Gene detail

Detailed information of OS493_003897-T1 in Lophelia pertusa

Genomic Location: scaffold_8:139380...146097
NR annotation: KAJ7386939.1, putative ATP-dependent RNA helicase ddx60 [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
Q8IY21	Probable ATP-dependent RNA helicase DDX60 OS=Homo sapiens OX=9606 GN=DDX60 PE=1 SV=3
Q5H9U9	Probable ATP-dependent RNA helicase DDX60-like OS=Homo sapiens OX=9606 GN=DDX60L PE=1 SV=3
Q09475	Uncharacterized helicase C28H8.3 OS=Caenorhabditis elegans OX=6239 GN=C28H8.3 PE=3 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001372 (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
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR052431 all species →	Family	SKI2 subfamily ATP-dependent RNA helicases	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan
IPR011545 all species →	Domain	DEAD/DEAH box helicase domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR44533 all species →	DEAD/H RNA HELICASE, PUTATIVE-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP 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_003897-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_003897-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

97TPM > 0

7Conditions

11.0Max TPM

3.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	3.69	6.76
polyp at pH7 6	18	12	2.75	6.71
coral polyp · control treatment	16	16	4.48	7.34
coral polyp · oil and dispersant treatment	16	15	3.41	7.49
coral polyp · oil treatment	16	16	3.27	7.55
coral polyp · dispersant treatment	16	14	5.31	10.97
Polyp	10	7	0.69	2.06

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	-	6.76
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.72
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.62
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.80
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.36
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.31
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.89
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.76
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.44
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.31
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.29
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.68
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.60
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.57
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.48
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.16
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.77
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.71
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.48
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.48
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.19
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.06
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.83
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.65
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.50
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.49
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.48
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.22
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.32
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
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
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.34
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.18
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.10
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.81
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.69
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.30
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.39
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.38
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.57
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.21
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.71
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.52
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.52
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.81
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.43
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.80
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.49
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.31
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.64
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.97
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.16
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.10
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.35
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.07
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.81
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.81
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.71
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.01
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.77
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.54
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.86
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.55
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.49
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.62
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.83
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.38
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.95
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.89
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.07
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.59
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.35
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.70
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.64
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.36
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.84
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.74
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.30
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.97
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.56
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.16
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.38
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.44
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.08
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.85
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.66
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.17
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.51
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.24
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.83
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.12
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.06
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.40
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.22
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.82
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.74
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.35
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.30
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
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.