Gene detail

Detailed information of OS493_005480-T1 in Lophelia pertusa

Genomic Location: scaffold_11:1720401...1721508
NR annotation: KAJ7365373.1, tRNA-splicing endonuclease subunit Sen34 [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
O60156	Probable tRNA-splicing endonuclease subunit sen34 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=sen34 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009655 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_005480-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR011856 all species →	Homologous_superfamily	tRNA endonuclease-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13070 all species →	TRNA-SPLICING ENDONUCLEASE SUBUNIT SEN34-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000213 all species →	Molecular Function	tRNA-intron endonuclease activity	Interproscan
GO:0000379 all species →	Biological Process	tRNA-type intron splice site recognition and cleavage	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid 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

No KEGG orthology assignment for OS493_005480-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_005480-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

107TPM > 0

7Conditions

8.3Max TPM

1.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	2.18	4.79
polyp at pH7 6	18	17	2.48	3.97
coral polyp · control treatment	16	16	2.12	8.33
coral polyp · oil and dispersant treatment	16	16	1.46	3.30
coral polyp · oil treatment	16	16	2.08	3.48
coral polyp · dispersant treatment	16	15	0.83	2.17
Polyp	10	9	1.25	2.24

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	-	4.79
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.42
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.71
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.72
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.22
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.19
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.14
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.13
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.90
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.87
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.67
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.53
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.52
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.37
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.37
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.33
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.28
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.14
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.97
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.51
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.49
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.46
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.78
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.75
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.73
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.72
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.53
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.52
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.50
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.43
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.26
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.11
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.00
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.46
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.35
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.33
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.38
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.91
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.39
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.17
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.99
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.98
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.64
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.56
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.35
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.27
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.11
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.00
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.98
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.92
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.87
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.30
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.35
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.33
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.93
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.93
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.52
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.41
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.35
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.26
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.01
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.99
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.96
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.93
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.81
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.76
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.44
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.48
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.39
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.37
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.39
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.29
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.27
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.11
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.09
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.92
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.84
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.63
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.60
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.59
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.51
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.07
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.69
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.17
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.50
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.40
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.07
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.90
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.85
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.80
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.77
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.70
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.68
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.67
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.53
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.53
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.51
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.19
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.24
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.11
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.06
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.91
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.71
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.45
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.55
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.26
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.22
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.