Gene detail

Detailed information of OS493_014724-T1 in Lophelia pertusa

Genomic Location: scaffold_42:959105...966278
NR annotation: KAJ7334413.1, hypothetical protein OS493_014724 [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
Q15477	Superkiller complex protein 2 OS=Homo sapiens OX=9606 GN=SKIC2 PE=1 SV=3
Q6NZR5	Superkiller complex protein 2 OS=Mus musculus OX=10090 GN=Skic2 PE=2 SV=1
F4JAA5	DExH-box ATP-dependent RNA helicase DExH11 OS=Arabidopsis thaliana OX=3702 GN=SKI2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001225 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13234 all species →	MTR4_beta-barrel	Mtr4-like, beta-barrel domain	Domain	Interproscan
PF08148 all species →	DSHCT	DSHCT (NUC185) domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR025696 all species →	Domain	Exosome RNA helicase MTR4-like, beta-barrel domain	Interproscan
IPR012961 all species →	Domain	ATP-dependent RNA helicase Ski2/MTR4, C-terminal	Interproscan
IPR050699 all species →	Family	RNA/DNA Helicase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12131 all species →	ATP-DEPENDENT RNA AND DNA HELICASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003724 all species →	Molecular Function	RNA helicase activity	Interproscan
GO:0006401 all species →	Biological Process	RNA catabolic process	Interproscan
GO:0055087 all species →	Cellular Component	Ski complex	Interproscan
GO:0070478 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay	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_014724-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_014724-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

167.9Max TPM

42.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	43.14	78.26
polyp at pH7 6	18	18	52.39	130.91
coral polyp · control treatment	16	16	50.30	161.97
coral polyp · oil and dispersant treatment	16	16	29.22	104.04
coral polyp · oil treatment	16	16	50.25	167.91
coral polyp · dispersant treatment	16	16	25.65	84.07
Polyp	10	9	44.25	157.33

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	78.26
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	77.64
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	69.35
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	68.57
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	67.82
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	66.61
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.61
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.32
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.76
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.46
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.02
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.06
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.58
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.50
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.17
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.05
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.73
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.09
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	130.91
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	125.90
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	125.90
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	117.39
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.58
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.55
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.26
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.71
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.79
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.17
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.83
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.01
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.59
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.69
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.88
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.68
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.16
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.95
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	161.97
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	130.90
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	125.49
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	81.10
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.06
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.39
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.41
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.28
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.69
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.63
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.05
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.58
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.83
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.47
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.09
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.87
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	104.04
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.49
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.40
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.52
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.05
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.27
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.05
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.18
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.00
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.32
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.51
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.35
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.00
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.83
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.32
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.20
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	167.91
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	132.10
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	115.11
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	110.22
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.93
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.85
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.84
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.76
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.67
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.73
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.15
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.55
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.52
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.84
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.70
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.08
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	84.07
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.46
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.62
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.80
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.74
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.61
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.13
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.67
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.51
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.77
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.54
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.52
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.46
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.10
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.08
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.36
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	157.33
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	126.95
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	44.48
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	32.48
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	31.83
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	28.23
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.92
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	7.69
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.57
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.