Gene detail

Detailed information of OS493_019279-T1 in Lophelia pertusa

Genomic Location: scaffold_66:1665910...1667161
NR annotation: KAJ7331685.1, hypothetical protein OS493_019279 [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
Q8ND04	Nonsense-mediated mRNA decay factor SMG8 OS=Homo sapiens OX=9606 GN=SMG8 PE=1 SV=1
Q8VE18	Nonsense-mediated mRNA decay factor SMG8 OS=Mus musculus OX=10090 GN=Smg8 PE=1 SV=1
A1A4J7	Nonsense-mediated mRNA decay factor SMG8 OS=Bos taurus OX=9913 GN=SMG8 PE=2 SV=2

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_019279-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_019279-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

32.2Max TPM

8.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.98	25.02
polyp at pH7 6	18	18	11.96	20.78
coral polyp · control treatment	16	16	6.36	17.99
coral polyp · oil and dispersant treatment	16	16	6.71	15.21
coral polyp · oil treatment	16	16	6.11	14.72
coral polyp · dispersant treatment	16	16	4.90	13.31
Polyp	10	10	13.63	32.18

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	-	25.02
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.39
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.30
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.32
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.91
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.77
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.72
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.56
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.41
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.24
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.87
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.55
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.58
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.19
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.85
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.70
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.73
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.47
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.78
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.82
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.92
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.41
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.25
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.88
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.05
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.05
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.38
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.12
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.77
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.59
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.85
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.48
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.17
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.12
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.07
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.99
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.29
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.11
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.84
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.81
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.10
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.30
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.50
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.42
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.24
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.34
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.34
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.16
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.07
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.04
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.22
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.21
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.64
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.41
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.27
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.10
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.01
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.27
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.10
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.88
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.99
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.81
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.99
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.76
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.20
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.09
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.66
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.72
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.50
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.78
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.52
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.88
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.01
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.64
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.35
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.89
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.64
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.57
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.50
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.21
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.99
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.50
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.02
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.31
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.37
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.36
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.65
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.25
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.82
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.71
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.22
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.66
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.63
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.30
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.57
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.46
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.28
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.95
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.84
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	32.18
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	22.88
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	16.41
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	14.69
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	10.35
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	9.74
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.03
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.28
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.91
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6.82

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.