Gene detail

Detailed information of OS493_015768-T1 in Lophelia pertusa

Genomic Location: scaffold_48:330762...335765
NR annotation: KAJ7333686.1, hypothetical protein OS493_015768 [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
O00560	Syntenin-1 OS=Homo sapiens OX=9606 GN=SDCBP PE=1 SV=1
O08992	Syntenin-1 OS=Mus musculus OX=10090 GN=Sdcbp PE=1 SV=1
Q9JI92	Syntenin-1 OS=Rattus norvegicus OX=10116 GN=Sdcbp PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008487 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00595 all species →	PDZ	PDZ domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036034 all species →	Homologous_superfamily	PDZ superfamily	Interproscan
IPR001478 all species →	Domain	PDZ domain	Interproscan
IPR051230 all species →	Family	Amyloid-beta A4 Precursor Protein-Binding	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12345 all species →	SYNTENIN RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005886 all species →	Cellular Component	plasma 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
K17254	SDCBP; syntenin-1	-	Exosome	ko04147	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_015768-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

1,133.6Max TPM

296.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	128.57	231.56
polyp at pH7 6	18	18	135.49	201.71
coral polyp · control treatment	16	16	283.68	605.93
coral polyp · oil and dispersant treatment	16	16	535.00	843.92
coral polyp · oil treatment	16	16	226.57	357.08
coral polyp · dispersant treatment	16	16	598.39	1,133.58
Polyp	10	10	160.28	320.11

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	231.56
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	197.07
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	152.71
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	146.89
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	139.29
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	138.20
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	131.79
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	129.76
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	124.21
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	123.70
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	119.78
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	112.48
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	110.68
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	96.88
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	94.98
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	94.41
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	91.13
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	78.79
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	201.71
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	187.69
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	183.28
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	179.29
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	168.29
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	165.85
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	157.27
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	154.25
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	145.06
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	144.74
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	119.71
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	118.83
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	116.62
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	104.58
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	83.47
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	74.23
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	73.75
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	60.28
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	605.93
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	458.48
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	349.03
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	341.30
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	318.82
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	307.07
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	303.77
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	289.44
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	262.27
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	238.04
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	231.66
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	227.68
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	208.01
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	163.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	118.53
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	115.79
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	843.92
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	790.89
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	653.17
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	631.45
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	630.25
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	621.15
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	613.96
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	572.34
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	566.97
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	547.98
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	544.45
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	388.88
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	365.67
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	306.14
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	295.29
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	187.52
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	357.08
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	337.45
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	286.14
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	274.90
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	271.43
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	263.45
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	252.43
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	249.30
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	229.80
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	218.42
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	214.98
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	183.27
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	148.99
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	120.68
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	115.12
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	101.68
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,133.58
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	977.12
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	885.20
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	765.68
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	740.32
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	700.99
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	666.71
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	666.65
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	629.88
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	591.05
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	433.34
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	416.33
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	412.46
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	311.51
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	139.26
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	104.18
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	320.11
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	306.87
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	259.25
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	201.53
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	154.48
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	98.96
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	74.50
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	70.31
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	67.60
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	49.19

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.