Gene detail

Detailed information of OS493_019272-T1 in Lophelia pertusa

Genomic Location: scaffold_66:1604520...1604876
NR annotation: KAJ7331679.1, hypothetical protein OS493_019272 [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
B0W730	Nonsense-mediated mRNA decay factor SMG8 OS=Culex quinquefasciatus OX=7176 GN=CPIJ003128 PE=3 SV=1
B4HWV2	Nonsense-mediated mRNA decay factor SMG8 OS=Drosophila sechellia OX=7238 GN=GM11479 PE=3 SV=1
B4Q9T2	Nonsense-mediated mRNA decay factor SMG8 OS=Drosophila simulans OX=7240 GN=GD22229 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005096 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10220 all species →	Smg8_Smg9	Smg8_Smg9	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019354 all species →	Family	Nonsense-mediated mRNA decay factor SMG8-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13091 all species →	AMPLIFIED IN BREAST CANCER 2-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000184 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, 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_019272-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_019272-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

110TPM > 0

7Conditions

50.7Max TPM

17.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	14.24	18.54
polyp at pH7 6	18	18	14.79	26.09
coral polyp · control treatment	16	16	23.37	50.66
coral polyp · oil and dispersant treatment	16	16	20.56	37.05
coral polyp · oil treatment	16	16	19.65	28.46
coral polyp · dispersant treatment	16	16	11.53	23.46
Polyp	10	10	15.97	38.79

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	-	18.54
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.48
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.06
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.85
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.57
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.56
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.80
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.36
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.88
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.86
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.64
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.55
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.37
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.56
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.18
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.98
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.75
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.34
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.09
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.84
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.03
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.72
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.40
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.96
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.97
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.90
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.22
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.26
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.91
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.70
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.03
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.18
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.11
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.49
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.01
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.38
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.66
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.01
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.89
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.60
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.77
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.43
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.05
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.05
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.94
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.31
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.81
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.81
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.60
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.93
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.47
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.52
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.05
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.67
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.06
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.33
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.27
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.62
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.38
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.63
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.50
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.42
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.08
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.05
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.56
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.54
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.90
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.95
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.46
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.60
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.38
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.98
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.45
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.95
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.34
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.18
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.58
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.23
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.14
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.76
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.50
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.44
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.56
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.81
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.46
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.07
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.00
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.97
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.94
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.57
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.79
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.50
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.23
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.12
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.69
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.86
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.15
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.62
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.73
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.79
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	38.79
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	20.97
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	18.46
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	16.19
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	14.44
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	13.31
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	12.08
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.08
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	8.96
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.40

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.