Gene detail

Detailed information of OS493_015476-T1 in Lophelia pertusa

Genomic Location: scaffold_46:2214193...2218444
NR annotation: KAJ7373006.1, putative ATP-dependent RNA helicase ddx4 [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
Q61496	ATP-dependent RNA helicase DDX4 OS=Mus musculus OX=10090 GN=Ddx4 PE=1 SV=2
Q6GWX0	Probable ATP-dependent RNA helicase DDX4 OS=Sus scrofa OX=9823 GN=DDX4 PE=2 SV=1
Q9NQI0	Probable ATP-dependent RNA helicase DDX4 OS=Homo sapiens OX=9606 GN=DDX4 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000987 (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
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
IPR000629 all species →	Conserved_site	ATP-dependent RNA helicase DEAD-box, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR47958 all species →	ATP-DEPENDENT RNA HELICASE DBP3	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003724 all species →	Molecular Function	RNA helicase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0007276 all species →	Biological Process	gamete generation	Interproscan
GO:0030154 all species →	Biological Process	cell differentiation	Interproscan
GO:0043186 all species →	Cellular Component	P granule	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_015476-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_015476-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

245.0Max TPM

37.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	25.12	53.37
polyp at pH7 6	18	18	25.38	47.24
coral polyp · control treatment	16	16	53.51	245.00
coral polyp · oil and dispersant treatment	16	16	63.53	160.12
coral polyp · oil treatment	16	16	33.38	47.19
coral polyp · dispersant treatment	16	16	41.90	74.64
Polyp	10	10	10.59	14.88

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.37
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.67
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.23
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.12
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.97
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.20
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.47
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.53
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.97
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.46
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.00
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.83
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.69
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.95
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.20
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.19
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.25
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.06
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.24
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.40
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.21
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.71
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.13
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.05
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.94
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.11
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.85
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.67
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.73
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.45
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.77
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.40
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.03
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.40
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.31
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	245.00
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.99
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.38
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.71
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.10
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.68
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.82
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.78
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.91
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.28
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.94
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.00
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.91
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.74
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.35
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.56
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	160.12
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.47
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.85
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.00
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	73.94
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.88
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	65.18
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.65
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.60
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.41
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.42
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.24
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.11
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.39
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.32
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.93
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.19
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.20
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.41
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.78
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.97
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.55
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.92
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.51
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.15
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.40
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.17
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.24
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.24
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.19
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.31
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.79
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.64
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.75
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.06
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.76
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.28
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.44
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.88
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.47
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.72
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.24
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.95
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.76
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.78
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.84
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.23
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.54
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	14.88
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.20
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	13.10
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	11.58
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	11.35
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	10.56
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.34
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	8.24
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.67
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.93

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.