Gene detail

Detailed information of OS493_003894-T1 in Lophelia pertusa

Genomic Location: scaffold_8:96544...103368
NR annotation: KAJ7386936.1, 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)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

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

Pfam domain

No Pfam domain signature was detected for OS493_003894-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_003894-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_003894-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

107TPM > 0

7Conditions

56.3Max TPM

9.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	9.60	17.85
polyp at pH7 6	18	16	8.11	15.69
coral polyp · control treatment	16	16	11.91	32.45
coral polyp · oil and dispersant treatment	16	16	11.58	56.33
coral polyp · oil treatment	16	16	9.11	16.30
coral polyp · dispersant treatment	16	16	11.61	22.14
Polyp	10	9	3.36	9.66

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	-	17.85
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.87
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.66
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.47
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.74
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.37
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.98
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.97
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.27
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.67
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.22
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.19
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.75
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.28
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.64
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.87
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.50
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.50
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.69
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.04
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.52
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.43
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.14
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.57
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.45
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.08
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.89
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.88
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.82
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.59
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.92
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.14
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.16
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.66
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
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.45
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.82
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.97
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.80
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.52
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.65
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.09
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.66
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.39
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.17
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.83
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.03
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.25
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.41
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.19
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.38
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.33
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.41
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.48
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.63
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.41
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.45
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.55
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.07
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.05
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.78
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.55
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.43
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.91
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.62
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.28
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.35
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.30
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.60
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.54
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.55
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.65
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.18
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.32
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.24
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.43
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.41
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.73
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.53
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.98
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.78
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.79
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.74
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.14
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.79
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.12
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.98
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.42
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.39
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.25
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.47
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.43
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.94
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.28
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.27
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.46
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.22
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.30
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.34
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.66
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.72
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.07
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.96
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.80
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.98
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.64
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.92
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.83
SRR7746667	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.