Gene detail

Detailed information of OS493_036704-T1 in Lophelia pertusa

Genomic Location: scaffold_380:165164...167279
NR annotation: KAJ7382154.1, decapping endonuclease targeting mRNA [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
Q5AYW6	Decapping nuclease RAI1 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) OX=227321 GN=rai1 PE=3 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002769 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08652 all species →	RAI1	RAI1 like PD-(D/E)XK nuclease	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039039 all species →	Family	RAI1-like family	Interproscan
IPR013961 all species →	Domain	RAI1-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12395 all species →	DOM-3 RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000956 all species →	Biological Process	nuclear-transcribed mRNA catabolic process	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0034353 all species →	Molecular Function	mRNA 5'-diphosphatase activity	Interproscan
GO:0090305 all species →	Biological Process	obsolete nucleic acid phosphodiester bond hydrolysis	Interproscan
GO:0110155 all species →	Biological Process	NAD-cap decapping	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_036704-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_036704-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

103TPM > 0

7Conditions

23.7Max TPM

4.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	5.72	22.46
polyp at pH7 6	18	15	3.02	8.19
coral polyp · control treatment	16	16	7.41	23.73
coral polyp · oil and dispersant treatment	16	15	3.72	9.21
coral polyp · oil treatment	16	16	5.16	11.38
coral polyp · dispersant treatment	16	16	3.06	9.43
Polyp	10	9	4.36	9.14

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.46
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.73
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.24
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.42
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.02
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.63
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.76
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.94
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.64
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.47
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.15
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.50
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.48
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.28
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.78
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.51
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.19
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.40
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.83
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.30
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.12
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.89
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.56
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.18
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.57
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.17
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.72
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.52
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.50
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.40
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.05
SRR11359500	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
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.73
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.54
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.25
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.18
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.20
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.61
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.38
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.94
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.93
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.38
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.09
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.80
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.32
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.24
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.53
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.38
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.21
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.87
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.46
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.69
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.92
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.37
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.68
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.27
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.05
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.59
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.58
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.24
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.08
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.46
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.09
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.38
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.11
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.67
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.22
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.16
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.97
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.54
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.23
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.10
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.49
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.54
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.35
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.35
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.96
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.34
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.14
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.43
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.23
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.62
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.94
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.36
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.14
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.85
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.30
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.98
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.89
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.58
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.46
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.02
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.01
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.68
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.46
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	9.14
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.33
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.87
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.21
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	4.57
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.29
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.10
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.21
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.91
SRR23025712	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.