Gene detail

Detailed information of OS493_038609-T1 in Lophelia pertusa

Genomic Location: scaffold_645:40105...41472
NR annotation: KAJ7375823.1, hypothetical protein OS493_038609 [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
Q06683	Putative ATP-dependent helicase IRC3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=IRC3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006668 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04851 all species →	ResIII	Type III restriction enzyme, res subunit	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR050742 all species →	Family	Helicase and Restriction-Modification Enzyme	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR006935 all species →	Domain	Helicase/UvrB, N-terminal	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR47396 all species →	TYPE I RESTRICTION ENZYME ECOKI R PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0016787 all species →	Molecular Function	hydrolase activity	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_038609-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_038609-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

74TPM > 0

7Conditions

6.6Max TPM

1.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	9	0.42	1.78
polyp at pH7 6	18	5	0.19	1.10
coral polyp · control treatment	16	11	1.60	4.92
coral polyp · oil and dispersant treatment	16	13	1.75	6.58
coral polyp · oil treatment	16	13	1.07	4.10
coral polyp · dispersant treatment	16	13	1.09	4.14
Polyp	10	10	1.78	4.91

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.78
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.53
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.38
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.06
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.84
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.63
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.15
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.12
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.06
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
SRR11359497	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
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359510	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
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.10
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.85
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.82
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.67
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.07
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
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359503	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
SRR11359505	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
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	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
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.92
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.10
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.02
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.58
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.48
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.13
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.70
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.57
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.94
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.80
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.36
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.58
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.19
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.28
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.09
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.40
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.24
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.81
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.63
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.11
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.92
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.64
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.03
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.02
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.10
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.14
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.95
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.90
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.83
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.45
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.25
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.50
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.35
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.34
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.30
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.01
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.01
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.14
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.20
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.02
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.00
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.67
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.33
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.97
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.79
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.63
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.41
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.15
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.08
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.04
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.91
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.38
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.36
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.97
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.29
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.82
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.68
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.57
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.43
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.36

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.