Gene detail

Detailed information of OS493_001012-T1 in Lophelia pertusa

Genomic Location: scaffold_2:3086363...3089925
NR annotation: KAJ7387674.1, 60S ribosomal protein L6 [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
P21533	Large ribosomal subunit protein eL6 OS=Rattus norvegicus OX=10116 GN=Rpl6 PE=1 SV=5
Q6QMZ4	Large ribosomal subunit protein eL6 OS=Chinchilla lanigera OX=34839 GN=RPL6 PE=2 SV=3
Q02878	Large ribosomal subunit protein eL6 OS=Homo sapiens OX=9606 GN=RPL6 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007850 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03868 all species →	Ribosomal_L6e_N	Ribosomal protein L6, N-terminal domain	Domain	Interproscan
PF01159 all species →	Ribosomal_L6e	Ribosomal protein L6e	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR005568 all species →	Domain	Large ribosomal subunit protein uL6, N-terminal	Interproscan
IPR014722 all species →	Homologous_superfamily	Large ribosomal subunit protein uL2, domain 2	Interproscan
IPR000915 all species →	Family	Large ribosomal subunit protein eL6	Interproscan
IPR008991 all species →	Homologous_superfamily	Translation protein SH3-like domain superfamily	Interproscan
IPR041997 all species →	Domain	Large ribosomal subunit protein eL6, KOW domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10715 all species →	60S RIBOSOMAL PROTEIN L6	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:0000027 all species →	Biological Process	ribosomal large subunit assembly	Interproscan
GO:0002181 all species →	Biological Process	cytoplasmic translation	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	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
K02934	RP-L6e, RPL6; large subunit ribosomal protein L6e	-	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_001012-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

8,619.3Max TPM

4,658.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	5,999.07	7,842.13
polyp at pH7 6	18	18	5,914.62	8,415.45
coral polyp · control treatment	16	16	3,803.87	6,788.34
coral polyp · oil and dispersant treatment	16	16	3,226.56	5,311.72
coral polyp · oil treatment	16	16	4,233.99	7,927.76
coral polyp · dispersant treatment	16	16	3,154.56	8,619.27
Polyp	10	10	6,723.62	8,199.13

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	-	7,842.13
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	7,699.12
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6,780.51
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6,714.41
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6,283.35
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	6,282.49
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6,079.54
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6,064.39
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6,036.60
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5,988.36
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	5,983.30
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5,976.13
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5,682.95
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5,625.32
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,917.94
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,861.60
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,596.50
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4,568.56
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	8,415.45
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8,314.99
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6,716.58
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6,615.75
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6,423.46
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6,419.11
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6,147.55
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6,137.19
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,626.83
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,619.47
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,226.81
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,217.44
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,169.96
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,151.94
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,030.72
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5,020.60
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,609.59
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4,599.66
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6,788.34
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4,970.58
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4,808.87
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4,410.32
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4,072.31
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4,048.52
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4,029.39
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,882.42
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,483.41
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,267.47
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,261.49
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3,251.99
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,876.97
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,769.06
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,569.77
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2,371.03
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5,311.72
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4,153.04
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,796.44
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,386.03
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,251.93
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,240.51
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,099.93
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3,059.48
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,986.03
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,978.51
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,939.84
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,790.58
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,760.40
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,676.38
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,675.69
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,518.39
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7,927.76
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5,503.33
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5,254.70
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5,108.71
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4,115.21
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4,072.55
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,895.49
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,805.08
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,751.85
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,733.29
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,718.72
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,672.22
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,628.50
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,314.35
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3,271.04
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2,971.01
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8,619.27
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7,162.10
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3,434.16
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,930.72
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,805.91
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,670.47
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,534.45
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,463.29
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,438.79
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,424.81
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,358.44
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,315.36
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,260.28
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,156.01
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,029.67
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,869.23
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8,199.13
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7,021.69
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	6,914.91
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6,760.54
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6,713.77
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	6,680.27
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6,674.07
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6,419.10
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	6,060.76
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5,791.99

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.