Gene detail

Detailed information of OS493_004589-T1 in Lophelia pertusa

Genomic Location: scaffold_9:2233506...2234012
NR annotation: KAJ7380995.1, 54S ribosomal protein L13 [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
Q3SYS1	Large ribosomal subunit protein uL13m OS=Bos taurus OX=9913 GN=MRPL13 PE=1 SV=1
Q9D1P0	Large ribosomal subunit protein uL13m OS=Mus musculus OX=10090 GN=Mrpl13 PE=1 SV=1
Q9BYD1	Large ribosomal subunit protein uL13m OS=Homo sapiens OX=9606 GN=MRPL13 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008178 (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
IPR005823 all species →	Family	Large ribosomal subunit protein uL13, bacterial-type	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:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005762 all species →	Cellular Component	mitochondrial large ribosomal subunit	Interproscan
GO:0017148 all species →	Biological Process	negative regulation of 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
K02871	RP-L13, MRPL13, rplM; large subunit ribosomal protein L13	-	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_004589-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

114.4Max TPM

27.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	25.36	50.58
polyp at pH7 6	18	18	21.41	28.20
coral polyp · control treatment	16	16	38.94	114.43
coral polyp · oil and dispersant treatment	16	16	31.97	107.30
coral polyp · oil treatment	16	16	33.39	44.78
coral polyp · dispersant treatment	16	16	16.86	31.37
Polyp	10	10	27.42	57.67

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	-	50.58
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.73
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.78
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.26
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.25
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.96
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.16
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.47
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.43
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.12
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.88
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.42
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.86
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.15
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.10
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.86
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.44
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.20
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.73
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.59
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.42
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.78
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.40
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.40
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.17
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.36
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.11
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.76
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.35
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.28
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.65
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.76
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.23
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.16
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.06
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	114.43
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.72
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.86
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.55
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.51
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.12
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.07
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.11
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.08
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.46
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.65
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.50
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.24
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.31
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.29
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.13
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	107.30
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.73
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.42
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.99
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.27
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.86
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.86
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.85
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.91
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.59
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.85
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.57
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.47
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.21
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.78
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.83
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.78
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.21
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.06
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.34
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.34
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.18
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.17
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.49
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.98
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.80
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.16
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.89
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.98
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.95
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.88
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.10
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.37
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.28
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.90
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.37
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.35
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.08
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.58
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.73
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.94
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.77
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.45
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.93
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.29
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.76
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.17
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.85
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	57.67
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	42.72
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	32.47
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	25.24
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	24.94
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	22.05
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	19.48
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	17.94
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	17.78
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	13.96

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.