Gene detail

Detailed information of OS493_036037-T1 in Lophelia pertusa

Genomic Location: scaffold_345:50176...59810
NR annotation: KAJ7376215.1, Syntaxin-18 [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
Q9P2W9	Syntaxin-18 OS=Homo sapiens OX=9606 GN=STX18 PE=1 SV=1
Q5REB4	Syntaxin-18 OS=Pongo abelii OX=9601 GN=STX18 PE=2 SV=1
Q8VDS8	Syntaxin-18 OS=Mus musculus OX=10090 GN=Stx18 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005970 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10496 all species →	Syntaxin-18_N	SNARE-complex protein Syntaxin-18 N-terminus	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR010989 all species →	Homologous_superfamily	SNARE	Interproscan
IPR019529 all species →	Domain	SNARE-complex protein Syntaxin-18, N-terminal	Interproscan
IPR000727 all species →	Domain	Target SNARE coiled-coil homology domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15959 all species →	SYNTAXIN-18	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0005783 all species →	Cellular Component	endoplasmic reticulum	Interproscan
GO:0006890 all species →	Biological Process	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	Interproscan
GO:0031201 all species →	Cellular Component	SNARE complex	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
K08492	STX18; syntaxin 18	-	Membrane trafficking	ko04131	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_036037-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

16.2Max TPM

7.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	9.01	16.18
polyp at pH7 6	18	18	9.15	15.28
coral polyp · control treatment	16	16	7.40	12.25
coral polyp · oil and dispersant treatment	16	16	5.18	7.62
coral polyp · oil treatment	16	16	7.30	10.55
coral polyp · dispersant treatment	16	16	5.35	9.02
Polyp	10	9	4.36	9.63

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.18
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.84
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.79
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.65
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.19
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.73
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.71
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.68
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.92
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.78
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.66
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.65
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.24
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.92
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.78
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.60
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.95
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.86
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.28
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.74
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.73
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.50
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.26
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.67
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.53
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.37
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.08
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.55
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.14
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.58
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.27
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.13
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.55
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.87
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.27
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.23
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.25
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.55
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.53
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.96
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.12
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.33
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.84
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.57
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.50
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.84
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.76
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.36
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.73
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.41
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.86
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.77
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.62
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.12
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.76
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.29
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.20
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.14
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.85
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.55
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.95
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.66
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.52
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.10
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.87
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.68
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.48
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.10
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.55
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.41
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.00
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.71
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.47
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.39
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.88
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.63
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.25
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.98
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.65
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.61
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.35
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.40
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.32
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.14
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.02
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.75
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.26
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.09
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.28
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.51
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.13
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.00
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.95
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.91
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.87
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.83
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.66
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.55
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.03
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.81
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	9.63
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.79
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.65
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	5.50
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.78
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.91
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.62
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.31
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.36
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.