Gene detail

Detailed information of OS493_029612-T1 in Lophelia pertusa

Genomic Location: scaffold_181:559401...563488
NR annotation: KAJ7389712.1, 40S ribosomal protein S3-1 [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
A7S3J7	Small ribosomal subunit protein eS1 OS=Nematostella vectensis OX=45351 GN=v1g242621 PE=3 SV=1
P49242	Small ribosomal subunit protein eS1 OS=Rattus norvegicus OX=10116 GN=Rps3a PE=1 SV=2
P61246	Small ribosomal subunit protein eS1 (Fragment) OS=Felis catus OX=9685 GN=RPS3A PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007928 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01015 all species →	Ribosomal_S3Ae	Ribosomal S3Ae family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027500 all species →	Family	Small ribosomal subunit protein eS1, eukaryotes	Interproscan
IPR001593 all species →	Family	Small ribosomal subunit protein eS1	Interproscan
IPR018281 all species →	Conserved_site	Small ribosomal subunit protein eS1, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11830 all species →	40S RIBOSOMAL PROTEIN S3A	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003735 all species →	Molecular Function	structural constituent of ribosome	Interproscan
GO:0005840 all species →	Cellular Component	ribosome	Interproscan
GO:0006412 all species →	Biological Process	translation	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	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
K02984	RP-S3Ae, RPS3A; small subunit ribosomal protein S3Ae	-	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_029612-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

7,411.3Max TPM

3,710.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4,056.63	4,995.26
polyp at pH7 6	18	18	4,046.55	5,208.63
coral polyp · control treatment	16	16	3,511.86	6,052.82
coral polyp · oil and dispersant treatment	16	16	3,121.53	5,265.17
coral polyp · oil treatment	16	16	3,931.47	6,121.98
coral polyp · dispersant treatment	16	16	2,872.52	7,411.31
Polyp	10	10	4,728.47	5,592.43

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	-	4,995.26
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,973.35
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,503.17
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,476.20
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,321.01
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,302.14
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,123.81
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,110.85
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,098.46
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,083.73
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,066.52
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,020.37
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,002.25
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3,985.47
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3,266.99
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3,246.66
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3,244.59
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3,198.59
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,208.63
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,179.94
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,970.75
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,887.03
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,382.61
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,360.63
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3,772.90
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3,768.28
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3,712.15
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3,704.60
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3,700.43
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3,698.23
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3,628.92
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3,618.91
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3,604.68
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3,589.76
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3,545.73
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3,503.68
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6,052.82
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4,975.79
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4,555.84
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4,509.87
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4,241.63
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4,007.75
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,691.95
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,202.16
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,072.21
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,034.18
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,957.55
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,827.88
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,610.15
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,402.52
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,337.52
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,709.90
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5,265.17
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4,247.92
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,610.63
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,517.91
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,238.05
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,158.83
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,055.90
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,005.59
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,859.10
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,807.19
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,788.41
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,702.15
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,469.15
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,448.93
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,444.76
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,324.86
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6,121.98
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5,527.93
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5,151.27
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4,639.79
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4,106.48
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4,054.90
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,910.89
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,815.59
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,750.85
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,699.17
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,522.34
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,350.45
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,088.07
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,854.96
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,711.81
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,597.08
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7,411.31
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6,144.02
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3,040.76
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,833.03
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,753.06
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,621.39
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,554.02
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,469.73
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,355.00
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,263.66
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,196.31
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,150.98
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,067.75
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,801.63
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,715.11
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,582.59
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5,592.43
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5,520.25
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5,242.28
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5,196.44
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	5,145.18
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4,555.50
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4,173.31
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3,962.83
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3,948.39
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3,948.13

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.