Gene detail

Detailed information of OS493_038236-T1 in Lophelia pertusa

Genomic Location: scaffold_536:37479...41653
NR annotation: KAJ7381932.1, hypothetical protein OS493_038236 [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
A7RKF6	RNA-splicing ligase RtcB homolog OS=Nematostella vectensis OX=45351 GN=v1g198406 PE=3 SV=1
Q6NZS4	RNA-splicing ligase RtcB homolog OS=Danio rerio OX=7955 GN=rtcb PE=2 SV=1
Q561P3	RNA-splicing ligase RtcB homolog OS=Xenopus tropicalis OX=8364 GN=rtcb PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003319 (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
IPR001233 all species →	Family	RNA-splicing ligase, RtcB	Interproscan
IPR036025 all species →	Homologous_superfamily	tRNA-splicing ligase RtcB-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11118 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000971 all species →	Biological Process	obsolete tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate	Interproscan
GO:0003972 all species →	Molecular Function	RNA ligase (ATP) activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0008452 all species →	Molecular Function	RNA ligase activity	Interproscan
GO:0072669 all species →	Cellular Component	tRNA-splicing ligase complex	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_038236-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_038236-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

57.7Max TPM

25.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	33.08	52.02
polyp at pH7 6	18	18	36.82	57.67
coral polyp · control treatment	16	16	21.57	30.22
coral polyp · oil and dispersant treatment	16	16	19.94	41.12
coral polyp · oil treatment	16	16	21.91	29.31
coral polyp · dispersant treatment	16	16	15.49	25.12
Polyp	10	9	28.87	55.40

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.02
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.78
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.23
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.20
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.68
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.01
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.02
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.42
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.33
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.21
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.02
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.42
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.04
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.53
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.59
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.80
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.46
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.66
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.67
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.75
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.33
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.82
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.60
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.35
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.32
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.30
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.16
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.50
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.04
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.35
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.93
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.50
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.86
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.20
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.07
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.91
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.22
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.19
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.38
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.19
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.58
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.02
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.35
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.46
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.92
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.07
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.79
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.99
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.39
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.01
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.41
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.22
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.12
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.54
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.46
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.40
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.28
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.91
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.13
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.54
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.70
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.28
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.14
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.82
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.52
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.41
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.68
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.14
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.31
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.17
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.28
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.61
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.72
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.57
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.20
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.88
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.72
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.98
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.87
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.46
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.57
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.53
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.49
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.15
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.12
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.26
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.79
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.61
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.05
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.05
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.43
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.24
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.66
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.22
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.88
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.24
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.06
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.66
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.20
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.36
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	55.40
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	46.03
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	35.47
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	34.21
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	32.06
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	29.54
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	23.21
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	19.96
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	12.82
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.