Gene detail

Detailed information of OS493_010346-T1 in Lophelia pertusa

Genomic Location: scaffold_25:1241555...1249947
NR annotation: KAJ7392695.1, putative ATP-dependent RNA helicase ddx6 [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
Q54E49	Probable ATP-dependent RNA helicase ddx6 OS=Dictyostelium discoideum OX=44689 GN=ddx6 PE=3 SV=1
Q7XMK8	DEAD-box ATP-dependent RNA helicase 6 OS=Oryza sativa subsp. japonica OX=39947 GN=Os04g0533000 PE=2 SV=1
P23128	ATP-dependent RNA helicase me31b OS=Drosophila melanogaster OX=7227 GN=me31B PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000794 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00270 all species →	DEAD	DEAD/DEAH box helicase	Domain	Interproscan
PF00271 all species →	Helicase_C	Helicase conserved C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000629 all species →	Conserved_site	ATP-dependent RNA helicase DEAD-box, conserved site	Interproscan
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
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	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:0000932 all species →	Cellular Component	P-body	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0010494 all species →	Cellular Component	cytoplasmic stress granule	Interproscan
GO:0017148 all species →	Biological Process	negative regulation of translation	Interproscan
GO:0033962 all species →	Biological Process	P-body assembly	Interproscan
GO:0034063 all species →	Biological Process	stress granule assembly	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K12614	DDX6, RCK, DHH1; ATP-dependent RNA helicase DDX6/DHH1	EC:5.6.2.7	Chromosome and associated proteins	ko03036	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_010346-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

110TPM > 0

7Conditions

156.5Max TPM

29.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	21.84	36.09
polyp at pH7 6	18	18	25.07	46.27
coral polyp · control treatment	16	16	46.19	156.46
coral polyp · oil and dispersant treatment	16	16	44.42	88.05
coral polyp · oil treatment	16	16	28.60	46.90
coral polyp · dispersant treatment	16	16	27.82	48.32
Polyp	10	10	8.96	17.14

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.09
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.25
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.91
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.34
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.10
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.56
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.24
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.96
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.26
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.63
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.03
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.88
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.85
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.67
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.10
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.44
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.93
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.86
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.27
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.45
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.15
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.22
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.58
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.69
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.14
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.44
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.39
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.92
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.32
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.57
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.78
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.08
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.33
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.24
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.35
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.35
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	156.46
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.54
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.00
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.05
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.97
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.24
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.19
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.82
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.65
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.93
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.51
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.77
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.61
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.66
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.33
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.29
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	88.05
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	73.24
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.72
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.03
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.96
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.56
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.52
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.29
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.29
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.35
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.46
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.75
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.09
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.60
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.84
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.94
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.90
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.66
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.05
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.07
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.79
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.71
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.96
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.91
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.56
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.51
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.75
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.47
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.39
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.30
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.52
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.98
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.32
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.28
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.38
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.23
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.74
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.62
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.43
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.44
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.80
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.81
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.01
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.21
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.22
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.04
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.60
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.94
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	17.14
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	14.17
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	11.19
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.10
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.06
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.25
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	6.43
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	5.64
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.03
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.60

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.