Gene detail

Detailed information of OS493_002791-T1 in Lophelia pertusa

Genomic Location: scaffold_6:388005...390555
NR annotation: KAJ7340068.1, Mitochondrial assembly of ribosomal large subunit protein 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
Q96EH3	Mitochondrial assembly of ribosomal large subunit protein 1 OS=Homo sapiens OX=9606 GN=MALSU1 PE=1 SV=1
Q9CWV0	Mitochondrial assembly of ribosomal large subunit protein 1 OS=Mus musculus OX=10090 GN=Malsu1 PE=1 SV=1
P0AAT7	Ribosomal silencing factor RsfS OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) OX=199310 GN=rsfS PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007095 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02410 all species →	RsfS	Ribosomal silencing factor during starvation	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR043519 all species →	Homologous_superfamily	Nucleotidyltransferase superfamily	Interproscan
IPR004394 all species →	Family	Protein Iojap/ribosomal silencing factor RsfS	Interproscan
IPR002048 all species →	Domain	EF-hand domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21043 all species →	IOJAP SUPERFAMILY ORTHOLOG	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0017148 all species →	Biological Process	negative regulation of translation	Interproscan
GO:0043023 all species →	Molecular Function	ribosomal large subunit binding	Interproscan
GO:0090071 all species →	Biological Process	negative regulation of ribosome biogenesis	Interproscan
GO:0005509 all species →	Molecular Function	calcium ion binding	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
K25803	MALSU1; mitochondrial assembly of ribosomal large subunit protein 1	-	Mitochondrial biogenesis	ko03029	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_002791-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

109TPM > 0

7Conditions

22.6Max TPM

10.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.47	22.55
polyp at pH7 6	18	18	11.45	16.99
coral polyp · control treatment	16	16	12.47	19.90
coral polyp · oil and dispersant treatment	16	16	9.61	13.86
coral polyp · oil treatment	16	16	11.25	15.16
coral polyp · dispersant treatment	16	16	4.44	9.86
Polyp	10	9	11.21	21.59

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.55
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.50
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.80
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.60
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.38
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.10
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.90
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.90
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.95
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.83
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.45
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.81
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.39
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.27
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.23
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.18
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.04
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.61
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.99
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.44
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.57
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.45
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.03
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.78
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.77
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.74
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.74
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.47
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.39
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.99
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.57
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.34
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.25
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.70
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.68
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.16
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.90
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.23
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.94
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.34
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.29
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.54
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.34
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.75
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.13
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.84
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.72
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.84
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.14
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.72
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.93
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.88
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.86
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.40
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.53
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.42
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.43
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.25
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.20
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.53
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.42
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.60
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.57
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.29
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.95
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.32
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.36
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.66
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.16
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.85
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.84
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.25
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.27
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.61
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.56
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.46
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.10
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.06
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.85
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.81
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.07
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.32
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.10
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.66
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.86
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.78
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.39
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.70
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.49
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.65
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.49
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.26
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.46
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.33
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.69
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.42
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.18
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.15
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.99
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.21
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	21.59
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	16.42
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	14.99
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	11.96
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	11.25
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	10.36
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	9.06
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.80
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.68
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.