Gene detail

Detailed information of OS493_003886-T1 in Lophelia pertusa

Genomic Location: scaffold_8:25504...27674
NR annotation: KAJ7386928.1, 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

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001372 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_003886-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR052431 all species →	Family	SKI2 subfamily ATP-dependent RNA helicases	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

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_003886-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_003886-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

96TPM > 0

7Conditions

23.0Max TPM

5.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	13	5.49	17.21
polyp at pH7 6	18	11	2.05	8.23
coral polyp · control treatment	16	16	6.24	13.36
coral polyp · oil and dispersant treatment	16	15	5.08	11.40
coral polyp · oil treatment	16	16	5.98	12.81
coral polyp · dispersant treatment	16	16	4.24	6.57
Polyp	10	9	7.63	22.98

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.21
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.28
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.32
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.19
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.02
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.20
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.09
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.56
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.36
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.19
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.96
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.85
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.56
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
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
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.23
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.25
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.59
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.54
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.53
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.47
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.08
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.74
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.37
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.28
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.81
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
SRR11359512	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
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.36
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.87
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.95
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.81
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.56
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.23
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.54
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.51
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.13
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.08
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.05
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.02
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.27
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.53
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.51
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.43
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.40
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.30
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.00
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.84
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.69
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.46
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.07
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.65
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.49
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.48
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.32
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.02
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.71
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.66
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.22
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.81
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.01
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.42
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.08
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.48
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.40
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.66
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.53
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.99
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.83
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.04
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.89
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.56
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.05
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.98
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.90
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.57
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.29
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.13
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.88
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.84
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.73
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.11
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.97
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.05
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.84
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.38
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.26
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.18
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.67
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.07
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.97
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	22.98
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	13.82
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.12
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.96
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	7.12
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.93
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.62
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.57
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.20
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.