Gene detail

Detailed information of OS493_015577-T1 in Lophelia pertusa

Genomic Location: scaffold_47:658940...661198
NR annotation: KAJ7360476.1, Integral membrane protein of the Golgi [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
A7S6Y0	Protein SYS1 homolog OS=Nematostella vectensis OX=45351 GN=sys1 PE=3 SV=1
Q78S06	Protein SYS1 homolog OS=Mus musculus OX=10090 GN=Sys1 PE=2 SV=1
Q8N2H4	Protein SYS1 homolog OS=Homo sapiens OX=9606 GN=SYS1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008699 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF09801 all species →	SYS1	Integral membrane protein S linking to the trans Golgi network	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019185 all species →	Family	Integral membrane protein SYS1-related	Interproscan
IPR016973 all species →	Family	Integral membrane protein SYS1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12952 all species →	SYS1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005802 all species →	Cellular Component	trans-Golgi network	Interproscan
GO:0006895 all species →	Biological Process	Golgi to endosome transport	Interproscan
GO:0030173 all species →	Cellular Component	obsolete integral component of Golgi membrane	Interproscan
GO:0034067 all species →	Biological Process	protein localization to Golgi apparatus	Interproscan
GO:0043001 all species →	Biological Process	Golgi to plasma membrane protein transport	Interproscan
GO:0000139 all species →	Cellular Component	Golgi membrane	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
K20318	SYS1; protein SYS1	-	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_015577-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

108TPM > 0

7Conditions

71.7Max TPM

20.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.81	10.65
polyp at pH7 6	18	18	8.56	13.35
coral polyp · control treatment	16	16	24.58	41.82
coral polyp · oil and dispersant treatment	16	16	35.29	50.03
coral polyp · oil treatment	16	16	19.52	36.61
coral polyp · dispersant treatment	16	16	37.00	71.66
Polyp	10	8	6.10	10.65

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.65
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.46
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.92
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.68
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.66
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.15
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.90
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.76
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.59
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.03
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.02
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.02
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.76
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.03
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.68
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.69
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.61
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.00
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.35
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.99
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.99
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.55
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.53
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.70
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.34
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.29
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.74
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.07
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.85
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.61
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.39
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.27
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.77
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.71
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.18
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.83
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.82
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.39
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.78
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.31
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.76
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.80
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.54
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.56
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.86
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.02
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.52
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.40
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.90
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.25
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.37
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.97
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.03
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.87
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.21
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.06
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.05
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.07
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.58
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.76
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.51
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.77
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.17
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.22
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.08
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.16
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.24
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.80
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.61
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.80
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.92
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.35
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.95
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.31
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.72
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.33
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.00
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.13
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.03
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.11
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.79
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.35
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.53
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.46
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	71.66
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.15
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.97
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	56.38
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.88
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.36
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.00
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.87
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.60
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.52
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.59
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.30
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.03
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.04
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.61
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	10.65
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.32
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.61
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.61
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.14
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.84
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.85
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.99
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.