Gene detail

Detailed information of OS493_002750-T1 in Lophelia pertusa

Genomic Location: scaffold_5:7483481...7487376
NR annotation: KAJ7366008.1, hypothetical protein OS493_002750 [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
Q3SZA5	Spermine synthase OS=Bos taurus OX=9913 GN=SMS PE=2 SV=1
P52788	Spermine synthase OS=Homo sapiens OX=9606 GN=SMS PE=1 SV=2
P97355	Spermine synthase OS=Mus musculus OX=10090 GN=Sms PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003794 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF17284 all species →	Spermine_synt_N	Spermidine synthase tetramerisation domain	Domain	Interproscan
PF01564 all species →	Spermine_synth	Spermine/spermidine synthase domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR030373 all species →	Conserved_site	Polyamine biosynthesis domain, conserved site	Interproscan
IPR037163 all species →	Homologous_superfamily	Spermidine synthase, tetramerisation domain superfamily	Interproscan
IPR035246 all species →	Domain	Spermidine synthase, tetramerisation domain	Interproscan
IPR030374 all species →	Domain	Polyamine biosynthesis domain	Interproscan
IPR015576 all species →	Family	Spermine synthase, animal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46315 all species →	SPERMINE SYNTHASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006597 all species →	Biological Process	spermine biosynthetic process	Interproscan
GO:0016768 all species →	Molecular Function	spermine synthase 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K00802	SMS; spermine synthase	EC:2.5.1.22	Glutathione metabolism	ko00480	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_002750-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

92TPM > 0

7Conditions

9.4Max TPM

2.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	14	3.32	8.72
polyp at pH7 6	18	9	1.33	3.91
coral polyp · control treatment	16	16	3.25	9.43
coral polyp · oil and dispersant treatment	16	15	1.31	2.60
coral polyp · oil treatment	16	16	1.93	5.25
coral polyp · dispersant treatment	16	15	1.59	3.57
Polyp	10	7	2.06	5.15

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.72
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.77
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.31
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.79
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.55
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.31
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.29
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.88
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.60
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.54
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.59
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.34
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.75
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.26
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.91
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.59
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.38
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.02
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.94
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.25
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.89
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.81
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.15
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.43
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.26
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.62
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.73
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.38
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.41
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.18
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.41
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.35
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.10
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.71
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.61
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.90
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.40
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.32
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.29
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.60
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.23
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.21
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.05
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.94
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.85
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.54
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.47
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.32
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.05
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.77
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.75
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.52
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.49
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.19
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.25
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.53
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.69
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.66
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.62
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.06
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.92
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.86
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.81
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.41
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.12
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.07
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.70
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.50
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.47
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.27
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.57
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.37
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.14
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.03
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.75
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.24
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.44
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.21
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.07
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.05
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.95
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.77
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.56
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.24
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.12
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.15
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.03
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.03
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.21
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.70
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.54
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.97
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
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.