Gene detail

Detailed information of OS493_036343-T1 in Lophelia pertusa

Genomic Location: scaffold_359:90344...93137
NR annotation: KAJ7351141.1, hypothetical protein OS493_036343 [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
Q835U7	Ribosome-binding factor A OS=Enterococcus faecalis (strain ATCC 700802 / V583) OX=226185 GN=rbfA PE=3 SV=1
Q6P3B9	Putative ribosome-binding factor A, mitochondrial OS=Mus musculus OX=10090 GN=Rbfa PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009212 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02033 all species →	RBFA	Ribosome-binding factor A	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR023799 all species →	Homologous_superfamily	Ribosome-binding factor A domain superfamily	Interproscan
IPR039212 all species →	Family	Ribosome-binding factor A, mitochondrial	Interproscan
IPR015946 all species →	Homologous_superfamily	K homology domain-like, alpha/beta	Interproscan
IPR000238 all species →	Family	Ribosome-binding factor A	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14725 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006364 all species →	Biological Process	rRNA processing	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

No KEGG orthology assignment for OS493_036343-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_036343-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

101TPM > 0

7Conditions

8.1Max TPM

3.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	4.15	6.49
polyp at pH7 6	18	15	3.96	8.15
coral polyp · control treatment	16	16	3.24	6.75
coral polyp · oil and dispersant treatment	16	15	2.04	6.43
coral polyp · oil treatment	16	16	3.42	6.31
coral polyp · dispersant treatment	16	15	2.07	4.87
Polyp	10	8	3.09	6.50

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	-	6.49
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.04
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.66
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.64
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.38
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.15
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.05
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.78
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.60
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.36
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.17
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.96
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.61
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.53
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.39
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.87
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.15
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.13
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.31
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.79
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.53
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.45
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.79
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.53
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.96
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.26
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.12
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.11
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.08
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.70
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.40
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.75
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.78
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.87
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.10
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.90
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.85
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.81
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.60
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.28
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.77
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.39
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.53
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.45
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.28
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.27
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.20
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.43
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.15
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.78
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.99
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.36
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.26
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.87
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.42
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.42
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.38
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.34
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.07
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.97
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.75
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.45
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.31
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.30
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.26
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.19
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.93
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.14
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.90
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.46
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.01
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.73
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.66
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.53
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.37
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.67
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.84
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.35
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.87
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.45
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.41
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.83
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.76
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.65
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.86
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.76
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.63
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.62
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.10
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.97
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.63
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.45
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.11
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.50
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.87
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.84
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.56
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.02
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.74
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.54
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.87
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
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.