Gene detail

Detailed information of OS493_023158-T1 in Lophelia pertusa

Genomic Location: scaffold_100:1041685...1043154
NR annotation: KAJ7371817.1, hypothetical protein OS493_023158 [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
P46850	RNA-splicing ligase RtcB OS=Escherichia coli (strain K12) OX=83333 GN=rtcB PE=1 SV=3
P0DX92	RNA-splicing ligase RtcB1 OS=Escherichia coli (strain ATCC 25922 / DSM 1103 / LMG 8223 / NCIMB 12210 / NCTC 12241 / WDCM 00013 / Seattle 1946) OX=1322345 GN=rtcB1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009009 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01139 all species →	RtcB	tRNA-splicing ligase RtcB	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR052915 all species →	Family	RNA-splicing ligase RtcB-like	Interproscan
IPR036025 all species →	Homologous_superfamily	tRNA-splicing ligase RtcB-like superfamily	Interproscan
IPR001233 all species →	Family	RNA-splicing ligase, RtcB	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43749 all species →	RNA-SPLICING LIGASE RTCB	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003909 all species →	Molecular Function	DNA ligase activity	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0008452 all species →	Molecular Function	RNA ligase activity	Interproscan
GO:0030145 all species →	Molecular Function	manganese ion binding	Interproscan
GO:0042245 all species →	Biological Process	RNA repair	Interproscan
GO:0006396 all species →	Biological Process	RNA 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_023158-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_023158-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

85TPM > 0

7Conditions

8.1Max TPM

2.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	11	2.44	7.55
polyp at pH7 6	18	9	1.75	5.86
coral polyp · control treatment	16	16	2.81	6.64
coral polyp · oil and dispersant treatment	16	14	1.99	5.34
coral polyp · oil treatment	16	16	2.95	4.84
coral polyp · dispersant treatment	16	14	2.55	8.12
Polyp	10	5	2.12	5.04

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.55
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.91
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.31
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.07
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.94
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.98
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.08
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.71
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.34
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.66
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.34
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.86
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.72
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.38
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.25
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.31
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.95
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.50
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.96
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.49
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	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
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.64
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.55
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.51
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.75
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.63
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.18
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.08
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.41
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.41
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.32
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.22
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.81
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.81
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.11
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.01
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.47
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.34
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.68
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.17
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.93
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.62
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.60
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.42
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.09
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.79
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.71
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.56
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.05
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.46
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.35
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.84
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.69
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.15
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.91
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.78
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.76
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.53
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.93
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.90
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.89
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.47
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.18
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.65
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.60
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.97
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.92
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.12
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.19
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.72
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.78
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.16
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.15
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.96
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.38
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.64
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.61
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.46
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.18
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.78
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.64
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.04
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.67
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.06
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.89
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.50
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	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.