Gene detail

Detailed information of OS493_032925-T1 in Lophelia pertusa

Genomic Location: scaffold_251:477736...483873
NR annotation: KAJ7352986.1, hypothetical protein OS493_032925 [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
Q9CWT6	Probable ATP-dependent RNA helicase DDX28 OS=Mus musculus OX=10090 GN=Ddx28 PE=2 SV=2
Q4R4T6	Probable ATP-dependent RNA helicase DDX28 OS=Macaca fascicularis OX=9541 GN=DDX28 PE=2 SV=1
Q9NUL7	Probable ATP-dependent RNA helicase DDX28 OS=Homo sapiens OX=9606 GN=DDX28 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004271 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00271 all species →	Helicase_C	Helicase conserved C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	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:0003729 all species →	Molecular Function	mRNA 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_032925-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_032925-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

109TPM > 0

7Conditions

19.4Max TPM

8.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	9.19	13.66
polyp at pH7 6	18	18	10.32	19.41
coral polyp · control treatment	16	16	8.09	13.52
coral polyp · oil and dispersant treatment	16	16	4.46	7.43
coral polyp · oil treatment	16	16	8.21	12.98
coral polyp · dispersant treatment	16	16	6.01	11.99
Polyp	10	9	10.71	18.39

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	-	13.66
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.79
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.59
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.42
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.35
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.23
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.95
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.67
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.36
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.33
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.10
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.82
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.76
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.31
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.56
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.26
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.09
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.21
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.41
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.09
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.53
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.52
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.19
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.02
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.56
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.15
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.31
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.27
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.57
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.18
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.63
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.53
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.16
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.08
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.02
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.50
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.52
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.49
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.62
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.37
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.74
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.57
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.34
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.26
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.21
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.01
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.10
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.62
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.17
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.64
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.57
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.15
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.43
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.39
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.29
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.62
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.50
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.47
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.46
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.43
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.03
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.79
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.53
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.48
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.08
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.07
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.88
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.86
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.98
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.32
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.28
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.16
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.42
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.76
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.61
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.23
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.13
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.74
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.73
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.84
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.97
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.93
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.92
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.39
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.99
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.91
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.65
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.67
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.51
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.37
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.99
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.89
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.38
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.35
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.86
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.81
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.38
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.58
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.90
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.94
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	18.39
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	15.70
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	15.56
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	12.10
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	11.92
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	11.16
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.72
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.76
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.75
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.