Gene detail

Detailed information of OS493_006090-T1 in Lophelia pertusa

Genomic Location: scaffold_12:4555805...4561558
NR annotation: KAJ7339681.1, 60S ribosomal protein L13A [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
Q3SZ90	Large ribosomal subunit protein uL13 OS=Bos taurus OX=9913 GN=RPL13A PE=2 SV=3
P40429	Large ribosomal subunit protein uL13 OS=Homo sapiens OX=9606 GN=RPL13A PE=1 SV=2
Q5RA38	Large ribosomal subunit protein uL13 OS=Pongo abelii OX=9601 GN=RPL13A PE=2 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006724 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00572 all species →	Ribosomal_L13	Ribosomal protein L13	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036899 all species →	Homologous_superfamily	Large ribosomal subunit protein uL13 superfamily	Interproscan
IPR005822 all species →	Family	Large ribosomal subunit protein uL13	Interproscan
IPR005755 all species →	Family	Large ribosomal subunit protein uL13, eukaryotic/archaeal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11545 all species →	RIBOSOMAL PROTEIN L13	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:0015934 all species →	Cellular Component	large ribosomal subunit	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0017148 all species →	Biological Process	negative regulation of translation	Interproscan
GO:0022625 all species →	Cellular Component	cytosolic large ribosomal subunit	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
K02872	RP-L13Ae, RPL13A; large subunit ribosomal protein L13Ae	-	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_006090-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

7,037.0Max TPM

3,635.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4,659.60	5,887.07
polyp at pH7 6	18	18	4,651.61	5,724.17
coral polyp · control treatment	16	16	2,964.66	5,230.54
coral polyp · oil and dispersant treatment	16	16	2,563.88	4,087.07
coral polyp · oil treatment	16	16	3,321.65	5,692.22
coral polyp · dispersant treatment	16	16	2,363.58	5,471.47
Polyp	10	10	5,286.31	7,036.97

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	-	5,887.07
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5,824.02
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5,655.70
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5,626.11
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5,329.35
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5,296.05
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,733.78
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,719.57
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,613.85
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,602.13
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,392.47
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,390.13
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,349.36
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,327.98
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3,610.72
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3,575.27
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3,473.35
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3,465.94
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,724.17
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,647.94
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,620.94
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,610.82
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,338.35
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,328.02
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,637.66
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,617.09
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,311.77
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,299.43
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,282.78
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,282.77
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,108.98
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,083.12
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,083.11
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,043.09
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3,855.66
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3,853.22
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5,230.54
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,942.85
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,772.43
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,441.79
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,369.95
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,246.71
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,154.18
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,141.61
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,723.65
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,633.76
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,521.68
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,221.72
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,177.36
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,123.38
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,121.87
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,611.02
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4,087.07
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,709.04
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,760.31
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,736.53
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,694.77
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,599.61
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,509.96
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,435.69
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,421.54
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,365.74
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,292.34
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,201.51
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,146.38
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,045.15
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,008.35
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,008.15
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5,692.22
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4,309.08
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,988.68
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,848.26
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,430.86
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,365.93
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,198.04
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,163.78
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,009.62
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,991.01
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,936.77
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,900.23
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,811.53
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,594.10
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,500.56
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,405.80
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5,471.47
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5,101.57
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,423.54
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,413.39
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,239.07
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,184.30
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,002.07
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,980.20
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,978.58
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,971.57
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,903.85
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,821.30
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,741.65
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,646.72
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,567.69
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,370.31
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7,036.97
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	6,592.99
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	6,115.96
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5,695.64
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5,497.45
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4,721.72
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4,654.03
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4,493.34
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4,050.65
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4,004.33

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.