Gene detail

Detailed information of OS493_032924-T1 in Lophelia pertusa

Genomic Location: scaffold_251:474165...477275
NR annotation: KAJ7352985.1, hypothetical protein OS493_032924 [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
Q56X76	DEAD-box ATP-dependent RNA helicase 39 OS=Arabidopsis thaliana OX=3702 GN=RH39 PE=2 SV=2
Q5VRY0	DEAD-box ATP-dependent RNA helicase 39 OS=Oryza sativa subsp. japonica OX=39947 GN=Os01g0184500 PE=2 SV=1
A1CIQ5	ATP-dependent RNA helicase has1 OS=Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1 / QM 1276 / 107) OX=344612 GN=has1 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004271 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00270 all species →	DEAD	DEAD/DEAH box helicase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR014014 all species →	Domain	RNA helicase, DEAD-box type, Q motif	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan
IPR011545 all species →	Domain	DEAD/DEAH box helicase domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR47960 all species →	DEAD-BOX ATP-DEPENDENT RNA HELICASE 50	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003724 all species →	Molecular Function	RNA helicase activity	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA 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_032924-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_032924-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

104TPM > 0

7Conditions

11.8Max TPM

4.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	5.09	8.03
polyp at pH7 6	18	14	4.29	7.66
coral polyp · control treatment	16	16	5.81	11.81
coral polyp · oil and dispersant treatment	16	15	3.30	6.70
coral polyp · oil treatment	16	16	5.18	8.60
coral polyp · dispersant treatment	16	16	4.82	10.18
Polyp	10	9	3.89	6.87

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.03
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.18
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.03
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.78
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.96
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.54
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.51
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.40
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.26
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.99
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.84
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.72
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.40
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.71
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.36
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.33
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.88
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.79
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.66
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.63
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.01
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.63
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.20
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.07
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.61
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.39
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.18
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.36
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.25
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.03
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.65
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.63
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
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
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.81
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.24
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.89
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.85
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.75
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.34
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.91
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.63
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.55
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.95
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.16
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.37
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.31
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.28
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.91
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.97
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.70
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.27
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.92
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.63
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.31
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.12
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.08
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.89
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.43
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.69
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.57
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.29
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.75
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.08
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.08
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.60
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.48
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.46
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.40
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.38
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.31
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.65
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.40
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.79
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.13
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.85
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.55
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.96
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.48
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.24
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.12
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.18
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.63
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.83
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.65
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.26
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.09
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.02
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.84
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.24
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.69
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.15
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.76
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.71
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.35
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.25
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.51
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6.87
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.65
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.91
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.67
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.75
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.68
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.13
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.66
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.62
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.