domain	RNA-binding S4 domain	Interproscan
IPR036986 all species →	Homologous_superfamily	RNA-binding S4 domain superfamily	Interproscan
IPR018079 all species →	Conserved_site	Small ribosomal subunit protein uS4, conserved site	Interproscan
IPR022801 all species →	Family	Small ribosomal subunit protein uS4	Interproscan
IPR001912 all species →	Domain	Small ribosomal subunit protein uS4, N-terminal	Interproscan
IPR005710 all species →	Family	Small ribosomal subunit protein uS4, eukaryotic/archaeal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11831 all species →	30S 40S RIBOSOMAL PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0019843 all species →	Molecular Function	rRNA binding	Interproscan
GO:0003735 all species →	Molecular Function	structural constituent of ribosome	Interproscan
GO:0015935 all species →	Cellular Component	small ribosomal subunit	Interproscan
GO:0022627 all species →	Cellular Component	cytosolic small ribosomal subunit	Interproscan
GO:0042274 all species →	Biological Process	ribosomal small subunit biogenesis	Interproscan
GO:0006412 all species →	Biological Process	translation	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
K02997	RP-S9e, RPS9; small subunit ribosomal protein S9e	-	Ribosome	ko03011	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_027798-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

5,235.8Max TPM

2,655.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	2,391.86	3,236.26
polyp at pH7 6	18	18	2,263.43	2,738.31
coral polyp · control treatment	16	16	3,136.05	5,235.83
coral polyp · oil and dispersant treatment	16	16	2,578.43	4,120.20
coral polyp · oil treatment	16	16	3,197.60	4,919.83
coral polyp · dispersant treatment	16	16	2,415.72	5,189.89
Polyp	10	10	2,707.55	3,019.78

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3,236.26
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3,221.92
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2,875.60
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2,777.84
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2,701.84
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2,683.50
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2,475.28
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2,409.68
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2,393.35
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2,375.52
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2,239.75
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2,238.79
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2,178.76
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2,134.49
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,804.82
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,778.16
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,767.85
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	1,760.00
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,738.31
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,695.58
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,581.74
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,508.65
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,422.94
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,421.37
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,414.35
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,371.38
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,332.03
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,217.60
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,215.88
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,197.70
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,187.96
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	2,003.63
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,898.28
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,856.75
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,843.37
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1,834.20
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5,235.83
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4,494.79
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,987.03
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,805.29
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,553.26
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,431.56
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,306.89
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,944.75
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,905.56
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,788.27
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,688.88
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,470.83
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,419.21
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,400.08
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,136.74
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,607.90
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4,120.20
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,432.72
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,149.33
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,847.95
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,686.23
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,526.04
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,476.87
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,453.56
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,431.27
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,406.42
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,326.43
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,164.05
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,152.29
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,077.78
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,029.06
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,974.63
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4,919.83
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4,048.07
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,913.24
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,816.65
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,609.93
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,217.92
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,213.84
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,024.94
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,011.89
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,977.21
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,876.89
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,826.64
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,792.77
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,352.16
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,306.90
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,252.73
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5,189.89
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4,291.84
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3,173.24
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,425.80
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,406.64
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,159.46
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,159.45
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,079.31
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,074.33
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,009.96
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,938.02
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,937.42
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,924.22
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,757.08
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,648.78
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,476.06
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3,019.78
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3,007.96
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2,800.70
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2,765.34
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2,677.54
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2,671.17
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2,627.79
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2,568.22
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2,538.68
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2,398.31

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.