Gene detail

Detailed information of OS493_020590-T1 in Lophelia pertusa

Genomic Location: scaffold_76:973963...976905
NR annotation: KAJ7372163.1, sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3) [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
Q5XHG1	Sphingomyelin phosphodiesterase 4 OS=Xenopus laevis OX=8355 GN=smpd4 PE=2 SV=2
Q9NXE4	Sphingomyelin phosphodiesterase 4 OS=Homo sapiens OX=9606 GN=SMPD4 PE=1 SV=3
Q6PFJ7	Sphingomyelin phosphodiesterase 4 OS=Danio rerio OX=7955 GN=smpd4 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004874 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14724 all species →	mit_SMPDase	Mitochondrial-associated sphingomyelin phosphodiesterase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR024129 all species →	Family	Sphingomyelin phosphodiesterase 4	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12988 all species →	SPHINGOMYELIN PHOSPHODIESTERASE 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006685 all species →	Biological Process	sphingomyelin catabolic process	Interproscan
GO:0046475 all species →	Biological Process	glycerophospholipid catabolic process	Interproscan
GO:0046513 all species →	Biological Process	ceramide biosynthetic process	Interproscan
GO:0050290 all species →	Molecular Function	sphingomyelin phosphodiesterase D activity	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_020590-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_020590-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

61.7Max TPM

23.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	20.71	30.35
polyp at pH7 6	18	18	24.02	38.44
coral polyp · control treatment	16	16	26.80	50.80
coral polyp · oil and dispersant treatment	16	16	23.44	41.12
coral polyp · oil treatment	16	16	26.39	40.23
coral polyp · dispersant treatment	16	16	14.69	22.64
Polyp	10	10	30.77	61.70

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.35
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.95
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.77
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.59
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.12
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.32
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.04
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.80
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.36
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.08
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.82
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.44
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.27
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.20
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.86
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.24
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.03
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.58
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.44
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.54
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.68
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.75
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.13
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.98
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.85
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.50
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.65
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.19
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.08
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.24
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.46
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.76
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.37
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.88
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.08
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.76
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.80
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.22
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.68
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.51
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.94
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.90
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.53
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.37
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.86
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.54
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.51
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.51
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.59
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.94
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.85
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.02
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.12
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.69
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.78
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.72
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.71
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.24
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.55
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.74
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.48
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.28
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.06
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.43
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.09
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.71
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.74
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.74
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.23
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.09
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.69
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.85
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.43
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.08
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.17
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.91
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.87
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.82
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.37
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.60
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.38
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.03
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.06
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.70
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.64
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.90
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.84
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.52
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.16
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.79
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.54
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.33
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.12
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.64
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.58
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.12
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.33
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.26
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.16
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.05
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	61.70
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	34.88
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	34.64
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	32.55
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	29.80
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	28.21
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	27.38
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	21.52
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	19.71
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	17.27

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.